Starting phenix.real_space_refine on Sat Mar 23 18:53:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x29_32962/03_2024/7x29_32962_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x29_32962/03_2024/7x29_32962.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x29_32962/03_2024/7x29_32962.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x29_32962/03_2024/7x29_32962.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x29_32962/03_2024/7x29_32962_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x29_32962/03_2024/7x29_32962_neut.pdb" } resolution = 2.49 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 5870 atoms to isotropic. 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 163 5.16 5 C 20536 2.51 5 N 5420 2.21 5 O 6334 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 32": "OE1" <-> "OE2" Residue "A PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 247": "OE1" <-> "OE2" Residue "A GLU 252": "OE1" <-> "OE2" Residue "A TYR 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 330": "OD1" <-> "OD2" Residue "A ASP 343": "OD1" <-> "OD2" Residue "A GLU 357": "OE1" <-> "OE2" Residue "A GLU 376": "OE1" <-> "OE2" Residue "A GLU 379": "OE1" <-> "OE2" Residue "A TYR 609": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 630": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 700": "NH1" <-> "NH2" Residue "A ASP 701": "OD1" <-> "OD2" Residue "A GLU 793": "OE1" <-> "OE2" Residue "A TYR 809": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 818": "OE1" <-> "OE2" Residue "A PHE 827": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 875": "OE1" <-> "OE2" Residue "A GLU 891": "OE1" <-> "OE2" Residue "A ASP 910": "OD1" <-> "OD2" Residue "A GLU 992": "OE1" <-> "OE2" Residue "A GLU 1017": "OE1" <-> "OE2" Residue "A PHE 1044": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1053": "OD1" <-> "OD2" Residue "A GLU 1062": "OE1" <-> "OE2" Residue "A TYR 1141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1179": "NH1" <-> "NH2" Residue "A GLU 1183": "OE1" <-> "OE2" Residue "A TYR 1186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 32": "OE1" <-> "OE2" Residue "B PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 216": "OD1" <-> "OD2" Residue "B TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 247": "OE1" <-> "OE2" Residue "B GLU 252": "OE1" <-> "OE2" Residue "B PHE 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 343": "OD1" <-> "OD2" Residue "B GLU 357": "OE1" <-> "OE2" Residue "B GLU 376": "OE1" <-> "OE2" Residue "B GLU 379": "OE1" <-> "OE2" Residue "B GLU 382": "OE1" <-> "OE2" Residue "B PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 499": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 505": "NH1" <-> "NH2" Residue "B ASP 510": "OD1" <-> "OD2" Residue "B GLU 536": "OE1" <-> "OE2" Residue "B GLU 589": "OE1" <-> "OE2" Residue "B PHE 617": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 635": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 666": "OE1" <-> "OE2" Residue "B GLU 680": "OE1" <-> "OE2" Residue "B ARG 700": "NH1" <-> "NH2" Residue "B GLU 725": "OE1" <-> "OE2" Residue "B GLU 793": "OE1" <-> "OE2" Residue "B TYR 809": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 818": "OE1" <-> "OE2" Residue "B TYR 824": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 827": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 869": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 875": "OE1" <-> "OE2" Residue "B GLU 891": "OE1" <-> "OE2" Residue "B PHE 895": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 910": "OD1" <-> "OD2" Residue "B TYR 978": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1044": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1053": "OD1" <-> "OD2" Residue "B GLU 1062": "OE1" <-> "OE2" Residue "B TYR 1141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1179": "NH1" <-> "NH2" Residue "B GLU 1183": "OE1" <-> "OE2" Residue "B TYR 1186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 32": "OE1" <-> "OE2" Residue "C PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 252": "OE1" <-> "OE2" Residue "C PHE 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 343": "OD1" <-> "OD2" Residue "C GLU 357": "OE1" <-> "OE2" Residue "C GLU 376": "OE1" <-> "OE2" Residue "C GLU 379": "OE1" <-> "OE2" Residue "C GLU 382": "OE1" <-> "OE2" Residue "C PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 499": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 505": "NH1" <-> "NH2" Residue "C GLU 536": "OE1" <-> "OE2" Residue "C TYR 577": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 589": "OE1" <-> "OE2" Residue "C PHE 590": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 593": "OD1" <-> "OD2" Residue "C PHE 617": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 635": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 666": "OE1" <-> "OE2" Residue "C GLU 680": "OE1" <-> "OE2" Residue "C ARG 700": "NH1" <-> "NH2" Residue "C GLU 725": "OE1" <-> "OE2" Residue "C GLU 793": "OE1" <-> "OE2" Residue "C TYR 809": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 818": "OE1" <-> "OE2" Residue "C PHE 827": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 869": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 875": "OE1" <-> "OE2" Residue "C GLU 891": "OE1" <-> "OE2" Residue "C ASP 910": "OD1" <-> "OD2" Residue "C TYR 978": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1001": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1044": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1059": "OD1" <-> "OD2" Residue "C GLU 1105": "OE1" <-> "OE2" Residue "C TYR 1141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 1179": "NH1" <-> "NH2" Residue "C GLU 1183": "OE1" <-> "OE2" Residue "C TYR 1186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 50": "NH1" <-> "NH2" Residue "F ARG 59": "NH1" <-> "NH2" Residue "F TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 89": "OD1" <-> "OD2" Residue "F ARG 98": "NH1" <-> "NH2" Residue "F GLU 99": "OE1" <-> "OE2" Residue "F ASP 105": "OD1" <-> "OD2" Residue "F ASP 108": "OD1" <-> "OD2" Residue "F PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 217": "NH1" <-> "NH2" Residue "G ARG 40": "NH1" <-> "NH2" Residue "G TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 109": "NH1" <-> "NH2" Residue "G PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 144": "OE1" <-> "OE2" Residue "G TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 196": "OE1" <-> "OE2" Residue "H ARG 50": "NH1" <-> "NH2" Residue "H ARG 59": "NH1" <-> "NH2" Residue "H PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 89": "OD1" <-> "OD2" Residue "H ARG 98": "NH1" <-> "NH2" Residue "H ASP 108": "OD1" <-> "OD2" Residue "H PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 217": "NH1" <-> "NH2" Residue "K ARG 40": "NH1" <-> "NH2" Residue "K TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 109": "NH1" <-> "NH2" Residue "K GLU 144": "OE1" <-> "OE2" Residue "K TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 196": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 32453 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 7657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 991, 7657 Classifications: {'peptide': 991} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 46, 'TRANS': 943} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 9186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1190, 9186 Classifications: {'peptide': 1190} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'CIS': 2, 'PTRANS': 59, 'TRANS': 1128} Chain breaks: 2 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "C" Number of atoms: 9186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1190, 9186 Classifications: {'peptide': 1190} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'CIS': 3, 'PTRANS': 59, 'TRANS': 1127} Chain breaks: 2 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "F" Number of atoms: 1589 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 214, 1583 Classifications: {'peptide': 214} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 201} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Conformer: "B" Number of residues, atoms: 214, 1583 Classifications: {'peptide': 214} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 201} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 bond proxies already assigned to first conformer: 1609 Chain: "G" Number of atoms: 1601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1601 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 199} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'PHE:plan': 1, 'TYR:plan': 1, 'ASP:plan': 1, 'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "H" Number of atoms: 1633 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 221, 1627 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 208} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Conformer: "B" Number of residues, atoms: 221, 1627 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 208} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 bond proxies already assigned to first conformer: 1655 Chain: "K" Number of atoms: 1601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1601 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 199} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'PHE:plan': 1, 'TYR:plan': 1, 'ASP:plan': 1, 'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 24 Time building chain proxies: 16.54, per 1000 atoms: 0.51 Number of scatterers: 32453 At special positions: 0 Unit cell: (152.632, 190.52, 240.315, 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 163 16.00 O 6334 8.00 N 5420 7.00 C 20536 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=52, symmetry=0 Simple disulfide: pdb=" SG CYS A 30 " - pdb=" SG CYS A 195 " distance=2.03 Simple disulfide: pdb=" SG CYS A 176 " - pdb=" SG CYS A 214 " distance=2.03 Simple disulfide: pdb=" SG CYS A 185 " - pdb=" SG CYS A 237 " distance=2.04 Simple disulfide: pdb=" SG CYS A 339 " - pdb=" SG CYS A 349 " distance=2.03 Simple disulfide: pdb=" SG CYS A 603 " - pdb=" SG CYS A 654 " distance=2.04 Simple disulfide: pdb=" SG CYS A 620 " - pdb=" SG CYS A 650 " distance=2.03 Simple disulfide: pdb=" SG CYS A 727 " - pdb=" SG CYS A 736 " distance=2.02 Simple disulfide: pdb=" SG CYS A 806 " - pdb=" SG CYS A 828 " distance=2.04 Simple disulfide: pdb=" SG CYS A 811 " - pdb=" SG CYS A 817 " distance=2.03 Simple disulfide: pdb=" SG CYS A 912 " - pdb=" SG CYS A 925 " distance=2.04 Simple disulfide: pdb=" SG CYS A1106 " - pdb=" SG CYS A1117 " distance=2.03 Simple disulfide: pdb=" SG CYS A1156 " - pdb=" SG CYS A1164 " distance=2.03 Simple disulfide: pdb=" SG CYS B 30 " - pdb=" SG CYS B 195 " distance=2.03 Simple disulfide: pdb=" SG CYS B 176 " - pdb=" SG CYS B 214 " distance=2.03 Simple disulfide: pdb=" SG CYS B 185 " - pdb=" SG CYS B 237 " distance=2.04 Simple disulfide: pdb=" SG CYS B 339 " - pdb=" SG CYS B 349 " distance=2.03 Simple disulfide: pdb=" SG CYS B 383 " - pdb=" SG CYS B 407 " distance=2.03 Simple disulfide: pdb=" SG CYS B 425 " - pdb=" SG CYS B 478 " distance=2.03 Simple disulfide: pdb=" SG CYS B 437 " - pdb=" SG CYS B 585 " distance=2.03 Simple disulfide: pdb=" SG CYS B 503 " - pdb=" SG CYS B 526 " distance=2.03 Simple disulfide: pdb=" SG CYS B 603 " - pdb=" SG CYS B 654 " distance=2.04 Simple disulfide: pdb=" SG CYS B 620 " - pdb=" SG CYS B 650 " distance=2.03 Simple disulfide: pdb=" SG CYS B 727 " - pdb=" SG CYS B 736 " distance=2.03 Simple disulfide: pdb=" SG CYS B 806 " - pdb=" SG CYS B 828 " distance=2.03 Simple disulfide: pdb=" SG CYS B 811 " - pdb=" SG CYS B 817 " distance=2.03 Simple disulfide: pdb=" SG CYS B 912 " - pdb=" SG CYS B 925 " distance=2.04 Simple disulfide: pdb=" SG CYS B1106 " - pdb=" SG CYS B1117 " distance=2.03 Simple disulfide: pdb=" SG CYS B1156 " - pdb=" SG CYS B1164 " distance=2.03 Simple disulfide: pdb=" SG CYS C 30 " - pdb=" SG CYS C 195 " distance=2.03 Simple disulfide: pdb=" SG CYS C 176 " - pdb=" SG CYS C 214 " distance=2.03 Simple disulfide: pdb=" SG CYS C 185 " - pdb=" SG CYS C 237 " distance=2.04 Simple disulfide: pdb=" SG CYS C 339 " - pdb=" SG CYS C 349 " distance=2.03 Simple disulfide: pdb=" SG CYS C 383 " - pdb=" SG CYS C 407 " distance=2.04 Simple disulfide: pdb=" SG CYS C 425 " - pdb=" SG CYS C 478 " distance=2.03 Simple disulfide: pdb=" SG CYS C 437 " - pdb=" SG CYS C 585 " distance=2.03 Simple disulfide: pdb=" SG CYS C 503 " - pdb=" SG CYS C 526 " distance=2.03 Simple disulfide: pdb=" SG CYS C 603 " - pdb=" SG CYS C 654 " distance=2.05 Simple disulfide: pdb=" SG CYS C 620 " - pdb=" SG CYS C 650 " distance=2.03 Simple disulfide: pdb=" SG CYS C 727 " - pdb=" SG CYS C 736 " distance=2.03 Simple disulfide: pdb=" SG CYS C 806 " - pdb=" SG CYS C 828 " distance=2.03 Simple disulfide: pdb=" SG CYS C 811 " - pdb=" SG CYS C 817 " distance=2.03 Simple disulfide: pdb=" SG CYS C 912 " - pdb=" SG CYS C 925 " distance=2.04 Simple disulfide: pdb=" SG CYS C1106 " - pdb=" SG CYS C1117 " distance=2.03 Simple disulfide: pdb=" SG CYS C1156 " - pdb=" SG CYS C1164 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 147 " - pdb=" SG CYS F 203 " distance=2.02 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 89 " distance=2.04 Simple disulfide: pdb=" SG CYS G 135 " - pdb=" SG CYS G 195 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 147 " - pdb=" SG CYS H 203 " distance=2.02 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 89 " distance=2.04 Simple disulfide: pdb=" SG CYS K 135 " - pdb=" SG CYS K 195 " distance=2.04 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: 11.70 Conformation dependent library (CDL) restraints added in 6.7 seconds 8408 Ramachandran restraints generated. 4204 Oldfield, 0 Emsley, 4204 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7840 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 72 sheets defined 20.7% alpha, 28.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.87 Creating SS restraints... Processing helix chain 'A' and resid 36 through 41 removed outlier: 3.648A pdb=" N PHE A 40 " --> pdb=" O GLN A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 231 removed outlier: 3.690A pdb=" N TYR A 231 " --> pdb=" O SER A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 273 removed outlier: 4.059A pdb=" N LEU A 273 " --> pdb=" O ARG A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 351 Processing helix chain 'A' and resid 805 through 812 Processing helix chain 'A' and resid 814 through 825 removed outlier: 3.763A pdb=" N LEU A 820 " --> pdb=" O LYS A 816 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLU A 823 " --> pdb=" O GLN A 819 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N TYR A 824 " --> pdb=" O LEU A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 825 through 854 removed outlier: 4.056A pdb=" N SER A 829 " --> pdb=" O GLY A 825 " (cutoff:3.500A) Processing helix chain 'A' and resid 888 through 898 Processing helix chain 'A' and resid 907 through 915 removed outlier: 3.668A pdb=" N GLN A 914 " --> pdb=" O ASP A 910 " (cutoff:3.500A) Processing helix chain 'A' and resid 922 through 931 removed outlier: 3.893A pdb=" N TYR A 928 " --> pdb=" O ILE A 924 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N VAL A 929 " --> pdb=" O CYS A 925 " (cutoff:3.500A) Processing helix chain 'A' and resid 940 through 957 removed outlier: 4.045A pdb=" N ALA A 956 " --> pdb=" O LEU A 952 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLY A 957 " --> pdb=" O GLY A 953 " (cutoff:3.500A) Processing helix chain 'A' and resid 971 through 984 Processing helix chain 'A' and resid 986 through 993 Processing helix chain 'A' and resid 993 through 1012 removed outlier: 3.604A pdb=" N MET A1008 " --> pdb=" O ALA A1004 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLN A1009 " --> pdb=" O LEU A1005 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N THR A1010 " --> pdb=" O GLY A1006 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N PHE A1012 " --> pdb=" O MET A1008 " (cutoff:3.500A) Processing helix chain 'A' and resid 1016 through 1042 removed outlier: 3.600A pdb=" N LEU A1033 " --> pdb=" O ASN A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1050 through 1058 Processing helix chain 'A' and resid 1059 through 1106 removed outlier: 3.913A pdb=" N ALA A1065 " --> pdb=" O PRO A1061 " (cutoff:3.500A) Processing helix chain 'A' and resid 1219 through 1223 Processing helix chain 'B' and resid 36 through 41 removed outlier: 3.737A pdb=" N PHE B 40 " --> pdb=" O GLN B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 53 Processing helix chain 'B' and resid 222 through 231 Processing helix chain 'B' and resid 268 through 273 removed outlier: 3.937A pdb=" N LEU B 273 " --> pdb=" O ARG B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 351 Processing helix chain 'B' and resid 410 through 418 removed outlier: 3.554A pdb=" N LEU B 414 " --> pdb=" O ASN B 410 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N PHE B 418 " --> pdb=" O LEU B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 435 removed outlier: 3.910A pdb=" N ALA B 434 " --> pdb=" O PRO B 430 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N SER B 435 " --> pdb=" O ALA B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 453 removed outlier: 3.545A pdb=" N MET B 452 " --> pdb=" O PRO B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 467 Processing helix chain 'B' and resid 805 through 812 Processing helix chain 'B' and resid 814 through 825 removed outlier: 3.728A pdb=" N TYR B 824 " --> pdb=" O LEU B 820 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLY B 825 " --> pdb=" O LEU B 821 " (cutoff:3.500A) Processing helix chain 'B' and resid 827 through 854 Processing helix chain 'B' and resid 888 through 898 Processing helix chain 'B' and resid 907 through 915 removed outlier: 3.753A pdb=" N GLN B 914 " --> pdb=" O ASP B 910 " (cutoff:3.500A) Processing helix chain 'B' and resid 922 through 931 removed outlier: 4.032A pdb=" N TYR B 928 " --> pdb=" O ILE B 924 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N VAL B 929 " --> pdb=" O CYS B 925 " (cutoff:3.500A) Processing helix chain 'B' and resid 940 through 957 removed outlier: 3.997A pdb=" N ALA B 956 " --> pdb=" O LEU B 952 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLY B 957 " --> pdb=" O GLY B 953 " (cutoff:3.500A) Processing helix chain 'B' and resid 971 through 984 Processing helix chain 'B' and resid 986 through 993 Processing helix chain 'B' and resid 993 through 1010 removed outlier: 3.842A pdb=" N THR B1010 " --> pdb=" O GLY B1006 " (cutoff:3.500A) Processing helix chain 'B' and resid 1016 through 1042 removed outlier: 3.716A pdb=" N LEU B1036 " --> pdb=" O ALA B1032 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER B1041 " --> pdb=" O ALA B1037 " (cutoff:3.500A) Processing helix chain 'B' and resid 1050 through 1058 Processing helix chain 'B' and resid 1059 through 1106 removed outlier: 3.881A pdb=" N ALA B1065 " --> pdb=" O PRO B1061 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLN B1066 " --> pdb=" O GLU B1062 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 41 removed outlier: 3.525A pdb=" N PHE C 40 " --> pdb=" O GLN C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 53 Processing helix chain 'C' and resid 222 through 231 removed outlier: 3.602A pdb=" N TYR C 231 " --> pdb=" O SER C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 268 through 273 removed outlier: 3.997A pdb=" N LEU C 273 " --> pdb=" O ARG C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 351 Processing helix chain 'C' and resid 385 through 390 Processing helix chain 'C' and resid 410 through 418 removed outlier: 3.681A pdb=" N LEU C 414 " --> pdb=" O ASN C 410 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 435 removed outlier: 3.551A pdb=" N ALA C 434 " --> pdb=" O PRO C 430 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N SER C 435 " --> pdb=" O ALA C 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 468 Processing helix chain 'C' and resid 524 through 529 removed outlier: 3.823A pdb=" N SER C 528 " --> pdb=" O PRO C 525 " (cutoff:3.500A) Processing helix chain 'C' and resid 805 through 812 Processing helix chain 'C' and resid 814 through 824 removed outlier: 3.562A pdb=" N GLU C 823 " --> pdb=" O GLN C 819 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N TYR C 824 " --> pdb=" O LEU C 820 " (cutoff:3.500A) Processing helix chain 'C' and resid 827 through 854 Processing helix chain 'C' and resid 888 through 898 Processing helix chain 'C' and resid 907 through 915 removed outlier: 3.760A pdb=" N GLN C 914 " --> pdb=" O ASP C 910 " (cutoff:3.500A) Processing helix chain 'C' and resid 922 through 931 removed outlier: 4.037A pdb=" N TYR C 928 " --> pdb=" O ILE C 924 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N VAL C 929 " --> pdb=" O CYS C 925 " (cutoff:3.500A) Processing helix chain 'C' and resid 940 through 957 removed outlier: 4.078A pdb=" N ALA C 956 " --> pdb=" O LEU C 952 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLY C 957 " --> pdb=" O GLY C 953 " (cutoff:3.500A) Processing helix chain 'C' and resid 971 through 984 Processing helix chain 'C' and resid 986 through 993 Processing helix chain 'C' and resid 993 through 1012 removed outlier: 3.574A pdb=" N MET C1008 " --> pdb=" O ALA C1004 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLN C1009 " --> pdb=" O LEU C1005 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N THR C1010 " --> pdb=" O GLY C1006 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N PHE C1012 " --> pdb=" O MET C1008 " (cutoff:3.500A) Processing helix chain 'C' and resid 1016 through 1042 removed outlier: 3.738A pdb=" N LEU C1036 " --> pdb=" O ALA C1032 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N SER C1041 " --> pdb=" O ALA C1037 " (cutoff:3.500A) Processing helix chain 'C' and resid 1050 through 1058 Processing helix chain 'C' and resid 1059 through 1106 removed outlier: 3.714A pdb=" N ALA C1065 " --> pdb=" O PRO C1061 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 91 Processing helix chain 'F' and resid 161 through 165 Processing helix chain 'G' and resid 80 through 84 removed outlier: 3.503A pdb=" N SER G 84 " --> pdb=" O PRO G 81 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 128 removed outlier: 4.066A pdb=" N LEU G 126 " --> pdb=" O SER G 122 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'K' and resid 80 through 84 removed outlier: 3.513A pdb=" N SER K 84 " --> pdb=" O PRO K 81 " (cutoff:3.500A) Processing helix chain 'K' and resid 122 through 127 removed outlier: 3.641A pdb=" N LYS K 127 " --> pdb=" O GLU K 124 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 33 through 35 removed outlier: 7.099A pdb=" N HIS A 91 " --> pdb=" O GLN A 98 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 63 through 64 removed outlier: 6.335A pdb=" N THR A 63 " --> pdb=" O TYR C 632 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N VAL C 639 " --> pdb=" O LEU C 651 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N GLY C 372 " --> pdb=" O CYS C 603 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 68 through 75 removed outlier: 4.261A pdb=" N ARG A 335 " --> pdb=" O ASP A 326 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 85 removed outlier: 5.936A pdb=" N SER A 267 " --> pdb=" O GLN A 280 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N GLN A 280 " --> pdb=" O SER A 267 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 88 through 89 removed outlier: 7.280A pdb=" N SER A 88 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N THR A 206 " --> pdb=" O SER A 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 110 through 111 Processing sheet with id=AA7, first strand: chain 'A' and resid 127 through 129 removed outlier: 3.840A pdb=" N ALA A 309 " --> pdb=" O THR A 139 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 187 through 189 Processing sheet with id=AA9, first strand: chain 'A' and resid 689 through 690 removed outlier: 4.470A pdb=" N VAL A 659 " --> pdb=" O VAL A 363 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N SER A 365 " --> pdb=" O VAL A 657 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N VAL A 657 " --> pdb=" O SER A 365 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 372 through 376 removed outlier: 6.534A pdb=" N GLY A 372 " --> pdb=" O GLU A 605 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N SER A 607 " --> pdb=" O GLY A 372 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N VAL A 374 " --> pdb=" O SER A 607 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N VAL A 639 " --> pdb=" O LEU A 651 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 717 through 724 removed outlier: 6.834A pdb=" N MET A 757 " --> pdb=" O VAL A 718 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N SER A 720 " --> pdb=" O MET A 757 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N LEU A 759 " --> pdb=" O SER A 720 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N LEU A 722 " --> pdb=" O LEU A 759 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLY A 732 " --> pdb=" O LEU A 735 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ALA A 737 " --> pdb=" O PRO A 730 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 768 through 769 removed outlier: 5.634A pdb=" N ILE A 768 " --> pdb=" O SER B 858 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 1121 through 1129 removed outlier: 5.921A pdb=" N HIS A1122 " --> pdb=" O TYR A1141 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N TYR A1141 " --> pdb=" O HIS A1122 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL A1124 " --> pdb=" O VAL A1139 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N VAL A1150 " --> pdb=" O LYS A1174 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N PHE A1172 " --> pdb=" O ALA A1152 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1121 through 1129 removed outlier: 5.921A pdb=" N HIS A1122 " --> pdb=" O TYR A1141 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N TYR A1141 " --> pdb=" O HIS A1122 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL A1124 " --> pdb=" O VAL A1139 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N HIS A1146 " --> pdb=" O PRO A 783 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N GLU A1148 " --> pdb=" O SER A 781 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N SER A 781 " --> pdb=" O GLU A1148 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N VAL A1150 " --> pdb=" O LYS A 779 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N LYS A 779 " --> pdb=" O VAL A1150 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N LYS A 779 " --> pdb=" O ALA B 969 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 802 through 804 Processing sheet with id=AB7, first strand: chain 'A' and resid 857 through 858 Processing sheet with id=AB8, first strand: chain 'A' and resid 967 through 968 removed outlier: 7.005A pdb=" N LYS C 779 " --> pdb=" O VAL C1150 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N VAL C1150 " --> pdb=" O LYS C 779 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N SER C 781 " --> pdb=" O GLU C1148 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N GLU C1148 " --> pdb=" O SER C 781 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N HIS C1146 " --> pdb=" O PRO C 783 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL C1124 " --> pdb=" O VAL C1139 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N TYR C1141 " --> pdb=" O HIS C1122 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N HIS C1122 " --> pdb=" O TYR C1141 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 967 through 968 removed outlier: 7.005A pdb=" N LYS C 779 " --> pdb=" O VAL C1150 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N VAL C1150 " --> pdb=" O LYS C 779 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N SER C 781 " --> pdb=" O GLU C1148 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N GLU C1148 " --> pdb=" O SER C 781 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N HIS C1146 " --> pdb=" O PRO C 783 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N VAL C1150 " --> pdb=" O LYS C1174 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N PHE C1172 " --> pdb=" O ALA C1152 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N GLU C1183 " --> pdb=" O THR C1175 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1202 through 1204 Processing sheet with id=AC2, first strand: chain 'B' and resid 33 through 35 removed outlier: 5.742A pdb=" N ASP B 34 " --> pdb=" O VAL B 102 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N HIS B 91 " --> pdb=" O GLN B 98 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 68 through 75 removed outlier: 4.262A pdb=" N ARG B 335 " --> pdb=" O ASP B 326 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 83 through 85 removed outlier: 5.972A pdb=" N SER B 267 " --> pdb=" O GLN B 280 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N GLN B 280 " --> pdb=" O SER B 267 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 88 through 89 removed outlier: 7.076A pdb=" N SER B 88 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N THR B 206 " --> pdb=" O SER B 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'B' and resid 110 through 111 Processing sheet with id=AC7, first strand: chain 'B' and resid 127 through 129 removed outlier: 3.679A pdb=" N ALA B 309 " --> pdb=" O THR B 139 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 153 through 154 Processing sheet with id=AC9, first strand: chain 'B' and resid 187 through 189 Processing sheet with id=AD1, first strand: chain 'B' and resid 689 through 690 removed outlier: 4.450A pdb=" N VAL B 659 " --> pdb=" O VAL B 363 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N SER B 365 " --> pdb=" O VAL B 657 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N VAL B 657 " --> pdb=" O SER B 365 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 372 through 376 removed outlier: 4.005A pdb=" N GLY B 372 " --> pdb=" O CYS B 603 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N VAL B 639 " --> pdb=" O LEU B 651 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 400 through 404 removed outlier: 3.627A pdb=" N LYS B 400 " --> pdb=" O TYR B 445 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE B 442 " --> pdb=" O THR B 574 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N THR B 483 " --> pdb=" O VAL B 420 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N VAL B 420 " --> pdb=" O THR B 483 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 408 through 409 Processing sheet with id=AD5, first strand: chain 'B' and resid 513 through 515 removed outlier: 5.799A pdb=" N SER B 498 " --> pdb=" O VAL B 561 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N VAL B 561 " --> pdb=" O SER B 498 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N ILE B 500 " --> pdb=" O SER B 559 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N SER B 559 " --> pdb=" O ILE B 500 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LYS B 502 " --> pdb=" O SER B 557 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 718 through 724 removed outlier: 7.958A pdb=" N SER B 761 " --> pdb=" O SER B 720 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N LEU B 722 " --> pdb=" O SER B 761 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N LEU B 735 " --> pdb=" O LEU B 731 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 768 through 769 removed outlier: 5.490A pdb=" N ILE B 768 " --> pdb=" O SER C 858 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'B' and resid 1121 through 1129 removed outlier: 5.755A pdb=" N HIS B1122 " --> pdb=" O TYR B1141 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N TYR B1141 " --> pdb=" O HIS B1122 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL B1124 " --> pdb=" O VAL B1139 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N VAL B1150 " --> pdb=" O LYS B1174 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N PHE B1172 " --> pdb=" O ALA B1152 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 1121 through 1129 removed outlier: 5.755A pdb=" N HIS B1122 " --> pdb=" O TYR B1141 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N TYR B1141 " --> pdb=" O HIS B1122 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL B1124 " --> pdb=" O VAL B1139 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N HIS B1146 " --> pdb=" O PRO B 783 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N GLU B1148 " --> pdb=" O SER B 781 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N SER B 781 " --> pdb=" O GLU B1148 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N VAL B1150 " --> pdb=" O LYS B 779 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N LYS B 779 " --> pdb=" O VAL B1150 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 802 through 804 Processing sheet with id=AE2, first strand: chain 'B' and resid 1202 through 1204 Processing sheet with id=AE3, first strand: chain 'C' and resid 33 through 35 removed outlier: 5.491A pdb=" N ASP C 34 " --> pdb=" O VAL C 102 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N THR C 96 " --> pdb=" O THR C 93 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N HIS C 91 " --> pdb=" O GLN C 98 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 68 through 75 removed outlier: 4.286A pdb=" N ARG C 335 " --> pdb=" O ASP C 326 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 83 through 85 removed outlier: 5.930A pdb=" N SER C 267 " --> pdb=" O GLN C 280 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N GLN C 280 " --> pdb=" O SER C 267 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 88 through 89 removed outlier: 7.256A pdb=" N SER C 88 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N THR C 206 " --> pdb=" O SER C 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'C' and resid 110 through 111 Processing sheet with id=AE8, first strand: chain 'C' and resid 127 through 129 Processing sheet with id=AE9, first strand: chain 'C' and resid 153 through 154 removed outlier: 3.624A pdb=" N ARG C 163 " --> pdb=" O GLY C 154 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 186 through 189 Processing sheet with id=AF2, first strand: chain 'C' and resid 689 through 690 removed outlier: 4.537A pdb=" N VAL C 659 " --> pdb=" O VAL C 363 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N SER C 365 " --> pdb=" O VAL C 657 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N VAL C 657 " --> pdb=" O SER C 365 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 400 through 404 removed outlier: 3.887A pdb=" N ILE C 442 " --> pdb=" O THR C 574 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N THR C 483 " --> pdb=" O VAL C 420 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N VAL C 420 " --> pdb=" O THR C 483 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 512 through 515 removed outlier: 6.919A pdb=" N THR C 512 " --> pdb=" O LEU C 507 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N SER C 498 " --> pdb=" O VAL C 561 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N VAL C 561 " --> pdb=" O SER C 498 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N ILE C 500 " --> pdb=" O SER C 559 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N SER C 559 " --> pdb=" O ILE C 500 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS C 502 " --> pdb=" O SER C 557 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N TRP C 553 " --> pdb=" O LEU C 506 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLY C 558 " --> pdb=" O ASP C 539 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 718 through 724 removed outlier: 7.885A pdb=" N SER C 761 " --> pdb=" O SER C 720 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N LEU C 722 " --> pdb=" O SER C 761 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N LEU C 735 " --> pdb=" O LEU C 731 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 802 through 804 Processing sheet with id=AF7, first strand: chain 'C' and resid 1202 through 1204 Processing sheet with id=AF8, first strand: chain 'F' and resid 5 through 6 removed outlier: 3.679A pdb=" N VAL F 5 " --> pdb=" O LYS F 23 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N THR F 78 " --> pdb=" O ASP F 73 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ASP F 73 " --> pdb=" O THR F 78 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'F' and resid 58 through 60 removed outlier: 5.210A pdb=" N TRP F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N ARG F 38 " --> pdb=" O TRP F 47 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'F' and resid 127 through 129 removed outlier: 3.742A pdb=" N LEU F 148 " --> pdb=" O PHE F 129 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N LEU F 148 " --> pdb=" O SER F 187 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N SER F 187 " --> pdb=" O LEU F 148 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N LYS F 150 " --> pdb=" O LEU F 185 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N LEU F 185 " --> pdb=" O LYS F 150 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR F 152 " --> pdb=" O TYR F 183 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR F 183 " --> pdb=" O TYR F 152 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU F 145 " --> pdb=" O VAL F 189 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'F' and resid 127 through 129 removed outlier: 3.742A pdb=" N LEU F 148 " --> pdb=" O PHE F 129 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N LEU F 148 " --> pdb=" O SER F 187 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N SER F 187 " --> pdb=" O LEU F 148 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N LYS F 150 " --> pdb=" O LEU F 185 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N LEU F 185 " --> pdb=" O LYS F 150 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR F 152 " --> pdb=" O TYR F 183 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR F 183 " --> pdb=" O TYR F 152 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N SER F 184 " --> pdb=" O ALA F 175 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N ALA F 175 " --> pdb=" O SER F 184 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER F 186 " --> pdb=" O PHE F 173 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'F' and resid 157 through 160 Processing sheet with id=AG4, first strand: chain 'F' and resid 201 through 202 Processing sheet with id=AG5, first strand: chain 'G' and resid 12 through 13 Processing sheet with id=AG6, first strand: chain 'G' and resid 19 through 24 Processing sheet with id=AG7, first strand: chain 'G' and resid 54 through 55 removed outlier: 3.734A pdb=" N SER G 54 " --> pdb=" O TYR G 50 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N TRP G 36 " --> pdb=" O LEU G 48 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N TYR G 50 " --> pdb=" O LEU G 34 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N LEU G 34 " --> pdb=" O TYR G 50 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'G' and resid 115 through 119 removed outlier: 3.814A pdb=" N VAL G 134 " --> pdb=" O PHE G 119 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER G 163 " --> pdb=" O SER G 177 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'G' and resid 154 through 155 removed outlier: 3.518A pdb=" N LYS G 146 " --> pdb=" O THR G 198 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'H' and resid 4 through 6 Processing sheet with id=AH2, first strand: chain 'H' and resid 10 through 11 removed outlier: 7.112A pdb=" N GLU H 10 " --> pdb=" O THR H 117 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'H' and resid 127 through 129 removed outlier: 3.539A pdb=" N LEU H 148 " --> pdb=" O PHE H 129 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N LEU H 148 " --> pdb=" O SER H 187 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N SER H 187 " --> pdb=" O LEU H 148 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N LYS H 150 " --> pdb=" O LEU H 185 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N LEU H 185 " --> pdb=" O LYS H 150 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'H' and resid 127 through 129 removed outlier: 3.539A pdb=" N LEU H 148 " --> pdb=" O PHE H 129 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N LEU H 148 " --> pdb=" O SER H 187 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N SER H 187 " --> pdb=" O LEU H 148 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N LYS H 150 " --> pdb=" O LEU H 185 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N LEU H 185 " --> pdb=" O LYS H 150 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N SER H 184 " --> pdb=" O ALA H 175 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ALA H 175 " --> pdb=" O SER H 184 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N SER H 186 " --> pdb=" O PHE H 173 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'H' and resid 158 through 160 removed outlier: 4.207A pdb=" N ASN H 204 " --> pdb=" O VAL H 214 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N VAL H 214 " --> pdb=" O ASN H 204 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ASN H 206 " --> pdb=" O THR H 212 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N THR H 212 " --> pdb=" O ASN H 206 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'K' and resid 11 through 13 removed outlier: 6.659A pdb=" N LEU K 34 " --> pdb=" O TYR K 50 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N TYR K 50 " --> pdb=" O LEU K 34 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N TRP K 36 " --> pdb=" O LEU K 48 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER K 54 " --> pdb=" O TYR K 50 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'K' and resid 19 through 24 Processing sheet with id=AH8, first strand: chain 'K' and resid 115 through 119 removed outlier: 4.085A pdb=" N ASN K 139 " --> pdb=" O TYR K 174 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N TYR K 174 " --> pdb=" O ASN K 139 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N SER K 163 " --> pdb=" O SER K 177 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'K' and resid 154 through 155 1246 hydrogen bonds defined for protein. 3373 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: 16.65 Time building geometry restraints manager: 12.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.41: 13754 1.41 - 1.61: 19228 1.61 - 1.82: 216 1.82 - 2.02: 1 2.02 - 2.23: 1 Bond restraints: 33200 Sorted by residual: bond pdb=" CD GLN A 377 " pdb=" OE1 GLN A 377 " ideal model delta sigma weight residual 1.231 1.894 -0.663 1.90e-02 2.77e+03 1.22e+03 bond pdb=" CG GLN A 377 " pdb=" CD GLN A 377 " ideal model delta sigma weight residual 1.516 2.228 -0.712 2.50e-02 1.60e+03 8.11e+02 bond pdb=" CD GLN A 377 " pdb=" NE2 GLN A 377 " ideal model delta sigma weight residual 1.328 1.727 -0.399 2.10e-02 2.27e+03 3.62e+02 bond pdb=" C SER F 160 " pdb=" O SER F 160 " ideal model delta sigma weight residual 1.235 1.367 -0.132 1.14e-02 7.69e+03 1.33e+02 bond pdb=" C SER H 160 " pdb=" O SER H 160 " ideal model delta sigma weight residual 1.236 1.368 -0.132 1.19e-02 7.06e+03 1.23e+02 ... (remaining 33195 not shown) Histogram of bond angle deviations from ideal: 10.05 - 34.92: 3 34.92 - 59.78: 0 59.78 - 84.64: 0 84.64 - 109.51: 4276 109.51 - 134.37: 40900 Bond angle restraints: 45179 Sorted by residual: angle pdb=" OE1 GLN A 377 " pdb=" CD GLN A 377 " pdb=" NE2 GLN A 377 " ideal model delta sigma weight residual 122.60 10.96 111.64 1.00e+00 1.00e+00 1.25e+04 angle pdb=" CG GLN A 377 " pdb=" CD GLN A 377 " pdb=" NE2 GLN A 377 " ideal model delta sigma weight residual 116.40 10.05 106.35 1.50e+00 4.44e-01 5.03e+03 angle pdb=" CG GLN A 377 " pdb=" CD GLN A 377 " pdb=" OE1 GLN A 377 " ideal model delta sigma weight residual 120.80 20.68 100.12 2.00e+00 2.50e-01 2.51e+03 angle pdb=" O SER F 186 " pdb=" C SER F 186 " pdb=" CA ASER F 186 " ideal model delta sigma weight residual 120.36 132.31 -11.95 1.08e+00 8.57e-01 1.22e+02 angle pdb=" O SER F 186 " pdb=" C SER F 186 " pdb=" CA BSER F 186 " ideal model delta sigma weight residual 120.36 132.27 -11.91 1.08e+00 8.57e-01 1.22e+02 ... (remaining 45174 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.68: 18189 18.68 - 37.36: 1286 37.36 - 56.04: 323 56.04 - 74.72: 57 74.72 - 93.40: 10 Dihedral angle restraints: 19865 sinusoidal: 7579 harmonic: 12286 Sorted by residual: dihedral pdb=" CA LEU A 588 " pdb=" C LEU A 588 " pdb=" N GLU A 589 " pdb=" CA GLU A 589 " ideal model delta harmonic sigma weight residual -180.00 -86.60 -93.40 0 5.00e+00 4.00e-02 3.49e+02 dihedral pdb=" C GLN A 377 " pdb=" N GLN A 377 " pdb=" CA GLN A 377 " pdb=" CB GLN A 377 " ideal model delta harmonic sigma weight residual -122.60 -159.32 36.72 0 2.50e+00 1.60e-01 2.16e+02 dihedral pdb=" N GLN A 377 " pdb=" C GLN A 377 " pdb=" CA GLN A 377 " pdb=" CB GLN A 377 " ideal model delta harmonic sigma weight residual 122.80 158.36 -35.56 0 2.50e+00 1.60e-01 2.02e+02 ... (remaining 19862 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.298: 5045 0.298 - 0.595: 24 0.595 - 0.893: 0 0.893 - 1.190: 1 1.190 - 1.488: 1 Chirality restraints: 5071 Sorted by residual: chirality pdb=" CA GLN A 377 " pdb=" N GLN A 377 " pdb=" C GLN A 377 " pdb=" CB GLN A 377 " both_signs ideal model delta sigma weight residual False 2.51 1.02 1.49 2.00e-01 2.50e+01 5.53e+01 chirality pdb=" CA ASN A 582 " pdb=" N ASN A 582 " pdb=" C ASN A 582 " pdb=" CB ASN A 582 " both_signs ideal model delta sigma weight residual False 2.51 1.55 0.96 2.00e-01 2.50e+01 2.30e+01 chirality pdb=" CA ASER H 186 " pdb=" N SER H 186 " pdb=" C SER H 186 " pdb=" CB ASER H 186 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.94e+00 ... (remaining 5068 not shown) Planarity restraints: 5872 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 374 " -0.017 2.00e-02 2.50e+03 3.30e-02 1.09e+01 pdb=" C VAL A 374 " 0.057 2.00e-02 2.50e+03 pdb=" O VAL A 374 " -0.021 2.00e-02 2.50e+03 pdb=" N VAL A 375 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO B 59 " 0.012 2.00e-02 2.50e+03 2.55e-02 6.50e+00 pdb=" C PRO B 59 " -0.044 2.00e-02 2.50e+03 pdb=" O PRO B 59 " 0.017 2.00e-02 2.50e+03 pdb=" N GLN B 60 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA C 678 " -0.012 2.00e-02 2.50e+03 2.44e-02 5.96e+00 pdb=" C ALA C 678 " 0.042 2.00e-02 2.50e+03 pdb=" O ALA C 678 " -0.016 2.00e-02 2.50e+03 pdb=" N CYS C 679 " -0.015 2.00e-02 2.50e+03 ... (remaining 5869 not shown) Histogram of nonbonded interaction distances: 1.14 - 1.89: 6 1.89 - 2.64: 235 2.64 - 3.39: 41369 3.39 - 4.15: 82364 4.15 - 4.90: 139994 Nonbonded interactions: 263968 Sorted by model distance: nonbonded pdb=" OD2 ASP A 49 " pdb=" NZ LYS A 52 " model vdw 1.135 2.520 nonbonded pdb=" O GLY A 154 " pdb=" CB ARG A 163 " model vdw 1.222 3.440 nonbonded pdb=" CG ASP A 49 " pdb=" NZ LYS A 52 " model vdw 1.237 3.350 nonbonded pdb=" CB ASP A 49 " pdb=" NZ LYS A 52 " model vdw 1.489 3.520 nonbonded pdb=" O GLY A 154 " pdb=" CG ARG A 163 " model vdw 1.806 3.440 ... (remaining 263963 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 'B' selection = chain 'C' } ncs_group { reference = (chain 'F' and (resid 1 through 159 or resid 161 through 185 or resid 187 throug \ h 221)) selection = (chain 'H' and (resid 1 through 24 or resid 32 through 159 or resid 161 through \ 185 or resid 187 through 221)) } ncs_group { reference = chain 'G' selection = chain 'K' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.40 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.210 Construct map_model_manager: 0.020 Extract box with map and model: 8.410 Check model and map are aligned: 0.390 Set scattering table: 0.230 Process input model: 85.700 Find NCS groups from input model: 1.490 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:12.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 111.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7101 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 : 0.014 0.712 33200 Z= 0.957 Angle : 1.755 111.639 45179 Z= 1.351 Chirality : 0.111 1.488 5071 Planarity : 0.004 0.033 5872 Dihedral : 13.582 93.401 11869 Min Nonbonded Distance : 1.135 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.60 % Allowed : 2.67 % Favored : 96.74 % Rotamer: Outliers : 8.77 % Allowed : 9.49 % Favored : 81.74 % Cbeta Deviations : 0.48 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 1.84 (0.13), residues: 4204 helix: 4.28 (0.18), residues: 744 sheet: 1.71 (0.16), residues: 1043 loop : 0.02 (0.12), residues: 2417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP H 110 HIS 0.004 0.001 HIS C 348 PHE 0.012 0.002 PHE A 850 TYR 0.024 0.002 TYR B 635 ARG 0.007 0.001 ARG A 758 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8408 Ramachandran restraints generated. 4204 Oldfield, 0 Emsley, 4204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8408 Ramachandran restraints generated. 4204 Oldfield, 0 Emsley, 4204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 906 residues out of total 3614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 312 poor density : 594 time to evaluate : 3.208 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: A 91 HIS cc_start: 0.5603 (m170) cc_final: 0.5258 (m170) REVERT: A 164 PHE cc_start: 0.7780 (m-80) cc_final: 0.7215 (m-80) REVERT: A 172 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8327 (pp) REVERT: A 189 PRO cc_start: 0.7837 (Cg_endo) cc_final: 0.7419 (Cg_exo) REVERT: A 234 LEU cc_start: 0.7649 (OUTLIER) cc_final: 0.7015 (mm) REVERT: A 587 LYS cc_start: 0.1126 (OUTLIER) cc_final: 0.0599 (mmtt) REVERT: A 609 TYR cc_start: 0.4175 (OUTLIER) cc_final: 0.3948 (m-10) REVERT: A 871 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8282 (pp) REVERT: A 960 TRP cc_start: 0.5711 (OUTLIER) cc_final: 0.5081 (p-90) REVERT: B 91 HIS cc_start: 0.5924 (m90) cc_final: 0.5393 (m170) REVERT: B 110 LYS cc_start: 0.7949 (OUTLIER) cc_final: 0.7634 (mtpt) REVERT: B 172 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8321 (pp) REVERT: B 189 PRO cc_start: 0.7548 (Cg_endo) cc_final: 0.7157 (Cg_exo) REVERT: B 234 LEU cc_start: 0.7534 (OUTLIER) cc_final: 0.6988 (mm) REVERT: B 960 TRP cc_start: 0.6401 (OUTLIER) cc_final: 0.5489 (m-90) REVERT: C 815 GLN cc_start: 0.7347 (OUTLIER) cc_final: 0.7093 (tm-30) REVERT: C 871 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8111 (pp) REVERT: C 960 TRP cc_start: 0.6254 (OUTLIER) cc_final: 0.5530 (m-90) outliers start: 312 outliers final: 54 residues processed: 846 average time/residue: 1.1660 time to fit residues: 1205.7125 Evaluate side-chains 385 residues out of total 3614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 318 time to evaluate : 3.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 208 HIS Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 367 GLU Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 587 LYS Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 609 TYR Chi-restraints excluded: chain A residue 802 VAL Chi-restraints excluded: chain A residue 828 CYS Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 872 THR Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 877 VAL Chi-restraints excluded: chain A residue 960 TRP Chi-restraints excluded: chain A residue 1054 ILE Chi-restraints excluded: chain A residue 1090 GLU Chi-restraints excluded: chain B residue 110 LYS Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 208 HIS Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain B residue 438 TYR Chi-restraints excluded: chain B residue 623 VAL Chi-restraints excluded: chain B residue 650 CYS Chi-restraints excluded: chain B residue 679 CYS Chi-restraints excluded: chain B residue 688 GLN Chi-restraints excluded: chain B residue 711 VAL Chi-restraints excluded: chain B residue 872 THR Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 877 VAL Chi-restraints excluded: chain B residue 960 TRP Chi-restraints excluded: chain B residue 983 VAL Chi-restraints excluded: chain B residue 1054 ILE Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 623 VAL Chi-restraints excluded: chain C residue 815 GLN Chi-restraints excluded: chain C residue 871 LEU Chi-restraints excluded: chain C residue 872 THR Chi-restraints excluded: chain C residue 873 LEU Chi-restraints excluded: chain C residue 874 LEU Chi-restraints excluded: chain C residue 877 VAL Chi-restraints excluded: chain C residue 960 TRP Chi-restraints excluded: chain C residue 1054 ILE Chi-restraints excluded: chain C residue 1180 ILE Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 6 GLN Chi-restraints excluded: chain F residue 54 ILE Chi-restraints excluded: chain F residue 70 ILE Chi-restraints excluded: chain F residue 118 VAL Chi-restraints excluded: chain G residue 190 HIS Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain K residue 111 VAL Chi-restraints excluded: chain K residue 116 VAL Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 164 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 422 random chunks: chunk 356 optimal weight: 20.0000 chunk 319 optimal weight: 0.9990 chunk 177 optimal weight: 0.9990 chunk 109 optimal weight: 0.9980 chunk 215 optimal weight: 0.8980 chunk 170 optimal weight: 3.9990 chunk 330 optimal weight: 1.9990 chunk 127 optimal weight: 5.9990 chunk 201 optimal weight: 0.9990 chunk 246 optimal weight: 6.9990 chunk 383 optimal weight: 0.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 GLN A 98 GLN A 167 HIS A 261 GLN A 377 GLN A 618 GLN A 628 GLN A 647 ASN A 812 ASN A 988 GLN A1009 GLN A1056 GLN A1145 ASN A1177 ASN A1208 GLN ** B 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 167 HIS B 244 ASN B 618 GLN B 637 ASN B 994 GLN B1056 GLN B1145 ASN B1160 ASN B1177 ASN C 72 GLN C 167 HIS C 516 GLN C 592 ASN C 618 GLN C 812 ASN ** C 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 819 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1020 GLN C1132 ASN C1145 ASN C1160 ASN C1177 ASN C1212 GLN F 178 GLN ** G 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 178 GLN H 199 GLN K 148 GLN Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 33200 Z= 0.234 Angle : 0.647 11.842 45179 Z= 0.345 Chirality : 0.046 0.232 5071 Planarity : 0.004 0.048 5872 Dihedral : 6.862 87.919 4703 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.36 % Favored : 97.43 % Rotamer: Outliers : 5.72 % Allowed : 16.71 % Favored : 77.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.15 % 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: 0.90 (0.12), residues: 4204 helix: 2.69 (0.18), residues: 769 sheet: 1.01 (0.15), residues: 1148 loop : -0.35 (0.12), residues: 2287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP F 47 HIS 0.010 0.001 HIS A 91 PHE 0.042 0.002 PHE C 418 TYR 0.034 0.001 TYR C 445 ARG 0.013 0.001 ARG A 629 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8408 Ramachandran restraints generated. 4204 Oldfield, 0 Emsley, 4204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8408 Ramachandran restraints generated. 4204 Oldfield, 0 Emsley, 4204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 533 residues out of total 3614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 202 poor density : 331 time to evaluate : 3.696 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: A 172 LEU cc_start: 0.8317 (pp) cc_final: 0.8086 (pp) REVERT: A 184 TYR cc_start: 0.6450 (OUTLIER) cc_final: 0.5287 (m-80) REVERT: A 251 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8676 (tp) REVERT: A 587 LYS cc_start: 0.1361 (OUTLIER) cc_final: 0.0680 (mmtt) REVERT: A 1175 THR cc_start: 0.7157 (OUTLIER) cc_final: 0.6912 (p) REVERT: B 172 LEU cc_start: 0.8551 (pp) cc_final: 0.8290 (pp) REVERT: B 184 TYR cc_start: 0.6185 (OUTLIER) cc_final: 0.5758 (m-80) REVERT: B 686 MET cc_start: 0.9059 (tpt) cc_final: 0.8508 (mmp) REVERT: C 110 LYS cc_start: 0.7942 (OUTLIER) cc_final: 0.7470 (mtpt) REVERT: C 184 TYR cc_start: 0.5680 (OUTLIER) cc_final: 0.5029 (m-80) REVERT: C 628 GLN cc_start: 0.7006 (OUTLIER) cc_final: 0.6208 (mt0) REVERT: C 808 GLN cc_start: 0.8871 (OUTLIER) cc_final: 0.8155 (tp40) REVERT: C 1180 ILE cc_start: 0.4617 (OUTLIER) cc_final: 0.4289 (pp) REVERT: H 208 LYS cc_start: 0.6990 (tppt) cc_final: 0.6778 (tptt) REVERT: K 101 GLN cc_start: 0.7039 (OUTLIER) cc_final: 0.6259 (mt0) outliers start: 202 outliers final: 78 residues processed: 507 average time/residue: 1.1255 time to fit residues: 704.0134 Evaluate side-chains 341 residues out of total 3614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 252 time to evaluate : 3.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 184 TYR Chi-restraints excluded: chain A residue 208 HIS Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 587 LYS Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 609 TYR Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 802 VAL Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 872 THR Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 877 VAL Chi-restraints excluded: chain A residue 960 TRP Chi-restraints excluded: chain A residue 1015 THR Chi-restraints excluded: chain A residue 1054 ILE Chi-restraints excluded: chain A residue 1175 THR Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 184 TYR Chi-restraints excluded: chain B residue 208 HIS Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 424 THR Chi-restraints excluded: chain B residue 438 TYR Chi-restraints excluded: chain B residue 502 LYS Chi-restraints excluded: chain B residue 623 VAL Chi-restraints excluded: chain B residue 661 VAL Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 688 GLN Chi-restraints excluded: chain B residue 779 LYS Chi-restraints excluded: chain B residue 872 THR Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 877 VAL Chi-restraints excluded: chain B residue 929 VAL Chi-restraints excluded: chain B residue 983 VAL Chi-restraints excluded: chain B residue 1015 THR Chi-restraints excluded: chain B residue 1043 THR Chi-restraints excluded: chain B residue 1054 ILE Chi-restraints excluded: chain C residue 110 LYS Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 181 ARG Chi-restraints excluded: chain C residue 184 TYR Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 426 SER Chi-restraints excluded: chain C residue 451 SER Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain C residue 496 LYS Chi-restraints excluded: chain C residue 628 GLN Chi-restraints excluded: chain C residue 662 ILE Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 808 GLN Chi-restraints excluded: chain C residue 872 THR Chi-restraints excluded: chain C residue 874 LEU Chi-restraints excluded: chain C residue 877 VAL Chi-restraints excluded: chain C residue 1015 THR Chi-restraints excluded: chain C residue 1054 ILE Chi-restraints excluded: chain C residue 1180 ILE Chi-restraints excluded: chain C residue 1216 THR Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 70 ILE Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 118 VAL Chi-restraints excluded: chain G residue 188 GLU Chi-restraints excluded: chain G residue 190 HIS Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 101 GLN Chi-restraints excluded: chain K residue 111 VAL Chi-restraints excluded: chain K residue 116 VAL Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 155 LEU Chi-restraints excluded: chain K residue 164 VAL Chi-restraints excluded: chain K residue 172 SER Chi-restraints excluded: chain K residue 206 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 422 random chunks: chunk 212 optimal weight: 0.9980 chunk 118 optimal weight: 0.0570 chunk 318 optimal weight: 1.9990 chunk 260 optimal weight: 5.9990 chunk 105 optimal weight: 0.9980 chunk 383 optimal weight: 5.9990 chunk 414 optimal weight: 6.9990 chunk 341 optimal weight: 5.9990 chunk 380 optimal weight: 0.9980 chunk 130 optimal weight: 4.9990 chunk 307 optimal weight: 2.9990 overall best weight: 1.0100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 GLN A 582 ASN A 994 GLN A1110 GLN ** B 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 501 ASN C 993 ASN C1029 ASN C1132 ASN ** G 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 39 GLN ** G 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 178 GLN H 199 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.3232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 33200 Z= 0.206 Angle : 0.591 11.023 45179 Z= 0.312 Chirality : 0.044 0.251 5071 Planarity : 0.004 0.043 5872 Dihedral : 6.056 89.048 4657 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.90 % Favored : 96.90 % Rotamer: Outliers : 5.27 % Allowed : 17.74 % Favored : 76.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.15 % 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: 0.64 (0.13), residues: 4204 helix: 2.42 (0.19), residues: 773 sheet: 0.80 (0.15), residues: 1132 loop : -0.46 (0.12), residues: 2299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP F 47 HIS 0.009 0.001 HIS F 207 PHE 0.026 0.002 PHE B 827 TYR 0.022 0.001 TYR C 445 ARG 0.010 0.001 ARG C1057 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8408 Ramachandran restraints generated. 4204 Oldfield, 0 Emsley, 4204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8408 Ramachandran restraints generated. 4204 Oldfield, 0 Emsley, 4204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 3614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 186 poor density : 282 time to evaluate : 3.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 LEU cc_start: 0.8313 (pp) cc_final: 0.8099 (pp) REVERT: A 184 TYR cc_start: 0.6365 (OUTLIER) cc_final: 0.4638 (m-80) REVERT: A 251 LEU cc_start: 0.9026 (OUTLIER) cc_final: 0.8769 (tp) REVERT: A 587 LYS cc_start: 0.0510 (OUTLIER) cc_final: -0.0001 (mmtt) REVERT: A 1175 THR cc_start: 0.7205 (OUTLIER) cc_final: 0.7005 (p) REVERT: B 67 ILE cc_start: 0.8864 (OUTLIER) cc_final: 0.8550 (pp) REVERT: B 110 LYS cc_start: 0.8045 (OUTLIER) cc_final: 0.7695 (mtpt) REVERT: B 172 LEU cc_start: 0.8572 (pp) cc_final: 0.8361 (pp) REVERT: B 184 TYR cc_start: 0.6227 (OUTLIER) cc_final: 0.4952 (m-80) REVERT: B 686 MET cc_start: 0.9160 (tpt) cc_final: 0.8628 (mmp) REVERT: B 929 VAL cc_start: 0.9003 (OUTLIER) cc_final: 0.8755 (p) REVERT: B 1008 MET cc_start: 0.7871 (OUTLIER) cc_final: 0.6986 (tpt) REVERT: C 110 LYS cc_start: 0.7970 (OUTLIER) cc_final: 0.7545 (mtpt) REVERT: C 148 MET cc_start: 0.8330 (ttm) cc_final: 0.8112 (ttm) REVERT: C 181 ARG cc_start: 0.8435 (OUTLIER) cc_final: 0.6997 (ptm160) REVERT: C 184 TYR cc_start: 0.5918 (OUTLIER) cc_final: 0.5117 (m-80) REVERT: C 628 GLN cc_start: 0.6990 (OUTLIER) cc_final: 0.6167 (mt0) REVERT: C 808 GLN cc_start: 0.8853 (OUTLIER) cc_final: 0.8107 (tp40) REVERT: C 907 GLN cc_start: 0.7586 (OUTLIER) cc_final: 0.7158 (pp30) REVERT: C 1180 ILE cc_start: 0.4587 (OUTLIER) cc_final: 0.4223 (pp) REVERT: H 29 PHE cc_start: 0.5922 (OUTLIER) cc_final: 0.5555 (t80) REVERT: K 101 GLN cc_start: 0.6957 (OUTLIER) cc_final: 0.6141 (mt0) outliers start: 186 outliers final: 85 residues processed: 439 average time/residue: 1.1168 time to fit residues: 608.6566 Evaluate side-chains 337 residues out of total 3614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 234 time to evaluate : 3.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 184 TYR Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 367 GLU Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 587 LYS Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 802 VAL Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 877 VAL Chi-restraints excluded: chain A residue 960 TRP Chi-restraints excluded: chain A residue 983 VAL Chi-restraints excluded: chain A residue 1054 ILE Chi-restraints excluded: chain A residue 1175 THR Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 110 LYS Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 184 TYR Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 424 THR Chi-restraints excluded: chain B residue 438 TYR Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 621 THR Chi-restraints excluded: chain B residue 623 VAL Chi-restraints excluded: chain B residue 679 CYS Chi-restraints excluded: chain B residue 682 ILE Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 688 GLN Chi-restraints excluded: chain B residue 779 LYS Chi-restraints excluded: chain B residue 862 ILE Chi-restraints excluded: chain B residue 871 LEU Chi-restraints excluded: chain B residue 872 THR Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 877 VAL Chi-restraints excluded: chain B residue 929 VAL Chi-restraints excluded: chain B residue 948 THR Chi-restraints excluded: chain B residue 1008 MET Chi-restraints excluded: chain B residue 1043 THR Chi-restraints excluded: chain B residue 1054 ILE Chi-restraints excluded: chain C residue 110 LYS Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 181 ARG Chi-restraints excluded: chain C residue 184 TYR Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 426 SER Chi-restraints excluded: chain C residue 451 SER Chi-restraints excluded: chain C residue 496 LYS Chi-restraints excluded: chain C residue 526 CYS Chi-restraints excluded: chain C residue 628 GLN Chi-restraints excluded: chain C residue 662 ILE Chi-restraints excluded: chain C residue 682 ILE Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 808 GLN Chi-restraints excluded: chain C residue 874 LEU Chi-restraints excluded: chain C residue 877 VAL Chi-restraints excluded: chain C residue 900 ILE Chi-restraints excluded: chain C residue 907 GLN Chi-restraints excluded: chain C residue 913 MET Chi-restraints excluded: chain C residue 964 LEU Chi-restraints excluded: chain C residue 1180 ILE Chi-restraints excluded: chain C residue 1216 THR Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 70 ILE Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 118 VAL Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 188 GLU Chi-restraints excluded: chain G residue 190 HIS Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain H residue 188 VAL Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 61 ASP Chi-restraints excluded: chain K residue 98 THR Chi-restraints excluded: chain K residue 101 GLN Chi-restraints excluded: chain K residue 105 VAL Chi-restraints excluded: chain K residue 116 VAL Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 155 LEU Chi-restraints excluded: chain K residue 164 VAL Chi-restraints excluded: chain K residue 197 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 422 random chunks: chunk 379 optimal weight: 1.9990 chunk 288 optimal weight: 3.9990 chunk 199 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 183 optimal weight: 0.9990 chunk 257 optimal weight: 20.0000 chunk 385 optimal weight: 3.9990 chunk 407 optimal weight: 0.5980 chunk 201 optimal weight: 4.9990 chunk 365 optimal weight: 30.0000 chunk 109 optimal weight: 6.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 GLN A 993 ASN A1110 GLN A1132 ASN ** B 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 GLN B 637 ASN B1056 GLN ** C 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 280 GLN ** C 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 647 ASN ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 GLN G 39 GLN ** G 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 62 GLN ** H 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.3817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 33200 Z= 0.360 Angle : 0.639 9.502 45179 Z= 0.339 Chirality : 0.047 0.459 5071 Planarity : 0.005 0.050 5872 Dihedral : 6.013 89.361 4642 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.33 % Favored : 96.40 % Rotamer: Outliers : 5.61 % Allowed : 17.93 % Favored : 76.46 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.15 % 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: 0.24 (0.12), residues: 4204 helix: 2.04 (0.19), residues: 760 sheet: 0.57 (0.15), residues: 1132 loop : -0.70 (0.12), residues: 2312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP F 47 HIS 0.009 0.001 HIS B1138 PHE 0.027 0.002 PHE B 827 TYR 0.020 0.002 TYR C 445 ARG 0.009 0.001 ARG A1057 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8408 Ramachandran restraints generated. 4204 Oldfield, 0 Emsley, 4204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8408 Ramachandran restraints generated. 4204 Oldfield, 0 Emsley, 4204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 3614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 198 poor density : 255 time to evaluate : 3.733 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: A 172 LEU cc_start: 0.8476 (pp) cc_final: 0.8260 (pp) REVERT: A 184 TYR cc_start: 0.6347 (OUTLIER) cc_final: 0.4971 (m-80) REVERT: A 225 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8611 (tp) REVERT: A 587 LYS cc_start: 0.0442 (OUTLIER) cc_final: -0.0053 (mmtt) REVERT: B 110 LYS cc_start: 0.8052 (OUTLIER) cc_final: 0.7611 (mtpt) REVERT: B 184 TYR cc_start: 0.6426 (OUTLIER) cc_final: 0.5596 (m-80) REVERT: B 219 TYR cc_start: 0.8076 (m-80) cc_final: 0.7813 (m-80) REVERT: B 872 THR cc_start: 0.9062 (OUTLIER) cc_final: 0.8827 (p) REVERT: B 1008 MET cc_start: 0.7831 (OUTLIER) cc_final: 0.6826 (tpt) REVERT: C 110 LYS cc_start: 0.8049 (OUTLIER) cc_final: 0.7638 (mtpt) REVERT: C 181 ARG cc_start: 0.8407 (OUTLIER) cc_final: 0.7021 (ptm160) REVERT: C 184 TYR cc_start: 0.5688 (OUTLIER) cc_final: 0.4855 (m-80) REVERT: C 628 GLN cc_start: 0.7352 (OUTLIER) cc_final: 0.6366 (mt0) REVERT: C 808 GLN cc_start: 0.8909 (OUTLIER) cc_final: 0.8115 (tp40) REVERT: C 907 GLN cc_start: 0.7745 (OUTLIER) cc_final: 0.7074 (pp30) REVERT: C 1180 ILE cc_start: 0.4918 (OUTLIER) cc_final: 0.4493 (pp) REVERT: F 118 VAL cc_start: -0.0229 (OUTLIER) cc_final: -0.0542 (t) REVERT: H 29 PHE cc_start: 0.6180 (OUTLIER) cc_final: 0.5839 (t80) REVERT: K 101 GLN cc_start: 0.7198 (OUTLIER) cc_final: 0.6396 (mt0) outliers start: 198 outliers final: 104 residues processed: 421 average time/residue: 1.0824 time to fit residues: 570.0883 Evaluate side-chains 352 residues out of total 3614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 231 time to evaluate : 3.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 184 TYR Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 367 GLU Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 587 LYS Chi-restraints excluded: chain A residue 612 SER Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 802 VAL Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 877 VAL Chi-restraints excluded: chain A residue 960 TRP Chi-restraints excluded: chain A residue 983 VAL Chi-restraints excluded: chain A residue 1015 THR Chi-restraints excluded: chain A residue 1054 ILE Chi-restraints excluded: chain A residue 1180 ILE Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 110 LYS Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 184 TYR Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 424 THR Chi-restraints excluded: chain B residue 438 TYR Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 502 LYS Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 621 THR Chi-restraints excluded: chain B residue 623 VAL Chi-restraints excluded: chain B residue 679 CYS Chi-restraints excluded: chain B residue 682 ILE Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 688 GLN Chi-restraints excluded: chain B residue 779 LYS Chi-restraints excluded: chain B residue 829 SER Chi-restraints excluded: chain B residue 871 LEU Chi-restraints excluded: chain B residue 872 THR Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 877 VAL Chi-restraints excluded: chain B residue 893 LEU Chi-restraints excluded: chain B residue 929 VAL Chi-restraints excluded: chain B residue 948 THR Chi-restraints excluded: chain B residue 1008 MET Chi-restraints excluded: chain B residue 1043 THR Chi-restraints excluded: chain B residue 1054 ILE Chi-restraints excluded: chain B residue 1055 ILE Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 110 LYS Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 181 ARG Chi-restraints excluded: chain C residue 184 TYR Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 451 SER Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain C residue 496 LYS Chi-restraints excluded: chain C residue 526 CYS Chi-restraints excluded: chain C residue 628 GLN Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 808 GLN Chi-restraints excluded: chain C residue 874 LEU Chi-restraints excluded: chain C residue 877 VAL Chi-restraints excluded: chain C residue 907 GLN Chi-restraints excluded: chain C residue 913 MET Chi-restraints excluded: chain C residue 964 LEU Chi-restraints excluded: chain C residue 1015 THR Chi-restraints excluded: chain C residue 1054 ILE Chi-restraints excluded: chain C residue 1180 ILE Chi-restraints excluded: chain C residue 1216 THR Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 70 ILE Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 118 VAL Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 190 THR Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 188 GLU Chi-restraints excluded: chain G residue 190 HIS Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain H residue 189 VAL Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 55 ARG Chi-restraints excluded: chain K residue 98 THR Chi-restraints excluded: chain K residue 101 GLN Chi-restraints excluded: chain K residue 103 THR Chi-restraints excluded: chain K residue 105 VAL Chi-restraints excluded: chain K residue 116 VAL Chi-restraints excluded: chain K residue 118 ILE Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 164 VAL Chi-restraints excluded: chain K residue 168 ASP Chi-restraints excluded: chain K residue 172 SER Chi-restraints excluded: chain K residue 197 VAL Chi-restraints excluded: chain K residue 206 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 422 random chunks: chunk 339 optimal weight: 10.0000 chunk 231 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 303 optimal weight: 5.9990 chunk 168 optimal weight: 0.9990 chunk 348 optimal weight: 40.0000 chunk 281 optimal weight: 0.8980 chunk 0 optimal weight: 9.9990 chunk 208 optimal weight: 0.7980 chunk 366 optimal weight: 9.9990 chunk 102 optimal weight: 0.6980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 HIS A 261 GLN ** A 681 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1110 GLN ** B 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 GLN ** B 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 576 GLN B1056 GLN ** C 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 91 HIS C 280 GLN ** C 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1029 ASN C1132 ASN ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 199 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.4082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.113 33200 Z= 0.257 Angle : 0.597 10.352 45179 Z= 0.314 Chirality : 0.046 0.636 5071 Planarity : 0.004 0.050 5872 Dihedral : 5.732 89.252 4640 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.52 % Favored : 96.24 % Rotamer: Outliers : 5.44 % Allowed : 18.48 % Favored : 76.08 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.15 % 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: 0.15 (0.12), residues: 4204 helix: 2.00 (0.19), residues: 755 sheet: 0.47 (0.15), residues: 1128 loop : -0.75 (0.12), residues: 2321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP F 47 HIS 0.008 0.001 HIS A1138 PHE 0.026 0.002 PHE B 827 TYR 0.019 0.001 TYR B 274 ARG 0.010 0.001 ARG A1057 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8408 Ramachandran restraints generated. 4204 Oldfield, 0 Emsley, 4204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8408 Ramachandran restraints generated. 4204 Oldfield, 0 Emsley, 4204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 3614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 192 poor density : 246 time to evaluate : 4.069 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 TYR cc_start: 0.6431 (OUTLIER) cc_final: 0.4838 (m-80) REVERT: A 225 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8580 (tp) REVERT: A 587 LYS cc_start: 0.0524 (OUTLIER) cc_final: 0.0105 (mmtt) REVERT: B 110 LYS cc_start: 0.7996 (OUTLIER) cc_final: 0.7585 (mtpt) REVERT: B 184 TYR cc_start: 0.6447 (OUTLIER) cc_final: 0.5340 (m-80) REVERT: B 219 TYR cc_start: 0.8289 (m-80) cc_final: 0.8025 (m-80) REVERT: B 235 ARG cc_start: 0.7352 (mmp80) cc_final: 0.7123 (mmt-90) REVERT: B 623 VAL cc_start: 0.8705 (OUTLIER) cc_final: 0.8430 (m) REVERT: B 1008 MET cc_start: 0.7680 (OUTLIER) cc_final: 0.6618 (tpt) REVERT: C 184 TYR cc_start: 0.5723 (OUTLIER) cc_final: 0.4897 (m-80) REVERT: C 225 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8375 (tp) REVERT: C 232 PHE cc_start: 0.8676 (m-80) cc_final: 0.8326 (m-80) REVERT: C 628 GLN cc_start: 0.7295 (OUTLIER) cc_final: 0.6273 (mt0) REVERT: C 808 GLN cc_start: 0.8915 (OUTLIER) cc_final: 0.8084 (tp40) REVERT: C 907 GLN cc_start: 0.7665 (OUTLIER) cc_final: 0.6920 (pp30) REVERT: C 1180 ILE cc_start: 0.5075 (OUTLIER) cc_final: 0.4668 (pp) REVERT: H 29 PHE cc_start: 0.6232 (OUTLIER) cc_final: 0.5961 (t80) REVERT: H 183 TYR cc_start: 0.5964 (OUTLIER) cc_final: 0.5457 (p90) outliers start: 192 outliers final: 99 residues processed: 407 average time/residue: 1.1384 time to fit residues: 576.9779 Evaluate side-chains 330 residues out of total 3614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 216 time to evaluate : 3.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 184 TYR Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 367 GLU Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 587 LYS Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 679 CYS Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 802 VAL Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 877 VAL Chi-restraints excluded: chain A residue 943 MET Chi-restraints excluded: chain A residue 960 TRP Chi-restraints excluded: chain A residue 983 VAL Chi-restraints excluded: chain A residue 1054 ILE Chi-restraints excluded: chain A residue 1180 ILE Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 110 LYS Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 184 TYR Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 424 THR Chi-restraints excluded: chain B residue 438 TYR Chi-restraints excluded: chain B residue 502 LYS Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 621 THR Chi-restraints excluded: chain B residue 623 VAL Chi-restraints excluded: chain B residue 662 ILE Chi-restraints excluded: chain B residue 679 CYS Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 688 GLN Chi-restraints excluded: chain B residue 779 LYS Chi-restraints excluded: chain B residue 829 SER Chi-restraints excluded: chain B residue 862 ILE Chi-restraints excluded: chain B residue 871 LEU Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 877 VAL Chi-restraints excluded: chain B residue 929 VAL Chi-restraints excluded: chain B residue 948 THR Chi-restraints excluded: chain B residue 1008 MET Chi-restraints excluded: chain B residue 1043 THR Chi-restraints excluded: chain B residue 1054 ILE Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 184 TYR Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 416 SER Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 451 SER Chi-restraints excluded: chain C residue 496 LYS Chi-restraints excluded: chain C residue 526 CYS Chi-restraints excluded: chain C residue 584 VAL Chi-restraints excluded: chain C residue 621 THR Chi-restraints excluded: chain C residue 628 GLN Chi-restraints excluded: chain C residue 679 CYS Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 808 GLN Chi-restraints excluded: chain C residue 874 LEU Chi-restraints excluded: chain C residue 877 VAL Chi-restraints excluded: chain C residue 907 GLN Chi-restraints excluded: chain C residue 964 LEU Chi-restraints excluded: chain C residue 1013 THR Chi-restraints excluded: chain C residue 1180 ILE Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 70 ILE Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 190 THR Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 188 GLU Chi-restraints excluded: chain G residue 190 HIS Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 57 ILE Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain H residue 183 TYR Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 98 THR Chi-restraints excluded: chain K residue 105 VAL Chi-restraints excluded: chain K residue 116 VAL Chi-restraints excluded: chain K residue 118 ILE Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 147 VAL Chi-restraints excluded: chain K residue 155 LEU Chi-restraints excluded: chain K residue 164 VAL Chi-restraints excluded: chain K residue 172 SER Chi-restraints excluded: chain K residue 197 VAL Chi-restraints excluded: chain K residue 206 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 422 random chunks: chunk 137 optimal weight: 2.9990 chunk 367 optimal weight: 5.9990 chunk 80 optimal weight: 0.9980 chunk 239 optimal weight: 8.9990 chunk 100 optimal weight: 0.7980 chunk 408 optimal weight: 7.9990 chunk 338 optimal weight: 8.9990 chunk 189 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 135 optimal weight: 3.9990 chunk 214 optimal weight: 0.8980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 HIS A 261 GLN ** A 681 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 GLN ** B 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1056 GLN B1217 ASN ** C 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 280 GLN ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1029 ASN C1132 ASN ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 199 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.4361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.100 33200 Z= 0.289 Angle : 0.618 12.158 45179 Z= 0.323 Chirality : 0.046 0.590 5071 Planarity : 0.004 0.053 5872 Dihedral : 5.650 87.526 4638 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.83 % Favored : 95.93 % Rotamer: Outliers : 5.33 % Allowed : 18.82 % Favored : 75.85 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.15 % 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: 0.03 (0.12), residues: 4204 helix: 1.91 (0.19), residues: 759 sheet: 0.33 (0.15), residues: 1161 loop : -0.80 (0.12), residues: 2284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP F 47 HIS 0.007 0.001 HIS B 208 PHE 0.027 0.002 PHE C 827 TYR 0.020 0.002 TYR C 445 ARG 0.009 0.001 ARG B 62 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8408 Ramachandran restraints generated. 4204 Oldfield, 0 Emsley, 4204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8408 Ramachandran restraints generated. 4204 Oldfield, 0 Emsley, 4204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 3614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 219 time to evaluate : 3.469 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: A 184 TYR cc_start: 0.6711 (OUTLIER) cc_final: 0.4988 (m-80) REVERT: A 225 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8529 (tp) REVERT: A 587 LYS cc_start: 0.0478 (OUTLIER) cc_final: 0.0085 (mmtt) REVERT: A 635 TYR cc_start: 0.8236 (m-80) cc_final: 0.7972 (m-80) REVERT: A 907 GLN cc_start: 0.7696 (OUTLIER) cc_final: 0.6590 (pp30) REVERT: B 110 LYS cc_start: 0.8010 (OUTLIER) cc_final: 0.7520 (mtpt) REVERT: B 174 ASP cc_start: 0.6885 (OUTLIER) cc_final: 0.6318 (m-30) REVERT: B 184 TYR cc_start: 0.6437 (OUTLIER) cc_final: 0.5415 (m-80) REVERT: B 219 TYR cc_start: 0.8281 (m-80) cc_final: 0.7972 (m-80) REVERT: B 330 ASP cc_start: 0.8390 (OUTLIER) cc_final: 0.8003 (p0) REVERT: B 623 VAL cc_start: 0.8679 (OUTLIER) cc_final: 0.8400 (m) REVERT: B 1090 GLU cc_start: 0.7533 (OUTLIER) cc_final: 0.7241 (mp0) REVERT: B 1105 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7667 (tt0) REVERT: C 110 LYS cc_start: 0.8081 (OUTLIER) cc_final: 0.7662 (mtpt) REVERT: C 169 LEU cc_start: 0.8470 (tt) cc_final: 0.8168 (tp) REVERT: C 184 TYR cc_start: 0.5767 (OUTLIER) cc_final: 0.4887 (m-80) REVERT: C 330 ASP cc_start: 0.8516 (OUTLIER) cc_final: 0.8169 (p0) REVERT: C 628 GLN cc_start: 0.7333 (OUTLIER) cc_final: 0.6314 (mt0) REVERT: C 808 GLN cc_start: 0.8951 (OUTLIER) cc_final: 0.8115 (tp40) REVERT: C 907 GLN cc_start: 0.7645 (OUTLIER) cc_final: 0.6808 (pp30) REVERT: C 1180 ILE cc_start: 0.5397 (OUTLIER) cc_final: 0.4987 (pp) REVERT: H 29 PHE cc_start: 0.6312 (OUTLIER) cc_final: 0.6036 (t80) REVERT: H 183 TYR cc_start: 0.5981 (OUTLIER) cc_final: 0.5237 (p90) REVERT: K 88 TYR cc_start: 0.7910 (m-80) cc_final: 0.7589 (m-80) outliers start: 188 outliers final: 114 residues processed: 380 average time/residue: 1.1251 time to fit residues: 528.2977 Evaluate side-chains 341 residues out of total 3614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 207 time to evaluate : 3.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 184 TYR Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 367 GLU Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 587 LYS Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 679 CYS Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 771 ASP Chi-restraints excluded: chain A residue 802 VAL Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 907 GLN Chi-restraints excluded: chain A residue 943 MET Chi-restraints excluded: chain A residue 960 TRP Chi-restraints excluded: chain A residue 983 VAL Chi-restraints excluded: chain A residue 1054 ILE Chi-restraints excluded: chain A residue 1180 ILE Chi-restraints excluded: chain A residue 1203 LYS Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 110 LYS Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 174 ASP Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 184 TYR Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain B residue 330 ASP Chi-restraints excluded: chain B residue 334 ARG Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 424 THR Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 438 TYR Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 502 LYS Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 621 THR Chi-restraints excluded: chain B residue 623 VAL Chi-restraints excluded: chain B residue 662 ILE Chi-restraints excluded: chain B residue 679 CYS Chi-restraints excluded: chain B residue 682 ILE Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 688 GLN Chi-restraints excluded: chain B residue 779 LYS Chi-restraints excluded: chain B residue 829 SER Chi-restraints excluded: chain B residue 862 ILE Chi-restraints excluded: chain B residue 871 LEU Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 929 VAL Chi-restraints excluded: chain B residue 948 THR Chi-restraints excluded: chain B residue 1043 THR Chi-restraints excluded: chain B residue 1054 ILE Chi-restraints excluded: chain B residue 1055 ILE Chi-restraints excluded: chain B residue 1090 GLU Chi-restraints excluded: chain B residue 1105 GLU Chi-restraints excluded: chain B residue 1180 ILE Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 110 LYS Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 184 TYR Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 330 ASP Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 451 SER Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 496 LYS Chi-restraints excluded: chain C residue 526 CYS Chi-restraints excluded: chain C residue 584 VAL Chi-restraints excluded: chain C residue 621 THR Chi-restraints excluded: chain C residue 623 VAL Chi-restraints excluded: chain C residue 628 GLN Chi-restraints excluded: chain C residue 669 THR Chi-restraints excluded: chain C residue 679 CYS Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 808 GLN Chi-restraints excluded: chain C residue 874 LEU Chi-restraints excluded: chain C residue 907 GLN Chi-restraints excluded: chain C residue 913 MET Chi-restraints excluded: chain C residue 964 LEU Chi-restraints excluded: chain C residue 1013 THR Chi-restraints excluded: chain C residue 1180 ILE Chi-restraints excluded: chain C residue 1216 THR Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 70 ILE Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 190 THR Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 188 GLU Chi-restraints excluded: chain G residue 190 HIS Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 57 ILE Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain H residue 183 TYR Chi-restraints excluded: chain H residue 189 VAL Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 78 ARG Chi-restraints excluded: chain K residue 98 THR Chi-restraints excluded: chain K residue 105 VAL Chi-restraints excluded: chain K residue 116 VAL Chi-restraints excluded: chain K residue 118 ILE Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 147 VAL Chi-restraints excluded: chain K residue 164 VAL Chi-restraints excluded: chain K residue 168 ASP Chi-restraints excluded: chain K residue 172 SER Chi-restraints excluded: chain K residue 197 VAL Chi-restraints excluded: chain K residue 206 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 422 random chunks: chunk 393 optimal weight: 6.9990 chunk 46 optimal weight: 5.9990 chunk 232 optimal weight: 9.9990 chunk 298 optimal weight: 2.9990 chunk 231 optimal weight: 1.9990 chunk 343 optimal weight: 0.1980 chunk 227 optimal weight: 1.9990 chunk 406 optimal weight: 9.9990 chunk 254 optimal weight: 6.9990 chunk 247 optimal weight: 3.9990 chunk 187 optimal weight: 10.0000 overall best weight: 2.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 HIS A 261 GLN A 681 HIS ** B 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 GLN B1217 ASN ** C 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 280 GLN ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 521 ASN ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 62 GLN H 199 GLN K 156 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.4620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.098 33200 Z= 0.349 Angle : 0.635 10.869 45179 Z= 0.334 Chirality : 0.047 0.584 5071 Planarity : 0.005 0.057 5872 Dihedral : 5.696 87.935 4634 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.10 % Favored : 95.64 % Rotamer: Outliers : 5.02 % Allowed : 19.04 % Favored : 75.94 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.15 % 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: -0.16 (0.12), residues: 4204 helix: 1.79 (0.19), residues: 759 sheet: 0.13 (0.14), residues: 1192 loop : -0.91 (0.12), residues: 2253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP F 47 HIS 0.008 0.001 HIS B1138 PHE 0.025 0.002 PHE B 827 TYR 0.017 0.002 TYR B 523 ARG 0.009 0.001 ARG B 921 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8408 Ramachandran restraints generated. 4204 Oldfield, 0 Emsley, 4204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8408 Ramachandran restraints generated. 4204 Oldfield, 0 Emsley, 4204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 3614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 232 time to evaluate : 3.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 TYR cc_start: 0.6513 (OUTLIER) cc_final: 0.4961 (m-80) REVERT: A 190 ARG cc_start: 0.6729 (mtp180) cc_final: 0.6379 (mtt180) REVERT: A 225 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8572 (tp) REVERT: A 907 GLN cc_start: 0.7717 (OUTLIER) cc_final: 0.6679 (pp30) REVERT: A 1180 ILE cc_start: 0.4265 (OUTLIER) cc_final: 0.3868 (pp) REVERT: B 42 LYS cc_start: 0.8539 (OUTLIER) cc_final: 0.8330 (mttm) REVERT: B 110 LYS cc_start: 0.8026 (OUTLIER) cc_final: 0.7479 (mtpt) REVERT: B 174 ASP cc_start: 0.6896 (OUTLIER) cc_final: 0.6362 (m-30) REVERT: B 184 TYR cc_start: 0.6490 (OUTLIER) cc_final: 0.5438 (m-80) REVERT: B 330 ASP cc_start: 0.8454 (OUTLIER) cc_final: 0.8109 (p0) REVERT: B 623 VAL cc_start: 0.8704 (OUTLIER) cc_final: 0.8425 (m) REVERT: B 1090 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.7401 (mp0) REVERT: B 1105 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7690 (tt0) REVERT: C 110 LYS cc_start: 0.8120 (OUTLIER) cc_final: 0.7691 (mtpt) REVERT: C 169 LEU cc_start: 0.8469 (tt) cc_final: 0.8173 (tp) REVERT: C 184 TYR cc_start: 0.5729 (OUTLIER) cc_final: 0.4826 (m-80) REVERT: C 225 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8434 (tp) REVERT: C 446 PHE cc_start: 0.5711 (OUTLIER) cc_final: 0.5448 (p90) REVERT: C 628 GLN cc_start: 0.7429 (OUTLIER) cc_final: 0.6374 (mt0) REVERT: C 808 GLN cc_start: 0.8957 (OUTLIER) cc_final: 0.8105 (tp40) REVERT: C 907 GLN cc_start: 0.7615 (OUTLIER) cc_final: 0.6730 (pp30) REVERT: C 1062 GLU cc_start: 0.7098 (OUTLIER) cc_final: 0.6838 (tp30) REVERT: F 68 ILE cc_start: 0.3393 (OUTLIER) cc_final: 0.2668 (tp) REVERT: H 29 PHE cc_start: 0.6688 (OUTLIER) cc_final: 0.6458 (t80) REVERT: H 183 TYR cc_start: 0.6081 (OUTLIER) cc_final: 0.5388 (p90) REVERT: K 88 TYR cc_start: 0.7960 (m-80) cc_final: 0.7691 (m-80) REVERT: K 101 GLN cc_start: 0.7435 (OUTLIER) cc_final: 0.6530 (mm-40) outliers start: 177 outliers final: 116 residues processed: 384 average time/residue: 1.2271 time to fit residues: 575.3036 Evaluate side-chains 355 residues out of total 3614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 215 time to evaluate : 3.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LYS Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 184 TYR Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 367 GLU Chi-restraints excluded: chain A residue 612 SER Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 679 CYS Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 771 ASP Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 907 GLN Chi-restraints excluded: chain A residue 943 MET Chi-restraints excluded: chain A residue 960 TRP Chi-restraints excluded: chain A residue 983 VAL Chi-restraints excluded: chain A residue 1054 ILE Chi-restraints excluded: chain A residue 1180 ILE Chi-restraints excluded: chain A residue 1203 LYS Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 110 LYS Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 174 ASP Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 184 TYR Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain B residue 330 ASP Chi-restraints excluded: chain B residue 334 ARG Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 420 VAL Chi-restraints excluded: chain B residue 424 THR Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 438 TYR Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 502 LYS Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 563 MET Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 621 THR Chi-restraints excluded: chain B residue 623 VAL Chi-restraints excluded: chain B residue 679 CYS Chi-restraints excluded: chain B residue 682 ILE Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 779 LYS Chi-restraints excluded: chain B residue 829 SER Chi-restraints excluded: chain B residue 862 ILE Chi-restraints excluded: chain B residue 871 LEU Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 877 VAL Chi-restraints excluded: chain B residue 893 LEU Chi-restraints excluded: chain B residue 929 VAL Chi-restraints excluded: chain B residue 948 THR Chi-restraints excluded: chain B residue 1043 THR Chi-restraints excluded: chain B residue 1054 ILE Chi-restraints excluded: chain B residue 1055 ILE Chi-restraints excluded: chain B residue 1090 GLU Chi-restraints excluded: chain B residue 1105 GLU Chi-restraints excluded: chain B residue 1180 ILE Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 110 LYS Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 156 PHE Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 184 TYR Chi-restraints excluded: chain C residue 212 THR Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 446 PHE Chi-restraints excluded: chain C residue 451 SER Chi-restraints excluded: chain C residue 496 LYS Chi-restraints excluded: chain C residue 526 CYS Chi-restraints excluded: chain C residue 584 VAL Chi-restraints excluded: chain C residue 621 THR Chi-restraints excluded: chain C residue 623 VAL Chi-restraints excluded: chain C residue 628 GLN Chi-restraints excluded: chain C residue 669 THR Chi-restraints excluded: chain C residue 679 CYS Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 808 GLN Chi-restraints excluded: chain C residue 874 LEU Chi-restraints excluded: chain C residue 907 GLN Chi-restraints excluded: chain C residue 913 MET Chi-restraints excluded: chain C residue 964 LEU Chi-restraints excluded: chain C residue 1013 THR Chi-restraints excluded: chain C residue 1062 GLU Chi-restraints excluded: chain C residue 1216 THR Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 68 ILE Chi-restraints excluded: chain F residue 70 ILE Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 190 THR Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 188 GLU Chi-restraints excluded: chain G residue 190 HIS Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 57 ILE Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain H residue 183 TYR Chi-restraints excluded: chain H residue 189 VAL Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 78 ARG Chi-restraints excluded: chain K residue 83 ASP Chi-restraints excluded: chain K residue 98 THR Chi-restraints excluded: chain K residue 101 GLN Chi-restraints excluded: chain K residue 105 VAL Chi-restraints excluded: chain K residue 116 VAL Chi-restraints excluded: chain K residue 118 ILE Chi-restraints excluded: chain K residue 147 VAL Chi-restraints excluded: chain K residue 172 SER Chi-restraints excluded: chain K residue 197 VAL Chi-restraints excluded: chain K residue 206 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 422 random chunks: chunk 251 optimal weight: 0.9990 chunk 162 optimal weight: 0.9980 chunk 242 optimal weight: 0.9980 chunk 122 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 258 optimal weight: 10.0000 chunk 277 optimal weight: 7.9990 chunk 201 optimal weight: 3.9990 chunk 37 optimal weight: 5.9990 chunk 319 optimal weight: 6.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 HIS A 261 GLN A1009 GLN ** B 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 GLN ** C 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 280 GLN ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1029 ASN C1132 ASN F 6 GLN ** G 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 199 GLN ** K 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.4692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.099 33200 Z= 0.250 Angle : 0.612 15.593 45179 Z= 0.317 Chirality : 0.045 0.561 5071 Planarity : 0.004 0.056 5872 Dihedral : 5.265 47.758 4621 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.93 % Favored : 95.86 % Rotamer: Outliers : 4.64 % Allowed : 19.48 % Favored : 75.88 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.15 % 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: -0.12 (0.13), residues: 4204 helix: 1.89 (0.19), residues: 758 sheet: 0.12 (0.14), residues: 1178 loop : -0.87 (0.12), residues: 2268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP F 47 HIS 0.006 0.001 HIS B 208 PHE 0.024 0.001 PHE C 827 TYR 0.021 0.001 TYR C 445 ARG 0.008 0.001 ARG A1057 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8408 Ramachandran restraints generated. 4204 Oldfield, 0 Emsley, 4204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8408 Ramachandran restraints generated. 4204 Oldfield, 0 Emsley, 4204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 3614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 216 time to evaluate : 3.626 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: A 184 TYR cc_start: 0.6583 (OUTLIER) cc_final: 0.4958 (m-80) REVERT: A 190 ARG cc_start: 0.6771 (mtp180) cc_final: 0.6561 (mtt180) REVERT: A 225 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8542 (tp) REVERT: A 700 ARG cc_start: 0.7083 (OUTLIER) cc_final: 0.6777 (pmt-80) REVERT: A 1180 ILE cc_start: 0.4173 (OUTLIER) cc_final: 0.3852 (pp) REVERT: B 42 LYS cc_start: 0.8533 (OUTLIER) cc_final: 0.8326 (mttm) REVERT: B 174 ASP cc_start: 0.6883 (OUTLIER) cc_final: 0.6360 (m-30) REVERT: B 184 TYR cc_start: 0.6350 (OUTLIER) cc_final: 0.5436 (m-80) REVERT: B 232 PHE cc_start: 0.8223 (m-80) cc_final: 0.7988 (m-80) REVERT: B 623 VAL cc_start: 0.8755 (OUTLIER) cc_final: 0.8430 (m) REVERT: B 1090 GLU cc_start: 0.7613 (OUTLIER) cc_final: 0.7361 (mp0) REVERT: C 110 LYS cc_start: 0.8049 (OUTLIER) cc_final: 0.7626 (mtpt) REVERT: C 169 LEU cc_start: 0.8500 (tt) cc_final: 0.8170 (tp) REVERT: C 184 TYR cc_start: 0.5719 (OUTLIER) cc_final: 0.4897 (m-80) REVERT: C 628 GLN cc_start: 0.7350 (OUTLIER) cc_final: 0.6344 (mm-40) REVERT: C 808 GLN cc_start: 0.8944 (OUTLIER) cc_final: 0.8100 (tp40) REVERT: C 907 GLN cc_start: 0.7617 (OUTLIER) cc_final: 0.6775 (pp30) REVERT: C 1180 ILE cc_start: 0.5512 (OUTLIER) cc_final: 0.5087 (pp) REVERT: H 29 PHE cc_start: 0.6823 (OUTLIER) cc_final: 0.6610 (t80) REVERT: H 183 TYR cc_start: 0.6067 (OUTLIER) cc_final: 0.5331 (p90) REVERT: K 88 TYR cc_start: 0.7904 (m-80) cc_final: 0.7602 (m-80) outliers start: 163 outliers final: 107 residues processed: 357 average time/residue: 1.1686 time to fit residues: 514.9530 Evaluate side-chains 329 residues out of total 3614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 205 time to evaluate : 3.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LYS Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 184 TYR Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 367 GLU Chi-restraints excluded: chain A residue 612 SER Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 679 CYS Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain A residue 700 ARG Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 960 TRP Chi-restraints excluded: chain A residue 983 VAL Chi-restraints excluded: chain A residue 1054 ILE Chi-restraints excluded: chain A residue 1180 ILE Chi-restraints excluded: chain A residue 1203 LYS Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 174 ASP Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 184 TYR Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain B residue 334 ARG Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 424 THR Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 438 TYR Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 502 LYS Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 563 MET Chi-restraints excluded: chain B residue 621 THR Chi-restraints excluded: chain B residue 623 VAL Chi-restraints excluded: chain B residue 679 CYS Chi-restraints excluded: chain B residue 682 ILE Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 779 LYS Chi-restraints excluded: chain B residue 829 SER Chi-restraints excluded: chain B residue 862 ILE Chi-restraints excluded: chain B residue 871 LEU Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 929 VAL Chi-restraints excluded: chain B residue 948 THR Chi-restraints excluded: chain B residue 1043 THR Chi-restraints excluded: chain B residue 1054 ILE Chi-restraints excluded: chain B residue 1090 GLU Chi-restraints excluded: chain B residue 1180 ILE Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 110 LYS Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 156 PHE Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 184 TYR Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 451 SER Chi-restraints excluded: chain C residue 496 LYS Chi-restraints excluded: chain C residue 526 CYS Chi-restraints excluded: chain C residue 584 VAL Chi-restraints excluded: chain C residue 621 THR Chi-restraints excluded: chain C residue 623 VAL Chi-restraints excluded: chain C residue 628 GLN Chi-restraints excluded: chain C residue 669 THR Chi-restraints excluded: chain C residue 679 CYS Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 808 GLN Chi-restraints excluded: chain C residue 829 SER Chi-restraints excluded: chain C residue 874 LEU Chi-restraints excluded: chain C residue 907 GLN Chi-restraints excluded: chain C residue 913 MET Chi-restraints excluded: chain C residue 948 THR Chi-restraints excluded: chain C residue 964 LEU Chi-restraints excluded: chain C residue 1180 ILE Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 70 ILE Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 190 THR Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 188 GLU Chi-restraints excluded: chain G residue 190 HIS Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 57 ILE Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain H residue 131 LEU Chi-restraints excluded: chain H residue 183 TYR Chi-restraints excluded: chain H residue 189 VAL Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 78 ARG Chi-restraints excluded: chain K residue 98 THR Chi-restraints excluded: chain K residue 105 VAL Chi-restraints excluded: chain K residue 116 VAL Chi-restraints excluded: chain K residue 118 ILE Chi-restraints excluded: chain K residue 147 VAL Chi-restraints excluded: chain K residue 197 VAL Chi-restraints excluded: chain K residue 206 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 422 random chunks: chunk 369 optimal weight: 7.9990 chunk 389 optimal weight: 2.9990 chunk 355 optimal weight: 50.0000 chunk 379 optimal weight: 0.4980 chunk 228 optimal weight: 7.9990 chunk 165 optimal weight: 7.9990 chunk 297 optimal weight: 6.9990 chunk 116 optimal weight: 0.0980 chunk 342 optimal weight: 50.0000 chunk 358 optimal weight: 40.0000 chunk 377 optimal weight: 50.0000 overall best weight: 3.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 HIS ** B 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 636 GLN ** G 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 148 GLN ** H 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.5002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.109 33200 Z= 0.538 Angle : 0.733 15.140 45179 Z= 0.385 Chirality : 0.051 0.571 5071 Planarity : 0.005 0.060 5872 Dihedral : 5.824 55.943 4621 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.29 % Allowed : 4.76 % Favored : 94.95 % Rotamer: Outliers : 4.66 % Allowed : 19.43 % Favored : 75.91 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.15 % 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: -0.47 (0.12), residues: 4204 helix: 1.52 (0.19), residues: 748 sheet: -0.09 (0.14), residues: 1153 loop : -1.06 (0.12), residues: 2303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP F 47 HIS 0.011 0.002 HIS A1138 PHE 0.025 0.003 PHE C 827 TYR 0.038 0.002 TYR C 445 ARG 0.009 0.001 ARG K 62 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8408 Ramachandran restraints generated. 4204 Oldfield, 0 Emsley, 4204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8408 Ramachandran restraints generated. 4204 Oldfield, 0 Emsley, 4204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 3614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 222 time to evaluate : 4.007 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 TYR cc_start: 0.6581 (OUTLIER) cc_final: 0.4972 (m-80) REVERT: A 190 ARG cc_start: 0.6815 (mtp180) cc_final: 0.6425 (mtt180) REVERT: A 225 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8638 (tp) REVERT: A 1180 ILE cc_start: 0.4358 (OUTLIER) cc_final: 0.3975 (pp) REVERT: B 42 LYS cc_start: 0.8596 (OUTLIER) cc_final: 0.8378 (mttm) REVERT: B 174 ASP cc_start: 0.7039 (OUTLIER) cc_final: 0.6422 (m-30) REVERT: B 184 TYR cc_start: 0.6508 (OUTLIER) cc_final: 0.5403 (m-80) REVERT: B 330 ASP cc_start: 0.8534 (OUTLIER) cc_final: 0.8207 (p0) REVERT: B 623 VAL cc_start: 0.8740 (OUTLIER) cc_final: 0.8469 (m) REVERT: B 907 GLN cc_start: 0.7690 (OUTLIER) cc_final: 0.7398 (pp30) REVERT: B 1008 MET cc_start: 0.8467 (tmm) cc_final: 0.8011 (ttp) REVERT: B 1090 GLU cc_start: 0.7714 (OUTLIER) cc_final: 0.7455 (mp0) REVERT: C 110 LYS cc_start: 0.8192 (OUTLIER) cc_final: 0.7753 (mtpt) REVERT: C 169 LEU cc_start: 0.8519 (tt) cc_final: 0.8211 (tp) REVERT: C 184 TYR cc_start: 0.5821 (OUTLIER) cc_final: 0.4872 (m-80) REVERT: C 628 GLN cc_start: 0.7648 (OUTLIER) cc_final: 0.6563 (mt0) REVERT: C 808 GLN cc_start: 0.8962 (OUTLIER) cc_final: 0.8099 (tp40) REVERT: C 907 GLN cc_start: 0.7632 (OUTLIER) cc_final: 0.6845 (pp30) REVERT: C 960 TRP cc_start: 0.6796 (OUTLIER) cc_final: 0.6182 (m-90) REVERT: C 1062 GLU cc_start: 0.7231 (OUTLIER) cc_final: 0.6963 (tp30) REVERT: C 1180 ILE cc_start: 0.5732 (OUTLIER) cc_final: 0.5304 (pp) REVERT: H 29 PHE cc_start: 0.7155 (OUTLIER) cc_final: 0.6916 (t80) REVERT: H 183 TYR cc_start: 0.6233 (OUTLIER) cc_final: 0.5314 (p90) REVERT: K 101 GLN cc_start: 0.7457 (OUTLIER) cc_final: 0.6512 (mm-40) outliers start: 164 outliers final: 107 residues processed: 364 average time/residue: 1.2675 time to fit residues: 573.8004 Evaluate side-chains 334 residues out of total 3614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 206 time to evaluate : 3.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 52 LYS Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 184 TYR Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 367 GLU Chi-restraints excluded: chain A residue 612 SER Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 679 CYS Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 960 TRP Chi-restraints excluded: chain A residue 983 VAL Chi-restraints excluded: chain A residue 1054 ILE Chi-restraints excluded: chain A residue 1180 ILE Chi-restraints excluded: chain A residue 1203 LYS Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 174 ASP Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 184 TYR Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain B residue 330 ASP Chi-restraints excluded: chain B residue 334 ARG Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 424 THR Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 438 TYR Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 502 LYS Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 563 MET Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 621 THR Chi-restraints excluded: chain B residue 623 VAL Chi-restraints excluded: chain B residue 679 CYS Chi-restraints excluded: chain B residue 682 ILE Chi-restraints excluded: chain B residue 779 LYS Chi-restraints excluded: chain B residue 829 SER Chi-restraints excluded: chain B residue 862 ILE Chi-restraints excluded: chain B residue 871 LEU Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 877 VAL Chi-restraints excluded: chain B residue 893 LEU Chi-restraints excluded: chain B residue 907 GLN Chi-restraints excluded: chain B residue 929 VAL Chi-restraints excluded: chain B residue 948 THR Chi-restraints excluded: chain B residue 1043 THR Chi-restraints excluded: chain B residue 1054 ILE Chi-restraints excluded: chain B residue 1055 ILE Chi-restraints excluded: chain B residue 1090 GLU Chi-restraints excluded: chain B residue 1180 ILE Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 110 LYS Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 156 PHE Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 184 TYR Chi-restraints excluded: chain C residue 212 THR Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 451 SER Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 496 LYS Chi-restraints excluded: chain C residue 526 CYS Chi-restraints excluded: chain C residue 621 THR Chi-restraints excluded: chain C residue 628 GLN Chi-restraints excluded: chain C residue 669 THR Chi-restraints excluded: chain C residue 679 CYS Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 808 GLN Chi-restraints excluded: chain C residue 829 SER Chi-restraints excluded: chain C residue 874 LEU Chi-restraints excluded: chain C residue 907 GLN Chi-restraints excluded: chain C residue 913 MET Chi-restraints excluded: chain C residue 948 THR Chi-restraints excluded: chain C residue 960 TRP Chi-restraints excluded: chain C residue 1062 GLU Chi-restraints excluded: chain C residue 1180 ILE Chi-restraints excluded: chain C residue 1216 THR Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 190 THR Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 188 GLU Chi-restraints excluded: chain G residue 190 HIS Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 57 ILE Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain H residue 183 TYR Chi-restraints excluded: chain H residue 189 VAL Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 83 ASP Chi-restraints excluded: chain K residue 98 THR Chi-restraints excluded: chain K residue 101 GLN Chi-restraints excluded: chain K residue 105 VAL Chi-restraints excluded: chain K residue 116 VAL Chi-restraints excluded: chain K residue 118 ILE Chi-restraints excluded: chain K residue 147 VAL Chi-restraints excluded: chain K residue 197 VAL Chi-restraints excluded: chain K residue 206 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 422 random chunks: chunk 248 optimal weight: 0.6980 chunk 400 optimal weight: 9.9990 chunk 244 optimal weight: 1.9990 chunk 190 optimal weight: 0.9990 chunk 278 optimal weight: 2.9990 chunk 420 optimal weight: 1.9990 chunk 386 optimal weight: 1.9990 chunk 334 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 258 optimal weight: 9.9990 chunk 205 optimal weight: 0.7980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 HIS A 261 GLN A1009 GLN ** B 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 280 GLN G 39 GLN ** G 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 190 HIS ** H 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 125 GLN ** K 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.4961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.107 33200 Z= 0.222 Angle : 0.627 13.985 45179 Z= 0.325 Chirality : 0.045 0.558 5071 Planarity : 0.004 0.057 5872 Dihedral : 5.343 49.456 4619 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.10 % Favored : 95.71 % Rotamer: Outliers : 3.16 % Allowed : 21.09 % Favored : 75.74 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.15 % 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: -0.21 (0.12), residues: 4204 helix: 1.91 (0.19), residues: 742 sheet: 0.02 (0.15), residues: 1150 loop : -0.92 (0.12), residues: 2312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.002 TRP F 47 HIS 0.006 0.001 HIS B 208 PHE 0.024 0.001 PHE C 827 TYR 0.025 0.001 TYR C 445 ARG 0.008 0.001 ARG A1057 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8408 Ramachandran restraints generated. 4204 Oldfield, 0 Emsley, 4204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8408 Ramachandran restraints generated. 4204 Oldfield, 0 Emsley, 4204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 3614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 212 time to evaluate : 3.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 TYR cc_start: 0.6428 (OUTLIER) cc_final: 0.4983 (m-80) REVERT: A 190 ARG cc_start: 0.6755 (mtp180) cc_final: 0.6429 (mtt180) REVERT: A 225 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8537 (tp) REVERT: A 1180 ILE cc_start: 0.4434 (OUTLIER) cc_final: 0.4094 (pp) REVERT: B 42 LYS cc_start: 0.8616 (OUTLIER) cc_final: 0.8407 (mttm) REVERT: B 174 ASP cc_start: 0.6885 (OUTLIER) cc_final: 0.6379 (m-30) REVERT: B 184 TYR cc_start: 0.6518 (OUTLIER) cc_final: 0.5493 (m-80) REVERT: B 232 PHE cc_start: 0.8121 (m-80) cc_final: 0.7711 (m-80) REVERT: B 235 ARG cc_start: 0.7358 (mmp80) cc_final: 0.7037 (mmp80) REVERT: B 330 ASP cc_start: 0.8475 (OUTLIER) cc_final: 0.8134 (p0) REVERT: B 623 VAL cc_start: 0.8701 (OUTLIER) cc_final: 0.8409 (m) REVERT: B 1090 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.7412 (mp0) REVERT: C 184 TYR cc_start: 0.5857 (OUTLIER) cc_final: 0.5065 (m-80) REVERT: C 628 GLN cc_start: 0.7397 (OUTLIER) cc_final: 0.6369 (mt0) REVERT: C 808 GLN cc_start: 0.8933 (OUTLIER) cc_final: 0.8089 (tp40) REVERT: C 1180 ILE cc_start: 0.5695 (OUTLIER) cc_final: 0.5260 (pp) REVERT: H 29 PHE cc_start: 0.7138 (OUTLIER) cc_final: 0.6877 (t80) outliers start: 110 outliers final: 84 residues processed: 309 average time/residue: 1.1717 time to fit residues: 446.2270 Evaluate side-chains 301 residues out of total 3614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 203 time to evaluate : 2.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LYS Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 184 TYR Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 367 GLU Chi-restraints excluded: chain A residue 612 SER Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 679 CYS Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 960 TRP Chi-restraints excluded: chain A residue 983 VAL Chi-restraints excluded: chain A residue 1054 ILE Chi-restraints excluded: chain A residue 1180 ILE Chi-restraints excluded: chain A residue 1203 LYS Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 174 ASP Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 184 TYR Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain B residue 330 ASP Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 424 THR Chi-restraints excluded: chain B residue 438 TYR Chi-restraints excluded: chain B residue 502 LYS Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 563 MET Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 623 VAL Chi-restraints excluded: chain B residue 679 CYS Chi-restraints excluded: chain B residue 682 ILE Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 779 LYS Chi-restraints excluded: chain B residue 829 SER Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 900 ILE Chi-restraints excluded: chain B residue 929 VAL Chi-restraints excluded: chain B residue 948 THR Chi-restraints excluded: chain B residue 1043 THR Chi-restraints excluded: chain B residue 1054 ILE Chi-restraints excluded: chain B residue 1090 GLU Chi-restraints excluded: chain B residue 1180 ILE Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 156 PHE Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 184 TYR Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain C residue 388 LEU Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 451 SER Chi-restraints excluded: chain C residue 526 CYS Chi-restraints excluded: chain C residue 628 GLN Chi-restraints excluded: chain C residue 679 CYS Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 808 GLN Chi-restraints excluded: chain C residue 829 SER Chi-restraints excluded: chain C residue 874 LEU Chi-restraints excluded: chain C residue 913 MET Chi-restraints excluded: chain C residue 948 THR Chi-restraints excluded: chain C residue 1180 ILE Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 190 THR Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 188 GLU Chi-restraints excluded: chain G residue 190 HIS Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 189 VAL Chi-restraints excluded: chain K residue 105 VAL Chi-restraints excluded: chain K residue 116 VAL Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 197 VAL Chi-restraints excluded: chain K residue 206 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 422 random chunks: chunk 265 optimal weight: 9.9990 chunk 356 optimal weight: 0.9990 chunk 102 optimal weight: 1.9990 chunk 308 optimal weight: 1.9990 chunk 49 optimal weight: 0.0870 chunk 93 optimal weight: 1.9990 chunk 335 optimal weight: 2.9990 chunk 140 optimal weight: 0.7980 chunk 344 optimal weight: 20.0000 chunk 42 optimal weight: 4.9990 chunk 61 optimal weight: 6.9990 overall best weight: 1.1764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 HIS A1009 GLN ** B 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1056 GLN ** C 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 280 GLN ** G 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 199 GLN K 125 GLN ** K 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.118274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.081781 restraints weight = 98645.628| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 3.30 r_work: 0.3101 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3129 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3129 r_free = 0.3129 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3129 r_free = 0.3129 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3129 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.5006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.098 33200 Z= 0.237 Angle : 0.621 12.513 45179 Z= 0.321 Chirality : 0.045 0.539 5071 Planarity : 0.004 0.058 5872 Dihedral : 5.238 46.729 4619 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.45 % Favored : 95.38 % Rotamer: Outliers : 3.39 % Allowed : 20.98 % Favored : 75.63 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.15 % 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: -0.17 (0.13), residues: 4204 helix: 1.98 (0.19), residues: 743 sheet: 0.05 (0.15), residues: 1149 loop : -0.90 (0.12), residues: 2312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.001 TRP F 47 HIS 0.006 0.001 HIS B 208 PHE 0.038 0.001 PHE C 165 TYR 0.024 0.001 TYR C 445 ARG 0.007 0.001 ARG A1057 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11599.41 seconds wall clock time: 210 minutes 58.94 seconds (12658.94 seconds total)