Starting phenix.real_space_refine on Wed Mar 13 12:02:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pp6_13580/03_2024/7pp6_13580_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pp6_13580/03_2024/7pp6_13580.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pp6_13580/03_2024/7pp6_13580.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pp6_13580/03_2024/7pp6_13580.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pp6_13580/03_2024/7pp6_13580_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pp6_13580/03_2024/7pp6_13580_trim.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.021 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 12 9.91 5 S 456 5.16 5 C 21562 2.51 5 N 6002 2.21 5 O 6828 1.98 5 H 31702 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 122": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 426": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 122": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 426": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 1142": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 868": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 890": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 923": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 949": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 984": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 1007": "OD1" <-> "OD2" Residue "C ASP 1185": "OD1" <-> "OD2" Residue "D PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 122": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 415": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 585": "OE1" <-> "OE2" Residue "D TYR 610": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 611": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 721": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 863": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 868": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 884": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 1143": "OE1" <-> "OE2" Residue "D ASP 1193": "OD1" <-> "OD2" Residue "E PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 122": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 132": "OD1" <-> "OD2" Residue "E TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 171": "OD1" <-> "OD2" Residue "E GLU 365": "OE1" <-> "OE2" Residue "E TYR 407": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 482": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 595": "OE1" <-> "OE2" Residue "E TYR 610": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ASP 827": "OD1" <-> "OD2" Residue "G TYR 863": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 868": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 884": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 932": "OE1" <-> "OE2" Residue "G TYR 984": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ASP 1016": "OD1" <-> "OD2" Residue "G PHE 1017": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ASP 1087": "OD1" <-> "OD2" Residue "G TYR 1123": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 1142": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 1159": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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: 66562 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 10088 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 708, 10053 Classifications: {'peptide': 708} Link IDs: {'PCIS': 3, 'PTRANS': 29, 'TRANS': 675} Chain breaks: 2 Unresolved non-hydrogen bonds: 166 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 134 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 6, 'TYR:plan': 2, 'HIS:plan': 1, 'GLU:plan': 11, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 114 Conformer: "B" Number of residues, atoms: 708, 10053 Classifications: {'peptide': 708} Link IDs: {'PCIS': 3, 'PTRANS': 29, 'TRANS': 675} Chain breaks: 2 Unresolved non-hydrogen bonds: 166 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 134 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 6, 'TYR:plan': 2, 'HIS:plan': 1, 'GLU:plan': 11, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 114 bond proxies already assigned to first conformer: 10135 Chain: "B" Number of atoms: 16569 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1148, 16499 Classifications: {'peptide': 1148} Link IDs: {'PCIS': 3, 'PTRANS': 52, 'TRANS': 1092} Chain breaks: 6 Unresolved non-hydrogen bonds: 231 Unresolved non-hydrogen angles: 292 Unresolved non-hydrogen dihedrals: 195 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 7, 'TYR:plan': 4, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 15, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 172 Conformer: "B" Number of residues, atoms: 1148, 16499 Classifications: {'peptide': 1148} Link IDs: {'PCIS': 3, 'PTRANS': 52, 'TRANS': 1092} Chain breaks: 6 Unresolved non-hydrogen bonds: 231 Unresolved non-hydrogen angles: 292 Unresolved non-hydrogen dihedrals: 195 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 7, 'TYR:plan': 4, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 15, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 172 bond proxies already assigned to first conformer: 16625 Chain: "C" Number of atoms: 6460 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 440, 6446 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 23, 'TRANS': 416} Chain breaks: 3 Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 61 Planarities with less than four sites: {'HIS:plan': 1, 'TYR:plan': 2, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 58 Conformer: "B" Number of residues, atoms: 440, 6446 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 23, 'TRANS': 416} Chain breaks: 3 Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 61 Planarities with less than four sites: {'HIS:plan': 1, 'TYR:plan': 2, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 58 bond proxies already assigned to first conformer: 6512 Chain: "D" Number of atoms: 16569 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1148, 16499 Classifications: {'peptide': 1148} Link IDs: {'PCIS': 3, 'PTRANS': 52, 'TRANS': 1092} Chain breaks: 6 Unresolved non-hydrogen bonds: 231 Unresolved non-hydrogen angles: 292 Unresolved non-hydrogen dihedrals: 195 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 7, 'TYR:plan': 4, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 15, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 172 Conformer: "B" Number of residues, atoms: 1148, 16499 Classifications: {'peptide': 1148} Link IDs: {'PCIS': 3, 'PTRANS': 52, 'TRANS': 1092} Chain breaks: 6 Unresolved non-hydrogen bonds: 231 Unresolved non-hydrogen angles: 292 Unresolved non-hydrogen dihedrals: 195 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 7, 'TYR:plan': 4, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 15, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 172 bond proxies already assigned to first conformer: 16625 Chain: "E" Number of atoms: 10088 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 708, 10053 Classifications: {'peptide': 708} Link IDs: {'PCIS': 3, 'PTRANS': 29, 'TRANS': 675} Chain breaks: 2 Unresolved non-hydrogen bonds: 166 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 134 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 6, 'TYR:plan': 2, 'HIS:plan': 1, 'GLU:plan': 11, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 114 Conformer: "B" Number of residues, atoms: 708, 10053 Classifications: {'peptide': 708} Link IDs: {'PCIS': 3, 'PTRANS': 29, 'TRANS': 675} Chain breaks: 2 Unresolved non-hydrogen bonds: 166 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 134 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 6, 'TYR:plan': 2, 'HIS:plan': 1, 'GLU:plan': 11, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 114 bond proxies already assigned to first conformer: 10135 Chain: "G" Number of atoms: 6460 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 440, 6446 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 23, 'TRANS': 416} Chain breaks: 3 Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 61 Planarities with less than four sites: {'HIS:plan': 1, 'TYR:plan': 2, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 58 Conformer: "B" Number of residues, atoms: 440, 6446 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 23, 'TRANS': 416} Chain breaks: 3 Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 61 Planarities with less than four sites: {'HIS:plan': 1, 'TYR:plan': 2, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 58 bond proxies already assigned to first conformer: 6512 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 30 Unusual residues: {' CA': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 31 Unusual residues: {' CA': 3, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 31 Unusual residues: {' CA': 3, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 30 Unusual residues: {' CA': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "B" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "C" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "D" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 24 Classifications: {'water': 24} Link IDs: {None: 23} Chain: "E" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "G" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Time building chain proxies: 42.50, per 1000 atoms: 0.64 Number of scatterers: 66562 At special positions: 0 Unit cell: (152.043, 248.681, 213.891, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 12 19.99 S 456 16.00 O 6828 8.00 N 6002 7.00 C 21562 6.00 H 31702 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=202, symmetry=0 Simple disulfide: pdb=" SG CYS A 37 " - pdb=" SG CYS A 169 " distance=2.03 Simple disulfide: pdb=" SG CYS A 59 " - pdb=" SG CYS A 206 " distance=2.03 Simple disulfide: pdb=" SG CYS A 67 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 255 " distance=2.03 Simple disulfide: pdb=" SG CYS A 225 " - pdb=" SG CYS A 250 " distance=2.03 Simple disulfide: pdb=" SG CYS A 237 " - pdb=" SG CYS A 275 " distance=2.03 Simple disulfide: pdb=" SG CYS A 257 " - pdb=" SG CYS A 263 " distance=2.03 Simple disulfide: pdb=" SG CYS A 265 " - pdb=" SG CYS A 291 " distance=2.03 Simple disulfide: pdb=" SG CYS A 295 " - pdb=" SG CYS A 329 " distance=2.03 Simple disulfide: pdb=" SG CYS A 308 " - pdb=" SG CYS A 321 " distance=2.03 Simple disulfide: pdb=" SG CYS A 312 " - pdb=" SG CYS A 351 " distance=2.03 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 345 " distance=2.03 Simple disulfide: pdb=" SG CYS A 353 " - pdb=" SG CYS A 375 " distance=2.03 Simple disulfide: pdb=" SG CYS A 370 " - pdb=" SG CYS A 387 " distance=2.03 Simple disulfide: pdb=" SG CYS A 373 " - pdb=" SG CYS A 382 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 528 " distance=2.03 Simple disulfide: pdb=" SG CYS A 413 " - pdb=" SG CYS A 563 " distance=2.03 Simple disulfide: pdb=" SG CYS A 435 " - pdb=" SG CYS A 443 " distance=2.03 Simple disulfide: pdb=" SG CYS A 574 " - pdb=" SG CYS A 619 " distance=2.03 Simple disulfide: pdb=" SG CYS A 588 " - pdb=" SG CYS A 614 " distance=2.03 Simple disulfide: pdb=" SG CYS A 601 " - pdb=" SG CYS A 639 " distance=2.03 Simple disulfide: pdb=" SG CYS A 621 " - pdb=" SG CYS A 627 " distance=2.03 Simple disulfide: pdb=" SG CYS A 629 " - pdb=" SG CYS A 654 " distance=2.03 Simple disulfide: pdb=" SG CYS A 661 " - pdb=" SG CYS A 698 " distance=2.03 Simple disulfide: pdb=" SG CYS A 674 " - pdb=" SG CYS A 688 " distance=2.03 Simple disulfide: pdb=" SG CYS A 678 " - pdb=" SG CYS A 718 " distance=2.03 Simple disulfide: pdb=" SG CYS A 700 " - pdb=" SG CYS A 712 " distance=2.03 Simple disulfide: pdb=" SG CYS A 720 " - pdb=" SG CYS A 742 " distance=2.03 Simple disulfide: pdb=" SG CYS A 740 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B 37 " - pdb=" SG CYS B 169 " distance=2.03 Simple disulfide: pdb=" SG CYS B 59 " - pdb=" SG CYS B 206 " distance=2.03 Simple disulfide: pdb=" SG CYS B 67 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 218 " - pdb=" SG CYS B 255 " distance=2.03 Simple disulfide: pdb=" SG CYS B 225 " - pdb=" SG CYS B 250 " distance=2.03 Simple disulfide: pdb=" SG CYS B 237 " - pdb=" SG CYS B 275 " distance=2.03 Simple disulfide: pdb=" SG CYS B 257 " - pdb=" SG CYS B 263 " distance=2.03 Simple disulfide: pdb=" SG CYS B 265 " - pdb=" SG CYS B 291 " distance=2.03 Simple disulfide: pdb=" SG CYS B 295 " - pdb=" SG CYS B 329 " distance=2.03 Simple disulfide: pdb=" SG CYS B 308 " - pdb=" SG CYS B 321 " distance=2.03 Simple disulfide: pdb=" SG CYS B 312 " - pdb=" SG CYS B 351 " distance=2.03 Simple disulfide: pdb=" SG CYS B 331 " - pdb=" SG CYS B 345 " distance=2.03 Simple disulfide: pdb=" SG CYS B 353 " - pdb=" SG CYS B 375 " distance=2.03 Simple disulfide: pdb=" SG CYS B 370 " - pdb=" SG CYS B 387 " distance=2.03 Simple disulfide: pdb=" SG CYS B 373 " - pdb=" SG CYS B 382 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 528 " distance=2.03 Simple disulfide: pdb=" SG CYS B 413 " - pdb=" SG CYS B 563 " distance=2.03 Simple disulfide: pdb=" SG CYS B 435 " - pdb=" SG CYS B 443 " distance=2.03 Simple disulfide: pdb=" SG CYS B 574 " - pdb=" SG CYS B 619 " distance=2.03 Simple disulfide: pdb=" SG CYS B 588 " - pdb=" SG CYS B 614 " distance=2.03 Simple disulfide: pdb=" SG CYS B 601 " - pdb=" SG CYS B 639 " distance=2.03 Simple disulfide: pdb=" SG CYS B 621 " - pdb=" SG CYS B 627 " distance=2.03 Simple disulfide: pdb=" SG CYS B 629 " - pdb=" SG CYS B 654 " distance=2.03 Simple disulfide: pdb=" SG CYS B 661 " - pdb=" SG CYS B 698 " distance=2.03 Simple disulfide: pdb=" SG CYS B 674 " - pdb=" SG CYS B 688 " distance=2.03 Simple disulfide: pdb=" SG CYS B 678 " - pdb=" SG CYS B 718 " distance=2.03 Simple disulfide: pdb=" SG CYS B 700 " - pdb=" SG CYS B 712 " distance=2.03 Simple disulfide: pdb=" SG CYS B 720 " - pdb=" SG CYS B 742 " distance=2.03 Simple disulfide: pdb=" SG CYS B 740 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B 784 " - pdb=" SG CYS B 820 " distance=2.03 Simple disulfide: pdb=" SG CYS B 802 " - pdb=" SG CYS B 814 " distance=2.03 Simple disulfide: pdb=" SG CYS B 822 " - pdb=" SG CYS B 844 " distance=2.03 Simple disulfide: pdb=" SG CYS B 839 " - pdb=" SG CYS B 856 " distance=2.03 Simple disulfide: pdb=" SG CYS B 842 " - pdb=" SG CYS B 851 " distance=2.03 Simple disulfide: pdb=" SG CYS B 860 " - pdb=" SG CYS B 992 " distance=2.03 Simple disulfide: pdb=" SG CYS B 882 " - pdb=" SG CYS B1027 " distance=2.03 Simple disulfide: pdb=" SG CYS B 891 " - pdb=" SG CYS B 989 " distance=2.03 Simple disulfide: pdb=" SG CYS B 909 " - pdb=" SG CYS B 916 " distance=2.03 Simple disulfide: pdb=" SG CYS B1037 " - pdb=" SG CYS B1080 " distance=2.03 Simple disulfide: pdb=" SG CYS B1051 " - pdb=" SG CYS B1075 " distance=2.03 Simple disulfide: pdb=" SG CYS B1062 " - pdb=" SG CYS B1102 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1090 " distance=2.03 Simple disulfide: pdb=" SG CYS B1092 " - pdb=" SG CYS B1117 " distance=2.03 Simple disulfide: pdb=" SG CYS B1108 " - pdb=" SG CYS B1137 " distance=2.03 Simple disulfide: pdb=" SG CYS B1121 " - pdb=" SG CYS B1163 " distance=2.03 Simple disulfide: pdb=" SG CYS B1130 " - pdb=" SG CYS G1130 " distance=2.03 Simple disulfide: pdb=" SG CYS B1145 " - pdb=" SG CYS B1187 " distance=2.03 Simple disulfide: pdb=" SG CYS B1167 " - pdb=" SG CYS B1181 " distance=2.03 Simple disulfide: pdb=" SG CYS B1189 " - pdb=" SG CYS B1213 " distance=2.03 Simple disulfide: pdb=" SG CYS B1208 " - pdb=" SG CYS B1238 " distance=2.03 Simple disulfide: pdb=" SG CYS B1211 " - pdb=" SG CYS B1221 " distance=2.03 Simple disulfide: pdb=" SG CYS C 784 " - pdb=" SG CYS C 820 " distance=2.03 Simple disulfide: pdb=" SG CYS C 802 " - pdb=" SG CYS C 814 " distance=2.03 Simple disulfide: pdb=" SG CYS C 822 " - pdb=" SG CYS C 844 " distance=2.03 Simple disulfide: pdb=" SG CYS C 839 " - pdb=" SG CYS C 856 " distance=2.03 Simple disulfide: pdb=" SG CYS C 842 " - pdb=" SG CYS C 851 " distance=2.03 Simple disulfide: pdb=" SG CYS C 860 " - pdb=" SG CYS C 992 " distance=2.03 Simple disulfide: pdb=" SG CYS C 882 " - pdb=" SG CYS C1027 " distance=2.03 Simple disulfide: pdb=" SG CYS C 891 " - pdb=" SG CYS C 989 " distance=2.03 Simple disulfide: pdb=" SG CYS C 909 " - pdb=" SG CYS C 916 " distance=2.03 Simple disulfide: pdb=" SG CYS C1037 " - pdb=" SG CYS C1080 " distance=2.03 Simple disulfide: pdb=" SG CYS C1051 " - pdb=" SG CYS C1075 " distance=2.03 Simple disulfide: pdb=" SG CYS C1062 " - pdb=" SG CYS C1102 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1090 " distance=2.03 Simple disulfide: pdb=" SG CYS C1092 " - pdb=" SG CYS C1117 " distance=2.03 Simple disulfide: pdb=" SG CYS C1108 " - pdb=" SG CYS C1137 " distance=2.03 Simple disulfide: pdb=" SG CYS C1121 " - pdb=" SG CYS C1163 " distance=2.03 Simple disulfide: pdb=" SG CYS C1130 " - pdb=" SG CYS D1130 " distance=2.03 Simple disulfide: pdb=" SG CYS C1145 " - pdb=" SG CYS C1187 " distance=2.04 Simple disulfide: pdb=" SG CYS C1167 " - pdb=" SG CYS C1181 " distance=2.03 Simple disulfide: pdb=" SG CYS C1189 " - pdb=" SG CYS C1213 " distance=2.03 Simple disulfide: pdb=" SG CYS C1208 " - pdb=" SG CYS C1238 " distance=2.03 Simple disulfide: pdb=" SG CYS C1211 " - pdb=" SG CYS C1221 " distance=2.03 Simple disulfide: pdb=" SG CYS D 37 " - pdb=" SG CYS D 169 " distance=2.03 Simple disulfide: pdb=" SG CYS D 59 " - pdb=" SG CYS D 206 " distance=2.03 Simple disulfide: pdb=" SG CYS D 67 " - pdb=" SG CYS D 166 " distance=2.03 Simple disulfide: pdb=" SG CYS D 218 " - pdb=" SG CYS D 255 " distance=2.03 Simple disulfide: pdb=" SG CYS D 225 " - pdb=" SG CYS D 250 " distance=2.03 Simple disulfide: pdb=" SG CYS D 237 " - pdb=" SG CYS D 275 " distance=2.03 Simple disulfide: pdb=" SG CYS D 257 " - pdb=" SG CYS D 263 " distance=2.03 Simple disulfide: pdb=" SG CYS D 265 " - pdb=" SG CYS D 291 " distance=2.03 Simple disulfide: pdb=" SG CYS D 295 " - pdb=" SG CYS D 329 " distance=2.03 Simple disulfide: pdb=" SG CYS D 308 " - pdb=" SG CYS D 321 " distance=2.03 Simple disulfide: pdb=" SG CYS D 312 " - pdb=" SG CYS D 351 " distance=2.02 Simple disulfide: pdb=" SG CYS D 331 " - pdb=" SG CYS D 345 " distance=2.03 Simple disulfide: pdb=" SG CYS D 353 " - pdb=" SG CYS D 375 " distance=2.03 Simple disulfide: pdb=" SG CYS D 370 " - pdb=" SG CYS D 387 " distance=2.03 Simple disulfide: pdb=" SG CYS D 373 " - pdb=" SG CYS D 382 " distance=2.03 Simple disulfide: pdb=" SG CYS D 391 " - pdb=" SG CYS D 528 " distance=2.03 Simple disulfide: pdb=" SG CYS D 413 " - pdb=" SG CYS D 563 " distance=2.03 Simple disulfide: pdb=" SG CYS D 435 " - pdb=" SG CYS D 443 " distance=2.03 Simple disulfide: pdb=" SG CYS D 574 " - pdb=" SG CYS D 619 " distance=2.03 Simple disulfide: pdb=" SG CYS D 588 " - pdb=" SG CYS D 614 " distance=2.03 Simple disulfide: pdb=" SG CYS D 601 " - pdb=" SG CYS D 639 " distance=2.03 Simple disulfide: pdb=" SG CYS D 621 " - pdb=" SG CYS D 627 " distance=2.03 Simple disulfide: pdb=" SG CYS D 629 " - pdb=" SG CYS D 654 " distance=2.03 Simple disulfide: pdb=" SG CYS D 661 " - pdb=" SG CYS D 698 " distance=2.03 Simple disulfide: pdb=" SG CYS D 674 " - pdb=" SG CYS D 688 " distance=2.03 Simple disulfide: pdb=" SG CYS D 678 " - pdb=" SG CYS D 718 " distance=2.03 Simple disulfide: pdb=" SG CYS D 700 " - pdb=" SG CYS D 712 " distance=2.03 Simple disulfide: pdb=" SG CYS D 720 " - pdb=" SG CYS D 742 " distance=2.03 Simple disulfide: pdb=" SG CYS D 740 " - pdb=" SG CYS D 749 " distance=2.03 Simple disulfide: pdb=" SG CYS D 784 " - pdb=" SG CYS D 820 " distance=2.03 Simple disulfide: pdb=" SG CYS D 802 " - pdb=" SG CYS D 814 " distance=2.03 Simple disulfide: pdb=" SG CYS D 822 " - pdb=" SG CYS D 844 " distance=2.03 Simple disulfide: pdb=" SG CYS D 839 " - pdb=" SG CYS D 856 " distance=2.03 Simple disulfide: pdb=" SG CYS D 842 " - pdb=" SG CYS D 851 " distance=2.03 Simple disulfide: pdb=" SG CYS D 860 " - pdb=" SG CYS D 992 " distance=2.03 Simple disulfide: pdb=" SG CYS D 882 " - pdb=" SG CYS D1027 " distance=2.03 Simple disulfide: pdb=" SG CYS D 891 " - pdb=" SG CYS D 989 " distance=2.03 Simple disulfide: pdb=" SG CYS D 909 " - pdb=" SG CYS D 916 " distance=2.03 Simple disulfide: pdb=" SG CYS D1037 " - pdb=" SG CYS D1080 " distance=2.03 Simple disulfide: pdb=" SG CYS D1051 " - pdb=" SG CYS D1075 " distance=2.03 Simple disulfide: pdb=" SG CYS D1062 " - pdb=" SG CYS D1102 " distance=2.03 Simple disulfide: pdb=" SG CYS D1082 " - pdb=" SG CYS D1090 " distance=2.04 Simple disulfide: pdb=" SG CYS D1092 " - pdb=" SG CYS D1117 " distance=2.03 Simple disulfide: pdb=" SG CYS D1108 " - pdb=" SG CYS D1137 " distance=2.04 Simple disulfide: pdb=" SG CYS D1121 " - pdb=" SG CYS D1163 " distance=2.03 Simple disulfide: pdb=" SG CYS D1145 " - pdb=" SG CYS D1187 " distance=2.03 Simple disulfide: pdb=" SG CYS D1167 " - pdb=" SG CYS D1181 " distance=2.03 Simple disulfide: pdb=" SG CYS D1189 " - pdb=" SG CYS D1213 " distance=2.03 Simple disulfide: pdb=" SG CYS D1208 " - pdb=" SG CYS D1238 " distance=2.03 Simple disulfide: pdb=" SG CYS D1211 " - pdb=" SG CYS D1221 " distance=2.03 Simple disulfide: pdb=" SG CYS E 37 " - pdb=" SG CYS E 169 " distance=2.03 Simple disulfide: pdb=" SG CYS E 59 " - pdb=" SG CYS E 206 " distance=2.03 Simple disulfide: pdb=" SG CYS E 67 " - pdb=" SG CYS E 166 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 255 " distance=2.03 Simple disulfide: pdb=" SG CYS E 225 " - pdb=" SG CYS E 250 " distance=2.03 Simple disulfide: pdb=" SG CYS E 237 " - pdb=" SG CYS E 275 " distance=2.03 Simple disulfide: pdb=" SG CYS E 257 " - pdb=" SG CYS E 263 " distance=2.03 Simple disulfide: pdb=" SG CYS E 265 " - pdb=" SG CYS E 291 " distance=2.03 Simple disulfide: pdb=" SG CYS E 295 " - pdb=" SG CYS E 329 " distance=2.03 Simple disulfide: pdb=" SG CYS E 308 " - pdb=" SG CYS E 321 " distance=2.03 Simple disulfide: pdb=" SG CYS E 312 " - pdb=" SG CYS E 351 " distance=2.03 Simple disulfide: pdb=" SG CYS E 331 " - pdb=" SG CYS E 345 " distance=2.03 Simple disulfide: pdb=" SG CYS E 353 " - pdb=" SG CYS E 375 " distance=2.03 Simple disulfide: pdb=" SG CYS E 370 " - pdb=" SG CYS E 387 " distance=2.04 Simple disulfide: pdb=" SG CYS E 373 " - pdb=" SG CYS E 382 " distance=2.03 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 528 " distance=2.03 Simple disulfide: pdb=" SG CYS E 413 " - pdb=" SG CYS E 563 " distance=2.03 Simple disulfide: pdb=" SG CYS E 435 " - pdb=" SG CYS E 443 " distance=2.03 Simple disulfide: pdb=" SG CYS E 574 " - pdb=" SG CYS E 619 " distance=2.03 Simple disulfide: pdb=" SG CYS E 588 " - pdb=" SG CYS E 614 " distance=2.03 Simple disulfide: pdb=" SG CYS E 601 " - pdb=" SG CYS E 639 " distance=2.03 Simple disulfide: pdb=" SG CYS E 621 " - pdb=" SG CYS E 627 " distance=2.03 Simple disulfide: pdb=" SG CYS E 629 " - pdb=" SG CYS E 654 " distance=2.03 Simple disulfide: pdb=" SG CYS E 661 " - pdb=" SG CYS E 698 " distance=2.03 Simple disulfide: pdb=" SG CYS E 674 " - pdb=" SG CYS E 688 " distance=2.03 Simple disulfide: pdb=" SG CYS E 678 " - pdb=" SG CYS E 718 " distance=2.03 Simple disulfide: pdb=" SG CYS E 700 " - pdb=" SG CYS E 712 " distance=2.03 Simple disulfide: pdb=" SG CYS E 720 " - pdb=" SG CYS E 742 " distance=2.03 Simple disulfide: pdb=" SG CYS E 740 " - pdb=" SG CYS E 749 " distance=2.03 Simple disulfide: pdb=" SG CYS G 784 " - pdb=" SG CYS G 820 " distance=2.03 Simple disulfide: pdb=" SG CYS G 802 " - pdb=" SG CYS G 814 " distance=2.03 Simple disulfide: pdb=" SG CYS G 822 " - pdb=" SG CYS G 844 " distance=2.03 Simple disulfide: pdb=" SG CYS G 839 " - pdb=" SG CYS G 856 " distance=2.03 Simple disulfide: pdb=" SG CYS G 842 " - pdb=" SG CYS G 851 " distance=2.03 Simple disulfide: pdb=" SG CYS G 860 " - pdb=" SG CYS G 992 " distance=2.03 Simple disulfide: pdb=" SG CYS G 882 " - pdb=" SG CYS G1027 " distance=2.03 Simple disulfide: pdb=" SG CYS G 891 " - pdb=" SG CYS G 989 " distance=2.03 Simple disulfide: pdb=" SG CYS G 909 " - pdb=" SG CYS G 916 " distance=2.03 Simple disulfide: pdb=" SG CYS G1037 " - pdb=" SG CYS G1080 " distance=2.03 Simple disulfide: pdb=" SG CYS G1051 " - pdb=" SG CYS G1075 " distance=2.03 Simple disulfide: pdb=" SG CYS G1062 " - pdb=" SG CYS G1102 " distance=2.03 Simple disulfide: pdb=" SG CYS G1082 " - pdb=" SG CYS G1090 " distance=2.03 Simple disulfide: pdb=" SG CYS G1092 " - pdb=" SG CYS G1117 " distance=2.03 Simple disulfide: pdb=" SG CYS G1108 " - pdb=" SG CYS G1137 " distance=2.03 Simple disulfide: pdb=" SG CYS G1121 " - pdb=" SG CYS G1163 " distance=2.03 Simple disulfide: pdb=" SG CYS G1145 " - pdb=" SG CYS G1187 " distance=2.03 Simple disulfide: pdb=" SG CYS G1167 " - pdb=" SG CYS G1181 " distance=2.03 Simple disulfide: pdb=" SG CYS G1189 " - pdb=" SG CYS G1213 " distance=2.03 Simple disulfide: pdb=" SG CYS G1208 " - pdb=" SG CYS G1238 " distance=2.03 Simple disulfide: pdb=" SG CYS G1211 " - pdb=" SG CYS G1221 " distance=2.03 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 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " NAG-ASN " NAG A2003 " - " ASN A 163 " " NAG A2004 " - " ASN A 670 " " NAG B2004 " - " ASN B 163 " " NAG B2005 " - " ASN B 670 " " NAG D2004 " - " ASN D 163 " " NAG D2005 " - " ASN D 670 " " NAG E2003 " - " ASN E 163 " " NAG E2004 " - " ASN E 670 " " NAG F 1 " - " ASN B1154 " " NAG H 1 " - " ASN C1154 " " NAG I 1 " - " ASN D1154 " " NAG J 1 " - " ASN G1154 " Time building additional restraints: 45.78 Conformation dependent library (CDL) restraints added in 10.6 seconds 9100 Ramachandran restraints generated. 4550 Oldfield, 0 Emsley, 4550 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8484 Finding SS restraints... Secondary structure from input PDB file: 111 helices and 63 sheets defined 20.8% alpha, 20.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.58 Creating SS restraints... Processing helix chain 'A' and resid 159 through 162 removed outlier: 3.573A pdb=" N ARG A 162 " --> pdb=" O THR A 159 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 159 through 162' Processing helix chain 'A' and resid 189 through 197 removed outlier: 3.793A pdb=" N GLN A 197 " --> pdb=" O PHE A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 230 Processing helix chain 'A' and resid 231 through 238 removed outlier: 3.532A pdb=" N PHE A 234 " --> pdb=" O ALA A 231 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N ASP A 236 " --> pdb=" O ALA A 233 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N CYS A 237 " --> pdb=" O PHE A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 257 removed outlier: 3.673A pdb=" N GLN A 252 " --> pdb=" O ARG A 248 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N CYS A 255 " --> pdb=" O GLN A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 279 removed outlier: 3.695A pdb=" N THR A 267 " --> pdb=" O CYS A 263 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL A 268 " --> pdb=" O VAL A 264 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ALA A 269 " --> pdb=" O CYS A 265 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLU A 270 " --> pdb=" O SER A 266 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLY A 279 " --> pdb=" O CYS A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 321 Processing helix chain 'A' and resid 347 through 351 removed outlier: 3.792A pdb=" N GLN A 350 " --> pdb=" O PRO A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 556 removed outlier: 3.958A pdb=" N PHE A 553 " --> pdb=" O THR A 549 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA A 554 " --> pdb=" O GLY A 550 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N THR A 556 " --> pdb=" O GLY A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 576 Processing helix chain 'A' and resid 577 through 589 removed outlier: 4.200A pdb=" N ASN A 582 " --> pdb=" O ILE A 578 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N TYR A 583 " --> pdb=" O GLU A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 593 Processing helix chain 'A' and resid 596 through 604 removed outlier: 3.572A pdb=" N SER A 603 " --> pdb=" O ARG A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 621 Processing helix chain 'A' and resid 623 through 639 removed outlier: 3.510A pdb=" N SER A 634 " --> pdb=" O ALA A 630 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N TYR A 635 " --> pdb=" O ALA A 631 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ALA A 636 " --> pdb=" O LEU A 632 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ARG A 637 " --> pdb=" O SER A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 642 No H-bonds generated for 'chain 'A' and resid 640 through 642' Processing helix chain 'A' and resid 657 through 661 removed outlier: 4.100A pdb=" N CYS A 661 " --> pdb=" O VAL A 658 " (cutoff:3.500A) Processing helix chain 'A' and resid 677 through 684 removed outlier: 3.558A pdb=" N LEU A 681 " --> pdb=" O THR A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 718 Processing helix chain 'B' and resid 159 through 162 removed outlier: 3.524A pdb=" N ARG B 162 " --> pdb=" O THR B 159 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 159 through 162' Processing helix chain 'B' and resid 189 through 197 removed outlier: 3.887A pdb=" N GLN B 197 " --> pdb=" O PHE B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 230 Processing helix chain 'B' and resid 234 through 238 removed outlier: 3.978A pdb=" N CYS B 237 " --> pdb=" O PHE B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 257 removed outlier: 3.690A pdb=" N GLN B 252 " --> pdb=" O ARG B 248 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N CYS B 255 " --> pdb=" O GLN B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 279 removed outlier: 3.857A pdb=" N VAL B 268 " --> pdb=" O VAL B 264 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA B 269 " --> pdb=" O CYS B 265 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLU B 270 " --> pdb=" O SER B 266 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLY B 279 " --> pdb=" O CYS B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 321 Processing helix chain 'B' and resid 347 through 351 removed outlier: 3.693A pdb=" N GLN B 350 " --> pdb=" O PRO B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 549 through 554 Processing helix chain 'B' and resid 555 through 558 removed outlier: 4.004A pdb=" N LYS B 558 " --> pdb=" O ASN B 555 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 555 through 558' Processing helix chain 'B' and resid 572 through 577 removed outlier: 3.648A pdb=" N LEU B 576 " --> pdb=" O ASP B 572 " (cutoff:3.500A) Processing helix chain 'B' and resid 577 through 589 removed outlier: 3.886A pdb=" N ASN B 582 " --> pdb=" O ILE B 578 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N TYR B 583 " --> pdb=" O GLU B 579 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N TRP B 587 " --> pdb=" O TYR B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 590 through 592 No H-bonds generated for 'chain 'B' and resid 590 through 592' Processing helix chain 'B' and resid 600 through 604 removed outlier: 4.017A pdb=" N SER B 603 " --> pdb=" O ARG B 600 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 621 removed outlier: 4.355A pdb=" N LYS B 612 " --> pdb=" O ALA B 608 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ARG B 613 " --> pdb=" O GLU B 609 " (cutoff:3.500A) Processing helix chain 'B' and resid 623 through 641 removed outlier: 3.660A pdb=" N CYS B 627 " --> pdb=" O ASN B 623 " (cutoff:3.500A) Processing helix chain 'B' and resid 657 through 661 removed outlier: 3.949A pdb=" N CYS B 661 " --> pdb=" O VAL B 658 " (cutoff:3.500A) Processing helix chain 'B' and resid 677 through 684 removed outlier: 3.919A pdb=" N GLU B 683 " --> pdb=" O ARG B 679 " (cutoff:3.500A) Processing helix chain 'B' and resid 1013 through 1020 Processing helix chain 'B' and resid 1035 through 1040 Processing helix chain 'B' and resid 1043 through 1051 Processing helix chain 'B' and resid 1052 through 1065 removed outlier: 6.006A pdb=" N SER B1057 " --> pdb=" O LEU B1054 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N VAL B1058 " --> pdb=" O LYS B1055 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N ILE B1061 " --> pdb=" O VAL B1058 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N SER B1064 " --> pdb=" O ILE B1061 " (cutoff:3.500A) Processing helix chain 'B' and resid 1068 through 1080 Processing helix chain 'B' and resid 1088 through 1105 removed outlier: 3.827A pdb=" N CYS B1092 " --> pdb=" O CYS B1088 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N SER B1093 " --> pdb=" O GLU B1089 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ALA B1094 " --> pdb=" O CYS B1090 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TYR B1098 " --> pdb=" O ALA B1094 " (cutoff:3.500A) Processing helix chain 'B' and resid 1146 through 1150 Processing helix chain 'C' and resid 982 through 985 removed outlier: 3.816A pdb=" N LYS C 985 " --> pdb=" O PRO C 982 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 982 through 985' Processing helix chain 'C' and resid 1013 through 1020 Processing helix chain 'C' and resid 1035 through 1040 Processing helix chain 'C' and resid 1043 through 1051 Processing helix chain 'C' and resid 1052 through 1056 Processing helix chain 'C' and resid 1060 through 1065 removed outlier: 3.537A pdb=" N HIS C1063 " --> pdb=" O SER C1060 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N SER C1064 " --> pdb=" O ILE C1061 " (cutoff:3.500A) Processing helix chain 'C' and resid 1068 through 1080 removed outlier: 3.721A pdb=" N ALA C1074 " --> pdb=" O PRO C1070 " (cutoff:3.500A) Processing helix chain 'C' and resid 1087 through 1105 removed outlier: 3.968A pdb=" N PHE C1091 " --> pdb=" O ASP C1087 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N CYS C1092 " --> pdb=" O CYS C1088 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER C1093 " --> pdb=" O GLU C1089 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA C1094 " --> pdb=" O CYS C1090 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N TYR C1098 " --> pdb=" O ALA C1094 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU C1101 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing helix chain 'C' and resid 1121 through 1125 Processing helix chain 'C' and resid 1146 through 1150 Processing helix chain 'D' and resid 159 through 162 removed outlier: 3.701A pdb=" N ARG D 162 " --> pdb=" O THR D 159 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 159 through 162' Processing helix chain 'D' and resid 189 through 197 removed outlier: 3.618A pdb=" N GLN D 197 " --> pdb=" O PHE D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 230 Processing helix chain 'D' and resid 231 through 238 removed outlier: 5.453A pdb=" N ASP D 236 " --> pdb=" O ALA D 233 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N CYS D 237 " --> pdb=" O PHE D 234 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLN D 238 " --> pdb=" O ALA D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 257 removed outlier: 3.613A pdb=" N GLN D 252 " --> pdb=" O ARG D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 279 removed outlier: 3.812A pdb=" N GLY D 279 " --> pdb=" O CYS D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 316 through 321 removed outlier: 3.627A pdb=" N SER D 319 " --> pdb=" O GLU D 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 347 through 351 removed outlier: 3.502A pdb=" N CYS D 351 " --> pdb=" O VAL D 348 " (cutoff:3.500A) Processing helix chain 'D' and resid 517 through 521 removed outlier: 3.535A pdb=" N GLN D 521 " --> pdb=" O GLN D 518 " (cutoff:3.500A) Processing helix chain 'D' and resid 549 through 555 Processing helix chain 'D' and resid 556 through 558 No H-bonds generated for 'chain 'D' and resid 556 through 558' Processing helix chain 'D' and resid 572 through 577 removed outlier: 3.675A pdb=" N LEU D 576 " --> pdb=" O ASP D 572 " (cutoff:3.500A) Processing helix chain 'D' and resid 577 through 589 removed outlier: 3.929A pdb=" N ASN D 582 " --> pdb=" O ILE D 578 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N TYR D 583 " --> pdb=" O GLU D 579 " (cutoff:3.500A) Processing helix chain 'D' and resid 590 through 592 No H-bonds generated for 'chain 'D' and resid 590 through 592' Processing helix chain 'D' and resid 598 through 602 Processing helix chain 'D' and resid 607 through 621 removed outlier: 3.751A pdb=" N LYS D 612 " --> pdb=" O ALA D 608 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG D 613 " --> pdb=" O GLU D 609 " (cutoff:3.500A) Processing helix chain 'D' and resid 623 through 641 removed outlier: 3.588A pdb=" N CYS D 627 " --> pdb=" O ASN D 623 " (cutoff:3.500A) Processing helix chain 'D' and resid 677 through 684 removed outlier: 3.877A pdb=" N LEU D 681 " --> pdb=" O THR D 677 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLU D 683 " --> pdb=" O ARG D 679 " (cutoff:3.500A) Processing helix chain 'D' and resid 714 through 718 removed outlier: 3.541A pdb=" N LYS D 717 " --> pdb=" O PRO D 714 " (cutoff:3.500A) Processing helix chain 'D' and resid 982 through 985 Processing helix chain 'D' and resid 1013 through 1020 removed outlier: 3.686A pdb=" N SER D1020 " --> pdb=" O ASP D1016 " (cutoff:3.500A) Processing helix chain 'D' and resid 1035 through 1040 Processing helix chain 'D' and resid 1043 through 1051 Processing helix chain 'D' and resid 1052 through 1060 removed outlier: 6.255A pdb=" N SER D1057 " --> pdb=" O LEU D1054 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N VAL D1058 " --> pdb=" O LYS D1055 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N PHE D1059 " --> pdb=" O SER D1056 " (cutoff:3.500A) Processing helix chain 'D' and resid 1068 through 1080 Processing helix chain 'D' and resid 1087 through 1105 removed outlier: 3.927A pdb=" N PHE D1091 " --> pdb=" O ASP D1087 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N CYS D1092 " --> pdb=" O CYS D1088 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N SER D1093 " --> pdb=" O GLU D1089 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N TYR D1098 " --> pdb=" O ALA D1094 " (cutoff:3.500A) Processing helix chain 'D' and resid 1121 through 1125 Processing helix chain 'D' and resid 1146 through 1150 Processing helix chain 'E' and resid 159 through 162 removed outlier: 3.625A pdb=" N ARG E 162 " --> pdb=" O THR E 159 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 159 through 162' Processing helix chain 'E' and resid 189 through 196 Processing helix chain 'E' and resid 218 through 220 No H-bonds generated for 'chain 'E' and resid 218 through 220' Processing helix chain 'E' and resid 221 through 230 Processing helix chain 'E' and resid 231 through 238 removed outlier: 5.610A pdb=" N ASP E 236 " --> pdb=" O ALA E 233 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N CYS E 237 " --> pdb=" O PHE E 234 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLN E 238 " --> pdb=" O ALA E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 243 through 257 removed outlier: 3.626A pdb=" N GLN E 252 " --> pdb=" O ARG E 248 " (cutoff:3.500A) Processing helix chain 'E' and resid 263 through 279 removed outlier: 3.564A pdb=" N THR E 267 " --> pdb=" O CYS E 263 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ALA E 269 " --> pdb=" O CYS E 265 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLU E 270 " --> pdb=" O SER E 266 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLY E 279 " --> pdb=" O CYS E 275 " (cutoff:3.500A) Processing helix chain 'E' and resid 316 through 321 removed outlier: 3.534A pdb=" N SER E 319 " --> pdb=" O GLU E 316 " (cutoff:3.500A) Processing helix chain 'E' and resid 347 through 351 Processing helix chain 'E' and resid 549 through 555 Processing helix chain 'E' and resid 556 through 558 No H-bonds generated for 'chain 'E' and resid 556 through 558' Processing helix chain 'E' and resid 572 through 577 removed outlier: 3.732A pdb=" N LEU E 576 " --> pdb=" O ASP E 572 " (cutoff:3.500A) Processing helix chain 'E' and resid 577 through 589 removed outlier: 3.916A pdb=" N ASN E 582 " --> pdb=" O ILE E 578 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N TYR E 583 " --> pdb=" O GLU E 579 " (cutoff:3.500A) Processing helix chain 'E' and resid 590 through 593 Processing helix chain 'E' and resid 596 through 604 removed outlier: 3.616A pdb=" N ARG E 600 " --> pdb=" O PRO E 597 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N SER E 603 " --> pdb=" O ARG E 600 " (cutoff:3.500A) Processing helix chain 'E' and resid 607 through 621 Processing helix chain 'E' and resid 623 through 640 removed outlier: 3.501A pdb=" N CYS E 627 " --> pdb=" O ASN E 623 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N TYR E 635 " --> pdb=" O ALA E 631 " (cutoff:3.500A) Processing helix chain 'E' and resid 677 through 684 removed outlier: 3.713A pdb=" N LEU E 681 " --> pdb=" O THR E 677 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLU E 683 " --> pdb=" O ARG E 679 " (cutoff:3.500A) Processing helix chain 'E' and resid 714 through 719 removed outlier: 4.695A pdb=" N SER E 719 " --> pdb=" O LEU E 715 " (cutoff:3.500A) Processing helix chain 'G' and resid 982 through 985 removed outlier: 3.690A pdb=" N LYS G 985 " --> pdb=" O PRO G 982 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 982 through 985' Processing helix chain 'G' and resid 1013 through 1018 Processing helix chain 'G' and resid 1019 through 1022 removed outlier: 3.641A pdb=" N LYS G1022 " --> pdb=" O ASN G1019 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 1019 through 1022' Processing helix chain 'G' and resid 1035 through 1040 Processing helix chain 'G' and resid 1043 through 1051 Processing helix chain 'G' and resid 1052 through 1060 removed outlier: 6.230A pdb=" N SER G1057 " --> pdb=" O LEU G1054 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N VAL G1058 " --> pdb=" O LYS G1055 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE G1059 " --> pdb=" O SER G1056 " (cutoff:3.500A) Processing helix chain 'G' and resid 1068 through 1080 Processing helix chain 'G' and resid 1087 through 1105 removed outlier: 3.862A pdb=" N PHE G1091 " --> pdb=" O ASP G1087 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N CYS G1092 " --> pdb=" O CYS G1088 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ALA G1094 " --> pdb=" O CYS G1090 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N TYR G1098 " --> pdb=" O ALA G1094 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLU G1101 " --> pdb=" O SER G1097 " (cutoff:3.500A) Processing helix chain 'G' and resid 1121 through 1125 Processing helix chain 'G' and resid 1146 through 1150 Processing sheet with id=AA1, first strand: chain 'A' and resid 50 through 54 removed outlier: 4.430A pdb=" N VAL A 52 " --> pdb=" O TYR A 45 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N TYR A 45 " --> pdb=" O VAL A 52 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU A 143 " --> pdb=" O SER A 139 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 61 through 65 removed outlier: 5.602A pdb=" N ASN A 62 " --> pdb=" O LEU A 78 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N LEU A 78 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ALA A 75 " --> pdb=" O LEU A 96 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N LEU A 96 " --> pdb=" O ALA A 75 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N HIS A 77 " --> pdb=" O ILE A 94 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N ILE A 94 " --> pdb=" O HIS A 77 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N LYS A 79 " --> pdb=" O GLU A 92 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASP A 101 " --> pdb=" O ILE A 98 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 300 through 305 removed outlier: 5.993A pdb=" N MET A 326 " --> pdb=" O SER A 304 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 353 through 354 Processing sheet with id=AA5, first strand: chain 'A' and resid 365 through 367 Processing sheet with id=AA6, first strand: chain 'A' and resid 404 through 407 removed outlier: 5.901A pdb=" N LYS A 405 " --> pdb=" O THR A 401 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N THR A 401 " --> pdb=" O LYS A 405 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL A 500 " --> pdb=" O MET A 496 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 442 through 444 removed outlier: 3.933A pdb=" N VAL A 448 " --> pdb=" O LEU A 429 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N THR A 446 " --> pdb=" O GLU A 431 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N LYS A 461 " --> pdb=" O SER A 465 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N SER A 465 " --> pdb=" O LYS A 461 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 442 through 444 removed outlier: 6.981A pdb=" N GLY A 430 " --> pdb=" O VAL A 416 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N VAL A 416 " --> pdb=" O GLY A 430 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N LEU A 432 " --> pdb=" O TYR A 414 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N TYR A 414 " --> pdb=" O LEU A 432 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN A 525 " --> pdb=" O LYS A 419 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 666 through 671 removed outlier: 4.126A pdb=" N ASN A 670 " --> pdb=" O VAL A 695 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N VAL A 695 " --> pdb=" O ASN A 670 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 50 through 54 removed outlier: 3.506A pdb=" N GLY B 50 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N VAL B 52 " --> pdb=" O TYR B 45 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N TYR B 45 " --> pdb=" O VAL B 52 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU B 143 " --> pdb=" O SER B 139 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE B 128 " --> pdb=" O HIS B 121 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 61 through 65 removed outlier: 5.343A pdb=" N ASN B 62 " --> pdb=" O LEU B 78 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N LEU B 78 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N SER B 93 " --> pdb=" O LYS B 79 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASP B 101 " --> pdb=" O ILE B 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 300 through 305 removed outlier: 6.338A pdb=" N MET B 326 " --> pdb=" O SER B 304 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 353 through 354 Processing sheet with id=AB5, first strand: chain 'B' and resid 365 through 367 Processing sheet with id=AB6, first strand: chain 'B' and resid 404 through 407 removed outlier: 3.538A pdb=" N GLY B 404 " --> pdb=" O THR B 401 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N THR B 406 " --> pdb=" O ILE B 399 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N ILE B 399 " --> pdb=" O THR B 406 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 442 through 444 removed outlier: 3.851A pdb=" N VAL B 448 " --> pdb=" O LEU B 429 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N THR B 446 " --> pdb=" O GLU B 431 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N LYS B 461 " --> pdb=" O SER B 465 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N SER B 465 " --> pdb=" O LYS B 461 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 442 through 444 removed outlier: 6.980A pdb=" N GLY B 430 " --> pdb=" O VAL B 416 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N VAL B 416 " --> pdb=" O GLY B 430 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N LEU B 432 " --> pdb=" O TYR B 414 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N TYR B 414 " --> pdb=" O LEU B 432 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLN B 525 " --> pdb=" O LYS B 419 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 666 through 671 removed outlier: 4.004A pdb=" N ASN B 670 " --> pdb=" O VAL B 695 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N VAL B 695 " --> pdb=" O ASN B 670 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 807 through 808 Processing sheet with id=AC2, first strand: chain 'B' and resid 822 through 824 Processing sheet with id=AC3, first strand: chain 'B' and resid 834 through 837 Processing sheet with id=AC4, first strand: chain 'B' and resid 875 through 877 removed outlier: 3.898A pdb=" N ILE B 966 " --> pdb=" O SER B 962 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 883 through 888 removed outlier: 5.607A pdb=" N SER B 883 " --> pdb=" O ASN B 906 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N ASN B 906 " --> pdb=" O SER B 883 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N VAL B 885 " --> pdb=" O THR B 904 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N THR B 904 " --> pdb=" O VAL B 885 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA B 919 " --> pdb=" O GLU B 905 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N VAL B 907 " --> pdb=" O SER B 917 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N SER B 917 " --> pdb=" O VAL B 907 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 1133 through 1135 removed outlier: 3.692A pdb=" N GLY B1162 " --> pdb=" O GLU B1135 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 1173 through 1175 Processing sheet with id=AC8, first strand: chain 'B' and resid 1201 through 1202 removed outlier: 4.018A pdb=" N CYS B1211 " --> pdb=" O VAL B1202 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 822 through 824 Processing sheet with id=AD1, first strand: chain 'C' and resid 835 through 837 Processing sheet with id=AD2, first strand: chain 'C' and resid 875 through 877 removed outlier: 3.859A pdb=" N ILE C 966 " --> pdb=" O SER C 962 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 883 through 888 removed outlier: 5.598A pdb=" N SER C 883 " --> pdb=" O ASN C 906 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N ASN C 906 " --> pdb=" O SER C 883 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N VAL C 885 " --> pdb=" O THR C 904 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N THR C 904 " --> pdb=" O VAL C 885 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N SER C 901 " --> pdb=" O ILE C 922 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N ILE C 922 " --> pdb=" O SER C 901 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N ILE C 903 " --> pdb=" O ILE C 920 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N ILE C 920 " --> pdb=" O ILE C 903 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N GLU C 905 " --> pdb=" O LYS C 918 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 1133 through 1135 removed outlier: 3.894A pdb=" N GLY C1162 " --> pdb=" O GLU C1135 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 1173 through 1175 Processing sheet with id=AD6, first strand: chain 'C' and resid 1201 through 1202 removed outlier: 3.989A pdb=" N CYS C1211 " --> pdb=" O VAL C1202 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 50 through 54 removed outlier: 4.394A pdb=" N VAL D 52 " --> pdb=" O TYR D 45 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N TYR D 45 " --> pdb=" O VAL D 52 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU D 143 " --> pdb=" O SER D 139 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 61 through 65 removed outlier: 5.386A pdb=" N ASN D 62 " --> pdb=" O LEU D 78 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N LEU D 78 " --> pdb=" O ASN D 62 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS D 79 " --> pdb=" O SER D 93 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER D 93 " --> pdb=" O LYS D 79 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ASP D 101 " --> pdb=" O ILE D 98 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 300 through 305 removed outlier: 5.132A pdb=" N TYR D 301 " --> pdb=" O PHE D 330 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N PHE D 330 " --> pdb=" O TYR D 301 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N GLU D 303 " --> pdb=" O GLY D 328 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N GLY D 328 " --> pdb=" O GLU D 303 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 353 through 354 Processing sheet with id=AE2, first strand: chain 'D' and resid 365 through 367 Processing sheet with id=AE3, first strand: chain 'D' and resid 404 through 407 removed outlier: 5.540A pdb=" N LYS D 405 " --> pdb=" O THR D 401 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N THR D 401 " --> pdb=" O LYS D 405 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 471 through 472 removed outlier: 5.364A pdb=" N SER D 465 " --> pdb=" O LYS D 461 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N LYS D 461 " --> pdb=" O SER D 465 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N LEU D 444 " --> pdb=" O ALA D 433 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ALA D 433 " --> pdb=" O LEU D 444 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N THR D 446 " --> pdb=" O GLU D 431 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL D 448 " --> pdb=" O LEU D 429 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N GLY D 430 " --> pdb=" O VAL D 416 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N VAL D 416 " --> pdb=" O GLY D 430 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N LEU D 432 " --> pdb=" O TYR D 414 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N TYR D 414 " --> pdb=" O LEU D 432 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 666 through 671 removed outlier: 3.782A pdb=" N ASN D 670 " --> pdb=" O VAL D 695 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N VAL D 695 " --> pdb=" O ASN D 670 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 822 through 824 Processing sheet with id=AE7, first strand: chain 'D' and resid 835 through 837 Processing sheet with id=AE8, first strand: chain 'D' and resid 875 through 877 removed outlier: 3.699A pdb=" N ILE D 966 " --> pdb=" O SER D 962 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 883 through 888 removed outlier: 5.636A pdb=" N SER D 883 " --> pdb=" O ASN D 906 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N ASN D 906 " --> pdb=" O SER D 883 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N VAL D 885 " --> pdb=" O THR D 904 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N THR D 904 " --> pdb=" O VAL D 885 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N SER D 901 " --> pdb=" O ILE D 922 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N ILE D 922 " --> pdb=" O SER D 901 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N ILE D 903 " --> pdb=" O ILE D 920 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N ILE D 920 " --> pdb=" O ILE D 903 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N GLU D 905 " --> pdb=" O LYS D 918 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 1132 through 1135 removed outlier: 3.911A pdb=" N GLY D1162 " --> pdb=" O GLU D1135 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 1173 through 1175 Processing sheet with id=AF3, first strand: chain 'D' and resid 1201 through 1202 removed outlier: 3.617A pdb=" N CYS D1211 " --> pdb=" O VAL D1202 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 50 through 54 removed outlier: 4.360A pdb=" N VAL E 52 " --> pdb=" O TYR E 45 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N TYR E 45 " --> pdb=" O VAL E 52 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU E 143 " --> pdb=" O SER E 139 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'E' and resid 61 through 65 removed outlier: 5.453A pdb=" N ASN E 62 " --> pdb=" O LEU E 78 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N LEU E 78 " --> pdb=" O ASN E 62 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASP E 101 " --> pdb=" O ILE E 98 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'E' and resid 300 through 305 removed outlier: 5.392A pdb=" N TYR E 301 " --> pdb=" O PHE E 330 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N PHE E 330 " --> pdb=" O TYR E 301 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N GLU E 303 " --> pdb=" O GLY E 328 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N GLY E 328 " --> pdb=" O GLU E 303 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N MET E 326 " --> pdb=" O GLY E 305 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'E' and resid 353 through 354 Processing sheet with id=AF8, first strand: chain 'E' and resid 365 through 367 Processing sheet with id=AF9, first strand: chain 'E' and resid 404 through 407 removed outlier: 3.533A pdb=" N GLY E 404 " --> pdb=" O THR E 401 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N THR E 406 " --> pdb=" O ILE E 399 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ILE E 399 " --> pdb=" O THR E 406 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL E 500 " --> pdb=" O MET E 496 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'E' and resid 471 through 472 removed outlier: 5.499A pdb=" N SER E 465 " --> pdb=" O LYS E 461 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N LYS E 461 " --> pdb=" O SER E 465 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N LEU E 444 " --> pdb=" O ALA E 433 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ALA E 433 " --> pdb=" O LEU E 444 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N THR E 446 " --> pdb=" O GLU E 431 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VAL E 448 " --> pdb=" O LEU E 429 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N GLY E 430 " --> pdb=" O VAL E 416 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N VAL E 416 " --> pdb=" O GLY E 430 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N LEU E 432 " --> pdb=" O TYR E 414 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N TYR E 414 " --> pdb=" O LEU E 432 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'E' and resid 666 through 671 removed outlier: 4.028A pdb=" N ASN E 670 " --> pdb=" O VAL E 695 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N VAL E 695 " --> pdb=" O ASN E 670 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'G' and resid 822 through 824 Processing sheet with id=AG4, first strand: chain 'G' and resid 834 through 837 Processing sheet with id=AG5, first strand: chain 'G' and resid 875 through 877 removed outlier: 4.153A pdb=" N ILE G 966 " --> pdb=" O SER G 962 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'G' and resid 883 through 888 removed outlier: 5.292A pdb=" N SER G 883 " --> pdb=" O ASN G 906 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ASN G 906 " --> pdb=" O SER G 883 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N VAL G 885 " --> pdb=" O THR G 904 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N THR G 904 " --> pdb=" O VAL G 885 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ALA G 919 " --> pdb=" O GLU G 905 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N VAL G 907 " --> pdb=" O SER G 917 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N SER G 917 " --> pdb=" O VAL G 907 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'G' and resid 1133 through 1135 removed outlier: 3.755A pdb=" N GLY G1162 " --> pdb=" O GLU G1135 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'G' and resid 1173 through 1175 Processing sheet with id=AG9, first strand: chain 'G' and resid 1200 through 1201 1116 hydrogen bonds defined for protein. 2788 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: 28.37 Time building geometry restraints manager: 48.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 31690 1.04 - 1.24: 4751 1.24 - 1.44: 10867 1.44 - 1.64: 19476 1.64 - 1.84: 504 Bond restraints: 67288 Sorted by residual: bond pdb=" C1 NAG E2003 " pdb=" O5 NAG E2003 " ideal model delta sigma weight residual 1.406 1.475 -0.069 2.00e-02 2.50e+03 1.18e+01 bond pdb=" C1 NAG A2003 " pdb=" O5 NAG A2003 " ideal model delta sigma weight residual 1.406 1.472 -0.066 2.00e-02 2.50e+03 1.09e+01 bond pdb=" C1 NAG B2004 " pdb=" O5 NAG B2004 " ideal model delta sigma weight residual 1.406 1.468 -0.062 2.00e-02 2.50e+03 9.48e+00 bond pdb=" C1 NAG D2004 " pdb=" O5 NAG D2004 " ideal model delta sigma weight residual 1.406 1.467 -0.061 2.00e-02 2.50e+03 9.43e+00 bond pdb=" CA GLY D 259 " pdb=" C GLY D 259 " ideal model delta sigma weight residual 1.530 1.514 0.016 1.04e-02 9.25e+03 2.40e+00 ... (remaining 67283 not shown) Histogram of bond angle deviations from ideal: 99.10 - 106.09: 913 106.09 - 113.07: 76056 113.07 - 120.06: 20564 120.06 - 127.04: 22868 127.04 - 134.02: 493 Bond angle restraints: 120894 Sorted by residual: angle pdb=" CA ARG A 149 " pdb=" C ARG A 149 " pdb=" N GLU A 150 " ideal model delta sigma weight residual 116.84 124.13 -7.29 1.71e+00 3.42e-01 1.82e+01 angle pdb=" N GLN G 785 " pdb=" CA GLN G 785 " pdb=" C GLN G 785 " ideal model delta sigma weight residual 114.31 109.00 5.31 1.29e+00 6.01e-01 1.69e+01 angle pdb=" N GLN D 785 " pdb=" CA GLN D 785 " pdb=" C GLN D 785 " ideal model delta sigma weight residual 113.72 108.63 5.09 1.30e+00 5.92e-01 1.53e+01 angle pdb=" N GLN C 785 " pdb=" CA GLN C 785 " pdb=" C GLN C 785 " ideal model delta sigma weight residual 114.31 109.51 4.80 1.29e+00 6.01e-01 1.38e+01 angle pdb=" N GLN B 785 " pdb=" CA GLN B 785 " pdb=" C GLN B 785 " ideal model delta sigma weight residual 114.31 109.71 4.60 1.29e+00 6.01e-01 1.27e+01 ... (remaining 120889 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.05: 31724 25.05 - 50.10: 1156 50.10 - 75.14: 244 75.14 - 100.19: 32 100.19 - 125.24: 28 Dihedral angle restraints: 33184 sinusoidal: 17556 harmonic: 15628 Sorted by residual: dihedral pdb=" CB CYS C 784 " pdb=" SG CYS C 784 " pdb=" SG CYS C 820 " pdb=" CB CYS C 820 " ideal model delta sinusoidal sigma weight residual -86.00 -174.60 88.60 1 1.00e+01 1.00e-02 9.37e+01 dihedral pdb=" CB CYS B 784 " pdb=" SG CYS B 784 " pdb=" SG CYS B 820 " pdb=" CB CYS B 820 " ideal model delta sinusoidal sigma weight residual 93.00 -178.84 -88.16 1 1.00e+01 1.00e-02 9.29e+01 dihedral pdb=" CB CYS D 784 " pdb=" SG CYS D 784 " pdb=" SG CYS D 820 " pdb=" CB CYS D 820 " ideal model delta sinusoidal sigma weight residual 93.00 -178.86 -88.14 1 1.00e+01 1.00e-02 9.29e+01 ... (remaining 33181 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 4539 0.055 - 0.110: 668 0.110 - 0.164: 157 0.164 - 0.219: 3 0.219 - 0.274: 3 Chirality restraints: 5370 Sorted by residual: chirality pdb=" C1 NAG A2003 " pdb=" ND2 ASN A 163 " pdb=" C2 NAG A2003 " pdb=" O5 NAG A2003 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" C1 NAG E2003 " pdb=" ND2 ASN E 163 " pdb=" C2 NAG E2003 " pdb=" O5 NAG E2003 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" C1 NAG B2004 " pdb=" ND2 ASN B 163 " pdb=" C2 NAG B2004 " pdb=" O5 NAG B2004 " both_signs ideal model delta sigma weight residual False -2.40 -2.17 -0.23 2.00e-01 2.50e+01 1.28e+00 ... (remaining 5367 not shown) Planarity restraints: 10702 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN D 201 " 0.093 5.00e-02 4.00e+02 1.42e-01 3.23e+01 pdb=" N PRO D 202 " -0.246 5.00e-02 4.00e+02 pdb=" CA PRO D 202 " 0.078 5.00e-02 4.00e+02 pdb=" CD PRO D 202 " 0.075 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG G1222 " 0.038 5.00e-02 4.00e+02 5.82e-02 5.42e+00 pdb=" N PRO G1223 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO G1223 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO G1223 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 147 " -0.021 2.00e-02 2.50e+03 1.10e-02 4.83e+00 pdb=" CG TRP D 147 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 TRP D 147 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 TRP D 147 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP D 147 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP D 147 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP D 147 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 147 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 147 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP D 147 " -0.003 2.00e-02 2.50e+03 pdb=" HD1 TRP D 147 " -0.006 2.00e-02 2.50e+03 pdb=" HE1 TRP D 147 " -0.003 2.00e-02 2.50e+03 pdb=" HE3 TRP D 147 " 0.002 2.00e-02 2.50e+03 pdb=" HZ2 TRP D 147 " -0.002 2.00e-02 2.50e+03 pdb=" HZ3 TRP D 147 " -0.003 2.00e-02 2.50e+03 pdb=" HH2 TRP D 147 " 0.000 2.00e-02 2.50e+03 ... (remaining 10699 not shown) Histogram of nonbonded interaction distances: 1.54 - 2.15: 2267 2.15 - 2.76: 121620 2.76 - 3.38: 169760 3.38 - 3.99: 220340 3.99 - 4.60: 342380 Nonbonded interactions: 856367 Sorted by model distance: nonbonded pdb=" O CYS E 370 " pdb=" H LEU E 385 " model vdw 1.541 1.850 nonbonded pdb=" OD1 ASN G1125 " pdb=" H TRP G1132 " model vdw 1.541 1.850 nonbonded pdb=" H CYS B 387 " pdb=" OE1 GLN B 518 " model vdw 1.551 1.850 nonbonded pdb="HD21 ASN E 532 " pdb=" OD2 ASP E 537 " model vdw 1.563 1.850 nonbonded pdb=" O THR D 618 " pdb="HD22 ASN D 624 " model vdw 1.572 1.850 ... (remaining 856362 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 35 through 313 or resid 315 through 612 or resid 614 throu \ gh 749 or resid 2001 through 2004)) selection = (chain 'E' and (resid 35 through 313 or resid 315 through 612 or resid 614 throu \ gh 749 or resid 2001 through 2004)) } ncs_group { reference = (chain 'B' and (resid 35 through 106 or resid 108 through 313 or resid 315 throu \ gh 612 or resid 614 through 996 or resid 998 through 1240 or resid 2001 through \ 2005)) selection = (chain 'D' and (resid 35 through 106 or resid 108 through 313 or resid 315 throu \ gh 612 or resid 614 through 996 or resid 998 through 1240 or resid 2001 through \ 2005)) } ncs_group { reference = (chain 'C' and (resid 780 through 996 or resid 998 through 1240 or resid 1301)) selection = (chain 'G' and (resid 780 through 996 or resid 998 through 1240 or resid 1301)) } ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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=0.50 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: 2.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.800 Extract box with map and model: 14.760 Check model and map are aligned: 0.730 Set scattering table: 0.500 Process input model: 200.990 Find NCS groups from input model: 2.310 Set up NCS constraints: 0.410 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 225.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 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 : 0.003 0.069 35586 Z= 0.187 Angle : 0.644 8.863 48402 Z= 0.383 Chirality : 0.044 0.274 5370 Planarity : 0.004 0.142 6332 Dihedral : 12.332 125.240 12782 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.02 % Allowed : 9.17 % Favored : 90.81 % Rotamer: Outliers : 0.19 % Allowed : 0.45 % Favored : 99.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.12), residues: 4550 helix: -0.27 (0.20), residues: 678 sheet: 0.02 (0.20), residues: 784 loop : -2.13 (0.11), residues: 3088 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP D 147 HIS 0.007 0.001 HIS E 652 PHE 0.017 0.001 PHE D 513 TYR 0.014 0.001 TYR D 172 ARG 0.010 0.000 ARG G1171 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9100 Ramachandran restraints generated. 4550 Oldfield, 0 Emsley, 4550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9100 Ramachandran restraints generated. 4550 Oldfield, 0 Emsley, 4550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 175 is missing expected H atoms. Skipping. Residue TYR 178 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue SER 183 is missing expected H atoms. Skipping. Residue VAL 186 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue VAL 213 is missing expected H atoms. Skipping. Residue SER 217 is missing expected H atoms. Skipping. Residue LYS 453 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue VAL 457 is missing expected H atoms. Skipping. Residue LYS 656 is missing expected H atoms. Skipping. Residue SER 686 is missing expected H atoms. Skipping. Residue LEU 689 is missing expected H atoms. Skipping. Residue LYS 709 is missing expected H atoms. Skipping. Residue LYS 717 is missing expected H atoms. Skipping. Residue TYR 726 is missing expected H atoms. Skipping. Residue LEU 727 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue TYR 178 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue SER 183 is missing expected H atoms. Skipping. Residue VAL 186 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue VAL 213 is missing expected H atoms. Skipping. Residue SER 217 is missing expected H atoms. Skipping. Residue LYS 453 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue VAL 457 is missing expected H atoms. Skipping. Residue LYS 656 is missing expected H atoms. Skipping. Residue SER 686 is missing expected H atoms. Skipping. Residue LEU 689 is missing expected H atoms. Skipping. Residue LYS 709 is missing expected H atoms. Skipping. Residue LYS 717 is missing expected H atoms. Skipping. Residue TYR 726 is missing expected H atoms. Skipping. Residue LEU 727 is missing expected H atoms. Skipping. Residue TYR 791 is missing expected H atoms. Skipping. Residue SER 1217 is missing expected H atoms. Skipping. Residue TYR 1239 is missing expected H atoms. Skipping. Residue TYR 791 is missing expected H atoms. Skipping. Residue SER 1217 is missing expected H atoms. Skipping. Residue TYR 1239 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue TYR 178 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue SER 183 is missing expected H atoms. Skipping. Residue VAL 186 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue VAL 213 is missing expected H atoms. Skipping. Residue SER 217 is missing expected H atoms. Skipping. Residue LYS 453 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue VAL 457 is missing expected H atoms. Skipping. Residue LYS 656 is missing expected H atoms. Skipping. Residue SER 686 is missing expected H atoms. Skipping. Residue LEU 689 is missing expected H atoms. Skipping. Residue LYS 709 is missing expected H atoms. Skipping. Residue LYS 717 is missing expected H atoms. Skipping. Residue TYR 726 is missing expected H atoms. Skipping. Residue LEU 727 is missing expected H atoms. Skipping. Residue TYR 791 is missing expected H atoms. Skipping. Residue SER 1217 is missing expected H atoms. Skipping. Residue TYR 1239 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue TYR 178 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue SER 183 is missing expected H atoms. Skipping. Residue VAL 186 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue VAL 213 is missing expected H atoms. Skipping. Residue SER 217 is missing expected H atoms. Skipping. Residue LYS 453 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue VAL 457 is missing expected H atoms. Skipping. Residue LYS 656 is missing expected H atoms. Skipping. Residue SER 686 is missing expected H atoms. Skipping. Residue LEU 689 is missing expected H atoms. Skipping. Residue LYS 709 is missing expected H atoms. Skipping. Residue LYS 717 is missing expected H atoms. Skipping. Residue TYR 726 is missing expected H atoms. Skipping. Residue LEU 727 is missing expected H atoms. Skipping. Residue TYR 791 is missing expected H atoms. Skipping. Residue SER 1217 is missing expected H atoms. Skipping. Residue TYR 1239 is missing expected H atoms. Skipping. Evaluate side-chains 140 residues out of total 3950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 140 time to evaluate : 4.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 TYR cc_start: 0.6704 (p90) cc_final: 0.6444 (p90) REVERT: A 92 GLU cc_start: 0.8740 (tp30) cc_final: 0.8250 (tp30) REVERT: A 706 LEU cc_start: 0.8344 (mm) cc_final: 0.7684 (tp) REVERT: E 99 LYS cc_start: 0.9229 (ptmm) cc_final: 0.9025 (ptmm) outliers start: 0 outliers final: 0 residues processed: 140 average time/residue: 0.8481 time to fit residues: 196.1450 Evaluate side-chains 108 residues out of total 3950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 4.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 385 optimal weight: 10.0000 chunk 345 optimal weight: 7.9990 chunk 191 optimal weight: 0.9980 chunk 118 optimal weight: 5.9990 chunk 233 optimal weight: 20.0000 chunk 184 optimal weight: 6.9990 chunk 357 optimal weight: 30.0000 chunk 138 optimal weight: 5.9990 chunk 217 optimal weight: 0.1980 chunk 266 optimal weight: 20.0000 chunk 414 optimal weight: 4.9990 overall best weight: 3.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 785 GLN C 785 GLN C 906 ASN ** D 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 881 HIS D 906 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.0870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 35586 Z= 0.381 Angle : 0.626 7.917 48402 Z= 0.335 Chirality : 0.045 0.303 5370 Planarity : 0.005 0.109 6332 Dihedral : 9.757 116.632 5282 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.02 % Allowed : 11.71 % Favored : 88.27 % Rotamer: Outliers : 0.51 % Allowed : 2.34 % Favored : 97.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.17 (0.12), residues: 4550 helix: -0.35 (0.19), residues: 704 sheet: -0.05 (0.20), residues: 744 loop : -2.22 (0.11), residues: 3102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP D 147 HIS 0.012 0.002 HIS E 652 PHE 0.024 0.002 PHE A 485 TYR 0.021 0.002 TYR D 337 ARG 0.006 0.001 ARG D 140 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9100 Ramachandran restraints generated. 4550 Oldfield, 0 Emsley, 4550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9100 Ramachandran restraints generated. 4550 Oldfield, 0 Emsley, 4550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 175 is missing expected H atoms. Skipping. Residue TYR 178 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue SER 183 is missing expected H atoms. Skipping. Residue VAL 186 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue VAL 213 is missing expected H atoms. Skipping. Residue SER 217 is missing expected H atoms. Skipping. Residue LYS 453 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue VAL 457 is missing expected H atoms. Skipping. Residue LYS 656 is missing expected H atoms. Skipping. Residue SER 686 is missing expected H atoms. Skipping. Residue LEU 689 is missing expected H atoms. Skipping. Residue LYS 709 is missing expected H atoms. Skipping. Residue LYS 717 is missing expected H atoms. Skipping. Residue TYR 726 is missing expected H atoms. Skipping. Residue LEU 727 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue TYR 178 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue SER 183 is missing expected H atoms. Skipping. Residue VAL 186 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue VAL 213 is missing expected H atoms. Skipping. Residue SER 217 is missing expected H atoms. Skipping. Residue LYS 453 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue VAL 457 is missing expected H atoms. Skipping. Residue LYS 656 is missing expected H atoms. Skipping. Residue SER 686 is missing expected H atoms. Skipping. Residue LEU 689 is missing expected H atoms. Skipping. Residue LYS 709 is missing expected H atoms. Skipping. Residue LYS 717 is missing expected H atoms. Skipping. Residue TYR 726 is missing expected H atoms. Skipping. Residue LEU 727 is missing expected H atoms. Skipping. Residue TYR 791 is missing expected H atoms. Skipping. Residue SER 1217 is missing expected H atoms. Skipping. Residue TYR 1239 is missing expected H atoms. Skipping. Residue TYR 791 is missing expected H atoms. Skipping. Residue SER 1217 is missing expected H atoms. Skipping. Residue TYR 1239 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue TYR 178 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue SER 183 is missing expected H atoms. Skipping. Residue VAL 186 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue VAL 213 is missing expected H atoms. Skipping. Residue SER 217 is missing expected H atoms. Skipping. Residue LYS 453 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue VAL 457 is missing expected H atoms. Skipping. Residue LYS 656 is missing expected H atoms. Skipping. Residue SER 686 is missing expected H atoms. Skipping. Residue LEU 689 is missing expected H atoms. Skipping. Residue LYS 709 is missing expected H atoms. Skipping. Residue LYS 717 is missing expected H atoms. Skipping. Residue TYR 726 is missing expected H atoms. Skipping. Residue LEU 727 is missing expected H atoms. Skipping. Residue TYR 791 is missing expected H atoms. Skipping. Residue SER 1217 is missing expected H atoms. Skipping. Residue TYR 1239 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue TYR 178 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue SER 183 is missing expected H atoms. Skipping. Residue VAL 186 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue VAL 213 is missing expected H atoms. Skipping. Residue SER 217 is missing expected H atoms. Skipping. Residue LYS 453 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue VAL 457 is missing expected H atoms. Skipping. Residue LYS 656 is missing expected H atoms. Skipping. Residue SER 686 is missing expected H atoms. Skipping. Residue LEU 689 is missing expected H atoms. Skipping. Residue LYS 709 is missing expected H atoms. Skipping. Residue LYS 717 is missing expected H atoms. Skipping. Residue TYR 726 is missing expected H atoms. Skipping. Residue LEU 727 is missing expected H atoms. Skipping. Residue TYR 791 is missing expected H atoms. Skipping. Residue SER 1217 is missing expected H atoms. Skipping. Residue TYR 1239 is missing expected H atoms. Skipping. Evaluate side-chains 119 residues out of total 3950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 108 time to evaluate : 4.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 TYR cc_start: 0.6819 (p90) cc_final: 0.6587 (p90) REVERT: E 99 LYS cc_start: 0.9259 (ptmm) cc_final: 0.9028 (ptmm) REVERT: E 154 MET cc_start: 0.7460 (OUTLIER) cc_final: 0.6634 (tmm) REVERT: E 600 ARG cc_start: 0.7385 (ptt180) cc_final: 0.6834 (ptt90) outliers start: 11 outliers final: 10 residues processed: 115 average time/residue: 0.8579 time to fit residues: 162.7543 Evaluate side-chains 114 residues out of total 3950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 103 time to evaluate : 4.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 703 HIS Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 155 LEU Chi-restraints excluded: chain D residue 490 TYR Chi-restraints excluded: chain E residue 154 MET Chi-restraints excluded: chain E residue 515 THR Chi-restraints excluded: chain E residue 564 HIS Chi-restraints excluded: chain E residue 668 LEU Chi-restraints excluded: chain E residue 687 HIS Chi-restraints excluded: chain G residue 920 ILE Chi-restraints excluded: chain G residue 1155 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 230 optimal weight: 10.0000 chunk 128 optimal weight: 5.9990 chunk 344 optimal weight: 9.9990 chunk 281 optimal weight: 9.9990 chunk 114 optimal weight: 7.9990 chunk 414 optimal weight: 10.0000 chunk 448 optimal weight: 5.9990 chunk 369 optimal weight: 20.0000 chunk 411 optimal weight: 10.0000 chunk 141 optimal weight: 30.0000 chunk 332 optimal weight: 0.0370 overall best weight: 6.0066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 505 GLN A 687 HIS ** B 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 503 GLN B1077 HIS B1195 HIS ** D 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1195 HIS ** E 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1033 ASN ** G1077 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.081 35586 Z= 0.594 Angle : 0.765 19.625 48402 Z= 0.414 Chirality : 0.050 0.359 5370 Planarity : 0.006 0.088 6332 Dihedral : 8.825 118.315 5282 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.04 % Allowed : 13.93 % Favored : 86.02 % Rotamer: Outliers : 0.77 % Allowed : 3.77 % Favored : 95.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.75 (0.12), residues: 4550 helix: -0.84 (0.18), residues: 706 sheet: -0.61 (0.20), residues: 730 loop : -2.56 (0.10), residues: 3114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP D 147 HIS 0.020 0.002 HIS G1077 PHE 0.037 0.003 PHE C1120 TYR 0.031 0.003 TYR A 414 ARG 0.009 0.001 ARG D 998 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9100 Ramachandran restraints generated. 4550 Oldfield, 0 Emsley, 4550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9100 Ramachandran restraints generated. 4550 Oldfield, 0 Emsley, 4550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 175 is missing expected H atoms. Skipping. Residue TYR 178 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue SER 183 is missing expected H atoms. Skipping. Residue VAL 186 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue VAL 213 is missing expected H atoms. Skipping. Residue SER 217 is missing expected H atoms. Skipping. Residue LYS 453 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue VAL 457 is missing expected H atoms. Skipping. Residue LYS 656 is missing expected H atoms. Skipping. Residue SER 686 is missing expected H atoms. Skipping. Residue LEU 689 is missing expected H atoms. Skipping. Residue LYS 709 is missing expected H atoms. Skipping. Residue LYS 717 is missing expected H atoms. Skipping. Residue TYR 726 is missing expected H atoms. Skipping. Residue LEU 727 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue TYR 178 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue SER 183 is missing expected H atoms. Skipping. Residue VAL 186 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue VAL 213 is missing expected H atoms. Skipping. Residue SER 217 is missing expected H atoms. Skipping. Residue LYS 453 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue VAL 457 is missing expected H atoms. Skipping. Residue LYS 656 is missing expected H atoms. Skipping. Residue SER 686 is missing expected H atoms. Skipping. Residue LEU 689 is missing expected H atoms. Skipping. Residue LYS 709 is missing expected H atoms. Skipping. Residue LYS 717 is missing expected H atoms. Skipping. Residue TYR 726 is missing expected H atoms. Skipping. Residue LEU 727 is missing expected H atoms. Skipping. Residue TYR 791 is missing expected H atoms. Skipping. Residue SER 1217 is missing expected H atoms. Skipping. Residue TYR 1239 is missing expected H atoms. Skipping. Residue TYR 791 is missing expected H atoms. Skipping. Residue SER 1217 is missing expected H atoms. Skipping. Residue TYR 1239 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue TYR 178 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue SER 183 is missing expected H atoms. Skipping. Residue VAL 186 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue VAL 213 is missing expected H atoms. Skipping. Residue SER 217 is missing expected H atoms. Skipping. Residue LYS 453 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue VAL 457 is missing expected H atoms. Skipping. Residue LYS 656 is missing expected H atoms. Skipping. Residue SER 686 is missing expected H atoms. Skipping. Residue LEU 689 is missing expected H atoms. Skipping. Residue LYS 709 is missing expected H atoms. Skipping. Residue LYS 717 is missing expected H atoms. Skipping. Residue TYR 726 is missing expected H atoms. Skipping. Residue LEU 727 is missing expected H atoms. Skipping. Residue TYR 791 is missing expected H atoms. Skipping. Residue SER 1217 is missing expected H atoms. Skipping. Residue TYR 1239 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue TYR 178 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue SER 183 is missing expected H atoms. Skipping. Residue VAL 186 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue VAL 213 is missing expected H atoms. Skipping. Residue SER 217 is missing expected H atoms. Skipping. Residue LYS 453 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue VAL 457 is missing expected H atoms. Skipping. Residue LYS 656 is missing expected H atoms. Skipping. Residue SER 686 is missing expected H atoms. Skipping. Residue LEU 689 is missing expected H atoms. Skipping. Residue LYS 709 is missing expected H atoms. Skipping. Residue LYS 717 is missing expected H atoms. Skipping. Residue TYR 726 is missing expected H atoms. Skipping. Residue LEU 727 is missing expected H atoms. Skipping. Residue TYR 791 is missing expected H atoms. Skipping. Residue SER 1217 is missing expected H atoms. Skipping. Residue TYR 1239 is missing expected H atoms. Skipping. Evaluate side-chains 128 residues out of total 3950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 107 time to evaluate : 4.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 TYR cc_start: 0.6871 (p90) cc_final: 0.6670 (p90) REVERT: E 326 MET cc_start: 0.4061 (mtt) cc_final: 0.3653 (mtt) REVERT: E 645 MET cc_start: 0.6085 (tmm) cc_final: 0.5371 (tmm) outliers start: 21 outliers final: 16 residues processed: 120 average time/residue: 0.8664 time to fit residues: 172.8816 Evaluate side-chains 119 residues out of total 3950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 103 time to evaluate : 4.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain A residue 703 HIS Chi-restraints excluded: chain B residue 652 HIS Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 971 ASP Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 163 ASN Chi-restraints excluded: chain E residue 309 MET Chi-restraints excluded: chain E residue 515 THR Chi-restraints excluded: chain E residue 668 LEU Chi-restraints excluded: chain E residue 687 HIS Chi-restraints excluded: chain E residue 718 CYS Chi-restraints excluded: chain G residue 920 ILE Chi-restraints excluded: chain G residue 1155 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 409 optimal weight: 0.3980 chunk 311 optimal weight: 0.6980 chunk 215 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 chunk 197 optimal weight: 0.7980 chunk 278 optimal weight: 8.9990 chunk 416 optimal weight: 7.9990 chunk 440 optimal weight: 1.9990 chunk 217 optimal weight: 0.7980 chunk 394 optimal weight: 10.0000 chunk 118 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 582 ASN ** G1077 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 35586 Z= 0.153 Angle : 0.559 9.287 48402 Z= 0.295 Chirality : 0.044 0.302 5370 Planarity : 0.004 0.082 6332 Dihedral : 7.899 116.175 5282 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.33 % Favored : 90.67 % Rotamer: Outliers : 0.69 % Allowed : 4.41 % Favored : 94.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.14 (0.12), residues: 4550 helix: -0.16 (0.19), residues: 716 sheet: -0.13 (0.20), residues: 750 loop : -2.23 (0.11), residues: 3084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP D 147 HIS 0.006 0.001 HIS D1128 PHE 0.015 0.001 PHE G 878 TYR 0.016 0.001 TYR A 414 ARG 0.004 0.000 ARG A 650 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9100 Ramachandran restraints generated. 4550 Oldfield, 0 Emsley, 4550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9100 Ramachandran restraints generated. 4550 Oldfield, 0 Emsley, 4550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 175 is missing expected H atoms. Skipping. Residue TYR 178 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue SER 183 is missing expected H atoms. Skipping. Residue VAL 186 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue VAL 213 is missing expected H atoms. Skipping. Residue SER 217 is missing expected H atoms. Skipping. Residue LYS 453 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue VAL 457 is missing expected H atoms. Skipping. Residue LYS 656 is missing expected H atoms. Skipping. Residue SER 686 is missing expected H atoms. Skipping. Residue LEU 689 is missing expected H atoms. Skipping. Residue LYS 709 is missing expected H atoms. Skipping. Residue LYS 717 is missing expected H atoms. Skipping. Residue TYR 726 is missing expected H atoms. Skipping. Residue LEU 727 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue TYR 178 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue SER 183 is missing expected H atoms. Skipping. Residue VAL 186 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue VAL 213 is missing expected H atoms. Skipping. Residue SER 217 is missing expected H atoms. Skipping. Residue LYS 453 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue VAL 457 is missing expected H atoms. Skipping. Residue LYS 656 is missing expected H atoms. Skipping. Residue SER 686 is missing expected H atoms. Skipping. Residue LEU 689 is missing expected H atoms. Skipping. Residue LYS 709 is missing expected H atoms. Skipping. Residue LYS 717 is missing expected H atoms. Skipping. Residue TYR 726 is missing expected H atoms. Skipping. Residue LEU 727 is missing expected H atoms. Skipping. Residue TYR 791 is missing expected H atoms. Skipping. Residue SER 1217 is missing expected H atoms. Skipping. Residue TYR 1239 is missing expected H atoms. Skipping. Residue TYR 791 is missing expected H atoms. Skipping. Residue SER 1217 is missing expected H atoms. Skipping. Residue TYR 1239 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue TYR 178 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue SER 183 is missing expected H atoms. Skipping. Residue VAL 186 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue VAL 213 is missing expected H atoms. Skipping. Residue SER 217 is missing expected H atoms. Skipping. Residue LYS 453 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue VAL 457 is missing expected H atoms. Skipping. Residue LYS 656 is missing expected H atoms. Skipping. Residue SER 686 is missing expected H atoms. Skipping. Residue LEU 689 is missing expected H atoms. Skipping. Residue LYS 709 is missing expected H atoms. Skipping. Residue LYS 717 is missing expected H atoms. Skipping. Residue TYR 726 is missing expected H atoms. Skipping. Residue LEU 727 is missing expected H atoms. Skipping. Residue TYR 791 is missing expected H atoms. Skipping. Residue SER 1217 is missing expected H atoms. Skipping. Residue TYR 1239 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue TYR 178 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue SER 183 is missing expected H atoms. Skipping. Residue VAL 186 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue VAL 213 is missing expected H atoms. Skipping. Residue SER 217 is missing expected H atoms. Skipping. Residue LYS 453 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue VAL 457 is missing expected H atoms. Skipping. Residue LYS 656 is missing expected H atoms. Skipping. Residue SER 686 is missing expected H atoms. Skipping. Residue LEU 689 is missing expected H atoms. Skipping. Residue LYS 709 is missing expected H atoms. Skipping. Residue LYS 717 is missing expected H atoms. Skipping. Residue TYR 726 is missing expected H atoms. Skipping. Residue LEU 727 is missing expected H atoms. Skipping. Residue TYR 791 is missing expected H atoms. Skipping. Residue SER 1217 is missing expected H atoms. Skipping. Residue TYR 1239 is missing expected H atoms. Skipping. Evaluate side-chains 120 residues out of total 3950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 102 time to evaluate : 5.064 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: E 326 MET cc_start: 0.4057 (mtt) cc_final: 0.3646 (mtt) REVERT: E 645 MET cc_start: 0.6014 (tmm) cc_final: 0.5345 (tmm) REVERT: G 846 ARG cc_start: 0.7459 (ppt170) cc_final: 0.7113 (ttp80) outliers start: 18 outliers final: 14 residues processed: 114 average time/residue: 0.8709 time to fit residues: 165.7105 Evaluate side-chains 112 residues out of total 3950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 98 time to evaluate : 4.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain A residue 326 MET Chi-restraints excluded: chain B residue 652 HIS Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 155 LEU Chi-restraints excluded: chain E residue 163 ASN Chi-restraints excluded: chain E residue 515 THR Chi-restraints excluded: chain E residue 668 LEU Chi-restraints excluded: chain E residue 687 HIS Chi-restraints excluded: chain E residue 715 LEU Chi-restraints excluded: chain G residue 877 ASP Chi-restraints excluded: chain G residue 920 ILE Chi-restraints excluded: chain G residue 1155 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 367 optimal weight: 0.6980 chunk 250 optimal weight: 9.9990 chunk 6 optimal weight: 2.9990 chunk 328 optimal weight: 0.9990 chunk 181 optimal weight: 5.9990 chunk 376 optimal weight: 4.9990 chunk 304 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 225 optimal weight: 7.9990 chunk 395 optimal weight: 0.9990 chunk 111 optimal weight: 4.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1077 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 35586 Z= 0.244 Angle : 0.551 9.311 48402 Z= 0.292 Chirality : 0.044 0.318 5370 Planarity : 0.004 0.078 6332 Dihedral : 7.631 115.336 5282 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.16 % Favored : 88.84 % Rotamer: Outliers : 0.61 % Allowed : 4.70 % Favored : 94.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.12), residues: 4550 helix: -0.01 (0.19), residues: 716 sheet: -0.09 (0.20), residues: 736 loop : -2.17 (0.11), residues: 3098 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP D 147 HIS 0.007 0.001 HIS D1128 PHE 0.019 0.001 PHE G 878 TYR 0.018 0.001 TYR B 61 ARG 0.004 0.000 ARG E 600 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9100 Ramachandran restraints generated. 4550 Oldfield, 0 Emsley, 4550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9100 Ramachandran restraints generated. 4550 Oldfield, 0 Emsley, 4550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 175 is missing expected H atoms. Skipping. Residue TYR 178 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue SER 183 is missing expected H atoms. Skipping. Residue VAL 186 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue VAL 213 is missing expected H atoms. Skipping. Residue SER 217 is missing expected H atoms. Skipping. Residue LYS 453 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue VAL 457 is missing expected H atoms. Skipping. Residue LYS 656 is missing expected H atoms. Skipping. Residue SER 686 is missing expected H atoms. Skipping. Residue LEU 689 is missing expected H atoms. Skipping. Residue LYS 709 is missing expected H atoms. Skipping. Residue LYS 717 is missing expected H atoms. Skipping. Residue TYR 726 is missing expected H atoms. Skipping. Residue LEU 727 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue TYR 178 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue SER 183 is missing expected H atoms. Skipping. Residue VAL 186 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue VAL 213 is missing expected H atoms. Skipping. Residue SER 217 is missing expected H atoms. Skipping. Residue LYS 453 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue VAL 457 is missing expected H atoms. Skipping. Residue LYS 656 is missing expected H atoms. Skipping. Residue SER 686 is missing expected H atoms. Skipping. Residue LEU 689 is missing expected H atoms. Skipping. Residue LYS 709 is missing expected H atoms. Skipping. Residue LYS 717 is missing expected H atoms. Skipping. Residue TYR 726 is missing expected H atoms. Skipping. Residue LEU 727 is missing expected H atoms. Skipping. Residue TYR 791 is missing expected H atoms. Skipping. Residue SER 1217 is missing expected H atoms. Skipping. Residue TYR 1239 is missing expected H atoms. Skipping. Residue TYR 791 is missing expected H atoms. Skipping. Residue SER 1217 is missing expected H atoms. Skipping. Residue TYR 1239 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue TYR 178 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue SER 183 is missing expected H atoms. Skipping. Residue VAL 186 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue VAL 213 is missing expected H atoms. Skipping. Residue SER 217 is missing expected H atoms. Skipping. Residue LYS 453 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue VAL 457 is missing expected H atoms. Skipping. Residue LYS 656 is missing expected H atoms. Skipping. Residue SER 686 is missing expected H atoms. Skipping. Residue LEU 689 is missing expected H atoms. Skipping. Residue LYS 709 is missing expected H atoms. Skipping. Residue LYS 717 is missing expected H atoms. Skipping. Residue TYR 726 is missing expected H atoms. Skipping. Residue LEU 727 is missing expected H atoms. Skipping. Residue TYR 791 is missing expected H atoms. Skipping. Residue SER 1217 is missing expected H atoms. Skipping. Residue TYR 1239 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue TYR 178 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue SER 183 is missing expected H atoms. Skipping. Residue VAL 186 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue VAL 213 is missing expected H atoms. Skipping. Residue SER 217 is missing expected H atoms. Skipping. Residue LYS 453 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue VAL 457 is missing expected H atoms. Skipping. Residue LYS 656 is missing expected H atoms. Skipping. Residue SER 686 is missing expected H atoms. Skipping. Residue LEU 689 is missing expected H atoms. Skipping. Residue LYS 709 is missing expected H atoms. Skipping. Residue LYS 717 is missing expected H atoms. Skipping. Residue TYR 726 is missing expected H atoms. Skipping. Residue LEU 727 is missing expected H atoms. Skipping. Residue TYR 791 is missing expected H atoms. Skipping. Residue SER 1217 is missing expected H atoms. Skipping. Residue TYR 1239 is missing expected H atoms. Skipping. Evaluate side-chains 117 residues out of total 3950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 102 time to evaluate : 4.167 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: B 326 MET cc_start: 0.5830 (mmt) cc_final: 0.5125 (mmt) REVERT: D 309 MET cc_start: 0.8172 (mtp) cc_final: 0.7277 (mmt) REVERT: E 326 MET cc_start: 0.3911 (mtt) cc_final: 0.3464 (mtt) REVERT: E 645 MET cc_start: 0.6026 (tmm) cc_final: 0.5548 (tmm) outliers start: 15 outliers final: 13 residues processed: 110 average time/residue: 0.8260 time to fit residues: 151.6099 Evaluate side-chains 111 residues out of total 3950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 98 time to evaluate : 4.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain B residue 652 HIS Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 155 LEU Chi-restraints excluded: chain D residue 369 ASP Chi-restraints excluded: chain E residue 163 ASN Chi-restraints excluded: chain E residue 515 THR Chi-restraints excluded: chain E residue 668 LEU Chi-restraints excluded: chain E residue 687 HIS Chi-restraints excluded: chain G residue 877 ASP Chi-restraints excluded: chain G residue 920 ILE Chi-restraints excluded: chain G residue 1155 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 148 optimal weight: 10.0000 chunk 396 optimal weight: 6.9990 chunk 87 optimal weight: 8.9990 chunk 258 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 chunk 441 optimal weight: 3.9990 chunk 366 optimal weight: 10.0000 chunk 204 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 145 optimal weight: 3.9990 chunk 231 optimal weight: 10.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1077 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 35586 Z= 0.340 Angle : 0.594 10.646 48402 Z= 0.318 Chirality : 0.045 0.300 5370 Planarity : 0.004 0.072 6332 Dihedral : 7.455 115.146 5282 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.24 % Favored : 87.76 % Rotamer: Outliers : 0.80 % Allowed : 5.00 % Favored : 94.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (0.12), residues: 4550 helix: -0.09 (0.19), residues: 718 sheet: -0.26 (0.20), residues: 752 loop : -2.20 (0.11), residues: 3080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.001 TRP D 147 HIS 0.009 0.001 HIS G1077 PHE 0.021 0.002 PHE G 878 TYR 0.021 0.002 TYR B 61 ARG 0.006 0.001 ARG E 600 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9100 Ramachandran restraints generated. 4550 Oldfield, 0 Emsley, 4550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9100 Ramachandran restraints generated. 4550 Oldfield, 0 Emsley, 4550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 175 is missing expected H atoms. Skipping. Residue TYR 178 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue SER 183 is missing expected H atoms. Skipping. Residue VAL 186 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue VAL 213 is missing expected H atoms. Skipping. Residue SER 217 is missing expected H atoms. Skipping. Residue LYS 453 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue VAL 457 is missing expected H atoms. Skipping. Residue LYS 656 is missing expected H atoms. Skipping. Residue SER 686 is missing expected H atoms. Skipping. Residue LEU 689 is missing expected H atoms. Skipping. Residue LYS 709 is missing expected H atoms. Skipping. Residue LYS 717 is missing expected H atoms. Skipping. Residue TYR 726 is missing expected H atoms. Skipping. Residue LEU 727 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue TYR 178 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue SER 183 is missing expected H atoms. Skipping. Residue VAL 186 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue VAL 213 is missing expected H atoms. Skipping. Residue SER 217 is missing expected H atoms. Skipping. Residue LYS 453 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue VAL 457 is missing expected H atoms. Skipping. Residue LYS 656 is missing expected H atoms. Skipping. Residue SER 686 is missing expected H atoms. Skipping. Residue LEU 689 is missing expected H atoms. Skipping. Residue LYS 709 is missing expected H atoms. Skipping. Residue LYS 717 is missing expected H atoms. Skipping. Residue TYR 726 is missing expected H atoms. Skipping. Residue LEU 727 is missing expected H atoms. Skipping. Residue TYR 791 is missing expected H atoms. Skipping. Residue SER 1217 is missing expected H atoms. Skipping. Residue TYR 1239 is missing expected H atoms. Skipping. Residue TYR 791 is missing expected H atoms. Skipping. Residue SER 1217 is missing expected H atoms. Skipping. Residue TYR 1239 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue TYR 178 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue SER 183 is missing expected H atoms. Skipping. Residue VAL 186 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue VAL 213 is missing expected H atoms. Skipping. Residue SER 217 is missing expected H atoms. Skipping. Residue LYS 453 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue VAL 457 is missing expected H atoms. Skipping. Residue LYS 656 is missing expected H atoms. Skipping. Residue SER 686 is missing expected H atoms. Skipping. Residue LEU 689 is missing expected H atoms. Skipping. Residue LYS 709 is missing expected H atoms. Skipping. Residue LYS 717 is missing expected H atoms. Skipping. Residue TYR 726 is missing expected H atoms. Skipping. Residue LEU 727 is missing expected H atoms. Skipping. Residue TYR 791 is missing expected H atoms. Skipping. Residue SER 1217 is missing expected H atoms. Skipping. Residue TYR 1239 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue TYR 178 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue SER 183 is missing expected H atoms. Skipping. Residue VAL 186 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue VAL 213 is missing expected H atoms. Skipping. Residue SER 217 is missing expected H atoms. Skipping. Residue LYS 453 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue VAL 457 is missing expected H atoms. Skipping. Residue LYS 656 is missing expected H atoms. Skipping. Residue SER 686 is missing expected H atoms. Skipping. Residue LEU 689 is missing expected H atoms. Skipping. Residue LYS 709 is missing expected H atoms. Skipping. Residue LYS 717 is missing expected H atoms. Skipping. Residue TYR 726 is missing expected H atoms. Skipping. Residue LEU 727 is missing expected H atoms. Skipping. Residue TYR 791 is missing expected H atoms. Skipping. Residue SER 1217 is missing expected H atoms. Skipping. Residue TYR 1239 is missing expected H atoms. Skipping. Evaluate side-chains 126 residues out of total 3950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 104 time to evaluate : 4.180 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: B 326 MET cc_start: 0.5760 (mmt) cc_final: 0.5047 (mmt) REVERT: D 309 MET cc_start: 0.8236 (mtp) cc_final: 0.7376 (mmt) REVERT: E 645 MET cc_start: 0.6064 (tmm) cc_final: 0.5309 (tmm) REVERT: G 846 ARG cc_start: 0.7320 (ppt170) cc_final: 0.7005 (ttp80) outliers start: 22 outliers final: 17 residues processed: 119 average time/residue: 0.8256 time to fit residues: 165.6270 Evaluate side-chains 116 residues out of total 3950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 99 time to evaluate : 4.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain B residue 652 HIS Chi-restraints excluded: chain C residue 971 ASP Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 155 LEU Chi-restraints excluded: chain D residue 369 ASP Chi-restraints excluded: chain E residue 163 ASN Chi-restraints excluded: chain E residue 515 THR Chi-restraints excluded: chain E residue 668 LEU Chi-restraints excluded: chain E residue 687 HIS Chi-restraints excluded: chain E residue 718 CYS Chi-restraints excluded: chain G residue 870 THR Chi-restraints excluded: chain G residue 877 ASP Chi-restraints excluded: chain G residue 920 ILE Chi-restraints excluded: chain G residue 1155 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 425 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 251 optimal weight: 20.0000 chunk 322 optimal weight: 0.4980 chunk 249 optimal weight: 6.9990 chunk 371 optimal weight: 6.9990 chunk 246 optimal weight: 9.9990 chunk 439 optimal weight: 0.7980 chunk 275 optimal weight: 8.9990 chunk 267 optimal weight: 20.0000 chunk 202 optimal weight: 0.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1077 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.2165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 35586 Z= 0.157 Angle : 0.527 10.296 48402 Z= 0.277 Chirality : 0.043 0.285 5370 Planarity : 0.004 0.070 6332 Dihedral : 7.140 114.293 5282 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.85 % Favored : 90.15 % Rotamer: Outliers : 0.64 % Allowed : 5.34 % Favored : 94.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.12), residues: 4550 helix: 0.18 (0.20), residues: 718 sheet: -0.01 (0.20), residues: 756 loop : -2.05 (0.11), residues: 3076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRP D 147 HIS 0.005 0.001 HIS E 356 PHE 0.012 0.001 PHE D1120 TYR 0.014 0.001 TYR B 61 ARG 0.003 0.000 ARG E 600 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9100 Ramachandran restraints generated. 4550 Oldfield, 0 Emsley, 4550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9100 Ramachandran restraints generated. 4550 Oldfield, 0 Emsley, 4550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 175 is missing expected H atoms. Skipping. Residue TYR 178 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue SER 183 is missing expected H atoms. Skipping. Residue VAL 186 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue VAL 213 is missing expected H atoms. Skipping. Residue SER 217 is missing expected H atoms. Skipping. Residue LYS 453 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue VAL 457 is missing expected H atoms. Skipping. Residue LYS 656 is missing expected H atoms. Skipping. Residue SER 686 is missing expected H atoms. Skipping. Residue LEU 689 is missing expected H atoms. Skipping. Residue LYS 709 is missing expected H atoms. Skipping. Residue LYS 717 is missing expected H atoms. Skipping. Residue TYR 726 is missing expected H atoms. Skipping. Residue LEU 727 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue TYR 178 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue SER 183 is missing expected H atoms. Skipping. Residue VAL 186 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue VAL 213 is missing expected H atoms. Skipping. Residue SER 217 is missing expected H atoms. Skipping. Residue LYS 453 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue VAL 457 is missing expected H atoms. Skipping. Residue LYS 656 is missing expected H atoms. Skipping. Residue SER 686 is missing expected H atoms. Skipping. Residue LEU 689 is missing expected H atoms. Skipping. Residue LYS 709 is missing expected H atoms. Skipping. Residue LYS 717 is missing expected H atoms. Skipping. Residue TYR 726 is missing expected H atoms. Skipping. Residue LEU 727 is missing expected H atoms. Skipping. Residue TYR 791 is missing expected H atoms. Skipping. Residue SER 1217 is missing expected H atoms. Skipping. Residue TYR 1239 is missing expected H atoms. Skipping. Residue TYR 791 is missing expected H atoms. Skipping. Residue SER 1217 is missing expected H atoms. Skipping. Residue TYR 1239 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue TYR 178 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue SER 183 is missing expected H atoms. Skipping. Residue VAL 186 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue VAL 213 is missing expected H atoms. Skipping. Residue SER 217 is missing expected H atoms. Skipping. Residue LYS 453 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue VAL 457 is missing expected H atoms. Skipping. Residue LYS 656 is missing expected H atoms. Skipping. Residue SER 686 is missing expected H atoms. Skipping. Residue LEU 689 is missing expected H atoms. Skipping. Residue LYS 709 is missing expected H atoms. Skipping. Residue LYS 717 is missing expected H atoms. Skipping. Residue TYR 726 is missing expected H atoms. Skipping. Residue LEU 727 is missing expected H atoms. Skipping. Residue TYR 791 is missing expected H atoms. Skipping. Residue SER 1217 is missing expected H atoms. Skipping. Residue TYR 1239 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue TYR 178 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue SER 183 is missing expected H atoms. Skipping. Residue VAL 186 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue VAL 213 is missing expected H atoms. Skipping. Residue SER 217 is missing expected H atoms. Skipping. Residue LYS 453 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue VAL 457 is missing expected H atoms. Skipping. Residue LYS 656 is missing expected H atoms. Skipping. Residue SER 686 is missing expected H atoms. Skipping. Residue LEU 689 is missing expected H atoms. Skipping. Residue LYS 709 is missing expected H atoms. Skipping. Residue LYS 717 is missing expected H atoms. Skipping. Residue TYR 726 is missing expected H atoms. Skipping. Residue LEU 727 is missing expected H atoms. Skipping. Residue TYR 791 is missing expected H atoms. Skipping. Residue SER 1217 is missing expected H atoms. Skipping. Residue TYR 1239 is missing expected H atoms. Skipping. Evaluate side-chains 113 residues out of total 3950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 97 time to evaluate : 4.360 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: A 706 LEU cc_start: 0.8508 (mm) cc_final: 0.7871 (tp) REVERT: D 309 MET cc_start: 0.8164 (mtp) cc_final: 0.7358 (mmt) REVERT: E 645 MET cc_start: 0.6147 (tmm) cc_final: 0.5309 (tmm) outliers start: 16 outliers final: 13 residues processed: 108 average time/residue: 0.8519 time to fit residues: 155.6477 Evaluate side-chains 110 residues out of total 3950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 97 time to evaluate : 4.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain B residue 652 HIS Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 155 LEU Chi-restraints excluded: chain D residue 369 ASP Chi-restraints excluded: chain E residue 163 ASN Chi-restraints excluded: chain E residue 515 THR Chi-restraints excluded: chain E residue 668 LEU Chi-restraints excluded: chain E residue 687 HIS Chi-restraints excluded: chain E residue 718 CYS Chi-restraints excluded: chain G residue 877 ASP Chi-restraints excluded: chain G residue 920 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 271 optimal weight: 8.9990 chunk 175 optimal weight: 9.9990 chunk 262 optimal weight: 5.9990 chunk 132 optimal weight: 10.0000 chunk 86 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 279 optimal weight: 20.0000 chunk 299 optimal weight: 5.9990 chunk 217 optimal weight: 0.0970 chunk 40 optimal weight: 0.8980 chunk 345 optimal weight: 20.0000 overall best weight: 2.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1077 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 35586 Z= 0.271 Angle : 0.551 10.329 48402 Z= 0.292 Chirality : 0.044 0.304 5370 Planarity : 0.004 0.067 6332 Dihedral : 7.019 114.018 5282 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.08 % Favored : 87.92 % Rotamer: Outliers : 0.61 % Allowed : 5.53 % Favored : 93.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (0.12), residues: 4550 helix: 0.17 (0.20), residues: 720 sheet: -0.05 (0.20), residues: 738 loop : -2.07 (0.11), residues: 3092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.001 TRP D 147 HIS 0.006 0.001 HIS A 410 PHE 0.019 0.001 PHE G 878 TYR 0.020 0.001 TYR B 61 ARG 0.004 0.000 ARG E 600 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9100 Ramachandran restraints generated. 4550 Oldfield, 0 Emsley, 4550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9100 Ramachandran restraints generated. 4550 Oldfield, 0 Emsley, 4550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 175 is missing expected H atoms. Skipping. Residue TYR 178 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue SER 183 is missing expected H atoms. Skipping. Residue VAL 186 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue VAL 213 is missing expected H atoms. Skipping. Residue SER 217 is missing expected H atoms. Skipping. Residue LYS 453 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue VAL 457 is missing expected H atoms. Skipping. Residue LYS 656 is missing expected H atoms. Skipping. Residue SER 686 is missing expected H atoms. Skipping. Residue LEU 689 is missing expected H atoms. Skipping. Residue LYS 709 is missing expected H atoms. Skipping. Residue LYS 717 is missing expected H atoms. Skipping. Residue TYR 726 is missing expected H atoms. Skipping. Residue LEU 727 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue TYR 178 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue SER 183 is missing expected H atoms. Skipping. Residue VAL 186 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue VAL 213 is missing expected H atoms. Skipping. Residue SER 217 is missing expected H atoms. Skipping. Residue LYS 453 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue VAL 457 is missing expected H atoms. Skipping. Residue LYS 656 is missing expected H atoms. Skipping. Residue SER 686 is missing expected H atoms. Skipping. Residue LEU 689 is missing expected H atoms. Skipping. Residue LYS 709 is missing expected H atoms. Skipping. Residue LYS 717 is missing expected H atoms. Skipping. Residue TYR 726 is missing expected H atoms. Skipping. Residue LEU 727 is missing expected H atoms. Skipping. Residue TYR 791 is missing expected H atoms. Skipping. Residue SER 1217 is missing expected H atoms. Skipping. Residue TYR 1239 is missing expected H atoms. Skipping. Residue TYR 791 is missing expected H atoms. Skipping. Residue SER 1217 is missing expected H atoms. Skipping. Residue TYR 1239 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue TYR 178 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue SER 183 is missing expected H atoms. Skipping. Residue VAL 186 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue VAL 213 is missing expected H atoms. Skipping. Residue SER 217 is missing expected H atoms. Skipping. Residue LYS 453 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue VAL 457 is missing expected H atoms. Skipping. Residue LYS 656 is missing expected H atoms. Skipping. Residue SER 686 is missing expected H atoms. Skipping. Residue LEU 689 is missing expected H atoms. Skipping. Residue LYS 709 is missing expected H atoms. Skipping. Residue LYS 717 is missing expected H atoms. Skipping. Residue TYR 726 is missing expected H atoms. Skipping. Residue LEU 727 is missing expected H atoms. Skipping. Residue TYR 791 is missing expected H atoms. Skipping. Residue SER 1217 is missing expected H atoms. Skipping. Residue TYR 1239 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue TYR 178 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue SER 183 is missing expected H atoms. Skipping. Residue VAL 186 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue VAL 213 is missing expected H atoms. Skipping. Residue SER 217 is missing expected H atoms. Skipping. Residue LYS 453 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue VAL 457 is missing expected H atoms. Skipping. Residue LYS 656 is missing expected H atoms. Skipping. Residue SER 686 is missing expected H atoms. Skipping. Residue LEU 689 is missing expected H atoms. Skipping. Residue LYS 709 is missing expected H atoms. Skipping. Residue LYS 717 is missing expected H atoms. Skipping. Residue TYR 726 is missing expected H atoms. Skipping. Residue LEU 727 is missing expected H atoms. Skipping. Residue TYR 791 is missing expected H atoms. Skipping. Residue SER 1217 is missing expected H atoms. Skipping. Residue TYR 1239 is missing expected H atoms. Skipping. Evaluate side-chains 112 residues out of total 3950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 97 time to evaluate : 4.172 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: B 326 MET cc_start: 0.5696 (mmt) cc_final: 0.5228 (mmt) REVERT: D 309 MET cc_start: 0.8156 (mtp) cc_final: 0.7385 (mmt) REVERT: E 645 MET cc_start: 0.6241 (tmm) cc_final: 0.5411 (tmm) REVERT: G 807 MET cc_start: 0.6215 (tpp) cc_final: 0.5870 (tpp) REVERT: G 846 ARG cc_start: 0.7530 (ppt170) cc_final: 0.7206 (ttp80) outliers start: 15 outliers final: 14 residues processed: 107 average time/residue: 0.8585 time to fit residues: 154.9820 Evaluate side-chains 110 residues out of total 3950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 96 time to evaluate : 4.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 652 HIS Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 155 LEU Chi-restraints excluded: chain D residue 369 ASP Chi-restraints excluded: chain E residue 163 ASN Chi-restraints excluded: chain E residue 515 THR Chi-restraints excluded: chain E residue 668 LEU Chi-restraints excluded: chain E residue 687 HIS Chi-restraints excluded: chain E residue 718 CYS Chi-restraints excluded: chain G residue 877 ASP Chi-restraints excluded: chain G residue 920 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 399 optimal weight: 6.9990 chunk 421 optimal weight: 1.9990 chunk 384 optimal weight: 6.9990 chunk 409 optimal weight: 0.0570 chunk 420 optimal weight: 1.9990 chunk 246 optimal weight: 10.0000 chunk 178 optimal weight: 0.3980 chunk 321 optimal weight: 2.9990 chunk 125 optimal weight: 5.9990 chunk 370 optimal weight: 0.9980 chunk 387 optimal weight: 0.4980 overall best weight: 0.7900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1077 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 35586 Z= 0.137 Angle : 0.513 10.531 48402 Z= 0.268 Chirality : 0.043 0.271 5370 Planarity : 0.004 0.067 6332 Dihedral : 6.574 112.711 5282 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.80 % Favored : 91.20 % Rotamer: Outliers : 0.51 % Allowed : 5.64 % Favored : 93.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.13), residues: 4550 helix: 0.40 (0.20), residues: 714 sheet: 0.15 (0.20), residues: 776 loop : -1.92 (0.11), residues: 3060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.001 TRP D 147 HIS 0.006 0.001 HIS E 356 PHE 0.012 0.001 PHE D1120 TYR 0.012 0.001 TYR A 407 ARG 0.003 0.000 ARG E 600 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9100 Ramachandran restraints generated. 4550 Oldfield, 0 Emsley, 4550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9100 Ramachandran restraints generated. 4550 Oldfield, 0 Emsley, 4550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 175 is missing expected H atoms. Skipping. Residue TYR 178 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue SER 183 is missing expected H atoms. Skipping. Residue VAL 186 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue VAL 213 is missing expected H atoms. Skipping. Residue SER 217 is missing expected H atoms. Skipping. Residue LYS 453 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue VAL 457 is missing expected H atoms. Skipping. Residue LYS 656 is missing expected H atoms. Skipping. Residue SER 686 is missing expected H atoms. Skipping. Residue LEU 689 is missing expected H atoms. Skipping. Residue LYS 709 is missing expected H atoms. Skipping. Residue LYS 717 is missing expected H atoms. Skipping. Residue TYR 726 is missing expected H atoms. Skipping. Residue LEU 727 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue TYR 178 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue SER 183 is missing expected H atoms. Skipping. Residue VAL 186 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue VAL 213 is missing expected H atoms. Skipping. Residue SER 217 is missing expected H atoms. Skipping. Residue LYS 453 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue VAL 457 is missing expected H atoms. Skipping. Residue LYS 656 is missing expected H atoms. Skipping. Residue SER 686 is missing expected H atoms. Skipping. Residue LEU 689 is missing expected H atoms. Skipping. Residue LYS 709 is missing expected H atoms. Skipping. Residue LYS 717 is missing expected H atoms. Skipping. Residue TYR 726 is missing expected H atoms. Skipping. Residue LEU 727 is missing expected H atoms. Skipping. Residue TYR 791 is missing expected H atoms. Skipping. Residue SER 1217 is missing expected H atoms. Skipping. Residue TYR 1239 is missing expected H atoms. Skipping. Residue TYR 791 is missing expected H atoms. Skipping. Residue SER 1217 is missing expected H atoms. Skipping. Residue TYR 1239 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue TYR 178 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue SER 183 is missing expected H atoms. Skipping. Residue VAL 186 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue VAL 213 is missing expected H atoms. Skipping. Residue SER 217 is missing expected H atoms. Skipping. Residue LYS 453 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue VAL 457 is missing expected H atoms. Skipping. Residue LYS 656 is missing expected H atoms. Skipping. Residue SER 686 is missing expected H atoms. Skipping. Residue LEU 689 is missing expected H atoms. Skipping. Residue LYS 709 is missing expected H atoms. Skipping. Residue LYS 717 is missing expected H atoms. Skipping. Residue TYR 726 is missing expected H atoms. Skipping. Residue LEU 727 is missing expected H atoms. Skipping. Residue TYR 791 is missing expected H atoms. Skipping. Residue SER 1217 is missing expected H atoms. Skipping. Residue TYR 1239 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue TYR 178 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue SER 183 is missing expected H atoms. Skipping. Residue VAL 186 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue VAL 213 is missing expected H atoms. Skipping. Residue SER 217 is missing expected H atoms. Skipping. Residue LYS 453 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue VAL 457 is missing expected H atoms. Skipping. Residue LYS 656 is missing expected H atoms. Skipping. Residue SER 686 is missing expected H atoms. Skipping. Residue LEU 689 is missing expected H atoms. Skipping. Residue LYS 709 is missing expected H atoms. Skipping. Residue LYS 717 is missing expected H atoms. Skipping. Residue TYR 726 is missing expected H atoms. Skipping. Residue LEU 727 is missing expected H atoms. Skipping. Residue TYR 791 is missing expected H atoms. Skipping. Residue SER 1217 is missing expected H atoms. Skipping. Residue TYR 1239 is missing expected H atoms. Skipping. Evaluate side-chains 111 residues out of total 3950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 100 time to evaluate : 4.127 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: A 706 LEU cc_start: 0.8445 (mm) cc_final: 0.7796 (tp) REVERT: E 645 MET cc_start: 0.6303 (tmm) cc_final: 0.5435 (tmm) REVERT: G 807 MET cc_start: 0.6259 (tpp) cc_final: 0.5898 (tpp) outliers start: 11 outliers final: 10 residues processed: 108 average time/residue: 0.8300 time to fit residues: 150.9234 Evaluate side-chains 106 residues out of total 3950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 96 time to evaluate : 4.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain B residue 652 HIS Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 155 LEU Chi-restraints excluded: chain E residue 163 ASN Chi-restraints excluded: chain E residue 668 LEU Chi-restraints excluded: chain E residue 687 HIS Chi-restraints excluded: chain E residue 718 CYS Chi-restraints excluded: chain G residue 877 ASP Chi-restraints excluded: chain G residue 920 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 408 optimal weight: 0.9990 chunk 268 optimal weight: 0.0570 chunk 433 optimal weight: 0.6980 chunk 264 optimal weight: 5.9990 chunk 205 optimal weight: 2.9990 chunk 301 optimal weight: 7.9990 chunk 454 optimal weight: 3.9990 chunk 418 optimal weight: 7.9990 chunk 361 optimal weight: 9.9990 chunk 37 optimal weight: 3.9990 chunk 279 optimal weight: 6.9990 overall best weight: 1.7504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1077 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 35586 Z= 0.202 Angle : 0.520 9.818 48402 Z= 0.273 Chirality : 0.043 0.287 5370 Planarity : 0.004 0.066 6332 Dihedral : 6.401 112.348 5282 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.54 % Favored : 89.46 % Rotamer: Outliers : 0.53 % Allowed : 5.66 % Favored : 93.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.13), residues: 4550 helix: 0.44 (0.20), residues: 714 sheet: 0.13 (0.20), residues: 768 loop : -1.88 (0.11), residues: 3068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.001 TRP D 147 HIS 0.005 0.001 HIS E 356 PHE 0.014 0.001 PHE G 878 TYR 0.017 0.001 TYR B 61 ARG 0.003 0.000 ARG E 501 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9100 Ramachandran restraints generated. 4550 Oldfield, 0 Emsley, 4550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9100 Ramachandran restraints generated. 4550 Oldfield, 0 Emsley, 4550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 175 is missing expected H atoms. Skipping. Residue TYR 178 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue SER 183 is missing expected H atoms. Skipping. Residue VAL 186 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue VAL 213 is missing expected H atoms. Skipping. Residue SER 217 is missing expected H atoms. Skipping. Residue LYS 453 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue VAL 457 is missing expected H atoms. Skipping. Residue LYS 656 is missing expected H atoms. Skipping. Residue SER 686 is missing expected H atoms. Skipping. Residue LEU 689 is missing expected H atoms. Skipping. Residue LYS 709 is missing expected H atoms. Skipping. Residue LYS 717 is missing expected H atoms. Skipping. Residue TYR 726 is missing expected H atoms. Skipping. Residue LEU 727 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue TYR 178 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue SER 183 is missing expected H atoms. Skipping. Residue VAL 186 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue VAL 213 is missing expected H atoms. Skipping. Residue SER 217 is missing expected H atoms. Skipping. Residue LYS 453 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue VAL 457 is missing expected H atoms. Skipping. Residue LYS 656 is missing expected H atoms. Skipping. Residue SER 686 is missing expected H atoms. Skipping. Residue LEU 689 is missing expected H atoms. Skipping. Residue LYS 709 is missing expected H atoms. Skipping. Residue LYS 717 is missing expected H atoms. Skipping. Residue TYR 726 is missing expected H atoms. Skipping. Residue LEU 727 is missing expected H atoms. Skipping. Residue TYR 791 is missing expected H atoms. Skipping. Residue SER 1217 is missing expected H atoms. Skipping. Residue TYR 1239 is missing expected H atoms. Skipping. Residue TYR 791 is missing expected H atoms. Skipping. Residue SER 1217 is missing expected H atoms. Skipping. Residue TYR 1239 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue TYR 178 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue SER 183 is missing expected H atoms. Skipping. Residue VAL 186 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue VAL 213 is missing expected H atoms. Skipping. Residue SER 217 is missing expected H atoms. Skipping. Residue LYS 453 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue VAL 457 is missing expected H atoms. Skipping. Residue LYS 656 is missing expected H atoms. Skipping. Residue SER 686 is missing expected H atoms. Skipping. Residue LEU 689 is missing expected H atoms. Skipping. Residue LYS 709 is missing expected H atoms. Skipping. Residue LYS 717 is missing expected H atoms. Skipping. Residue TYR 726 is missing expected H atoms. Skipping. Residue LEU 727 is missing expected H atoms. Skipping. Residue TYR 791 is missing expected H atoms. Skipping. Residue SER 1217 is missing expected H atoms. Skipping. Residue TYR 1239 is missing expected H atoms. Skipping. Residue LEU 175 is missing expected H atoms. Skipping. Residue TYR 178 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue SER 183 is missing expected H atoms. Skipping. Residue VAL 186 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue VAL 213 is missing expected H atoms. Skipping. Residue SER 217 is missing expected H atoms. Skipping. Residue LYS 453 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue VAL 457 is missing expected H atoms. Skipping. Residue LYS 656 is missing expected H atoms. Skipping. Residue SER 686 is missing expected H atoms. Skipping. Residue LEU 689 is missing expected H atoms. Skipping. Residue LYS 709 is missing expected H atoms. Skipping. Residue LYS 717 is missing expected H atoms. Skipping. Residue TYR 726 is missing expected H atoms. Skipping. Residue LEU 727 is missing expected H atoms. Skipping. Residue TYR 791 is missing expected H atoms. Skipping. Residue SER 1217 is missing expected H atoms. Skipping. Residue TYR 1239 is missing expected H atoms. Skipping. Evaluate side-chains 109 residues out of total 3950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 97 time to evaluate : 4.191 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: A 706 LEU cc_start: 0.8463 (mm) cc_final: 0.7827 (tp) REVERT: E 493 MET cc_start: 0.7187 (mpp) cc_final: 0.6862 (mpp) REVERT: E 645 MET cc_start: 0.6343 (tmm) cc_final: 0.5476 (tmm) outliers start: 12 outliers final: 11 residues processed: 107 average time/residue: 0.8868 time to fit residues: 160.9743 Evaluate side-chains 108 residues out of total 3950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 97 time to evaluate : 4.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 652 HIS Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 155 LEU Chi-restraints excluded: chain E residue 163 ASN Chi-restraints excluded: chain E residue 668 LEU Chi-restraints excluded: chain E residue 687 HIS Chi-restraints excluded: chain E residue 718 CYS Chi-restraints excluded: chain G residue 877 ASP Chi-restraints excluded: chain G residue 920 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 221 optimal weight: 0.3980 chunk 287 optimal weight: 9.9990 chunk 385 optimal weight: 9.9990 chunk 110 optimal weight: 7.9990 chunk 333 optimal weight: 0.0770 chunk 53 optimal weight: 0.0470 chunk 100 optimal weight: 0.0050 chunk 362 optimal weight: 6.9990 chunk 151 optimal weight: 2.9990 chunk 372 optimal weight: 8.9990 chunk 45 optimal weight: 0.0270 overall best weight: 0.1108 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1077 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.106286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.074305 restraints weight = 516174.394| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 6.76 r_work: 0.3169 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3164 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3164 r_free = 0.3164 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3164 r_free = 0.3164 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3164 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 35586 Z= 0.128 Angle : 0.497 10.553 48402 Z= 0.259 Chirality : 0.043 0.261 5370 Planarity : 0.004 0.067 6332 Dihedral : 6.018 110.614 5282 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 0.51 % Allowed : 5.74 % Favored : 93.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.13), residues: 4550 helix: 0.57 (0.20), residues: 714 sheet: 0.25 (0.20), residues: 802 loop : -1.71 (0.12), residues: 3034 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.001 TRP D 147 HIS 0.006 0.001 HIS E 356 PHE 0.010 0.001 PHE B1120 TYR 0.011 0.001 TYR G1123 ARG 0.003 0.000 ARG G 846 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8851.46 seconds wall clock time: 155 minutes 36.77 seconds (9336.77 seconds total)