Starting phenix.real_space_refine on Thu Feb 22 14:31:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kmz_22932/02_2024/7kmz_22932.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kmz_22932/02_2024/7kmz_22932.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kmz_22932/02_2024/7kmz_22932.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kmz_22932/02_2024/7kmz_22932.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kmz_22932/02_2024/7kmz_22932.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kmz_22932/02_2024/7kmz_22932.pdb" } resolution = 3.62 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= 0.033 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 167 5.16 5 C 21969 2.51 5 N 5637 2.21 5 O 6680 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 158": "NH1" <-> "NH2" Residue "C TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 214": "NH1" <-> "NH2" Residue "C TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 287": "OD1" <-> "OD2" Residue "C ASP 294": "OD1" <-> "OD2" Residue "C ARG 319": "NH1" <-> "NH2" Residue "C PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 357": "NH1" <-> "NH2" Residue "C TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 420": "OD1" <-> "OD2" Residue "C GLU 465": "OE1" <-> "OE2" Residue "C TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 583": "OE1" <-> "OE2" Residue "C PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 619": "OE1" <-> "OE2" Residue "C GLU 661": "OE1" <-> "OE2" Residue "C ASP 663": "OD1" <-> "OD2" Residue "C TYR 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 702": "OE1" <-> "OE2" Residue "C TYR 741": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 780": "OE1" <-> "OE2" Residue "C ASP 796": "OD1" <-> "OD2" Residue "C ARG 815": "NH1" <-> "NH2" Residue "C PHE 817": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 918": "OE1" <-> "OE2" Residue "C ASP 979": "OD1" <-> "OD2" Residue "C ASP 994": "OD1" <-> "OD2" Residue "C TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1072": "OE1" <-> "OE2" Residue "C GLU 1092": "OE1" <-> "OE2" Residue "C PHE 1095": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1111": "OE1" <-> "OE2" Residue "C ASP 1118": "OD1" <-> "OD2" Residue "C ASP 1127": "OD1" <-> "OD2" Residue "A TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 96": "OE1" <-> "OE2" Residue "A PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 158": "NH1" <-> "NH2" Residue "A PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 191": "OE1" <-> "OE2" Residue "A PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 319": "NH1" <-> "NH2" Residue "A PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 357": "NH1" <-> "NH2" Residue "A TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 406": "OE1" <-> "OE2" Residue "A ASP 420": "OD1" <-> "OD2" Residue "A PHE 429": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 465": "OE1" <-> "OE2" Residue "A TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 702": "OE1" <-> "OE2" Residue "A PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 796": "OD1" <-> "OD2" Residue "A ARG 815": "NH1" <-> "NH2" Residue "A PHE 817": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 904": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 38": "OD1" <-> "OD2" Residue "E TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 115": "NH1" <-> "NH2" Residue "E ARG 169": "NH1" <-> "NH2" Residue "E ARG 177": "NH1" <-> "NH2" Residue "E GLU 182": "OE1" <-> "OE2" Residue "E GLU 189": "OE1" <-> "OE2" Residue "E ARG 192": "NH1" <-> "NH2" Residue "E TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 206": "OD1" <-> "OD2" Residue "E TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 213": "OD1" <-> "OD2" Residue "E ASP 216": "OD1" <-> "OD2" Residue "E TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 232": "OE1" <-> "OE2" Residue "E ARG 245": "NH1" <-> "NH2" Residue "E ARG 273": "NH1" <-> "NH2" Residue "E PHE 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 357": "NH1" <-> "NH2" Residue "E TYR 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 402": "OE1" <-> "OE2" Residue "E PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 516": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 518": "NH1" <-> "NH2" Residue "E GLU 527": "OE1" <-> "OE2" Residue "E ARG 559": "NH1" <-> "NH2" Residue "E GLU 564": "OE1" <-> "OE2" Residue "E TYR 587": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 96": "OE1" <-> "OE2" Residue "B PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 158": "NH1" <-> "NH2" Residue "B TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 228": "OD1" <-> "OD2" Residue "B TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 287": "OD1" <-> "OD2" Residue "B GLU 298": "OE1" <-> "OE2" Residue "B GLU 309": "OE1" <-> "OE2" Residue "B ARG 319": "NH1" <-> "NH2" Residue "B PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 357": "NH1" <-> "NH2" Residue "B TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 420": "OD1" <-> "OD2" Residue "B PHE 429": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 465": "OE1" <-> "OE2" Residue "B TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 619": "OE1" <-> "OE2" Residue "B PHE 643": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 654": "OE1" <-> "OE2" Residue "B TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 815": "NH1" <-> "NH2" Residue "B GLU 819": "OE1" <-> "OE2" Residue "B PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 904": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 979": "OD1" <-> "OD2" Residue "B GLU 1031": "OE1" <-> "OE2" Residue "B TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1139": "OD1" <-> "OD2" Residue "D ASP 38": "OD1" <-> "OD2" Residue "D ASP 67": "OD1" <-> "OD2" Residue "D ARG 115": "NH1" <-> "NH2" Residue "D ARG 169": "NH1" <-> "NH2" Residue "D ARG 177": "NH1" <-> "NH2" Residue "D GLU 189": "OE1" <-> "OE2" Residue "D ARG 192": "NH1" <-> "NH2" Residue "D ASP 206": "OD1" <-> "OD2" Residue "D TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 216": "OD1" <-> "OD2" Residue "D TYR 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 245": "NH1" <-> "NH2" Residue "D ARG 273": "NH1" <-> "NH2" Residue "D ASP 299": "OD1" <-> "OD2" Residue "D ASP 350": "OD1" <-> "OD2" Residue "D PHE 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 357": "NH1" <-> "NH2" Residue "D TYR 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 402": "OE1" <-> "OE2" Residue "D GLU 406": "OE1" <-> "OE2" Residue "D ASP 427": "OD1" <-> "OD2" Residue "D PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 510": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 518": "NH1" <-> "NH2" Residue "D GLU 527": "OE1" <-> "OE2" Residue "D GLU 536": "OE1" <-> "OE2" Residue "D PHE 555": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 559": "NH1" <-> "NH2" Residue "D GLU 564": "OE1" <-> "OE2" Residue "D TYR 587": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 34453 Number of models: 1 Model: "" Number of chains: 14 Chain: "C" Number of atoms: 7837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1007, 7837 Classifications: {'peptide': 1007} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 49, 'TRANS': 957} Chain breaks: 8 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "A" Number of atoms: 8020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1030, 8020 Classifications: {'peptide': 1030} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 51, 'TRANS': 978} Chain breaks: 7 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "E" Number of atoms: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 27, 'TRANS': 568} Chain: "B" Number of atoms: 8018 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1031, 8018 Classifications: {'peptide': 1031} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 51, 'TRANS': 979} Chain breaks: 7 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "D" Number of atoms: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 27, 'TRANS': 568} 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: "G" 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: "C" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "A" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 196 Unusual residues: {'NAG': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 14 Chain: "E" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 196 Unusual residues: {'NAG': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 14 Chain: "D" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 18.74, per 1000 atoms: 0.54 Number of scatterers: 34453 At special positions: 0 Unit cell: (136.482, 162.932, 242.282, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 167 16.00 O 6680 8.00 N 5637 7.00 C 21969 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.04 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.04 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS E 133 " - pdb=" SG CYS E 141 " distance=2.03 Simple disulfide: pdb=" SG CYS E 344 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 530 " - pdb=" SG CYS E 542 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.03 Simple disulfide: pdb=" SG CYS D 344 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " 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 G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " NAG-ASN " NAG A1301 " - " ASN A 331 " " NAG A1302 " - " ASN A1134 " " NAG A1303 " - " ASN A1098 " " NAG A1304 " - " ASN A 282 " " NAG A1305 " - " ASN A 657 " " NAG A1306 " - " ASN A 616 " " NAG A1307 " - " ASN A 801 " " NAG A1308 " - " ASN A 709 " " NAG A1309 " - " ASN A1074 " " NAG A1310 " - " ASN A 61 " " NAG A1311 " - " ASN A 234 " " NAG A1312 " - " ASN A 165 " " NAG A1313 " - " ASN A 343 " " NAG A1314 " - " ASN A 603 " " NAG B1301 " - " ASN B 331 " " NAG B1302 " - " ASN B1134 " " NAG B1303 " - " ASN B1098 " " NAG B1304 " - " ASN B 282 " " NAG B1305 " - " ASN B 657 " " NAG B1306 " - " ASN B 616 " " NAG B1307 " - " ASN B 801 " " NAG B1308 " - " ASN B 709 " " NAG B1309 " - " ASN B1074 " " NAG B1310 " - " ASN B 61 " " NAG B1311 " - " ASN B 234 " " NAG B1312 " - " ASN B 165 " " NAG B1313 " - " ASN B 343 " " NAG B1314 " - " ASN B 603 " " NAG C1301 " - " ASN C 331 " " NAG C1302 " - " ASN C1134 " " NAG C1303 " - " ASN C1098 " " NAG C1304 " - " ASN C 282 " " NAG C1305 " - " ASN C 616 " " NAG C1306 " - " ASN C 801 " " NAG C1307 " - " ASN C 709 " " NAG C1308 " - " ASN C1074 " " NAG C1309 " - " ASN C 61 " " NAG C1310 " - " ASN C 234 " " NAG C1311 " - " ASN C 603 " " NAG C1312 " - " ASN C 165 " " NAG C1313 " - " ASN C 657 " " NAG D 701 " - " ASN D 546 " " NAG D 702 " - " ASN D 322 " " NAG D 703 " - " ASN D 432 " " NAG D 704 " - " ASN D 103 " " NAG D 705 " - " ASN D 90 " " NAG D 706 " - " ASN D 53 " " NAG E 701 " - " ASN E 546 " " NAG E 702 " - " ASN E 322 " " NAG E 703 " - " ASN E 432 " " NAG E 704 " - " ASN E 103 " " NAG E 705 " - " ASN E 90 " " NAG E 706 " - " ASN E 53 " " NAG F 1 " - " ASN C 717 " " NAG G 1 " - " ASN C 343 " " NAG H 1 " - " ASN A 717 " " NAG I 1 " - " ASN B 717 " Time building additional restraints: 13.38 Conformation dependent library (CDL) restraints added in 6.3 seconds 8412 Ramachandran restraints generated. 4206 Oldfield, 0 Emsley, 4206 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8012 Finding SS restraints... Secondary structure from input PDB file: 122 helices and 47 sheets defined 35.8% alpha, 16.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.46 Creating SS restraints... Processing helix chain 'C' and resid 294 through 304 removed outlier: 3.631A pdb=" N LYS C 300 " --> pdb=" O LEU C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 365 through 370 removed outlier: 3.932A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ASN C 370 " --> pdb=" O SER C 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 365 through 370' Processing helix chain 'C' and resid 385 through 390 removed outlier: 4.127A pdb=" N ASP C 389 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 407 No H-bonds generated for 'chain 'C' and resid 405 through 407' Processing helix chain 'C' and resid 417 through 422 Processing helix chain 'C' and resid 542 through 546 removed outlier: 3.842A pdb=" N GLY C 545 " --> pdb=" O ASN C 542 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 757 removed outlier: 4.009A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N TYR C 756 " --> pdb=" O LEU C 752 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY C 757 " --> pdb=" O LEU C 753 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.611A pdb=" N GLU C 773 " --> pdb=" O GLY C 769 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LYS C 776 " --> pdb=" O VAL C 772 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 824 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.674A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.287A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS C 964 " --> pdb=" O ASN C 960 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLN C 965 " --> pdb=" O THR C 961 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 removed outlier: 4.045A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER C 982 " --> pdb=" O ASN C 978 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.834A pdb=" N GLU C 990 " --> pdb=" O PRO C 986 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLN C1002 " --> pdb=" O THR C 998 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1145 removed outlier: 3.794A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 304 removed outlier: 3.542A pdb=" N CYS A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N THR A 302 " --> pdb=" O GLU A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 341 Processing helix chain 'A' and resid 365 through 370 removed outlier: 3.951A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ASN A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 365 through 370' Processing helix chain 'A' and resid 405 through 410 removed outlier: 5.173A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 619 through 623 Processing helix chain 'A' and resid 738 through 743 removed outlier: 3.543A pdb=" N CYS A 743 " --> pdb=" O THR A 739 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.691A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.658A pdb=" N GLU A 773 " --> pdb=" O GLY A 769 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.672A pdb=" N LYS A 825 " --> pdb=" O LEU A 821 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 884 removed outlier: 3.632A pdb=" N ALA A 871 " --> pdb=" O ASP A 867 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N GLN A 872 " --> pdb=" O GLU A 868 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N TYR A 873 " --> pdb=" O MET A 869 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.636A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 removed outlier: 3.581A pdb=" N MET A 902 " --> pdb=" O PHE A 898 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG A 905 " --> pdb=" O GLN A 901 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.671A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 removed outlier: 3.527A pdb=" N LEU A 938 " --> pdb=" O ILE A 934 " (cutoff:3.500A) Processing helix chain 'A' and resid 946 through 965 removed outlier: 3.531A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASN A 953 " --> pdb=" O GLN A 949 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 983 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.919A pdb=" N GLU A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1118 No H-bonds generated for 'chain 'A' and resid 1116 through 1118' Processing helix chain 'A' and resid 1140 through 1148 removed outlier: 3.901A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE A1148 " --> pdb=" O GLU A1144 " (cutoff:3.500A) Processing helix chain 'E' and resid 20 through 53 removed outlier: 3.668A pdb=" N THR E 27 " --> pdb=" O GLU E 23 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N HIS E 34 " --> pdb=" O ASP E 30 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASN E 49 " --> pdb=" O LEU E 45 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N TYR E 50 " --> pdb=" O ALA E 46 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ASN E 51 " --> pdb=" O SER E 47 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N THR E 52 " --> pdb=" O TRP E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 80 removed outlier: 3.874A pdb=" N VAL E 59 " --> pdb=" O THR E 55 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N GLN E 60 " --> pdb=" O GLU E 56 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ASN E 63 " --> pdb=" O VAL E 59 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LYS E 68 " --> pdb=" O ASN E 64 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU E 73 " --> pdb=" O TRP E 69 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS E 74 " --> pdb=" O SER E 70 " (cutoff:3.500A) Processing helix chain 'E' and resid 91 through 101 removed outlier: 3.889A pdb=" N GLN E 96 " --> pdb=" O THR E 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 128 removed outlier: 3.505A pdb=" N LYS E 114 " --> pdb=" O GLU E 110 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ARG E 115 " --> pdb=" O ASP E 111 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LEU E 116 " --> pdb=" O LYS E 112 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ASN E 117 " --> pdb=" O SER E 113 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N THR E 122 " --> pdb=" O THR E 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 154 removed outlier: 3.920A pdb=" N ASN E 149 " --> pdb=" O GLU E 145 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N GLU E 150 " --> pdb=" O PRO E 146 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ILE E 151 " --> pdb=" O GLY E 147 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 170 removed outlier: 3.883A pdb=" N ARG E 161 " --> pdb=" O ASP E 157 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N TRP E 168 " --> pdb=" O ALA E 164 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG E 169 " --> pdb=" O TRP E 165 " (cutoff:3.500A) Processing helix chain 'E' and resid 173 through 175 No H-bonds generated for 'chain 'E' and resid 173 through 175' Processing helix chain 'E' and resid 176 through 188 removed outlier: 3.509A pdb=" N GLU E 181 " --> pdb=" O ARG E 177 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N GLU E 182 " --> pdb=" O PRO E 178 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU E 186 " --> pdb=" O GLU E 182 " (cutoff:3.500A) Processing helix chain 'E' and resid 189 through 194 removed outlier: 3.503A pdb=" N ALA E 193 " --> pdb=" O GLU E 189 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 204 removed outlier: 3.713A pdb=" N TRP E 203 " --> pdb=" O TYR E 199 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ARG E 204 " --> pdb=" O GLY E 200 " (cutoff:3.500A) Processing helix chain 'E' and resid 218 through 252 removed outlier: 4.072A pdb=" N LEU E 222 " --> pdb=" O SER E 218 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ILE E 223 " --> pdb=" O ARG E 219 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLU E 224 " --> pdb=" O GLY E 220 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLU E 231 " --> pdb=" O GLU E 227 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N GLU E 232 " --> pdb=" O HIS E 228 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ILE E 233 " --> pdb=" O THR E 229 " (cutoff:3.500A) Proline residue: E 235 - end of helix removed outlier: 3.546A pdb=" N ARG E 245 " --> pdb=" O HIS E 241 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ALA E 246 " --> pdb=" O ALA E 242 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N LYS E 247 " --> pdb=" O TYR E 243 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LEU E 248 " --> pdb=" O VAL E 244 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N MET E 249 " --> pdb=" O ARG E 245 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ASN E 250 " --> pdb=" O ALA E 246 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ALA E 251 " --> pdb=" O LYS E 247 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N TYR E 252 " --> pdb=" O LEU E 248 " (cutoff:3.500A) Processing helix chain 'E' and resid 277 through 282 removed outlier: 4.425A pdb=" N LEU E 281 " --> pdb=" O ASN E 277 " (cutoff:3.500A) Processing helix chain 'E' and resid 293 through 299 removed outlier: 3.768A pdb=" N MET E 297 " --> pdb=" O VAL E 293 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL E 298 " --> pdb=" O THR E 294 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ASP E 299 " --> pdb=" O ASP E 295 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 293 through 299' Processing helix chain 'E' and resid 303 through 319 removed outlier: 3.616A pdb=" N LYS E 313 " --> pdb=" O LYS E 309 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N PHE E 314 " --> pdb=" O GLU E 310 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N PHE E 315 " --> pdb=" O ALA E 311 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL E 316 " --> pdb=" O GLU E 312 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 383 removed outlier: 3.579A pdb=" N HIS E 378 " --> pdb=" O HIS E 374 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE E 379 " --> pdb=" O GLU E 375 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N MET E 383 " --> pdb=" O ILE E 379 " (cutoff:3.500A) Processing helix chain 'E' and resid 384 through 386 No H-bonds generated for 'chain 'E' and resid 384 through 386' Processing helix chain 'E' and resid 397 through 413 removed outlier: 3.865A pdb=" N HIS E 401 " --> pdb=" O ASN E 397 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N GLU E 402 " --> pdb=" O GLU E 398 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLY E 405 " --> pdb=" O HIS E 401 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU E 406 " --> pdb=" O GLU E 402 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N MET E 408 " --> pdb=" O VAL E 404 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N SER E 409 " --> pdb=" O GLY E 405 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N SER E 411 " --> pdb=" O ILE E 407 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 422 Processing helix chain 'E' and resid 431 through 447 removed outlier: 3.772A pdb=" N GLU E 435 " --> pdb=" O ASP E 431 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR E 445 " --> pdb=" O LYS E 441 " (cutoff:3.500A) Processing helix chain 'E' and resid 448 through 466 removed outlier: 4.566A pdb=" N PHE E 452 " --> pdb=" O GLY E 448 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N MET E 462 " --> pdb=" O LYS E 458 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL E 463 " --> pdb=" O TRP E 459 " (cutoff:3.500A) Processing helix chain 'E' and resid 469 through 471 No H-bonds generated for 'chain 'E' and resid 469 through 471' Processing helix chain 'E' and resid 472 through 484 removed outlier: 4.050A pdb=" N MET E 480 " --> pdb=" O LYS E 476 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LYS E 481 " --> pdb=" O TRP E 477 " (cutoff:3.500A) Processing helix chain 'E' and resid 498 through 502 removed outlier: 3.533A pdb=" N ALA E 501 " --> pdb=" O CYS E 498 " (cutoff:3.500A) Processing helix chain 'E' and resid 503 through 508 Processing helix chain 'E' and resid 512 through 534 removed outlier: 4.283A pdb=" N TYR E 516 " --> pdb=" O PHE E 512 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR E 517 " --> pdb=" O ILE E 513 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N THR E 519 " --> pdb=" O TYR E 515 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N LEU E 520 " --> pdb=" O TYR E 516 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE E 523 " --> pdb=" O THR E 519 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLN E 524 " --> pdb=" O LEU E 520 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA E 532 " --> pdb=" O ALA E 528 " (cutoff:3.500A) Processing helix chain 'E' and resid 538 through 542 Processing helix chain 'E' and resid 547 through 559 Processing helix chain 'E' and resid 565 through 572 removed outlier: 3.706A pdb=" N ALA E 569 " --> pdb=" O PRO E 565 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU E 570 " --> pdb=" O TRP E 566 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLU E 571 " --> pdb=" O THR E 567 " (cutoff:3.500A) Processing helix chain 'E' and resid 581 through 585 removed outlier: 3.595A pdb=" N LEU E 585 " --> pdb=" O ARG E 582 " (cutoff:3.500A) Processing helix chain 'E' and resid 588 through 599 removed outlier: 3.818A pdb=" N ASP E 597 " --> pdb=" O THR E 593 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N GLN E 598 " --> pdb=" O TRP E 594 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASN E 599 " --> pdb=" O LEU E 595 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 removed outlier: 3.748A pdb=" N LYS B 300 " --> pdb=" O LEU B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.647A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 370 removed outlier: 4.138A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 738 through 743 removed outlier: 3.617A pdb=" N ILE B 742 " --> pdb=" O CYS B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.692A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.606A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLU B 773 " --> pdb=" O GLY B 769 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 884 removed outlier: 3.942A pdb=" N ALA B 871 " --> pdb=" O ASP B 867 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N GLN B 872 " --> pdb=" O GLU B 868 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N TYR B 873 " --> pdb=" O MET B 869 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.613A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 removed outlier: 3.747A pdb=" N MET B 902 " --> pdb=" O PHE B 898 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG B 905 " --> pdb=" O GLN B 901 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.731A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 938 removed outlier: 3.670A pdb=" N LEU B 938 " --> pdb=" O ILE B 934 " (cutoff:3.500A) Processing helix chain 'B' and resid 946 through 967 removed outlier: 4.415A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N ASN B 953 " --> pdb=" O GLN B 949 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASN B 955 " --> pdb=" O VAL B 951 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS B 964 " --> pdb=" O ASN B 960 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLN B 965 " --> pdb=" O THR B 961 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LEU B 966 " --> pdb=" O LEU B 962 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N SER B 967 " --> pdb=" O VAL B 963 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 removed outlier: 4.259A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU B 984 " --> pdb=" O ILE B 980 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.685A pdb=" N GLU B 990 " --> pdb=" O PRO B 986 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1148 removed outlier: 4.025A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 51 removed outlier: 4.183A pdb=" N LYS D 31 " --> pdb=" O THR D 27 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TRP D 48 " --> pdb=" O SER D 44 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ASN D 49 " --> pdb=" O LEU D 45 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N TYR D 50 " --> pdb=" O ALA D 46 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASN D 51 " --> pdb=" O SER D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 80 removed outlier: 4.127A pdb=" N GLN D 60 " --> pdb=" O GLU D 56 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LYS D 68 " --> pdb=" O ASN D 64 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU D 73 " --> pdb=" O TRP D 69 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LYS D 74 " --> pdb=" O SER D 70 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR D 78 " --> pdb=" O LYS D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 101 removed outlier: 3.580A pdb=" N LYS D 94 " --> pdb=" O ASN D 90 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU D 95 " --> pdb=" O LEU D 91 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLN D 96 " --> pdb=" O THR D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 108 removed outlier: 4.105A pdb=" N VAL D 107 " --> pdb=" O GLY D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 129 removed outlier: 4.098A pdb=" N ARG D 115 " --> pdb=" O ASP D 111 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N LEU D 116 " --> pdb=" O LYS D 112 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ASN D 117 " --> pdb=" O SER D 113 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR D 118 " --> pdb=" O LYS D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 154 removed outlier: 3.811A pdb=" N ASN D 149 " --> pdb=" O GLU D 145 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N GLU D 150 " --> pdb=" O PRO D 146 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N MET D 152 " --> pdb=" O LEU D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 170 removed outlier: 3.663A pdb=" N TRP D 168 " --> pdb=" O ALA D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 188 removed outlier: 4.235A pdb=" N LEU D 179 " --> pdb=" O GLN D 175 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU D 182 " --> pdb=" O PRO D 178 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU D 186 " --> pdb=" O GLU D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 194 Processing helix chain 'D' and resid 198 through 204 removed outlier: 3.798A pdb=" N TRP D 203 " --> pdb=" O TYR D 199 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ARG D 204 " --> pdb=" O GLY D 200 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 229 removed outlier: 3.754A pdb=" N GLU D 224 " --> pdb=" O GLY D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 232 through 249 removed outlier: 4.241A pdb=" N LEU D 236 " --> pdb=" O GLU D 232 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA D 246 " --> pdb=" O ALA D 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 267 No H-bonds generated for 'chain 'D' and resid 265 through 267' Processing helix chain 'D' and resid 277 through 282 removed outlier: 4.303A pdb=" N LEU D 281 " --> pdb=" O ASN D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 300 removed outlier: 3.509A pdb=" N VAL D 298 " --> pdb=" O THR D 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 319 removed outlier: 3.524A pdb=" N PHE D 308 " --> pdb=" O ALA D 304 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA D 311 " --> pdb=" O ILE D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 329 removed outlier: 4.430A pdb=" N TRP D 328 " --> pdb=" O THR D 324 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N GLU D 329 " --> pdb=" O GLN D 325 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 324 through 329' Processing helix chain 'D' and resid 365 through 385 removed outlier: 3.565A pdb=" N GLY D 377 " --> pdb=" O HIS D 373 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N HIS D 378 " --> pdb=" O HIS D 374 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE D 379 " --> pdb=" O GLU D 375 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N TYR D 385 " --> pdb=" O TYR D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 397 through 413 removed outlier: 3.856A pdb=" N HIS D 401 " --> pdb=" O ASN D 397 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLU D 402 " --> pdb=" O GLU D 398 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLY D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLU D 406 " --> pdb=" O GLU D 402 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N SER D 409 " --> pdb=" O GLY D 405 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER D 411 " --> pdb=" O ILE D 407 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 422 Processing helix chain 'D' and resid 431 through 447 removed outlier: 4.263A pdb=" N PHE D 438 " --> pdb=" O THR D 434 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 466 removed outlier: 4.390A pdb=" N PHE D 452 " --> pdb=" O GLY D 448 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N TRP D 459 " --> pdb=" O MET D 455 " (cutoff:3.500A) Processing helix chain 'D' and resid 469 through 471 No H-bonds generated for 'chain 'D' and resid 469 through 471' Processing helix chain 'D' and resid 472 through 484 Processing helix chain 'D' and resid 498 through 502 Processing helix chain 'D' and resid 503 through 508 Processing helix chain 'D' and resid 513 through 533 removed outlier: 3.593A pdb=" N THR D 519 " --> pdb=" O TYR D 515 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU D 520 " --> pdb=" O TYR D 516 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 542 Processing helix chain 'D' and resid 547 through 559 removed outlier: 3.621A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 572 removed outlier: 3.506A pdb=" N ALA D 569 " --> pdb=" O PRO D 565 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLU D 571 " --> pdb=" O THR D 567 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 583 No H-bonds generated for 'chain 'D' and resid 581 through 583' Processing helix chain 'D' and resid 584 through 599 removed outlier: 4.143A pdb=" N PHE D 588 " --> pdb=" O LEU D 584 " (cutoff:3.500A) Proline residue: D 590 - end of helix removed outlier: 3.621A pdb=" N ASP D 597 " --> pdb=" O THR D 593 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 29 through 31 removed outlier: 3.828A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 8.591A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 42 through 43 removed outlier: 5.513A pdb=" N PHE C 43 " --> pdb=" O ARG B 567 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU B 583 " --> pdb=" O ASP B 578 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY B 550 " --> pdb=" O VAL B 539 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 48 through 51 removed outlier: 4.058A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 54 through 55 Processing sheet with id=AA5, first strand: chain 'C' and resid 104 through 107 Processing sheet with id=AA6, first strand: chain 'C' and resid 118 through 121 removed outlier: 3.802A pdb=" N LEU C 118 " --> pdb=" O LYS C 129 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 311 through 318 removed outlier: 5.244A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLY C 593 " --> pdb=" O PHE C 318 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 354 through 356 removed outlier: 3.901A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL C 510 " --> pdb=" O PHE C 400 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'C' and resid 539 through 541 removed outlier: 3.501A pdb=" N THR C 588 " --> pdb=" O VAL C 551 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 653 through 655 removed outlier: 3.661A pdb=" N ALA C 694 " --> pdb=" O GLU C 654 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 703 through 704 removed outlier: 6.938A pdb=" N ASN C 703 " --> pdb=" O LYS A 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 712 through 728 removed outlier: 6.280A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY C1059 " --> pdb=" O ALA C1056 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.404A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 1122 through 1125 removed outlier: 4.325A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AB8, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.511A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ARG A 190 " --> pdb=" O SER A 94 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.511A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ARG A 190 " --> pdb=" O SER A 94 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.665A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AC3, first strand: chain 'A' and resid 311 through 318 removed outlier: 7.126A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 354 through 356 removed outlier: 3.974A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS A 356 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE A 400 " --> pdb=" O VAL A 510 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 452 through 453 removed outlier: 3.756A pdb=" N GLN A 493 " --> pdb=" O TYR A 453 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 538 through 542 removed outlier: 3.519A pdb=" N GLY A 550 " --> pdb=" O VAL A 539 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 654 through 655 Processing sheet with id=AC8, first strand: chain 'A' and resid 703 through 704 removed outlier: 7.211A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'A' and resid 712 through 728 removed outlier: 6.610A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLU A 725 " --> pdb=" O PHE A1062 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 712 through 728 removed outlier: 6.610A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLU A 725 " --> pdb=" O PHE A1062 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLY A1059 " --> pdb=" O ALA A1056 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AD3, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.683A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AD5, first strand: chain 'E' and resid 347 through 352 removed outlier: 6.077A pdb=" N ALA E 348 " --> pdb=" O LEU E 359 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N LEU E 359 " --> pdb=" O ALA E 348 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N ASP E 350 " --> pdb=" O ARG E 357 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N ARG E 357 " --> pdb=" O ASP E 350 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.703A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL B 90 " --> pdb=" O PHE B 194 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL B 193 " --> pdb=" O TYR B 204 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N TYR B 204 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N LYS B 195 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LYS B 202 " --> pdb=" O LYS B 195 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 48 through 51 removed outlier: 3.818A pdb=" N HIS B 49 " --> pdb=" O LEU B 277 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU B 277 " --> pdb=" O HIS B 49 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 54 through 55 Processing sheet with id=AD9, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.583A pdb=" N ARG B 237 " --> pdb=" O GLY B 107 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLY B 107 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLN B 239 " --> pdb=" O ILE B 105 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TYR B 170 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL B 130 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 187 through 189 removed outlier: 3.955A pdb=" N LYS B 187 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE B 210 " --> pdb=" O LYS B 187 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N THR B 208 " --> pdb=" O LEU B 189 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 311 through 318 removed outlier: 3.506A pdb=" N THR B 315 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU B 650 " --> pdb=" O PHE B 643 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N PHE B 643 " --> pdb=" O LEU B 650 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 354 through 356 removed outlier: 3.802A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LYS B 356 " --> pdb=" O ALA B 397 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N PHE B 400 " --> pdb=" O VAL B 510 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL B 510 " --> pdb=" O PHE B 400 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE B 402 " --> pdb=" O TYR B 508 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 452 through 453 removed outlier: 3.673A pdb=" N GLN B 493 " --> pdb=" O TYR B 453 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.259A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.644A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 712 through 728 removed outlier: 6.598A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AE8, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.617A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AF1, first strand: chain 'D' and resid 262 through 263 removed outlier: 6.416A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'D' and resid 347 through 352 removed outlier: 6.219A pdb=" N ALA D 348 " --> pdb=" O LEU D 359 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N LEU D 359 " --> pdb=" O ALA D 348 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N ASP D 350 " --> pdb=" O ARG D 357 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N ARG D 357 " --> pdb=" O ASP D 350 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY D 352 " --> pdb=" O ASP D 355 " (cutoff:3.500A) 1226 hydrogen bonds defined for protein. 3429 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: 13.61 Time building geometry restraints manager: 14.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 10972 1.34 - 1.46: 8813 1.46 - 1.58: 15246 1.58 - 1.70: 0 1.70 - 1.82: 237 Bond restraints: 35268 Sorted by residual: bond pdb=" C PHE A 329 " pdb=" N PRO A 330 " ideal model delta sigma weight residual 1.328 1.355 -0.027 1.25e-02 6.40e+03 4.78e+00 bond pdb=" C1 NAG G 1 " pdb=" O5 NAG G 1 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.61e+00 bond pdb=" C1 NAG A1311 " pdb=" O5 NAG A1311 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.54e+00 bond pdb=" C1 NAG C1312 " pdb=" O5 NAG C1312 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.39e+00 bond pdb=" C1 NAG C1308 " pdb=" O5 NAG C1308 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.19e+00 ... (remaining 35263 not shown) Histogram of bond angle deviations from ideal: 99.11 - 106.09: 771 106.09 - 113.07: 19204 113.07 - 120.05: 11900 120.05 - 127.03: 15695 127.03 - 134.01: 399 Bond angle restraints: 47969 Sorted by residual: angle pdb=" N ILE D 259 " pdb=" CA ILE D 259 " pdb=" C ILE D 259 " ideal model delta sigma weight residual 113.71 110.18 3.53 9.50e-01 1.11e+00 1.38e+01 angle pdb=" N THR B 33 " pdb=" CA THR B 33 " pdb=" C THR B 33 " ideal model delta sigma weight residual 114.56 111.74 2.82 1.27e+00 6.20e-01 4.91e+00 angle pdb=" CA ILE D 259 " pdb=" C ILE D 259 " pdb=" N GLY D 260 " ideal model delta sigma weight residual 119.87 117.02 2.85 1.34e+00 5.57e-01 4.53e+00 angle pdb=" N ASN D 338 " pdb=" CA ASN D 338 " pdb=" C ASN D 338 " ideal model delta sigma weight residual 113.18 110.44 2.74 1.33e+00 5.65e-01 4.26e+00 angle pdb=" N PRO A 330 " pdb=" CA PRO A 330 " pdb=" C PRO A 330 " ideal model delta sigma weight residual 111.03 114.53 -3.50 1.78e+00 3.16e-01 3.86e+00 ... (remaining 47964 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 19562 17.91 - 35.83: 1701 35.83 - 53.74: 366 53.74 - 71.65: 92 71.65 - 89.56: 34 Dihedral angle restraints: 21755 sinusoidal: 9323 harmonic: 12432 Sorted by residual: dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -151.97 65.97 1 1.00e+01 1.00e-02 5.69e+01 dihedral pdb=" CB CYS C 738 " pdb=" SG CYS C 738 " pdb=" SG CYS C 760 " pdb=" CB CYS C 760 " ideal model delta sinusoidal sigma weight residual 93.00 37.74 55.26 1 1.00e+01 1.00e-02 4.13e+01 dihedral pdb=" CB CYS A 336 " pdb=" SG CYS A 336 " pdb=" SG CYS A 361 " pdb=" CB CYS A 361 " ideal model delta sinusoidal sigma weight residual 93.00 39.46 53.54 1 1.00e+01 1.00e-02 3.90e+01 ... (remaining 21752 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 4825 0.060 - 0.119: 637 0.119 - 0.179: 48 0.179 - 0.239: 4 0.239 - 0.298: 3 Chirality restraints: 5517 Sorted by residual: chirality pdb=" C1 NAG A1311 " pdb=" ND2 ASN A 234 " pdb=" C2 NAG A1311 " pdb=" O5 NAG A1311 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.22e+00 chirality pdb=" C1 NAG A1312 " pdb=" ND2 ASN A 165 " pdb=" C2 NAG A1312 " pdb=" O5 NAG A1312 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.18e+00 chirality pdb=" C1 NAG C1312 " pdb=" ND2 ASN C 165 " pdb=" C2 NAG C1312 " pdb=" O5 NAG C1312 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.17e+00 ... (remaining 5514 not shown) Planarity restraints: 6184 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA C 520 " 0.048 5.00e-02 4.00e+02 7.31e-02 8.54e+00 pdb=" N PRO C 521 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO C 521 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO C 521 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 811 " 0.034 5.00e-02 4.00e+02 5.18e-02 4.30e+00 pdb=" N PRO A 812 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO A 812 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 812 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 811 " -0.029 5.00e-02 4.00e+02 4.35e-02 3.03e+00 pdb=" N PRO B 812 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO B 812 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 812 " -0.024 5.00e-02 4.00e+02 ... (remaining 6181 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.58: 367 2.58 - 3.16: 30083 3.16 - 3.74: 51904 3.74 - 4.32: 70834 4.32 - 4.90: 116820 Nonbonded interactions: 270008 Sorted by model distance: nonbonded pdb=" OG1 THR B 323 " pdb=" OE1 GLU B 324 " model vdw 2.006 2.440 nonbonded pdb=" OD1 ASN A 540 " pdb=" OG1 THR A 549 " model vdw 2.017 2.440 nonbonded pdb=" OD2 ASP A 398 " pdb=" OH TYR A 423 " model vdw 2.135 2.440 nonbonded pdb=" O ALA E 501 " pdb=" OG SER E 507 " model vdw 2.147 2.440 nonbonded pdb=" OG1 THR B1116 " pdb=" OD1 ASP B1118 " model vdw 2.201 2.440 ... (remaining 270003 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 26 through 59 or (resid 60 and (name N or name CA or name \ C or name O or name CB )) or resid 61 through 66 or (resid 81 and (name N or nam \ e CA or name C or name O or name CB )) or resid 82 through 114 or (resid 115 and \ (name N or name CA or name C or name O or name CB )) or resid 116 through 141 o \ r resid 156 through 176 or (resid 187 through 188 and (name N or name CA or name \ C or name O or name CB )) or resid 189 through 194 or (resid 195 through 198 an \ d (name N or name CA or name C or name O or name CB )) or resid 199 or (resid 20 \ 0 and (name N or name CA or name C or name O or name CB )) or resid 201 through \ 243 or resid 264 through 620 or resid 640 through 811 or resid 815 through 828 o \ r resid 853 through 1147 or resid 1302 through 1314)) selection = (chain 'B' and (resid 26 through 66 or resid 81 through 141 or resid 156 through \ 176 or (resid 187 through 188 and (name N or name CA or name C or name O or nam \ e CB )) or resid 189 through 194 or (resid 195 through 198 and (name N or name C \ A or name C or name O or name CB )) or resid 199 or (resid 200 and (name N or na \ me CA or name C or name O or name CB )) or resid 201 through 243 or resid 264 th \ rough 620 or resid 640 through 811 or resid 815 through 828 or resid 853 through \ 1147 or resid 1302 through 1314)) selection = (chain 'C' and (resid 26 through 59 or (resid 60 and (name N or name CA or name \ C or name O or name CB )) or resid 61 through 66 or (resid 81 and (name N or nam \ e CA or name C or name O or name CB )) or resid 82 through 114 or (resid 115 and \ (name N or name CA or name C or name O or name CB )) or resid 116 through 134 o \ r (resid 135 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 36 through 163 or (resid 164 and (name N or name CA or name C or name O or name \ CB )) or resid 165 through 189 or (resid 190 and (name N or name CA or name C or \ name O or name CB )) or resid 191 through 209 or (resid 210 and (name N or name \ CA or name C or name O or name CB )) or resid 211 through 280 or (resid 281 and \ (name N or name CA or name C or name O or name CB )) or resid 282 through 289 o \ r (resid 290 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 91 through 620 or resid 640 through 676 or resid 690 through 1147 or resid 1301 \ through 1313)) } ncs_group { reference = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.890 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: 0.030 Extract box with map and model: 17.520 Check model and map are aligned: 0.510 Set scattering table: 0.290 Process input model: 90.160 Find NCS groups from input model: 2.440 Set up NCS constraints: 0.220 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 118.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 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 0.036 35268 Z= 0.190 Angle : 0.483 6.862 47969 Z= 0.235 Chirality : 0.042 0.298 5517 Planarity : 0.003 0.073 6127 Dihedral : 14.197 89.565 13608 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.13), residues: 4206 helix: 1.18 (0.16), residues: 1224 sheet: 0.00 (0.23), residues: 518 loop : -0.71 (0.13), residues: 2464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP D 594 HIS 0.003 0.000 HIS E 540 PHE 0.012 0.001 PHE B 275 TYR 0.007 0.000 TYR C 904 ARG 0.020 0.000 ARG B 815 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8412 Ramachandran restraints generated. 4206 Oldfield, 0 Emsley, 4206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8412 Ramachandran restraints generated. 4206 Oldfield, 0 Emsley, 4206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 3735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 4.009 Fit side-chains REVERT: C 697 MET cc_start: 0.8294 (mpp) cc_final: 0.7660 (mpp) REVERT: A 153 MET cc_start: 0.3500 (ptt) cc_final: 0.2662 (ppp) REVERT: E 82 MET cc_start: 0.6135 (pmm) cc_final: 0.5864 (pmm) REVERT: E 190 MET cc_start: 0.0475 (ppp) cc_final: 0.0218 (ppp) REVERT: D 579 MET cc_start: 0.2114 (tpt) cc_final: 0.1522 (tpp) outliers start: 0 outliers final: 0 residues processed: 114 average time/residue: 0.4331 time to fit residues: 86.7209 Evaluate side-chains 94 residues out of total 3735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 3.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 358 optimal weight: 1.9990 chunk 321 optimal weight: 4.9990 chunk 178 optimal weight: 4.9990 chunk 109 optimal weight: 1.9990 chunk 216 optimal weight: 40.0000 chunk 171 optimal weight: 2.9990 chunk 332 optimal weight: 4.9990 chunk 128 optimal weight: 7.9990 chunk 202 optimal weight: 8.9990 chunk 247 optimal weight: 20.0000 chunk 385 optimal weight: 20.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN C 935 GLN A 115 GLN A 625 HIS E 188 ASN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN B 907 ASN ** B1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1083 HIS ** D 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 522 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 35268 Z= 0.368 Angle : 0.630 9.104 47969 Z= 0.324 Chirality : 0.046 0.302 5517 Planarity : 0.004 0.064 6127 Dihedral : 7.095 58.962 5836 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 0.40 % Allowed : 6.96 % Favored : 92.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.13), residues: 4206 helix: 0.53 (0.14), residues: 1295 sheet: -0.50 (0.20), residues: 599 loop : -0.94 (0.13), residues: 2312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 886 HIS 0.006 0.001 HIS C1083 PHE 0.029 0.002 PHE B 759 TYR 0.024 0.002 TYR A1067 ARG 0.023 0.001 ARG A 905 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8412 Ramachandran restraints generated. 4206 Oldfield, 0 Emsley, 4206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8412 Ramachandran restraints generated. 4206 Oldfield, 0 Emsley, 4206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 3735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 104 time to evaluate : 4.119 Fit side-chains REVERT: A 153 MET cc_start: 0.3463 (ptt) cc_final: 0.2829 (ppp) REVERT: A 697 MET cc_start: 0.8675 (mmp) cc_final: 0.8274 (mmp) REVERT: A 869 MET cc_start: 0.9255 (ptp) cc_final: 0.8661 (ptp) REVERT: E 557 MET cc_start: 0.6795 (ttt) cc_final: 0.6346 (ppp) REVERT: B 200 TYR cc_start: 0.8725 (m-80) cc_final: 0.8474 (t80) REVERT: B 902 MET cc_start: 0.9100 (mmt) cc_final: 0.8686 (tpt) REVERT: D 579 MET cc_start: 0.1307 (tpt) cc_final: 0.0836 (tpp) outliers start: 15 outliers final: 6 residues processed: 116 average time/residue: 0.4579 time to fit residues: 95.3219 Evaluate side-chains 98 residues out of total 3735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 92 time to evaluate : 4.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 365 TYR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain E residue 360 MET Chi-restraints excluded: chain E residue 427 ASP Chi-restraints excluded: chain E residue 548 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 213 optimal weight: 7.9990 chunk 119 optimal weight: 3.9990 chunk 320 optimal weight: 0.9990 chunk 262 optimal weight: 10.0000 chunk 106 optimal weight: 1.9990 chunk 385 optimal weight: 5.9990 chunk 416 optimal weight: 20.0000 chunk 343 optimal weight: 4.9990 chunk 382 optimal weight: 0.3980 chunk 131 optimal weight: 0.6980 chunk 309 optimal weight: 4.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 87 ASN C 487 ASN ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 625 HIS ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 926 GLN ** B 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.1769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 35268 Z= 0.199 Angle : 0.496 9.356 47969 Z= 0.255 Chirality : 0.043 0.304 5517 Planarity : 0.003 0.054 6127 Dihedral : 6.407 59.464 5836 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.65 % Allowed : 9.33 % Favored : 90.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.13), residues: 4206 helix: 0.60 (0.15), residues: 1307 sheet: -0.52 (0.20), residues: 594 loop : -0.91 (0.13), residues: 2305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 165 HIS 0.007 0.001 HIS A 625 PHE 0.024 0.001 PHE B 759 TYR 0.019 0.001 TYR A1067 ARG 0.002 0.000 ARG C 214 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8412 Ramachandran restraints generated. 4206 Oldfield, 0 Emsley, 4206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8412 Ramachandran restraints generated. 4206 Oldfield, 0 Emsley, 4206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 3735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 97 time to evaluate : 4.476 Fit side-chains REVERT: C 745 ASP cc_start: 0.6969 (t70) cc_final: 0.6767 (t0) REVERT: A 153 MET cc_start: 0.3471 (ptt) cc_final: 0.2826 (ppp) REVERT: A 697 MET cc_start: 0.8565 (mmp) cc_final: 0.8257 (mmp) REVERT: A 900 MET cc_start: 0.8415 (pmm) cc_final: 0.8202 (pmm) REVERT: A 1031 GLU cc_start: 0.8543 (OUTLIER) cc_final: 0.8126 (mp0) REVERT: E 557 MET cc_start: 0.6780 (ttt) cc_final: 0.6353 (ppp) REVERT: D 579 MET cc_start: 0.1677 (tpt) cc_final: 0.1169 (tpp) outliers start: 24 outliers final: 10 residues processed: 118 average time/residue: 0.4146 time to fit residues: 89.0008 Evaluate side-chains 101 residues out of total 3735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 90 time to evaluate : 4.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain E residue 228 HIS Chi-restraints excluded: chain E residue 360 MET Chi-restraints excluded: chain E residue 427 ASP Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain D residue 374 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 381 optimal weight: 7.9990 chunk 290 optimal weight: 5.9990 chunk 200 optimal weight: 5.9990 chunk 42 optimal weight: 3.9990 chunk 184 optimal weight: 0.8980 chunk 259 optimal weight: 10.0000 chunk 387 optimal weight: 30.0000 chunk 409 optimal weight: 30.0000 chunk 202 optimal weight: 9.9990 chunk 366 optimal weight: 20.0000 chunk 110 optimal weight: 0.2980 overall best weight: 3.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 935 GLN ** C1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 ASN A1083 HIS ** E 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 GLN ** B 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 239 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 35268 Z= 0.369 Angle : 0.622 16.295 47969 Z= 0.316 Chirality : 0.048 1.154 5517 Planarity : 0.004 0.054 6127 Dihedral : 6.326 59.047 5836 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 1.35 % Allowed : 12.25 % Favored : 86.40 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.13), residues: 4206 helix: 0.52 (0.14), residues: 1299 sheet: -0.82 (0.19), residues: 606 loop : -1.04 (0.13), residues: 2301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 48 HIS 0.007 0.001 HIS A1088 PHE 0.026 0.002 PHE B 759 TYR 0.021 0.001 TYR A1067 ARG 0.007 0.001 ARG C1107 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8412 Ramachandran restraints generated. 4206 Oldfield, 0 Emsley, 4206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8412 Ramachandran restraints generated. 4206 Oldfield, 0 Emsley, 4206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 3735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 99 time to evaluate : 3.955 Fit side-chains REVERT: A 153 MET cc_start: 0.3841 (ptt) cc_final: 0.3143 (ppp) REVERT: A 869 MET cc_start: 0.9085 (ptp) cc_final: 0.8588 (ptp) REVERT: A 1031 GLU cc_start: 0.8546 (OUTLIER) cc_final: 0.8061 (mp0) REVERT: A 1116 THR cc_start: 0.9190 (OUTLIER) cc_final: 0.8944 (p) REVERT: E 557 MET cc_start: 0.6798 (ttt) cc_final: 0.6260 (ppp) REVERT: B 200 TYR cc_start: 0.8910 (OUTLIER) cc_final: 0.8637 (t80) REVERT: B 275 PHE cc_start: 0.8786 (OUTLIER) cc_final: 0.7626 (m-80) REVERT: B 697 MET cc_start: 0.8722 (mmm) cc_final: 0.7882 (tpt) REVERT: D 579 MET cc_start: 0.1825 (tpt) cc_final: 0.1269 (tpp) outliers start: 50 outliers final: 27 residues processed: 142 average time/residue: 0.4348 time to fit residues: 111.5157 Evaluate side-chains 123 residues out of total 3735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 92 time to evaluate : 5.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 544 ASN Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain E residue 228 HIS Chi-restraints excluded: chain E residue 548 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain D residue 374 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 341 optimal weight: 2.9990 chunk 232 optimal weight: 0.9980 chunk 5 optimal weight: 5.9990 chunk 305 optimal weight: 20.0000 chunk 169 optimal weight: 4.9990 chunk 349 optimal weight: 0.8980 chunk 283 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 209 optimal weight: 0.0670 chunk 367 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 overall best weight: 0.7518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 81 ASN C 317 ASN ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN C 935 GLN A1108 ASN E 58 ASN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.2441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 35268 Z= 0.146 Angle : 0.487 9.485 47969 Z= 0.248 Chirality : 0.044 0.659 5517 Planarity : 0.003 0.054 6127 Dihedral : 5.644 55.232 5836 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.21 % Allowed : 13.14 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.13), residues: 4206 helix: 0.69 (0.15), residues: 1308 sheet: -0.60 (0.20), residues: 613 loop : -0.96 (0.13), residues: 2285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 165 HIS 0.004 0.001 HIS D 417 PHE 0.016 0.001 PHE B 759 TYR 0.017 0.001 TYR A1067 ARG 0.003 0.000 ARG C 214 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8412 Ramachandran restraints generated. 4206 Oldfield, 0 Emsley, 4206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8412 Ramachandran restraints generated. 4206 Oldfield, 0 Emsley, 4206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 3735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 99 time to evaluate : 4.317 Fit side-chains revert: symmetry clash REVERT: C 754 LEU cc_start: 0.9195 (mt) cc_final: 0.8959 (pp) REVERT: A 153 MET cc_start: 0.3751 (ptt) cc_final: 0.2989 (ppp) REVERT: A 869 MET cc_start: 0.9110 (ptp) cc_final: 0.8768 (ptp) REVERT: A 1116 THR cc_start: 0.9101 (OUTLIER) cc_final: 0.8864 (p) REVERT: E 408 MET cc_start: -0.2261 (ttt) cc_final: -0.2806 (ttt) REVERT: E 455 MET cc_start: 0.4859 (mtt) cc_final: 0.4636 (mtt) REVERT: E 462 MET cc_start: 0.6280 (mpp) cc_final: 0.5945 (pmm) REVERT: E 557 MET cc_start: 0.6835 (ttt) cc_final: 0.6284 (ppp) REVERT: D 579 MET cc_start: 0.1993 (tpt) cc_final: 0.1387 (tpp) outliers start: 45 outliers final: 20 residues processed: 141 average time/residue: 0.3998 time to fit residues: 102.5231 Evaluate side-chains 113 residues out of total 3735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 92 time to evaluate : 3.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain E residue 228 HIS Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 374 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 137 optimal weight: 20.0000 chunk 369 optimal weight: 0.9990 chunk 81 optimal weight: 3.9990 chunk 240 optimal weight: 6.9990 chunk 101 optimal weight: 3.9990 chunk 410 optimal weight: 5.9990 chunk 340 optimal weight: 2.9990 chunk 189 optimal weight: 2.9990 chunk 34 optimal weight: 10.0000 chunk 135 optimal weight: 20.0000 chunk 215 optimal weight: 6.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 317 ASN ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1011 GLN ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 24 GLN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN ** B1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 599 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.2882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 35268 Z= 0.323 Angle : 0.581 13.252 47969 Z= 0.293 Chirality : 0.045 0.535 5517 Planarity : 0.004 0.054 6127 Dihedral : 5.658 56.381 5836 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 1.54 % Allowed : 14.00 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.13), residues: 4206 helix: 0.61 (0.15), residues: 1307 sheet: -0.83 (0.19), residues: 623 loop : -1.05 (0.13), residues: 2276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 168 HIS 0.005 0.001 HIS A1088 PHE 0.026 0.002 PHE B 759 TYR 0.021 0.001 TYR A 904 ARG 0.009 0.000 ARG C1107 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8412 Ramachandran restraints generated. 4206 Oldfield, 0 Emsley, 4206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8412 Ramachandran restraints generated. 4206 Oldfield, 0 Emsley, 4206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 3735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 97 time to evaluate : 4.187 Fit side-chains revert: symmetry clash REVERT: C 1011 GLN cc_start: 0.9106 (OUTLIER) cc_final: 0.8868 (tp40) REVERT: A 153 MET cc_start: 0.3919 (ptt) cc_final: 0.3573 (ppp) REVERT: A 1031 GLU cc_start: 0.8492 (OUTLIER) cc_final: 0.7834 (mp0) REVERT: A 1116 THR cc_start: 0.9170 (OUTLIER) cc_final: 0.8940 (p) REVERT: E 215 TYR cc_start: 0.3604 (OUTLIER) cc_final: 0.3312 (m-10) REVERT: E 455 MET cc_start: 0.4903 (mtt) cc_final: 0.4693 (mtt) REVERT: B 275 PHE cc_start: 0.8818 (OUTLIER) cc_final: 0.7722 (m-80) REVERT: D 579 MET cc_start: 0.2219 (tpt) cc_final: 0.1596 (tpp) outliers start: 57 outliers final: 32 residues processed: 146 average time/residue: 0.4103 time to fit residues: 108.1650 Evaluate side-chains 132 residues out of total 3735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 95 time to evaluate : 3.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1011 GLN Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 544 ASN Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain E residue 215 TYR Chi-restraints excluded: chain E residue 228 HIS Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 1083 HIS Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 374 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 395 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 233 optimal weight: 8.9990 chunk 299 optimal weight: 7.9990 chunk 232 optimal weight: 5.9990 chunk 345 optimal weight: 3.9990 chunk 229 optimal weight: 0.9990 chunk 408 optimal weight: 4.9990 chunk 255 optimal weight: 20.0000 chunk 249 optimal weight: 10.0000 chunk 188 optimal weight: 0.5980 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1011 GLN A 544 ASN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.3027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 35268 Z= 0.253 Angle : 0.537 14.306 47969 Z= 0.272 Chirality : 0.044 0.446 5517 Planarity : 0.003 0.054 6127 Dihedral : 5.472 54.292 5836 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 1.78 % Allowed : 14.22 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.13), residues: 4206 helix: 0.69 (0.15), residues: 1299 sheet: -0.80 (0.19), residues: 637 loop : -1.06 (0.13), residues: 2270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP D 168 HIS 0.004 0.001 HIS E 540 PHE 0.039 0.001 PHE B 759 TYR 0.016 0.001 TYR A1067 ARG 0.005 0.000 ARG A 328 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8412 Ramachandran restraints generated. 4206 Oldfield, 0 Emsley, 4206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8412 Ramachandran restraints generated. 4206 Oldfield, 0 Emsley, 4206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 3735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 96 time to evaluate : 3.762 Fit side-chains revert: symmetry clash REVERT: C 754 LEU cc_start: 0.9211 (mt) cc_final: 0.8920 (pp) REVERT: A 153 MET cc_start: 0.4044 (ptt) cc_final: 0.3635 (ppp) REVERT: A 869 MET cc_start: 0.9120 (ptp) cc_final: 0.8757 (ptp) REVERT: A 1031 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.7931 (mp0) REVERT: A 1050 MET cc_start: 0.8889 (OUTLIER) cc_final: 0.8659 (pmm) REVERT: A 1116 THR cc_start: 0.9152 (OUTLIER) cc_final: 0.8920 (p) REVERT: E 215 TYR cc_start: 0.3411 (OUTLIER) cc_final: 0.2868 (m-10) REVERT: E 323 MET cc_start: -0.2235 (tpt) cc_final: -0.2626 (tpt) REVERT: B 29 THR cc_start: 0.8853 (OUTLIER) cc_final: 0.8629 (p) REVERT: B 563 GLN cc_start: 0.8620 (OUTLIER) cc_final: 0.7798 (mm110) REVERT: B 900 MET cc_start: 0.8998 (ptp) cc_final: 0.8793 (ptp) REVERT: D 376 MET cc_start: 0.5599 (ppp) cc_final: 0.5159 (ptt) REVERT: D 579 MET cc_start: 0.2372 (tpt) cc_final: 0.1716 (tpp) outliers start: 66 outliers final: 36 residues processed: 153 average time/residue: 0.3971 time to fit residues: 109.3386 Evaluate side-chains 135 residues out of total 3735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 93 time to evaluate : 3.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 544 ASN Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain E residue 215 TYR Chi-restraints excluded: chain E residue 228 HIS Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 563 GLN Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 374 HIS Chi-restraints excluded: chain D residue 383 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 252 optimal weight: 0.0040 chunk 163 optimal weight: 0.8980 chunk 244 optimal weight: 8.9990 chunk 123 optimal weight: 0.8980 chunk 80 optimal weight: 3.9990 chunk 79 optimal weight: 0.8980 chunk 259 optimal weight: 2.9990 chunk 278 optimal weight: 0.9990 chunk 202 optimal weight: 0.0010 chunk 38 optimal weight: 9.9990 chunk 321 optimal weight: 4.9990 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 317 ASN C 487 ASN ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 544 ASN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 949 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.3023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.089 35268 Z= 0.138 Angle : 0.499 13.001 47969 Z= 0.251 Chirality : 0.043 0.400 5517 Planarity : 0.003 0.055 6127 Dihedral : 5.100 55.306 5836 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 1.43 % Allowed : 14.81 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.13), residues: 4206 helix: 0.79 (0.15), residues: 1295 sheet: -0.68 (0.19), residues: 648 loop : -1.00 (0.13), residues: 2263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 168 HIS 0.003 0.000 HIS E 540 PHE 0.031 0.001 PHE B 759 TYR 0.016 0.001 TYR A1067 ARG 0.004 0.000 ARG C 905 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8412 Ramachandran restraints generated. 4206 Oldfield, 0 Emsley, 4206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8412 Ramachandran restraints generated. 4206 Oldfield, 0 Emsley, 4206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 3735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 94 time to evaluate : 4.051 Fit side-chains revert: symmetry clash REVERT: C 487 ASN cc_start: 0.6933 (OUTLIER) cc_final: 0.6633 (p0) REVERT: C 754 LEU cc_start: 0.9166 (mt) cc_final: 0.8880 (pp) REVERT: A 169 GLU cc_start: 0.6407 (OUTLIER) cc_final: 0.5584 (mm-30) REVERT: A 869 MET cc_start: 0.9081 (ptp) cc_final: 0.8709 (ptp) REVERT: A 900 MET cc_start: 0.8539 (ptp) cc_final: 0.8324 (ptp) REVERT: A 1050 MET cc_start: 0.8871 (OUTLIER) cc_final: 0.8617 (pmm) REVERT: A 1116 THR cc_start: 0.9083 (OUTLIER) cc_final: 0.8880 (p) REVERT: E 215 TYR cc_start: 0.3423 (OUTLIER) cc_final: 0.2938 (m-10) REVERT: E 323 MET cc_start: -0.2403 (tpt) cc_final: -0.2668 (tpt) REVERT: B 29 THR cc_start: 0.8840 (OUTLIER) cc_final: 0.8624 (p) REVERT: B 900 MET cc_start: 0.8916 (ptp) cc_final: 0.8625 (ptp) REVERT: D 332 MET cc_start: 0.2955 (pmm) cc_final: 0.1838 (ppp) REVERT: D 376 MET cc_start: 0.5174 (ppp) cc_final: 0.4648 (ptt) REVERT: D 579 MET cc_start: 0.1866 (tpt) cc_final: 0.1193 (tpp) outliers start: 53 outliers final: 36 residues processed: 141 average time/residue: 0.4195 time to fit residues: 108.4919 Evaluate side-chains 135 residues out of total 3735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 93 time to evaluate : 4.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 544 ASN Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain E residue 215 TYR Chi-restraints excluded: chain E residue 228 HIS Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 140 GLU Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 374 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 371 optimal weight: 6.9990 chunk 391 optimal weight: 0.9990 chunk 357 optimal weight: 2.9990 chunk 380 optimal weight: 20.0000 chunk 229 optimal weight: 0.9980 chunk 165 optimal weight: 4.9990 chunk 299 optimal weight: 2.9990 chunk 116 optimal weight: 5.9990 chunk 344 optimal weight: 0.0010 chunk 360 optimal weight: 2.9990 chunk 379 optimal weight: 5.9990 overall best weight: 1.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 544 ASN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.3125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 35268 Z= 0.198 Angle : 0.517 13.397 47969 Z= 0.259 Chirality : 0.047 1.306 5517 Planarity : 0.003 0.054 6127 Dihedral : 5.263 57.549 5836 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 1.40 % Allowed : 15.19 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.13), residues: 4206 helix: 0.82 (0.15), residues: 1294 sheet: -0.67 (0.19), residues: 621 loop : -1.01 (0.13), residues: 2291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 168 HIS 0.003 0.001 HIS E 540 PHE 0.036 0.001 PHE B 759 TYR 0.016 0.001 TYR A1067 ARG 0.004 0.000 ARG C1107 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8412 Ramachandran restraints generated. 4206 Oldfield, 0 Emsley, 4206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8412 Ramachandran restraints generated. 4206 Oldfield, 0 Emsley, 4206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 3735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 92 time to evaluate : 3.859 Fit side-chains revert: symmetry clash REVERT: A 169 GLU cc_start: 0.6565 (OUTLIER) cc_final: 0.5713 (mm-30) REVERT: A 869 MET cc_start: 0.9093 (ptp) cc_final: 0.8749 (ptp) REVERT: A 1050 MET cc_start: 0.8908 (OUTLIER) cc_final: 0.8629 (pmm) REVERT: A 1116 THR cc_start: 0.9089 (OUTLIER) cc_final: 0.8884 (p) REVERT: E 215 TYR cc_start: 0.3252 (OUTLIER) cc_final: 0.2572 (m-10) REVERT: E 323 MET cc_start: -0.2217 (tpt) cc_final: -0.2440 (tpt) REVERT: B 29 THR cc_start: 0.8842 (OUTLIER) cc_final: 0.8626 (p) REVERT: B 563 GLN cc_start: 0.8522 (OUTLIER) cc_final: 0.7968 (mm110) REVERT: D 132 VAL cc_start: 0.1713 (OUTLIER) cc_final: 0.1431 (m) REVERT: D 332 MET cc_start: 0.2998 (pmm) cc_final: 0.1880 (ppp) REVERT: D 376 MET cc_start: 0.5180 (ppp) cc_final: 0.4634 (ptt) REVERT: D 579 MET cc_start: 0.2058 (tpt) cc_final: 0.1315 (tpp) outliers start: 52 outliers final: 42 residues processed: 138 average time/residue: 0.3965 time to fit residues: 99.1561 Evaluate side-chains 141 residues out of total 3735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 92 time to evaluate : 4.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 544 ASN Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain E residue 215 TYR Chi-restraints excluded: chain E residue 228 HIS Chi-restraints excluded: chain E residue 270 MET Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 563 GLN Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 140 GLU Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 374 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 250 optimal weight: 0.5980 chunk 402 optimal weight: 20.0000 chunk 245 optimal weight: 20.0000 chunk 191 optimal weight: 0.9980 chunk 279 optimal weight: 10.0000 chunk 422 optimal weight: 3.9990 chunk 388 optimal weight: 7.9990 chunk 336 optimal weight: 0.0070 chunk 34 optimal weight: 5.9990 chunk 259 optimal weight: 30.0000 chunk 206 optimal weight: 9.9990 overall best weight: 2.3202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 317 ASN ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 544 ASN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN ** B1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.3261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 35268 Z= 0.255 Angle : 0.538 13.078 47969 Z= 0.271 Chirality : 0.044 0.328 5517 Planarity : 0.003 0.053 6127 Dihedral : 5.137 54.245 5836 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 1.48 % Allowed : 15.08 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.13), residues: 4206 helix: 0.80 (0.15), residues: 1296 sheet: -0.74 (0.19), residues: 622 loop : -1.03 (0.13), residues: 2288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 168 HIS 0.004 0.001 HIS A 655 PHE 0.040 0.001 PHE B 759 TYR 0.016 0.001 TYR A1067 ARG 0.005 0.000 ARG C1107 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8412 Ramachandran restraints generated. 4206 Oldfield, 0 Emsley, 4206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8412 Ramachandran restraints generated. 4206 Oldfield, 0 Emsley, 4206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 3735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 94 time to evaluate : 4.059 Fit side-chains revert: symmetry clash REVERT: C 754 LEU cc_start: 0.9175 (mt) cc_final: 0.8894 (pp) REVERT: C 869 MET cc_start: 0.8621 (ptp) cc_final: 0.8408 (mtm) REVERT: A 169 GLU cc_start: 0.6697 (OUTLIER) cc_final: 0.5450 (mp0) REVERT: A 869 MET cc_start: 0.9132 (ptp) cc_final: 0.8833 (ptp) REVERT: A 1050 MET cc_start: 0.8930 (OUTLIER) cc_final: 0.8574 (pmm) REVERT: A 1116 THR cc_start: 0.9135 (OUTLIER) cc_final: 0.8923 (p) REVERT: E 215 TYR cc_start: 0.3058 (OUTLIER) cc_final: 0.2369 (m-10) REVERT: B 29 THR cc_start: 0.8844 (OUTLIER) cc_final: 0.8623 (p) REVERT: B 563 GLN cc_start: 0.8561 (OUTLIER) cc_final: 0.7943 (mm110) REVERT: B 1029 MET cc_start: 0.9039 (tpp) cc_final: 0.8671 (ttm) REVERT: D 132 VAL cc_start: 0.1511 (OUTLIER) cc_final: 0.1231 (m) REVERT: D 332 MET cc_start: 0.3078 (pmm) cc_final: 0.1956 (ppp) REVERT: D 376 MET cc_start: 0.5122 (ppp) cc_final: 0.4577 (ptt) REVERT: D 579 MET cc_start: 0.2099 (tpt) cc_final: 0.1369 (tpp) outliers start: 55 outliers final: 42 residues processed: 142 average time/residue: 0.3823 time to fit residues: 99.5298 Evaluate side-chains 143 residues out of total 3735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 94 time to evaluate : 3.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 544 ASN Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain E residue 215 TYR Chi-restraints excluded: chain E residue 228 HIS Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 563 GLN Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 140 GLU Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 374 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 267 optimal weight: 3.9990 chunk 358 optimal weight: 2.9990 chunk 103 optimal weight: 0.0770 chunk 310 optimal weight: 3.9990 chunk 49 optimal weight: 9.9990 chunk 93 optimal weight: 4.9990 chunk 336 optimal weight: 4.9990 chunk 140 optimal weight: 7.9990 chunk 345 optimal weight: 0.9980 chunk 42 optimal weight: 6.9990 chunk 62 optimal weight: 1.9990 overall best weight: 2.0144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 544 ASN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.094278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.060855 restraints weight = 188492.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 67)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.060824 restraints weight = 77529.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.061423 restraints weight = 46145.998| |-----------------------------------------------------------------------------| r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.3383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 35268 Z= 0.228 Angle : 0.537 14.410 47969 Z= 0.267 Chirality : 0.043 0.315 5517 Planarity : 0.003 0.053 6127 Dihedral : 5.075 54.471 5836 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 1.43 % Allowed : 15.27 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.13), residues: 4206 helix: 0.81 (0.15), residues: 1293 sheet: -0.76 (0.19), residues: 616 loop : -1.03 (0.13), residues: 2297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 168 HIS 0.004 0.001 HIS E 540 PHE 0.038 0.001 PHE B 759 TYR 0.015 0.001 TYR A1067 ARG 0.004 0.000 ARG C1107 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5975.20 seconds wall clock time: 111 minutes 24.92 seconds (6684.92 seconds total)