Starting phenix.real_space_refine (version: dev) on Fri Dec 16 14:58:06 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m0r_23613/12_2022/7m0r_23613.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m0r_23613/12_2022/7m0r_23613.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m0r_23613/12_2022/7m0r_23613.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m0r_23613/12_2022/7m0r_23613.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m0r_23613/12_2022/7m0r_23613.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m0r_23613/12_2022/7m0r_23613.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.002 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "E GLU 34": "OE1" <-> "OE2" Residue "E TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 52": "OE1" <-> "OE2" Residue "E GLU 62": "OE1" <-> "OE2" Residue "E TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 137": "NH1" <-> "NH2" Residue "E TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 101": "OD1" <-> "OD2" Residue "C TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 159": "OD1" <-> "OD2" Residue "C GLU 163": "OE1" <-> "OE2" Residue "C PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 219": "NH1" <-> "NH2" Residue "C GLU 234": "OE1" <-> "OE2" Residue "C TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 414": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 429": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 516": "NH1" <-> "NH2" Residue "C TYR 520": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 34": "OE1" <-> "OE2" Residue "F TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 52": "OE1" <-> "OE2" Residue "F GLU 62": "OE1" <-> "OE2" Residue "F TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 137": "NH1" <-> "NH2" Residue "F TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 101": "OD1" <-> "OD2" Residue "D TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 159": "OD1" <-> "OD2" Residue "D GLU 163": "OE1" <-> "OE2" Residue "D PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 219": "NH1" <-> "NH2" Residue "D GLU 234": "OE1" <-> "OE2" Residue "D TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 414": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 429": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 516": "NH1" <-> "NH2" Residue "D TYR 520": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 56": "OD1" <-> "OD2" Residue "A TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 123": "OE1" <-> "OE2" Residue "A TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 164": "OE1" <-> "OE2" Residue "A PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 179": "OD1" <-> "OD2" Residue "A ASP 180": "OD1" <-> "OD2" Residue "A PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 208": "OE1" <-> "OE2" Residue "A ASP 231": "OD1" <-> "OD2" Residue "A PHE 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 294": "OE1" <-> "OE2" Residue "A GLU 305": "OE1" <-> "OE2" Residue "A TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 330": "OD1" <-> "OD2" Residue "A GLU 377": "OE1" <-> "OE2" Residue "A ASP 381": "OD1" <-> "OD2" Residue "A ASP 389": "OD1" <-> "OD2" Residue "A PHE 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 458": "NH1" <-> "NH2" Residue "A ASP 460": "OD1" <-> "OD2" Residue "A TYR 469": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 550": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 553": "OE1" <-> "OE2" Residue "A TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 653": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 676": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 801": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 907": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 948": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1065": "OD1" <-> "OD2" Residue "A TYR 1137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 56": "OD1" <-> "OD2" Residue "B TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 123": "OE1" <-> "OE2" Residue "B TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 164": "OE1" <-> "OE2" Residue "B PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 179": "OD1" <-> "OD2" Residue "B ASP 180": "OD1" <-> "OD2" Residue "B PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 208": "OE1" <-> "OE2" Residue "B ASP 231": "OD1" <-> "OD2" Residue "B PHE 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 294": "OE1" <-> "OE2" Residue "B GLU 305": "OE1" <-> "OE2" Residue "B TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 330": "OD1" <-> "OD2" Residue "B GLU 377": "OE1" <-> "OE2" Residue "B ASP 381": "OD1" <-> "OD2" Residue "B ASP 389": "OD1" <-> "OD2" Residue "B PHE 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 458": "NH1" <-> "NH2" Residue "B ASP 460": "OD1" <-> "OD2" Residue "B TYR 469": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 550": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 553": "OE1" <-> "OE2" Residue "B TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 653": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 676": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 801": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 907": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 948": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1065": "OD1" <-> "OD2" Residue "B TYR 1137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1220": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 30898 Number of models: 1 Model: "" Number of chains: 8 Chain: "E" Number of atoms: 2915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 2915 Classifications: {'peptide': 458} Incomplete info: {'truncation_to_alanine': 205} Link IDs: {'PCIS': 2, 'PTRANS': 27, 'TRANS': 428} Chain breaks: 12 Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 758 Unresolved non-hydrogen angles: 973 Unresolved non-hydrogen dihedrals: 635 Unresolved non-hydrogen chiralities: 71 Planarities with less than four sites: {'GLN:plan1': 9, 'ARG:plan': 17, 'TYR:plan': 9, 'ASN:plan1': 10, 'TRP:plan': 5, 'HIS:plan': 1, 'PHE:plan': 10, 'GLU:plan': 18, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 420 Chain: "C" Number of atoms: 4492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 588, 4492 Classifications: {'peptide': 588} Incomplete info: {'truncation_to_alanine': 68} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 555} Chain breaks: 8 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 140 Unresolved non-hydrogen angles: 208 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'UNK:plan-1': 65} Unresolved non-hydrogen planarities: 69 Chain: "F" Number of atoms: 2915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 2915 Classifications: {'peptide': 458} Incomplete info: {'truncation_to_alanine': 205} Link IDs: {'PCIS': 2, 'PTRANS': 27, 'TRANS': 428} Chain breaks: 12 Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 758 Unresolved non-hydrogen angles: 973 Unresolved non-hydrogen dihedrals: 635 Unresolved non-hydrogen chiralities: 71 Planarities with less than four sites: {'GLN:plan1': 9, 'ARG:plan': 17, 'TYR:plan': 9, 'ASN:plan1': 10, 'TRP:plan': 5, 'HIS:plan': 1, 'PHE:plan': 10, 'GLU:plan': 18, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 420 Chain: "D" Number of atoms: 4492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 588, 4492 Classifications: {'peptide': 588} Incomplete info: {'truncation_to_alanine': 68} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 555} Chain breaks: 8 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 140 Unresolved non-hydrogen angles: 208 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'UNK:plan-1': 65} Unresolved non-hydrogen planarities: 69 Chain: "A" Number of atoms: 8040 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1133, 8040 Classifications: {'peptide': 1133} Incomplete info: {'truncation_to_alanine': 214} Link IDs: {'PCIS': 2, 'PTRANS': 61, 'TRANS': 1069} Chain breaks: 7 Unresolved non-hydrogen bonds: 858 Unresolved non-hydrogen angles: 1054 Unresolved non-hydrogen dihedrals: 693 Unresolved non-hydrogen chiralities: 38 Planarities with less than four sites: {'GLN:plan1': 24, 'HIS:plan': 5, 'TYR:plan': 2, 'ASN:plan1': 17, 'TRP:plan': 1, 'ASP:plan': 14, 'PHE:plan': 4, 'GLU:plan': 45, 'ARG:plan': 29} Unresolved non-hydrogen planarities: 586 Chain: "B" Number of atoms: 8040 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1133, 8040 Classifications: {'peptide': 1133} Incomplete info: {'truncation_to_alanine': 214} Link IDs: {'PCIS': 2, 'PTRANS': 61, 'TRANS': 1069} Chain breaks: 7 Unresolved non-hydrogen bonds: 858 Unresolved non-hydrogen angles: 1054 Unresolved non-hydrogen dihedrals: 693 Unresolved non-hydrogen chiralities: 38 Planarities with less than four sites: {'GLN:plan1': 24, 'HIS:plan': 5, 'TYR:plan': 2, 'ASN:plan1': 17, 'TRP:plan': 1, 'ASP:plan': 14, 'PHE:plan': 4, 'GLU:plan': 45, 'ARG:plan': 29} Unresolved non-hydrogen planarities: 586 Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 17.65, per 1000 atoms: 0.57 Number of scatterers: 30898 At special positions: 0 Unit cell: (232.2, 135, 177.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 4 19.99 S 202 16.00 O 5838 8.00 N 5316 7.00 C 19538 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=70, symmetry=0 Simple disulfide: pdb=" SG CYS E 27 " - pdb=" SG CYS E 54 " distance=2.04 Simple disulfide: pdb=" SG CYS E 82 " - pdb=" SG CYS E 104 " distance=2.03 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 173 " distance=2.03 Simple disulfide: pdb=" SG CYS E 206 " - pdb=" SG CYS E 228 " distance=2.03 Simple disulfide: pdb=" SG CYS C 103 " - pdb=" SG CYS C 114 " distance=2.03 Simple disulfide: pdb=" SG CYS C 132 " - pdb=" SG CYS C 141 " distance=2.03 Simple disulfide: pdb=" SG CYS C 269 " - pdb=" SG CYS C 381 " distance=2.03 Simple disulfide: pdb=" SG CYS C 293 " - pdb=" SG CYS C 341 " distance=2.03 Simple disulfide: pdb=" SG CYS C 517 " - pdb=" SG CYS C 535 " distance=2.03 Simple disulfide: pdb=" SG CYS C 524 " - pdb=" SG CYS C 567 " distance=2.03 Simple disulfide: pdb=" SG CYS C 527 " - pdb=" SG CYS C 542 " distance=2.03 Simple disulfide: pdb=" SG CYS F 27 " - pdb=" SG CYS F 54 " distance=2.04 Simple disulfide: pdb=" SG CYS F 82 " - pdb=" SG CYS F 104 " distance=2.03 Simple disulfide: pdb=" SG CYS F 147 " - pdb=" SG CYS F 173 " distance=2.03 Simple disulfide: pdb=" SG CYS F 206 " - pdb=" SG CYS F 228 " distance=2.03 Simple disulfide: pdb=" SG CYS D 103 " - pdb=" SG CYS D 114 " distance=2.03 Simple disulfide: pdb=" SG CYS D 132 " - pdb=" SG CYS D 141 " distance=2.03 Simple disulfide: pdb=" SG CYS D 269 " - pdb=" SG CYS D 381 " distance=2.03 Simple disulfide: pdb=" SG CYS D 293 " - pdb=" SG CYS D 341 " distance=2.03 Simple disulfide: pdb=" SG CYS D 517 " - pdb=" SG CYS D 535 " distance=2.03 Simple disulfide: pdb=" SG CYS D 524 " - pdb=" SG CYS D 567 " distance=2.03 Simple disulfide: pdb=" SG CYS D 527 " - pdb=" SG CYS D 542 " distance=2.03 Simple disulfide: pdb=" SG CYS A 94 " - pdb=" SG CYS A 103 " distance=2.03 Simple disulfide: pdb=" SG CYS A 129 " - pdb=" SG CYS A 137 " distance=2.03 Simple disulfide: pdb=" SG CYS A 283 " - pdb=" SG CYS A 404 " distance=2.03 Simple disulfide: pdb=" SG CYS A 299 " - pdb=" SG CYS A 355 " distance=2.03 Simple disulfide: pdb=" SG CYS A 373 " - pdb=" SG CYS A 392 " distance=2.03 Simple disulfide: pdb=" SG CYS A 509 " - pdb=" SG CYS A 526 " distance=2.03 Simple disulfide: pdb=" SG CYS A 515 " - pdb=" SG CYS A 557 " distance=2.04 Simple disulfide: pdb=" SG CYS A 518 " - pdb=" SG CYS A 535 " distance=2.03 Simple disulfide: pdb=" SG CYS A 529 " - pdb=" SG CYS A 541 " distance=2.03 Simple disulfide: pdb=" SG CYS A 592 " - pdb=" SG CYS A 611 " distance=2.03 Simple disulfide: pdb=" SG CYS A 655 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 661 " - pdb=" SG CYS A 700 " distance=2.03 Simple disulfide: pdb=" SG CYS A 664 " - pdb=" SG CYS A 680 " distance=2.03 Simple disulfide: pdb=" SG CYS A 674 " - pdb=" SG CYS A 687 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 761 " distance=2.03 Simple disulfide: pdb=" SG CYS A 803 " - pdb=" SG CYS A 822 " distance=2.03 Simple disulfide: pdb=" SG CYS A 810 " - pdb=" SG CYS A 854 " distance=2.03 Simple disulfide: pdb=" SG CYS A 813 " - pdb=" SG CYS A 831 " distance=2.03 Simple disulfide: pdb=" SG CYS A 825 " - pdb=" SG CYS A 837 " distance=2.03 Simple disulfide: pdb=" SG CYS A 900 " - pdb=" SG CYS A 915 " distance=2.03 Simple disulfide: pdb=" SG CYS A 932 " - pdb=" SG CYS A 936 " distance=2.03 Simple disulfide: pdb=" SG CYS A 993 " - pdb=" SG CYS A1005 " distance=2.04 Simple disulfide: pdb=" SG CYS A1085 " - pdb=" SG CYS A1095 " distance=2.03 Simple disulfide: pdb=" SG CYS A1189 " - pdb=" SG CYS A1200 " distance=2.04 Simple disulfide: pdb=" SG CYS B 94 " - pdb=" SG CYS B 103 " distance=2.03 Simple disulfide: pdb=" SG CYS B 129 " - pdb=" SG CYS B 137 " distance=2.03 Simple disulfide: pdb=" SG CYS B 283 " - pdb=" SG CYS B 404 " distance=2.03 Simple disulfide: pdb=" SG CYS B 299 " - pdb=" SG CYS B 355 " distance=2.03 Simple disulfide: pdb=" SG CYS B 373 " - pdb=" SG CYS B 392 " distance=2.03 Simple disulfide: pdb=" SG CYS B 509 " - pdb=" SG CYS B 526 " distance=2.03 Simple disulfide: pdb=" SG CYS B 515 " - pdb=" SG CYS B 557 " distance=2.03 Simple disulfide: pdb=" SG CYS B 518 " - pdb=" SG CYS B 535 " distance=2.03 Simple disulfide: pdb=" SG CYS B 529 " - pdb=" SG CYS B 541 " distance=2.03 Simple disulfide: pdb=" SG CYS B 592 " - pdb=" SG CYS B 611 " distance=2.03 Simple disulfide: pdb=" SG CYS B 655 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 661 " - pdb=" SG CYS B 700 " distance=2.03 Simple disulfide: pdb=" SG CYS B 664 " - pdb=" SG CYS B 680 " distance=2.03 Simple disulfide: pdb=" SG CYS B 674 " - pdb=" SG CYS B 687 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 761 " distance=2.03 Simple disulfide: pdb=" SG CYS B 803 " - pdb=" SG CYS B 822 " distance=2.03 Simple disulfide: pdb=" SG CYS B 810 " - pdb=" SG CYS B 854 " distance=2.03 Simple disulfide: pdb=" SG CYS B 813 " - pdb=" SG CYS B 831 " distance=2.04 Simple disulfide: pdb=" SG CYS B 825 " - pdb=" SG CYS B 837 " distance=2.04 Simple disulfide: pdb=" SG CYS B 900 " - pdb=" SG CYS B 915 " distance=2.03 Simple disulfide: pdb=" SG CYS B 932 " - pdb=" SG CYS B 936 " distance=2.03 Simple disulfide: pdb=" SG CYS B 993 " - pdb=" SG CYS B1005 " distance=2.04 Simple disulfide: pdb=" SG CYS B1085 " - pdb=" SG CYS B1095 " distance=2.03 Simple disulfide: pdb=" SG CYS B1189 " - pdb=" SG CYS B1200 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 12.53 Conformation dependent library (CDL) restraints added in 5.0 seconds 8264 Ramachandran restraints generated. 4132 Oldfield, 0 Emsley, 4132 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8092 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 86 sheets defined 8.7% alpha, 36.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.88 Creating SS restraints... Processing helix chain 'E' and resid 302 through 306 Processing helix chain 'E' and resid 425 through 429 removed outlier: 3.686A pdb=" N TYR E 429 " --> pdb=" O ILE E 426 " (cutoff:3.500A) Processing helix chain 'E' and resid 459 through 463 removed outlier: 3.590A pdb=" N ARG E 463 " --> pdb=" O GLU E 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 42 Processing helix chain 'C' and resid 96 through 107 Processing helix chain 'C' and resid 149 through 153 Processing helix chain 'C' and resid 237 through 240 Processing helix chain 'C' and resid 345 through 353 Processing helix chain 'C' and resid 391 through 395 Processing helix chain 'C' and resid 396 through 406 Processing helix chain 'C' and resid 415 through 419 removed outlier: 3.720A pdb=" N ARG C 419 " --> pdb=" O ILE C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 517 through 521 Processing helix chain 'C' and resid 523 through 530 Processing helix chain 'F' and resid 302 through 306 Processing helix chain 'F' and resid 425 through 429 removed outlier: 3.685A pdb=" N TYR F 429 " --> pdb=" O ILE F 426 " (cutoff:3.500A) Processing helix chain 'F' and resid 459 through 463 removed outlier: 3.590A pdb=" N ARG F 463 " --> pdb=" O GLU F 460 " (cutoff:3.500A) Processing helix chain 'D' and resid 35 through 42 Processing helix chain 'D' and resid 96 through 107 Processing helix chain 'D' and resid 149 through 153 Processing helix chain 'D' and resid 237 through 240 Processing helix chain 'D' and resid 345 through 353 Processing helix chain 'D' and resid 391 through 395 Processing helix chain 'D' and resid 396 through 406 Processing helix chain 'D' and resid 415 through 419 removed outlier: 3.721A pdb=" N ARG D 419 " --> pdb=" O ILE D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 517 through 521 Processing helix chain 'D' and resid 523 through 530 Processing helix chain 'A' and resid 154 through 158 Processing helix chain 'A' and resid 229 through 236 removed outlier: 3.875A pdb=" N PHE A 233 " --> pdb=" O PRO A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 326 removed outlier: 3.522A pdb=" N THR A 324 " --> pdb=" O VAL A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 375 Processing helix chain 'A' and resid 382 through 386 removed outlier: 3.559A pdb=" N LEU A 385 " --> pdb=" O LEU A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 521 Processing helix chain 'A' and resid 617 through 624 removed outlier: 4.033A pdb=" N ARG A 621 " --> pdb=" O LYS A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 658 removed outlier: 3.634A pdb=" N VAL A 657 " --> pdb=" O ASN A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 661 through 667 removed outlier: 3.511A pdb=" N SER A 667 " --> pdb=" O SER A 663 " (cutoff:3.500A) Processing helix chain 'A' and resid 809 through 816 removed outlier: 3.546A pdb=" N ALA A 816 " --> pdb=" O LEU A 812 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 821 Processing helix chain 'A' and resid 885 through 890 Processing helix chain 'A' and resid 1124 through 1129 Processing helix chain 'B' and resid 154 through 158 Processing helix chain 'B' and resid 229 through 236 removed outlier: 3.875A pdb=" N PHE B 233 " --> pdb=" O PRO B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 326 removed outlier: 3.522A pdb=" N THR B 324 " --> pdb=" O VAL B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 375 Processing helix chain 'B' and resid 382 through 386 removed outlier: 3.560A pdb=" N LEU B 385 " --> pdb=" O LEU B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 514 through 521 Processing helix chain 'B' and resid 617 through 624 removed outlier: 4.034A pdb=" N ARG B 621 " --> pdb=" O LYS B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 654 through 658 removed outlier: 3.634A pdb=" N VAL B 657 " --> pdb=" O ASN B 654 " (cutoff:3.500A) Processing helix chain 'B' and resid 661 through 667 removed outlier: 3.512A pdb=" N SER B 667 " --> pdb=" O SER B 663 " (cutoff:3.500A) Processing helix chain 'B' and resid 809 through 816 removed outlier: 3.547A pdb=" N ALA B 816 " --> pdb=" O LEU B 812 " (cutoff:3.500A) Processing helix chain 'B' and resid 817 through 821 Processing helix chain 'B' and resid 885 through 890 Processing helix chain 'B' and resid 1124 through 1129 Processing sheet with id=AA1, first strand: chain 'E' and resid 29 through 32 removed outlier: 5.944A pdb=" N ASP E 91 " --> pdb=" O LEU E 99 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N LEU E 99 " --> pdb=" O ASP E 91 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 37 through 40 Processing sheet with id=AA3, first strand: chain 'E' and resid 148 through 151 removed outlier: 6.677A pdb=" N ILE E 213 " --> pdb=" O ILE E 224 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 155 through 159 removed outlier: 6.916A pdb=" N GLY E 257 " --> pdb=" O PHE E 192 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N PHE E 192 " --> pdb=" O GLY E 257 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N SER E 259 " --> pdb=" O GLU E 190 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 277 through 278 removed outlier: 7.056A pdb=" N CYS E 424 " --> pdb=" O VAL E 336 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N VAL E 336 " --> pdb=" O CYS E 424 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N ARG E 402 " --> pdb=" O LEU E 330 " (cutoff:3.500A) removed outlier: 9.785A pdb=" N LEU E 332 " --> pdb=" O ILE E 400 " (cutoff:3.500A) removed outlier: 8.693A pdb=" N ILE E 400 " --> pdb=" O LEU E 332 " (cutoff:3.500A) removed outlier: 9.512A pdb=" N ARG E 334 " --> pdb=" O PRO E 398 " (cutoff:3.500A) removed outlier: 10.643A pdb=" N VAL E 336 " --> pdb=" O SER E 396 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N SER E 396 " --> pdb=" O VAL E 336 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ALA E 338 " --> pdb=" O VAL E 394 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N VAL E 394 " --> pdb=" O ALA E 338 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N GLY E 340 " --> pdb=" O LEU E 392 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N LEU E 392 " --> pdb=" O GLY E 340 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N THR E 357 " --> pdb=" O VAL E 409 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N TRP E 411 " --> pdb=" O VAL E 355 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N VAL E 355 " --> pdb=" O TRP E 411 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 433 through 434 removed outlier: 7.087A pdb=" N CYS E 583 " --> pdb=" O VAL E 495 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N VAL E 495 " --> pdb=" O CYS E 583 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 433 through 434 removed outlier: 7.087A pdb=" N CYS E 583 " --> pdb=" O VAL E 495 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N VAL E 495 " --> pdb=" O CYS E 583 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N ARG E 560 " --> pdb=" O LEU E 489 " (cutoff:3.500A) removed outlier: 10.392A pdb=" N ASP E 491 " --> pdb=" O SER E 558 " (cutoff:3.500A) removed outlier: 9.331A pdb=" N SER E 558 " --> pdb=" O ASP E 491 " (cutoff:3.500A) removed outlier: 9.584A pdb=" N LYS E 493 " --> pdb=" O PRO E 556 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N VAL E 495 " --> pdb=" O PHE E 554 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N PHE E 554 " --> pdb=" O VAL E 495 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N GLY E 497 " --> pdb=" O ARG E 552 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ARG E 552 " --> pdb=" O GLY E 497 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ILE E 499 " --> pdb=" O GLU E 550 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N GLU E 550 " --> pdb=" O ILE E 499 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 32 through 34 removed outlier: 6.768A pdb=" N LYS C 460 " --> pdb=" O LEU C 477 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N GLU C 479 " --> pdb=" O VAL C 458 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N VAL C 458 " --> pdb=" O GLU C 479 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N THR C 457 " --> pdb=" O THR C 453 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLN C 433 " --> pdb=" O GLY C 452 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 46 through 48 Processing sheet with id=AB1, first strand: chain 'C' and resid 60 through 63 Processing sheet with id=AB2, first strand: chain 'C' and resid 116 through 123 removed outlier: 6.779A pdb=" N CYS C 132 " --> pdb=" O LYS C 119 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LEU C 121 " --> pdb=" O TYR C 130 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N TYR C 130 " --> pdb=" O LEU C 121 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N ALA C 123 " --> pdb=" O HIS C 128 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N HIS C 128 " --> pdb=" O ALA C 123 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 116 through 123 removed outlier: 6.779A pdb=" N CYS C 132 " --> pdb=" O LYS C 119 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LEU C 121 " --> pdb=" O TYR C 130 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N TYR C 130 " --> pdb=" O LEU C 121 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N ALA C 123 " --> pdb=" O HIS C 128 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N HIS C 128 " --> pdb=" O ALA C 123 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 178 through 182 Processing sheet with id=AB5, first strand: chain 'C' and resid 225 through 232 removed outlier: 3.644A pdb=" N ARG C 248 " --> pdb=" O ARG C 225 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N PHE C 246 " --> pdb=" O ILE C 227 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ALA C 229 " --> pdb=" O TYR C 244 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N TYR C 244 " --> pdb=" O ALA C 229 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N LEU C 231 " --> pdb=" O LYS C 242 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N LYS C 242 " --> pdb=" O LEU C 231 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 294 through 296 Processing sheet with id=AB7, first strand: chain 'C' and resid 307 through 314 removed outlier: 5.808A pdb=" N LEU C 308 " --> pdb=" O THR C 329 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N THR C 329 " --> pdb=" O LEU C 308 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ASP C 310 " --> pdb=" O VAL C 327 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N MET C 422 " --> pdb=" O VAL C 340 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 535 through 537 Processing sheet with id=AB9, first strand: chain 'C' and resid 593 through 595 removed outlier: 5.258A pdb=" N UNK C 666 " --> pdb=" O UNK C 658 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N UNK C 658 " --> pdb=" O UNK C 666 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N UNK C 668 " --> pdb=" O UNK C 656 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N UNK C 656 " --> pdb=" O UNK C 668 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 602 through 604 Processing sheet with id=AC2, first strand: chain 'F' and resid 29 through 32 removed outlier: 5.944A pdb=" N ASP F 91 " --> pdb=" O LEU F 99 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N LEU F 99 " --> pdb=" O ASP F 91 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 37 through 40 Processing sheet with id=AC4, first strand: chain 'F' and resid 148 through 151 removed outlier: 6.677A pdb=" N ILE F 213 " --> pdb=" O ILE F 224 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 155 through 159 removed outlier: 6.915A pdb=" N GLY F 257 " --> pdb=" O PHE F 192 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N PHE F 192 " --> pdb=" O GLY F 257 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N SER F 259 " --> pdb=" O GLU F 190 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 277 through 278 removed outlier: 7.056A pdb=" N CYS F 424 " --> pdb=" O VAL F 336 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N VAL F 336 " --> pdb=" O CYS F 424 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N ARG F 402 " --> pdb=" O LEU F 330 " (cutoff:3.500A) removed outlier: 9.785A pdb=" N LEU F 332 " --> pdb=" O ILE F 400 " (cutoff:3.500A) removed outlier: 8.693A pdb=" N ILE F 400 " --> pdb=" O LEU F 332 " (cutoff:3.500A) removed outlier: 9.513A pdb=" N ARG F 334 " --> pdb=" O PRO F 398 " (cutoff:3.500A) removed outlier: 10.643A pdb=" N VAL F 336 " --> pdb=" O SER F 396 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N SER F 396 " --> pdb=" O VAL F 336 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ALA F 338 " --> pdb=" O VAL F 394 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N VAL F 394 " --> pdb=" O ALA F 338 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N GLY F 340 " --> pdb=" O LEU F 392 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N LEU F 392 " --> pdb=" O GLY F 340 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N THR F 357 " --> pdb=" O VAL F 409 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N TRP F 411 " --> pdb=" O VAL F 355 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N VAL F 355 " --> pdb=" O TRP F 411 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 433 through 434 removed outlier: 7.088A pdb=" N CYS F 583 " --> pdb=" O VAL F 495 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N VAL F 495 " --> pdb=" O CYS F 583 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 433 through 434 removed outlier: 7.088A pdb=" N CYS F 583 " --> pdb=" O VAL F 495 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N VAL F 495 " --> pdb=" O CYS F 583 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N ARG F 560 " --> pdb=" O LEU F 489 " (cutoff:3.500A) removed outlier: 10.392A pdb=" N ASP F 491 " --> pdb=" O SER F 558 " (cutoff:3.500A) removed outlier: 9.330A pdb=" N SER F 558 " --> pdb=" O ASP F 491 " (cutoff:3.500A) removed outlier: 9.583A pdb=" N LYS F 493 " --> pdb=" O PRO F 556 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N VAL F 495 " --> pdb=" O PHE F 554 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N PHE F 554 " --> pdb=" O VAL F 495 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N GLY F 497 " --> pdb=" O ARG F 552 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ARG F 552 " --> pdb=" O GLY F 497 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ILE F 499 " --> pdb=" O GLU F 550 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N GLU F 550 " --> pdb=" O ILE F 499 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 32 through 34 removed outlier: 6.768A pdb=" N LYS D 460 " --> pdb=" O LEU D 477 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N GLU D 479 " --> pdb=" O VAL D 458 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N VAL D 458 " --> pdb=" O GLU D 479 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N THR D 457 " --> pdb=" O THR D 453 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLN D 433 " --> pdb=" O GLY D 452 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 46 through 48 Processing sheet with id=AD2, first strand: chain 'D' and resid 60 through 63 Processing sheet with id=AD3, first strand: chain 'D' and resid 116 through 123 removed outlier: 6.779A pdb=" N CYS D 132 " --> pdb=" O LYS D 119 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LEU D 121 " --> pdb=" O TYR D 130 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N TYR D 130 " --> pdb=" O LEU D 121 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N ALA D 123 " --> pdb=" O HIS D 128 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N HIS D 128 " --> pdb=" O ALA D 123 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 116 through 123 removed outlier: 6.779A pdb=" N CYS D 132 " --> pdb=" O LYS D 119 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LEU D 121 " --> pdb=" O TYR D 130 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N TYR D 130 " --> pdb=" O LEU D 121 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N ALA D 123 " --> pdb=" O HIS D 128 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N HIS D 128 " --> pdb=" O ALA D 123 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 178 through 182 Processing sheet with id=AD6, first strand: chain 'D' and resid 225 through 232 removed outlier: 3.644A pdb=" N ARG D 248 " --> pdb=" O ARG D 225 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N PHE D 246 " --> pdb=" O ILE D 227 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ALA D 229 " --> pdb=" O TYR D 244 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N TYR D 244 " --> pdb=" O ALA D 229 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N LEU D 231 " --> pdb=" O LYS D 242 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N LYS D 242 " --> pdb=" O LEU D 231 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 294 through 296 Processing sheet with id=AD8, first strand: chain 'D' and resid 307 through 314 removed outlier: 5.809A pdb=" N LEU D 308 " --> pdb=" O THR D 329 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N THR D 329 " --> pdb=" O LEU D 308 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ASP D 310 " --> pdb=" O VAL D 327 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N MET D 422 " --> pdb=" O VAL D 340 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 535 through 537 Processing sheet with id=AE1, first strand: chain 'D' and resid 593 through 595 removed outlier: 5.260A pdb=" N UNK D 666 " --> pdb=" O UNK D 658 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N UNK D 658 " --> pdb=" O UNK D 666 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N UNK D 668 " --> pdb=" O UNK D 656 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N UNK D 656 " --> pdb=" O UNK D 668 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 602 through 604 Processing sheet with id=AE3, first strand: chain 'A' and resid 41 through 43 Processing sheet with id=AE4, first strand: chain 'A' and resid 50 through 55 removed outlier: 3.570A pdb=" N VAL A 81 " --> pdb=" O LYS A 72 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'A' and resid 88 through 90 Processing sheet with id=AE6, first strand: chain 'A' and resid 114 through 120 removed outlier: 3.558A pdb=" N MET A 116 " --> pdb=" O CYS A 129 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG A 125 " --> pdb=" O ASP A 120 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY A 149 " --> pdb=" O LEU A 139 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'A' and resid 168 through 173 removed outlier: 3.718A pdb=" N ILE A 198 " --> pdb=" O ILE A 226 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'A' and resid 242 through 249 removed outlier: 6.759A pdb=" N LEU A 256 " --> pdb=" O VAL A 244 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N GLY A 246 " --> pdb=" O TYR A 254 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N TYR A 254 " --> pdb=" O GLY A 246 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N SER A 248 " --> pdb=" O PHE A 252 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N PHE A 252 " --> pdb=" O SER A 248 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N VAL A 274 " --> pdb=" O GLU A 261 " (cutoff:3.500A) removed outlier: 14.206A pdb=" N TYR A 275 " --> pdb=" O CYS A 299 " (cutoff:3.500A) removed outlier: 10.724A pdb=" N CYS A 299 " --> pdb=" O TYR A 275 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N SER A 277 " --> pdb=" O ILE A 297 " (cutoff:3.500A) removed outlier: 8.853A pdb=" N VAL A 418 " --> pdb=" O GLU A 294 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'A' and resid 412 through 413 removed outlier: 19.702A pdb=" N VAL A 293 " --> pdb=" O ALA A 312 " (cutoff:3.500A) removed outlier: 17.152A pdb=" N ALA A 312 " --> pdb=" O VAL A 293 " (cutoff:3.500A) removed outlier: 17.418A pdb=" N VAL A 295 " --> pdb=" O GLN A 310 " (cutoff:3.500A) removed outlier: 13.354A pdb=" N GLN A 310 " --> pdb=" O VAL A 295 " (cutoff:3.500A) removed outlier: 10.069A pdb=" N ILE A 297 " --> pdb=" O LEU A 308 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N LEU A 308 " --> pdb=" O ILE A 297 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N VAL A 337 " --> pdb=" O GLN A 310 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ALA A 312 " --> pdb=" O PHE A 335 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N PHE A 335 " --> pdb=" O ALA A 312 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N LEU A 314 " --> pdb=" O LEU A 333 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LEU A 333 " --> pdb=" O LEU A 314 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N SER A 352 " --> pdb=" O THR A 425 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N THR A 425 " --> pdb=" O SER A 352 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N LEU A 354 " --> pdb=" O VAL A 423 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'A' and resid 434 through 435 removed outlier: 6.305A pdb=" N LEU A 454 " --> pdb=" O THR A 471 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N THR A 471 " --> pdb=" O LEU A 454 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N LYS A 456 " --> pdb=" O TYR A 469 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'A' and resid 527 through 529 Processing sheet with id=AF3, first strand: chain 'A' and resid 559 through 562 Processing sheet with id=AF4, first strand: chain 'A' and resid 566 through 568 removed outlier: 6.329A pdb=" N THR A 644 " --> pdb=" O SER A 638 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N SER A 638 " --> pdb=" O THR A 644 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA A 646 " --> pdb=" O LEU A 636 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL A 590 " --> pdb=" O GLY A 602 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N ASP A 601 " --> pdb=" O TYR A 612 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N TYR A 612 " --> pdb=" O ASP A 601 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'A' and resid 679 through 681 Processing sheet with id=AF6, first strand: chain 'A' and resid 710 through 712 Processing sheet with id=AF7, first strand: chain 'A' and resid 710 through 712 Processing sheet with id=AF8, first strand: chain 'A' and resid 715 through 722 removed outlier: 5.658A pdb=" N VAL A 715 " --> pdb=" O SER A 765 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N SER A 765 " --> pdb=" O VAL A 715 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N LYS A 717 " --> pdb=" O ASN A 763 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ASN A 763 " --> pdb=" O LYS A 717 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'A' and resid 824 through 825 removed outlier: 3.779A pdb=" N GLN A 830 " --> pdb=" O CYS A 825 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'A' and resid 858 through 859 removed outlier: 5.615A pdb=" N VAL A 929 " --> pdb=" O SER A 944 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL A 893 " --> pdb=" O CYS A 900 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'A' and resid 954 through 957 removed outlier: 7.075A pdb=" N THR A 974 " --> pdb=" O ALA A 956 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ASN A1006 " --> pdb=" O PHE A 995 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N PHE A 995 " --> pdb=" O ASN A1006 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'A' and resid 962 through 963 Processing sheet with id=AG4, first strand: chain 'A' and resid 987 through 988 Processing sheet with id=AG5, first strand: chain 'A' and resid 1040 through 1044 removed outlier: 5.282A pdb=" N ILE A1041 " --> pdb=" O THR A1062 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N THR A1062 " --> pdb=" O ILE A1041 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N ILE A1084 " --> pdb=" O GLN A1096 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLU A1116 " --> pdb=" O LYS A1075 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'A' and resid 1048 through 1050 removed outlier: 6.020A pdb=" N SER A1049 " --> pdb=" O TYR A1138 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG6 Processing sheet with id=AG7, first strand: chain 'A' and resid 1142 through 1143 Processing sheet with id=AG8, first strand: chain 'A' and resid 1180 through 1183 Processing sheet with id=AG9, first strand: chain 'B' and resid 41 through 43 Processing sheet with id=AH1, first strand: chain 'B' and resid 50 through 55 removed outlier: 3.571A pdb=" N VAL B 81 " --> pdb=" O LYS B 72 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'B' and resid 88 through 90 Processing sheet with id=AH3, first strand: chain 'B' and resid 114 through 120 removed outlier: 3.557A pdb=" N MET B 116 " --> pdb=" O CYS B 129 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG B 125 " --> pdb=" O ASP B 120 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY B 149 " --> pdb=" O LEU B 139 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'B' and resid 168 through 173 removed outlier: 3.718A pdb=" N ILE B 198 " --> pdb=" O ILE B 226 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'B' and resid 242 through 249 removed outlier: 6.759A pdb=" N LEU B 256 " --> pdb=" O VAL B 244 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N GLY B 246 " --> pdb=" O TYR B 254 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N TYR B 254 " --> pdb=" O GLY B 246 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N SER B 248 " --> pdb=" O PHE B 252 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N PHE B 252 " --> pdb=" O SER B 248 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N VAL B 274 " --> pdb=" O GLU B 261 " (cutoff:3.500A) removed outlier: 14.206A pdb=" N TYR B 275 " --> pdb=" O CYS B 299 " (cutoff:3.500A) removed outlier: 10.723A pdb=" N CYS B 299 " --> pdb=" O TYR B 275 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N SER B 277 " --> pdb=" O ILE B 297 " (cutoff:3.500A) removed outlier: 8.853A pdb=" N VAL B 418 " --> pdb=" O GLU B 294 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'B' and resid 412 through 413 removed outlier: 19.702A pdb=" N VAL B 293 " --> pdb=" O ALA B 312 " (cutoff:3.500A) removed outlier: 17.152A pdb=" N ALA B 312 " --> pdb=" O VAL B 293 " (cutoff:3.500A) removed outlier: 17.418A pdb=" N VAL B 295 " --> pdb=" O GLN B 310 " (cutoff:3.500A) removed outlier: 13.354A pdb=" N GLN B 310 " --> pdb=" O VAL B 295 " (cutoff:3.500A) removed outlier: 10.069A pdb=" N ILE B 297 " --> pdb=" O LEU B 308 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N LEU B 308 " --> pdb=" O ILE B 297 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N VAL B 337 " --> pdb=" O GLN B 310 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ALA B 312 " --> pdb=" O PHE B 335 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N PHE B 335 " --> pdb=" O ALA B 312 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N LEU B 314 " --> pdb=" O LEU B 333 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N LEU B 333 " --> pdb=" O LEU B 314 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N SER B 352 " --> pdb=" O THR B 425 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N THR B 425 " --> pdb=" O SER B 352 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N LEU B 354 " --> pdb=" O VAL B 423 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'B' and resid 434 through 435 removed outlier: 6.305A pdb=" N LEU B 454 " --> pdb=" O THR B 471 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N THR B 471 " --> pdb=" O LEU B 454 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N LYS B 456 " --> pdb=" O TYR B 469 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'B' and resid 527 through 529 Processing sheet with id=AH9, first strand: chain 'B' and resid 559 through 562 Processing sheet with id=AI1, first strand: chain 'B' and resid 566 through 568 removed outlier: 6.329A pdb=" N THR B 644 " --> pdb=" O SER B 638 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N SER B 638 " --> pdb=" O THR B 644 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA B 646 " --> pdb=" O LEU B 636 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL B 590 " --> pdb=" O GLY B 602 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N ASP B 601 " --> pdb=" O TYR B 612 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N TYR B 612 " --> pdb=" O ASP B 601 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'B' and resid 679 through 681 Processing sheet with id=AI3, first strand: chain 'B' and resid 710 through 712 Processing sheet with id=AI4, first strand: chain 'B' and resid 710 through 712 Processing sheet with id=AI5, first strand: chain 'B' and resid 715 through 722 removed outlier: 5.657A pdb=" N VAL B 715 " --> pdb=" O SER B 765 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N SER B 765 " --> pdb=" O VAL B 715 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N LYS B 717 " --> pdb=" O ASN B 763 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ASN B 763 " --> pdb=" O LYS B 717 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'B' and resid 824 through 825 removed outlier: 3.779A pdb=" N GLN B 830 " --> pdb=" O CYS B 825 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'B' and resid 858 through 859 removed outlier: 5.615A pdb=" N VAL B 929 " --> pdb=" O SER B 944 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL B 893 " --> pdb=" O CYS B 900 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'B' and resid 954 through 957 removed outlier: 7.075A pdb=" N THR B 974 " --> pdb=" O ALA B 956 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ASN B1006 " --> pdb=" O PHE B 995 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N PHE B 995 " --> pdb=" O ASN B1006 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'B' and resid 962 through 963 Processing sheet with id=AJ1, first strand: chain 'B' and resid 987 through 988 Processing sheet with id=AJ2, first strand: chain 'B' and resid 1040 through 1044 removed outlier: 5.282A pdb=" N ILE B1041 " --> pdb=" O THR B1062 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N THR B1062 " --> pdb=" O ILE B1041 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N ILE B1084 " --> pdb=" O GLN B1096 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLU B1116 " --> pdb=" O LYS B1075 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'B' and resid 1048 through 1050 removed outlier: 6.020A pdb=" N SER B1049 " --> pdb=" O TYR B1138 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ3 Processing sheet with id=AJ4, first strand: chain 'B' and resid 1142 through 1143 Processing sheet with id=AJ5, first strand: chain 'B' and resid 1180 through 1183 1088 hydrogen bonds defined for protein. 2760 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: 19.68 Time building geometry restraints manager: 13.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 10292 1.35 - 1.47: 7588 1.47 - 1.59: 13410 1.59 - 1.71: 0 1.71 - 1.83: 262 Bond restraints: 31552 Sorted by residual: bond pdb=" N ALA A 896 " pdb=" CA ALA A 896 " ideal model delta sigma weight residual 1.458 1.483 -0.025 1.23e-02 6.61e+03 4.06e+00 bond pdb=" N ALA B 896 " pdb=" CA ALA B 896 " ideal model delta sigma weight residual 1.458 1.483 -0.025 1.23e-02 6.61e+03 4.06e+00 bond pdb=" C HIS D 406 " pdb=" N PRO D 407 " ideal model delta sigma weight residual 1.331 1.316 0.015 7.90e-03 1.60e+04 3.75e+00 bond pdb=" N ALA A1025 " pdb=" CA ALA A1025 " ideal model delta sigma weight residual 1.457 1.479 -0.022 1.17e-02 7.31e+03 3.53e+00 bond pdb=" C SER D 188 " pdb=" N GLY D 189 " ideal model delta sigma weight residual 1.332 1.323 0.009 5.00e-03 4.00e+04 3.50e+00 ... (remaining 31547 not shown) Histogram of bond angle deviations from ideal: 99.92 - 106.74: 1087 106.74 - 113.55: 17478 113.55 - 120.37: 10683 120.37 - 127.19: 13456 127.19 - 134.01: 350 Bond angle restraints: 43054 Sorted by residual: angle pdb=" N PRO C 465 " pdb=" CA PRO C 465 " pdb=" CB PRO C 465 " ideal model delta sigma weight residual 103.00 110.41 -7.41 1.10e+00 8.26e-01 4.54e+01 angle pdb=" N PRO D 465 " pdb=" CA PRO D 465 " pdb=" CB PRO D 465 " ideal model delta sigma weight residual 103.00 110.40 -7.40 1.10e+00 8.26e-01 4.53e+01 angle pdb=" N GLY E 101 " pdb=" CA GLY E 101 " pdb=" C GLY E 101 " ideal model delta sigma weight residual 111.37 116.93 -5.56 1.29e+00 6.01e-01 1.86e+01 angle pdb=" N GLY F 101 " pdb=" CA GLY F 101 " pdb=" C GLY F 101 " ideal model delta sigma weight residual 111.37 116.91 -5.54 1.29e+00 6.01e-01 1.84e+01 angle pdb=" N VAL A 895 " pdb=" CA VAL A 895 " pdb=" C VAL A 895 " ideal model delta sigma weight residual 109.58 104.98 4.60 1.29e+00 6.01e-01 1.27e+01 ... (remaining 43049 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 17354 18.00 - 36.00: 1172 36.00 - 54.01: 216 54.01 - 72.01: 54 72.01 - 90.01: 28 Dihedral angle restraints: 18824 sinusoidal: 6276 harmonic: 12548 Sorted by residual: dihedral pdb=" CB CYS A 825 " pdb=" SG CYS A 825 " pdb=" SG CYS A 837 " pdb=" CB CYS A 837 " ideal model delta sinusoidal sigma weight residual -86.00 -176.01 90.01 1 1.00e+01 1.00e-02 9.60e+01 dihedral pdb=" CB CYS B 825 " pdb=" SG CYS B 825 " pdb=" SG CYS B 837 " pdb=" CB CYS B 837 " ideal model delta sinusoidal sigma weight residual -86.00 -176.00 90.00 1 1.00e+01 1.00e-02 9.60e+01 dihedral pdb=" CB CYS B 993 " pdb=" SG CYS B 993 " pdb=" SG CYS B1005 " pdb=" CB CYS B1005 " ideal model delta sinusoidal sigma weight residual 93.00 177.80 -84.80 1 1.00e+01 1.00e-02 8.73e+01 ... (remaining 18821 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 3806 0.047 - 0.095: 809 0.095 - 0.142: 332 0.142 - 0.189: 19 0.189 - 0.237: 4 Chirality restraints: 4970 Sorted by residual: chirality pdb=" CA PRO C 465 " pdb=" N PRO C 465 " pdb=" C PRO C 465 " pdb=" CB PRO C 465 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CA PRO D 465 " pdb=" N PRO D 465 " pdb=" C PRO D 465 " pdb=" CB PRO D 465 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CA VAL A 783 " pdb=" N VAL A 783 " pdb=" C VAL A 783 " pdb=" CB VAL A 783 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 9.21e-01 ... (remaining 4967 not shown) Planarity restraints: 5652 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP C 318 " 0.028 5.00e-02 4.00e+02 4.21e-02 2.84e+00 pdb=" N PRO C 319 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO C 319 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 319 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP D 318 " 0.028 5.00e-02 4.00e+02 4.21e-02 2.83e+00 pdb=" N PRO D 319 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO D 319 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO D 319 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 295 " 0.027 5.00e-02 4.00e+02 4.01e-02 2.58e+00 pdb=" N PRO B 296 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO B 296 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 296 " 0.022 5.00e-02 4.00e+02 ... (remaining 5649 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.62: 495 2.62 - 3.19: 28224 3.19 - 3.76: 48924 3.76 - 4.33: 66806 4.33 - 4.90: 108093 Nonbonded interactions: 252542 Sorted by model distance: nonbonded pdb=" O ILE F 253 " pdb="CA CA F 602 " model vdw 2.056 2.510 nonbonded pdb=" O ILE E 253 " pdb="CA CA E 602 " model vdw 2.056 2.510 nonbonded pdb=" OG1 THR B 41 " pdb=" OE1 GLN B 500 " model vdw 2.160 2.440 nonbonded pdb=" OG1 THR A 41 " pdb=" OE1 GLN A 500 " model vdw 2.160 2.440 nonbonded pdb=" OH TYR A 768 " pdb=" O ILE A 773 " model vdw 2.173 2.440 ... (remaining 252537 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' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 4 9.91 5 S 202 5.16 5 C 19538 2.51 5 N 5316 2.21 5 O 5838 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.040 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: 0.000 Extract box with map and model: 8.670 Check model and map are aligned: 0.440 Convert atoms to be neutral: 0.240 Process input model: 87.990 Find NCS groups from input model: 1.620 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Set scattering table: 0.020 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 104.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 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 : 0.004 0.043 31552 Z= 0.281 Angle : 0.711 8.913 43054 Z= 0.421 Chirality : 0.046 0.237 4970 Planarity : 0.004 0.042 5652 Dihedral : 12.838 89.852 10522 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 17.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer Outliers : 1.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.49 (0.12), residues: 4132 helix: -2.20 (0.25), residues: 292 sheet: -1.13 (0.13), residues: 1368 loop : -1.94 (0.11), residues: 2472 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8264 Ramachandran restraints generated. 4132 Oldfield, 0 Emsley, 4132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8264 Ramachandran restraints generated. 4132 Oldfield, 0 Emsley, 4132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 3732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 207 time to evaluate : 3.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 8 residues processed: 237 average time/residue: 0.4598 time to fit residues: 171.3343 Evaluate side-chains 126 residues out of total 3732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 118 time to evaluate : 3.673 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.2570 time to fit residues: 8.9061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 364 optimal weight: 9.9990 chunk 327 optimal weight: 9.9990 chunk 181 optimal weight: 6.9990 chunk 111 optimal weight: 9.9990 chunk 220 optimal weight: 9.9990 chunk 174 optimal weight: 6.9990 chunk 338 optimal weight: 6.9990 chunk 131 optimal weight: 50.0000 chunk 205 optimal weight: 40.0000 chunk 252 optimal weight: 10.0000 chunk 392 optimal weight: 8.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 59 GLN E 130 HIS E 149 GLN E 150 ASN E 223 HIS ** C 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 HIS C 209 HIS ** C 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 256 HIS C 281 ASN C 309 GLN ** C 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 411 ASN C 433 GLN C 445 GLN C 566 HIS F 59 GLN F 130 HIS F 149 GLN F 150 ASN F 223 HIS ** D 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 76 HIS D 209 HIS ** D 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 309 GLN ** D 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 411 ASN D 433 GLN D 445 GLN D 566 HIS A 51 ASN A 114 ASN A 124 ASN A 206 ASN A 218 HIS A 273 GLN ** A 630 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 977 ASN A 979 ASN B 51 ASN B 114 ASN B 124 ASN B 218 HIS B 273 GLN B 371 GLN ** B 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 977 ASN B 979 ASN Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.112 31552 Z= 0.491 Angle : 0.709 8.311 43054 Z= 0.370 Chirality : 0.048 0.249 4970 Planarity : 0.005 0.048 5652 Dihedral : 5.443 27.120 4584 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 18.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer Outliers : 2.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.06 (0.12), residues: 4132 helix: -1.54 (0.29), residues: 282 sheet: -0.92 (0.14), residues: 1356 loop : -1.63 (0.12), residues: 2494 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8264 Ramachandran restraints generated. 4132 Oldfield, 0 Emsley, 4132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8264 Ramachandran restraints generated. 4132 Oldfield, 0 Emsley, 4132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 3732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 117 time to evaluate : 3.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 75 outliers final: 41 residues processed: 184 average time/residue: 0.3501 time to fit residues: 113.5592 Evaluate side-chains 156 residues out of total 3732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 115 time to evaluate : 3.557 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 0 residues processed: 41 average time/residue: 0.2612 time to fit residues: 25.1818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 218 optimal weight: 7.9990 chunk 121 optimal weight: 9.9990 chunk 326 optimal weight: 10.0000 chunk 267 optimal weight: 8.9990 chunk 108 optimal weight: 5.9990 chunk 393 optimal weight: 4.9990 chunk 424 optimal weight: 5.9990 chunk 350 optimal weight: 4.9990 chunk 389 optimal weight: 20.0000 chunk 133 optimal weight: 50.0000 chunk 315 optimal weight: 40.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 44 ASN ** C 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 358 HIS D 44 ASN ** D 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 358 HIS A 371 GLN ** A 630 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 725 ASN ** A 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 979 ASN ** B 630 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 725 ASN ** B 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 979 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.089 31552 Z= 0.370 Angle : 0.629 8.790 43054 Z= 0.327 Chirality : 0.046 0.194 4970 Planarity : 0.005 0.044 5652 Dihedral : 5.258 24.365 4584 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 17.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer Outliers : 2.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.13), residues: 4132 helix: -1.44 (0.29), residues: 294 sheet: -0.88 (0.14), residues: 1370 loop : -1.41 (0.12), residues: 2468 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8264 Ramachandran restraints generated. 4132 Oldfield, 0 Emsley, 4132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8264 Ramachandran restraints generated. 4132 Oldfield, 0 Emsley, 4132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 3732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 117 time to evaluate : 3.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 82 outliers final: 24 residues processed: 193 average time/residue: 0.3608 time to fit residues: 125.0244 Evaluate side-chains 134 residues out of total 3732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 110 time to evaluate : 4.121 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.3272 time to fit residues: 20.9572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 388 optimal weight: 20.0000 chunk 295 optimal weight: 30.0000 chunk 203 optimal weight: 50.0000 chunk 43 optimal weight: 40.0000 chunk 187 optimal weight: 4.9990 chunk 263 optimal weight: 0.5980 chunk 394 optimal weight: 20.0000 chunk 417 optimal weight: 20.0000 chunk 206 optimal weight: 8.9990 chunk 373 optimal weight: 0.0470 chunk 112 optimal weight: 20.0000 overall best weight: 6.9286 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 630 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 979 ASN ** B 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 630 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.104 31552 Z= 0.433 Angle : 0.667 10.477 43054 Z= 0.345 Chirality : 0.047 0.182 4970 Planarity : 0.005 0.055 5652 Dihedral : 5.436 27.447 4584 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 19.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer Outliers : 4.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.13), residues: 4132 helix: -1.32 (0.29), residues: 282 sheet: -0.89 (0.14), residues: 1386 loop : -1.35 (0.12), residues: 2464 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8264 Ramachandran restraints generated. 4132 Oldfield, 0 Emsley, 4132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8264 Ramachandran restraints generated. 4132 Oldfield, 0 Emsley, 4132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 3732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 107 time to evaluate : 3.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 122 outliers final: 57 residues processed: 222 average time/residue: 0.4072 time to fit residues: 159.0394 Evaluate side-chains 163 residues out of total 3732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 106 time to evaluate : 3.621 Switching outliers to nearest non-outliers outliers start: 57 outliers final: 0 residues processed: 57 average time/residue: 0.3160 time to fit residues: 39.0042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 347 optimal weight: 10.0000 chunk 237 optimal weight: 3.9990 chunk 6 optimal weight: 5.9990 chunk 310 optimal weight: 4.9990 chunk 172 optimal weight: 3.9990 chunk 356 optimal weight: 9.9990 chunk 288 optimal weight: 20.0000 chunk 0 optimal weight: 30.0000 chunk 213 optimal weight: 4.9990 chunk 374 optimal weight: 10.0000 chunk 105 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 630 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 206 ASN ** B 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.2696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.066 31552 Z= 0.311 Angle : 0.606 10.051 43054 Z= 0.313 Chirality : 0.046 0.180 4970 Planarity : 0.004 0.050 5652 Dihedral : 5.213 27.556 4584 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 17.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer Outliers : 2.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.13), residues: 4132 helix: -0.84 (0.31), residues: 270 sheet: -0.79 (0.14), residues: 1360 loop : -1.22 (0.12), residues: 2502 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8264 Ramachandran restraints generated. 4132 Oldfield, 0 Emsley, 4132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8264 Ramachandran restraints generated. 4132 Oldfield, 0 Emsley, 4132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 3732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 112 time to evaluate : 3.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 62 outliers final: 22 residues processed: 166 average time/residue: 0.3676 time to fit residues: 107.9197 Evaluate side-chains 130 residues out of total 3732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 108 time to evaluate : 3.381 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.2871 time to fit residues: 15.7357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 140 optimal weight: 30.0000 chunk 376 optimal weight: 9.9990 chunk 82 optimal weight: 1.9990 chunk 245 optimal weight: 4.9990 chunk 103 optimal weight: 30.0000 chunk 417 optimal weight: 7.9990 chunk 346 optimal weight: 5.9990 chunk 193 optimal weight: 5.9990 chunk 34 optimal weight: 40.0000 chunk 138 optimal weight: 20.0000 chunk 219 optimal weight: 5.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 979 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.2913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.140 31552 Z= 0.330 Angle : 0.607 10.105 43054 Z= 0.314 Chirality : 0.046 0.180 4970 Planarity : 0.004 0.051 5652 Dihedral : 5.183 27.673 4584 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 17.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer Outliers : 2.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.13), residues: 4132 helix: -0.73 (0.31), residues: 270 sheet: -0.76 (0.14), residues: 1384 loop : -1.19 (0.12), residues: 2478 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8264 Ramachandran restraints generated. 4132 Oldfield, 0 Emsley, 4132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8264 Ramachandran restraints generated. 4132 Oldfield, 0 Emsley, 4132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 3732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 114 time to evaluate : 3.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 68 outliers final: 24 residues processed: 175 average time/residue: 0.3499 time to fit residues: 109.3184 Evaluate side-chains 132 residues out of total 3732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 108 time to evaluate : 3.673 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.2790 time to fit residues: 17.4983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 402 optimal weight: 50.0000 chunk 47 optimal weight: 0.0770 chunk 238 optimal weight: 1.9990 chunk 305 optimal weight: 6.9990 chunk 236 optimal weight: 20.0000 chunk 351 optimal weight: 2.9990 chunk 233 optimal weight: 8.9990 chunk 416 optimal weight: 8.9990 chunk 260 optimal weight: 1.9990 chunk 253 optimal weight: 8.9990 chunk 192 optimal weight: 5.9990 overall best weight: 2.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 566 ASN ** A 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.3032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.066 31552 Z= 0.215 Angle : 0.573 8.879 43054 Z= 0.295 Chirality : 0.045 0.167 4970 Planarity : 0.004 0.046 5652 Dihedral : 5.016 27.791 4584 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 15.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer Outliers : 1.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.13), residues: 4132 helix: -0.40 (0.32), residues: 270 sheet: -0.60 (0.14), residues: 1350 loop : -1.12 (0.12), residues: 2512 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8264 Ramachandran restraints generated. 4132 Oldfield, 0 Emsley, 4132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8264 Ramachandran restraints generated. 4132 Oldfield, 0 Emsley, 4132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 3732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 114 time to evaluate : 3.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 47 outliers final: 22 residues processed: 158 average time/residue: 0.3513 time to fit residues: 99.8926 Evaluate side-chains 130 residues out of total 3732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 108 time to evaluate : 3.436 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.2747 time to fit residues: 16.1639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 257 optimal weight: 20.0000 chunk 166 optimal weight: 3.9990 chunk 248 optimal weight: 20.0000 chunk 125 optimal weight: 7.9990 chunk 81 optimal weight: 9.9990 chunk 80 optimal weight: 4.9990 chunk 264 optimal weight: 8.9990 chunk 283 optimal weight: 0.8980 chunk 205 optimal weight: 50.0000 chunk 38 optimal weight: 40.0000 chunk 327 optimal weight: 10.0000 overall best weight: 5.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 892 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 979 ASN ** B 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.3204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.078 31552 Z= 0.343 Angle : 0.617 9.016 43054 Z= 0.317 Chirality : 0.046 0.196 4970 Planarity : 0.004 0.050 5652 Dihedral : 5.119 29.481 4584 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 17.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer Outliers : 1.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.13), residues: 4132 helix: -0.44 (0.32), residues: 270 sheet: -0.65 (0.14), residues: 1354 loop : -1.17 (0.12), residues: 2508 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8264 Ramachandran restraints generated. 4132 Oldfield, 0 Emsley, 4132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8264 Ramachandran restraints generated. 4132 Oldfield, 0 Emsley, 4132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 3732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 110 time to evaluate : 3.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 22 residues processed: 135 average time/residue: 0.3810 time to fit residues: 92.2511 Evaluate side-chains 132 residues out of total 3732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 110 time to evaluate : 3.858 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.3039 time to fit residues: 17.7771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 378 optimal weight: 9.9990 chunk 398 optimal weight: 50.0000 chunk 363 optimal weight: 10.0000 chunk 388 optimal weight: 8.9990 chunk 233 optimal weight: 10.0000 chunk 169 optimal weight: 4.9990 chunk 304 optimal weight: 2.9990 chunk 119 optimal weight: 9.9990 chunk 350 optimal weight: 4.9990 chunk 366 optimal weight: 10.0000 chunk 386 optimal weight: 5.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 892 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 892 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.3408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.078 31552 Z= 0.351 Angle : 0.622 9.244 43054 Z= 0.320 Chirality : 0.046 0.204 4970 Planarity : 0.004 0.049 5652 Dihedral : 5.177 31.085 4584 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 18.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer Outliers : 0.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.13), residues: 4132 helix: -0.48 (0.32), residues: 270 sheet: -0.74 (0.14), residues: 1366 loop : -1.16 (0.12), residues: 2496 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8264 Ramachandran restraints generated. 4132 Oldfield, 0 Emsley, 4132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8264 Ramachandran restraints generated. 4132 Oldfield, 0 Emsley, 4132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 3732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 114 time to evaluate : 3.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 4 residues processed: 125 average time/residue: 0.3763 time to fit residues: 84.0853 Evaluate side-chains 114 residues out of total 3732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 110 time to evaluate : 3.572 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2787 time to fit residues: 6.8474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 254 optimal weight: 1.9990 chunk 410 optimal weight: 5.9990 chunk 250 optimal weight: 7.9990 chunk 194 optimal weight: 2.9990 chunk 285 optimal weight: 50.0000 chunk 430 optimal weight: 1.9990 chunk 396 optimal weight: 0.9990 chunk 342 optimal weight: 1.9990 chunk 35 optimal weight: 50.0000 chunk 264 optimal weight: 5.9990 chunk 210 optimal weight: 10.0000 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 775 ASN ** A 892 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 892 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.3494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 31552 Z= 0.185 Angle : 0.568 9.128 43054 Z= 0.291 Chirality : 0.045 0.179 4970 Planarity : 0.004 0.049 5652 Dihedral : 4.868 30.387 4584 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 15.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer Outliers : 0.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.13), residues: 4132 helix: -0.16 (0.33), residues: 270 sheet: -0.56 (0.14), residues: 1338 loop : -1.07 (0.12), residues: 2524 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8264 Ramachandran restraints generated. 4132 Oldfield, 0 Emsley, 4132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8264 Ramachandran restraints generated. 4132 Oldfield, 0 Emsley, 4132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 3732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 113 time to evaluate : 3.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 7 residues processed: 121 average time/residue: 0.3800 time to fit residues: 82.9281 Evaluate side-chains 117 residues out of total 3732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 110 time to evaluate : 3.597 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2947 time to fit residues: 8.6939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 272 optimal weight: 3.9990 chunk 365 optimal weight: 10.0000 chunk 104 optimal weight: 5.9990 chunk 316 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 chunk 95 optimal weight: 5.9990 chunk 343 optimal weight: 0.8980 chunk 143 optimal weight: 50.0000 chunk 352 optimal weight: 10.0000 chunk 43 optimal weight: 0.4980 chunk 63 optimal weight: 7.9990 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 892 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 892 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.075478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.050946 restraints weight = 187824.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.052572 restraints weight = 98758.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.052210 restraints weight = 53908.026| |-----------------------------------------------------------------------------| r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.3585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 31552 Z= 0.214 Angle : 0.571 13.361 43054 Z= 0.291 Chirality : 0.045 0.175 4970 Planarity : 0.004 0.047 5652 Dihedral : 4.811 29.668 4584 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 15.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.13), residues: 4132 helix: -0.13 (0.33), residues: 270 sheet: -0.52 (0.14), residues: 1348 loop : -1.06 (0.12), residues: 2514 =============================================================================== Job complete usr+sys time: 4233.10 seconds wall clock time: 79 minutes 38.60 seconds (4778.60 seconds total)