Starting phenix.real_space_refine on Sat Feb 17 21:20:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i02_35092/02_2024/8i02_35092_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i02_35092/02_2024/8i02_35092.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i02_35092/02_2024/8i02_35092.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i02_35092/02_2024/8i02_35092.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i02_35092/02_2024/8i02_35092_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i02_35092/02_2024/8i02_35092_neut.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.102 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians K 2 8.98 5 Zn 6 6.06 5 S 103 5.16 5 C 12702 2.51 5 N 3377 2.21 5 O 3686 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "F ASP 118": "OD1" <-> "OD2" Residue "F GLU 133": "OE1" <-> "OE2" Residue "F PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 145": "OE1" <-> "OE2" Residue "F GLU 155": "OE1" <-> "OE2" Residue "F ASP 183": "OD1" <-> "OD2" Residue "F TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 218": "OE1" <-> "OE2" Residue "F TYR 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 372": "OE1" <-> "OE2" Residue "A ASP 38": "OD1" <-> "OD2" Residue "A TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 70": "OE1" <-> "OE2" Residue "A PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 144": "NH1" <-> "NH2" Residue "A PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 161": "OE1" <-> "OE2" Residue "A PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 168": "OD1" <-> "OD2" Residue "A PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 200": "OE1" <-> "OE2" Residue "A PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 243": "NH1" <-> "NH2" Residue "A PHE 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 270": "OD1" <-> "OD2" Residue "A TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 321": "OE1" <-> "OE2" Residue "A PHE 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 333": "OD1" <-> "OD2" Residue "A GLU 347": "OE1" <-> "OE2" Residue "A GLU 348": "OE1" <-> "OE2" Residue "A ASP 358": "OD1" <-> "OD2" Residue "A PHE 359": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 377": "OE1" <-> "OE2" Residue "A ARG 385": "NH1" <-> "NH2" Residue "A TYR 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 398": "OE1" <-> "OE2" Residue "A TYR 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 402": "OE1" <-> "OE2" Residue "A ARG 405": "NH1" <-> "NH2" Residue "A GLU 408": "OE1" <-> "OE2" Residue "A ARG 423": "NH1" <-> "NH2" Residue "A GLU 426": "OE1" <-> "OE2" Residue "A GLU 429": "OE1" <-> "OE2" Residue "A GLU 433": "OE1" <-> "OE2" Residue "A TYR 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 439": "OE1" <-> "OE2" Residue "A TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 470": "OE1" <-> "OE2" Residue "A GLU 486": "OE1" <-> "OE2" Residue "A GLU 490": "OE1" <-> "OE2" Residue "A GLU 506": "OE1" <-> "OE2" Residue "A TYR 520": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 521": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 537": "OE1" <-> "OE2" Residue "A ASP 539": "OD1" <-> "OD2" Residue "A ARG 552": "NH1" <-> "NH2" Residue "A GLU 558": "OE1" <-> "OE2" Residue "A GLU 566": "OE1" <-> "OE2" Residue "A TYR 574": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 592": "OE1" <-> "OE2" Residue "A PHE 603": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 606": "OE1" <-> "OE2" Residue "A PHE 610": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 714": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 723": "OE1" <-> "OE2" Residue "A GLU 742": "OE1" <-> "OE2" Residue "A TYR 746": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 750": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 752": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 761": "OE1" <-> "OE2" Residue "A TYR 764": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 765": "OE1" <-> "OE2" Residue "A GLU 770": "OE1" <-> "OE2" Residue "A ASP 794": "OD1" <-> "OD2" Residue "A ARG 795": "NH1" <-> "NH2" Residue "A TYR 809": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 825": "OD1" <-> "OD2" Residue "A PHE 829": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 830": "OE1" <-> "OE2" Residue "A TYR 832": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 835": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 886": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 887": "OD1" <-> "OD2" Residue "A ASP 888": "OD1" <-> "OD2" Residue "A PHE 889": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 894": "OE1" <-> "OE2" Residue "A GLU 896": "OE1" <-> "OE2" Residue "A PHE 906": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 961": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 971": "OE1" <-> "OE2" Residue "A GLU 973": "OE1" <-> "OE2" Residue "A ARG 974": "NH1" <-> "NH2" Residue "A GLU 992": "OE1" <-> "OE2" Residue "A ASP 1004": "OD1" <-> "OD2" Residue "A PHE 1006": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1010": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1015": "OE1" <-> "OE2" Residue "A ASP 1016": "OD1" <-> "OD2" Residue "A ASP 1028": "OD1" <-> "OD2" Residue "A ASP 1030": "OD1" <-> "OD2" Residue "A PHE 1031": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1033": "OD1" <-> "OD2" Residue "B TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 46": "OE1" <-> "OE2" Residue "B TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 96": "OD1" <-> "OD2" Residue "B PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 101": "OD1" <-> "OD2" Residue "B TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 105": "OE1" <-> "OE2" Residue "B PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 159": "OE1" <-> "OE2" Residue "B TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 173": "OD1" <-> "OD2" Residue "B GLU 182": "OE1" <-> "OE2" Residue "B TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 227": "OD1" <-> "OD2" Residue "B ASP 230": "OD1" <-> "OD2" Residue "B ASP 231": "OD1" <-> "OD2" Residue "B GLU 235": "OE1" <-> "OE2" Residue "B PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 283": "OD1" <-> "OD2" Residue "B PHE 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 312": "OE1" <-> "OE2" Residue "B GLU 319": "OE1" <-> "OE2" Residue "B GLU 323": "OE1" <-> "OE2" Residue "B TYR 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 348": "OE1" <-> "OE2" Residue "B TYR 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 362": "OE1" <-> "OE2" Residue "B PHE 372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 23": "OE1" <-> "OE2" Residue "C GLU 28": "OE1" <-> "OE2" Residue "C GLU 29": "OE1" <-> "OE2" Residue "C TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 61": "OE1" <-> "OE2" Residue "C TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 141": "OD1" <-> "OD2" Residue "C ASP 154": "OD1" <-> "OD2" Residue "C PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 161": "OE1" <-> "OE2" Residue "C GLU 164": "OE1" <-> "OE2" Residue "C TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 206": "OD1" <-> "OD2" Residue "C ASP 213": "OD1" <-> "OD2" Residue "C GLU 234": "OE1" <-> "OE2" Residue "C ASP 239": "OD1" <-> "OD2" Residue "C ASP 268": "OD1" <-> "OD2" Residue "C ASP 303": "OD1" <-> "OD2" Residue "C ASP 326": "OD1" <-> "OD2" Residue "C PHE 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 337": "OE1" <-> "OE2" Residue "C GLU 338": "OE1" <-> "OE2" Residue "C GLU 366": "OE1" <-> "OE2" Residue "C GLU 373": "OE1" <-> "OE2" Residue "C ASP 389": "OD1" <-> "OD2" Residue "C TYR 394": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 404": "OD1" <-> "OD2" Residue "D ASP 176": "OD1" <-> "OD2" Residue "D ASP 185": "OD1" <-> "OD2" Residue "D GLU 187": "OE1" <-> "OE2" Residue "D PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 213": "OE1" <-> "OE2" Residue "D GLU 222": "OE1" <-> "OE2" Residue "D PHE 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 229": "OE1" <-> "OE2" Residue "D TYR 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 252": "OE1" <-> "OE2" Residue "D TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 258": "OE1" <-> "OE2" Residue "D TYR 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 265": "OD1" <-> "OD2" Residue "D TYR 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 275": "OE1" <-> "OE2" Residue "D GLU 286": "OE1" <-> "OE2" Residue "D GLU 299": "OE1" <-> "OE2" Residue "D GLU 306": "OE1" <-> "OE2" Residue "D PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 317": "OD1" <-> "OD2" Residue "D GLU 323": "OE1" <-> "OE2" Residue "D TYR 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 176": "OD1" <-> "OD2" Residue "E PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 222": "OE1" <-> "OE2" Residue "E GLU 229": "OE1" <-> "OE2" Residue "E PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 289": "OD1" <-> "OD2" Residue "E ASP 294": "OD1" <-> "OD2" Residue "E GLU 299": "OE1" <-> "OE2" Residue "E GLU 306": "OE1" <-> "OE2" Residue "E TYR 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 318": "OE1" <-> "OE2" Residue "E GLU 323": "OE1" <-> "OE2" Residue "G TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 301": "OD1" <-> "OD2" Residue "G PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 376": "OE1" <-> "OE2" Residue "G TYR 431": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 521": "OE1" <-> "OE2" Residue "G GLU 543": "OE1" <-> "OE2" Residue "G PHE 550": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 576": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 585": "NH1" <-> "NH2" Residue "G PHE 599": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 19876 Number of models: 1 Model: "" Number of chains: 10 Chain: "F" Number of atoms: 1702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1702 Classifications: {'peptide': 235} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 19, 'TRANS': 215} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 169 Unresolved non-hydrogen angles: 212 Unresolved non-hydrogen dihedrals: 155 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 2, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 87 Chain: "A" Number of atoms: 7173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 864, 7173 Classifications: {'peptide': 864} Link IDs: {'PTRANS': 36, 'TRANS': 827} Chain breaks: 6 Chain: "B" Number of atoms: 2957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2957 Classifications: {'peptide': 369} Link IDs: {'PTRANS': 15, 'TRANS': 353} Chain: "C" Number of atoms: 3046 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 3046 Classifications: {'peptide': 380} Link IDs: {'PTRANS': 20, 'TRANS': 359} Chain breaks: 1 Chain: "D" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1378 Classifications: {'peptide': 165} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 157} Chain breaks: 1 Chain: "E" Number of atoms: 1337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1337 Classifications: {'peptide': 160} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 152} Chain breaks: 1 Chain: "G" Number of atoms: 2275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2275 Classifications: {'peptide': 284} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 22, 'TRANS': 261} Chain breaks: 3 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' K': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 171 SG CYS F 137 57.666 35.100 80.932 1.00 77.48 S ATOM 353 SG CYS F 160 56.585 38.764 77.543 1.00 79.66 S ATOM 60 SG CYS F 120 49.847 28.802 79.913 1.00 75.07 S ATOM 218 SG CYS F 143 45.468 30.262 78.727 1.00 76.69 S ATOM 17635 SG CYS G 266 80.671 67.521 131.409 1.00 58.13 S ATOM 17652 SG CYS G 269 77.934 69.167 129.364 1.00 51.87 S ATOM 17798 SG CYS G 289 76.676 68.440 132.695 1.00 51.11 S ATOM 18455 SG CYS G 409 58.407 95.813 97.741 1.00 15.88 S ATOM 18483 SG CYS G 412 57.406 99.479 97.015 1.00 14.69 S ATOM 18673 SG CYS G 436 56.697 98.367 100.584 1.00 17.31 S ATOM 18576 SG CYS G 425 61.214 84.100 100.203 1.00 16.98 S ATOM 18809 SG CYS G 453 57.664 85.341 99.638 1.00 18.08 S Time building chain proxies: 10.69, per 1000 atoms: 0.54 Number of scatterers: 19876 At special positions: 0 Unit cell: (108.7, 148.919, 191.312, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 6 29.99 K 2 19.00 S 103 16.00 O 3686 8.00 N 3377 7.00 C 12702 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.53 Conformation dependent library (CDL) restraints added in 3.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 501 " pdb="ZN ZN B 501 " - pdb=" ND1 HIS B 175 " pdb=" ZN F 501 " pdb="ZN ZN F 501 " - pdb=" SG CYS F 160 " pdb="ZN ZN F 501 " - pdb=" SG CYS F 137 " pdb=" ZN F 502 " pdb="ZN ZN F 502 " - pdb=" ND1 HIS F 140 " pdb="ZN ZN F 502 " - pdb=" SG CYS F 120 " pdb="ZN ZN F 502 " - pdb=" SG CYS F 143 " pdb=" ZN G 701 " pdb="ZN ZN G 701 " - pdb=" SG CYS G 266 " pdb="ZN ZN G 701 " - pdb=" SG CYS G 269 " pdb="ZN ZN G 701 " - pdb=" SG CYS G 289 " pdb="ZN ZN G 701 " - pdb=" ND1 HIS G 286 " pdb=" ZN G 702 " pdb="ZN ZN G 702 " - pdb=" SG CYS G 436 " pdb="ZN ZN G 702 " - pdb=" SG CYS G 412 " pdb="ZN ZN G 702 " - pdb=" SG CYS G 409 " pdb=" ZN G 703 " pdb="ZN ZN G 703 " - pdb=" SG CYS G 453 " pdb="ZN ZN G 703 " - pdb=" SG CYS G 425 " pdb="ZN ZN G 703 " - pdb=" NE2 HIS G 456 " Number of angles added : 3 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4704 Finding SS restraints... Secondary structure from input PDB file: 89 helices and 20 sheets defined 43.1% alpha, 7.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.09 Creating SS restraints... Processing helix chain 'F' and resid 149 through 153 removed outlier: 3.888A pdb=" N ASN F 152 " --> pdb=" O THR F 149 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE F 153 " --> pdb=" O PRO F 150 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 149 through 153' Processing helix chain 'F' and resid 160 through 165 Processing helix chain 'F' and resid 178 through 188 removed outlier: 3.550A pdb=" N GLN F 188 " --> pdb=" O TRP F 184 " (cutoff:3.500A) Processing helix chain 'F' and resid 196 through 201 removed outlier: 3.612A pdb=" N HIS F 201 " --> pdb=" O ASP F 197 " (cutoff:3.500A) Processing helix chain 'F' and resid 268 through 272 Processing helix chain 'F' and resid 343 through 371 removed outlier: 3.564A pdb=" N ASN F 364 " --> pdb=" O LYS F 360 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU F 371 " --> pdb=" O LYS F 367 " (cutoff:3.500A) Processing helix chain 'F' and resid 390 through 403 removed outlier: 3.692A pdb=" N ALA F 394 " --> pdb=" O ASN F 390 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ARG F 396 " --> pdb=" O PRO F 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 50 Processing helix chain 'A' and resid 53 through 69 removed outlier: 3.872A pdb=" N TYR A 57 " --> pdb=" O ARG A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 85 Processing helix chain 'A' and resid 88 through 96 Processing helix chain 'A' and resid 137 through 156 removed outlier: 3.781A pdb=" N THR A 141 " --> pdb=" O ASP A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 176 removed outlier: 3.797A pdb=" N SER A 169 " --> pdb=" O LYS A 165 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU A 170 " --> pdb=" O LEU A 166 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N LYS A 172 " --> pdb=" O ASP A 168 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N PHE A 173 " --> pdb=" O SER A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 191 removed outlier: 4.136A pdb=" N THR A 185 " --> pdb=" O SER A 181 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ILE A 186 " --> pdb=" O GLU A 182 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER A 189 " --> pdb=" O THR A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 204 Processing helix chain 'A' and resid 236 through 241 removed outlier: 3.845A pdb=" N GLN A 241 " --> pdb=" O ASP A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 268 removed outlier: 4.053A pdb=" N PHE A 261 " --> pdb=" O SER A 257 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LYS A 262 " --> pdb=" O SER A 258 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ASN A 263 " --> pdb=" O ASP A 259 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LYS A 265 " --> pdb=" O PHE A 261 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASN A 266 " --> pdb=" O LYS A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 286 removed outlier: 3.646A pdb=" N HIS A 275 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N GLU A 276 " --> pdb=" O GLU A 272 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE A 277 " --> pdb=" O THR A 273 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 298 Processing helix chain 'A' and resid 307 through 316 removed outlier: 3.521A pdb=" N SER A 314 " --> pdb=" O ARG A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 328 removed outlier: 3.653A pdb=" N LEU A 324 " --> pdb=" O PRO A 320 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N SER A 325 " --> pdb=" O GLU A 321 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N ASN A 328 " --> pdb=" O LEU A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 351 removed outlier: 3.745A pdb=" N ASN A 350 " --> pdb=" O GLU A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 425 removed outlier: 3.586A pdb=" N LEU A 396 " --> pdb=" O ALA A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 435 removed outlier: 3.590A pdb=" N TYR A 435 " --> pdb=" O ARG A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 457 removed outlier: 4.218A pdb=" N TYR A 449 " --> pdb=" O SER A 445 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE A 453 " --> pdb=" O TYR A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 460 No H-bonds generated for 'chain 'A' and resid 458 through 460' Processing helix chain 'A' and resid 461 through 472 removed outlier: 4.218A pdb=" N MET A 465 " --> pdb=" O HIS A 461 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG A 471 " --> pdb=" O LYS A 467 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N MET A 472 " --> pdb=" O ALA A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 497 removed outlier: 4.180A pdb=" N LEU A 479 " --> pdb=" O LEU A 475 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG A 483 " --> pdb=" O LEU A 479 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER A 497 " --> pdb=" O SER A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 510 removed outlier: 3.815A pdb=" N LYS A 508 " --> pdb=" O SER A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 514 removed outlier: 3.670A pdb=" N LEU A 514 " --> pdb=" O ASP A 511 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 511 through 514' Processing helix chain 'A' and resid 516 through 529 removed outlier: 3.872A pdb=" N TYR A 520 " --> pdb=" O SER A 516 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N LYS A 522 " --> pdb=" O CYS A 518 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N ALA A 523 " --> pdb=" O VAL A 519 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LYS A 526 " --> pdb=" O LYS A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 549 removed outlier: 3.734A pdb=" N LEU A 534 " --> pdb=" O SER A 530 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N LEU A 547 " --> pdb=" O SER A 543 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N HIS A 548 " --> pdb=" O GLN A 544 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N PHE A 549 " --> pdb=" O ALA A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 584 removed outlier: 3.869A pdb=" N ASP A 571 " --> pdb=" O ILE A 567 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N CYS A 573 " --> pdb=" O LEU A 569 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE A 580 " --> pdb=" O VAL A 576 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N CYS A 582 " --> pdb=" O THR A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 604 removed outlier: 4.640A pdb=" N LEU A 599 " --> pdb=" O PHE A 595 " (cutoff:3.500A) Proline residue: A 600 - end of helix Processing helix chain 'A' and resid 609 through 614 Processing helix chain 'A' and resid 614 through 619 removed outlier: 4.183A pdb=" N PHE A 618 " --> pdb=" O LEU A 614 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ARG A 619 " --> pdb=" O ASP A 615 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 614 through 619' Processing helix chain 'A' and resid 746 through 770 removed outlier: 3.698A pdb=" N PHE A 752 " --> pdb=" O SER A 748 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASN A 757 " --> pdb=" O PHE A 753 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLU A 770 " --> pdb=" O LEU A 766 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 788 Processing helix chain 'A' and resid 807 through 822 removed outlier: 3.590A pdb=" N ASN A 811 " --> pdb=" O THR A 807 " (cutoff:3.500A) Processing helix chain 'A' and resid 825 through 838 removed outlier: 3.532A pdb=" N TYR A 836 " --> pdb=" O TYR A 832 " (cutoff:3.500A) Processing helix chain 'A' and resid 846 through 859 removed outlier: 3.647A pdb=" N VAL A 851 " --> pdb=" O ILE A 847 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 877 removed outlier: 4.206A pdb=" N VAL A 870 " --> pdb=" O LYS A 866 " (cutoff:3.500A) Processing helix chain 'A' and resid 887 through 896 Processing helix chain 'A' and resid 976 through 989 removed outlier: 3.539A pdb=" N ARG A 989 " --> pdb=" O THR A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 1022 through 1026 removed outlier: 3.637A pdb=" N LEU A1026 " --> pdb=" O TYR A1023 " (cutoff:3.500A) Processing helix chain 'A' and resid 1029 through 1051 removed outlier: 3.598A pdb=" N ASP A1033 " --> pdb=" O THR A1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 19 removed outlier: 4.164A pdb=" N GLY B 17 " --> pdb=" O GLU B 14 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASN B 18 " --> pdb=" O ASP B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 66 through 74 removed outlier: 3.772A pdb=" N PHE B 72 " --> pdb=" O GLU B 68 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N TRP B 74 " --> pdb=" O ILE B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 91 removed outlier: 3.639A pdb=" N LYS B 90 " --> pdb=" O PRO B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 123 removed outlier: 3.608A pdb=" N PHE B 106 " --> pdb=" O GLY B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 161 removed outlier: 4.202A pdb=" N LEU B 158 " --> pdb=" O ALA B 154 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU B 159 " --> pdb=" O LEU B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 183 removed outlier: 3.606A pdb=" N GLU B 181 " --> pdb=" O GLY B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 249 removed outlier: 3.605A pdb=" N GLU B 235 " --> pdb=" O ASP B 231 " (cutoff:3.500A) Proline residue: B 240 - end of helix Processing helix chain 'B' and resid 274 through 286 removed outlier: 4.969A pdb=" N CYS B 281 " --> pdb=" O GLY B 277 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N VAL B 282 " --> pdb=" O HIS B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 289 No H-bonds generated for 'chain 'B' and resid 287 through 289' Processing helix chain 'B' and resid 301 through 317 removed outlier: 3.675A pdb=" N ARG B 307 " --> pdb=" O ARG B 303 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR B 310 " --> pdb=" O ALA B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 335 removed outlier: 3.943A pdb=" N GLY B 335 " --> pdb=" O GLN B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 369 removed outlier: 3.573A pdb=" N ASN B 369 " --> pdb=" O GLU B 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 40 Proline residue: C 38 - end of helix Processing helix chain 'C' and resid 159 through 165 Processing helix chain 'C' and resid 355 through 358 removed outlier: 3.727A pdb=" N ILE C 358 " --> pdb=" O LEU C 355 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 355 through 358' Processing helix chain 'C' and resid 413 through 418 removed outlier: 3.778A pdb=" N TRP C 417 " --> pdb=" O SER C 413 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 191 Processing helix chain 'D' and resid 205 through 216 removed outlier: 4.172A pdb=" N PHE D 211 " --> pdb=" O ALA D 207 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N SER D 214 " --> pdb=" O ALA D 210 " (cutoff:3.500A) Processing helix chain 'D' and resid 217 through 219 No H-bonds generated for 'chain 'D' and resid 217 through 219' Processing helix chain 'D' and resid 221 through 240 Processing helix chain 'D' and resid 249 through 251 No H-bonds generated for 'chain 'D' and resid 249 through 251' Processing helix chain 'D' and resid 252 through 263 Processing helix chain 'D' and resid 267 through 271 Processing helix chain 'D' and resid 277 through 283 Processing helix chain 'D' and resid 296 through 314 removed outlier: 3.518A pdb=" N TYR D 304 " --> pdb=" O CYS D 300 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU D 314 " --> pdb=" O LYS D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 328 through 335 removed outlier: 4.259A pdb=" N SER D 333 " --> pdb=" O PRO D 329 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LEU D 334 " --> pdb=" O ASN D 330 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N VAL D 335 " --> pdb=" O TYR D 331 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 178 No H-bonds generated for 'chain 'E' and resid 177 through 178' Processing helix chain 'E' and resid 180 through 180 No H-bonds generated for 'chain 'E' and resid 180 through 180' Processing helix chain 'E' and resid 181 through 191 removed outlier: 3.788A pdb=" N ILE E 189 " --> pdb=" O ASP E 185 " (cutoff:3.500A) Processing helix chain 'E' and resid 204 through 216 removed outlier: 3.506A pdb=" N ALA E 209 " --> pdb=" O ARG E 205 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ALA E 210 " --> pdb=" O ALA E 206 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLU E 213 " --> pdb=" O ALA E 209 " (cutoff:3.500A) Processing helix chain 'E' and resid 221 through 244 removed outlier: 3.603A pdb=" N VAL E 225 " --> pdb=" O ASN E 221 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N GLY E 244 " --> pdb=" O ASN E 240 " (cutoff:3.500A) Processing helix chain 'E' and resid 253 through 263 removed outlier: 3.601A pdb=" N GLN E 261 " --> pdb=" O LEU E 257 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLN E 262 " --> pdb=" O GLU E 258 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TYR E 263 " --> pdb=" O ILE E 259 " (cutoff:3.500A) Processing helix chain 'E' and resid 267 through 271 removed outlier: 3.816A pdb=" N LEU E 271 " --> pdb=" O MET E 268 " (cutoff:3.500A) Processing helix chain 'E' and resid 276 through 284 Processing helix chain 'E' and resid 284 through 289 Processing helix chain 'E' and resid 294 through 315 Processing helix chain 'G' and resid 334 through 345 removed outlier: 3.666A pdb=" N TRP G 338 " --> pdb=" O MET G 334 " (cutoff:3.500A) Processing helix chain 'G' and resid 356 through 361 removed outlier: 3.511A pdb=" N SER G 360 " --> pdb=" O PRO G 356 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER G 361 " --> pdb=" O HIS G 357 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 356 through 361' Processing helix chain 'G' and resid 518 through 545 removed outlier: 3.639A pdb=" N ILE G 542 " --> pdb=" O GLU G 538 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU G 543 " --> pdb=" O GLN G 539 " (cutoff:3.500A) Processing helix chain 'G' and resid 547 through 568 removed outlier: 3.691A pdb=" N THR G 553 " --> pdb=" O ASP G 549 " (cutoff:3.500A) Proline residue: G 559 - end of helix Processing helix chain 'G' and resid 575 through 587 removed outlier: 3.688A pdb=" N ALA G 579 " --> pdb=" O ASP G 575 " (cutoff:3.500A) Processing helix chain 'G' and resid 600 through 605 Processing sheet with id=AA1, first strand: chain 'F' and resid 254 through 256 Processing sheet with id=AA2, first strand: chain 'G' and resid 472 through 474 removed outlier: 6.642A pdb=" N LEU F 339 " --> pdb=" O ILE G 473 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N TYR F 340 " --> pdb=" O VAL G 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 115 through 117 Processing sheet with id=AA4, first strand: chain 'A' and resid 134 through 135 Processing sheet with id=AA5, first strand: chain 'A' and resid 342 through 343 Processing sheet with id=AA6, first strand: chain 'A' and resid 743 through 745 removed outlier: 4.020A pdb=" N GLY A 918 " --> pdb=" O CYS A 909 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 743 through 745 removed outlier: 6.705A pdb=" N LEU A 905 " --> pdb=" O MET A 922 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 992 through 995 removed outlier: 3.840A pdb=" N LEU C 43 " --> pdb=" O THR C 411 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU C 407 " --> pdb=" O ARG C 47 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASP C 387 " --> pdb=" O ALA C 401 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 49 through 51 removed outlier: 6.142A pdb=" N TYR B 10 " --> pdb=" O ILE B 51 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N SER B 9 " --> pdb=" O ILE B 130 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL B 254 " --> pdb=" O ILE B 293 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N VAL B 295 " --> pdb=" O VAL B 254 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N LEU B 256 " --> pdb=" O VAL B 295 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N LEU B 168 " --> pdb=" O ILE B 255 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N GLN B 257 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N ILE B 170 " --> pdb=" O GLN B 257 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N VAL B 221 " --> pdb=" O VAL B 190 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N THR B 192 " --> pdb=" O VAL B 221 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N VAL B 223 " --> pdb=" O THR B 192 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N SER B 194 " --> pdb=" O VAL B 223 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N LEU B 225 " --> pdb=" O SER B 194 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N HIS B 196 " --> pdb=" O LEU B 225 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 212 through 213 Processing sheet with id=AB2, first strand: chain 'C' and resid 70 through 82 removed outlier: 3.854A pdb=" N VAL C 79 " --> pdb=" O LEU C 87 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU C 87 " --> pdb=" O VAL C 79 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N LYS C 85 " --> pdb=" O ALA C 81 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N LEU C 88 " --> pdb=" O LEU C 125 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N LEU C 125 " --> pdb=" O LEU C 88 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N VAL C 90 " --> pdb=" O SER C 123 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 145 through 148 Processing sheet with id=AB4, first strand: chain 'C' and resid 187 through 192 removed outlier: 7.027A pdb=" N GLY C 203 " --> pdb=" O THR C 188 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N VAL C 190 " --> pdb=" O VAL C 201 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N VAL C 201 " --> pdb=" O VAL C 190 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 239 through 241 removed outlier: 4.128A pdb=" N ASP C 239 " --> pdb=" O VAL C 253 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 284 through 287 removed outlier: 7.138A pdb=" N CYS C 300 " --> pdb=" O HIS C 285 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N VAL C 287 " --> pdb=" O ALA C 298 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ALA C 298 " --> pdb=" O VAL C 287 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LEU C 308 " --> pdb=" O HIS C 319 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N HIS C 319 " --> pdb=" O LEU C 308 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 328 through 333 removed outlier: 3.913A pdb=" N LEU C 341 " --> pdb=" O TRP C 353 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 194 through 195 Processing sheet with id=AB9, first strand: chain 'G' and resid 276 through 277 Processing sheet with id=AC1, first strand: chain 'G' and resid 367 through 368 Processing sheet with id=AC2, first strand: chain 'G' and resid 423 through 424 715 hydrogen bonds defined for protein. 2013 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: 6.09 Time building geometry restraints manager: 8.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.01 - 1.17: 22 1.17 - 1.33: 5661 1.33 - 1.49: 6677 1.49 - 1.66: 7868 1.66 - 1.82: 139 Bond restraints: 20367 Sorted by residual: bond pdb=" C CYS A 337 " pdb=" O CYS A 337 " ideal model delta sigma weight residual 1.235 1.010 0.226 1.26e-02 6.30e+03 3.21e+02 bond pdb=" N PRO A 372 " pdb=" CA PRO A 372 " ideal model delta sigma weight residual 1.469 1.696 -0.228 1.28e-02 6.10e+03 3.17e+02 bond pdb=" C PHE A 359 " pdb=" O PHE A 359 " ideal model delta sigma weight residual 1.236 1.086 0.150 1.15e-02 7.56e+03 1.70e+02 bond pdb=" C SER A 370 " pdb=" O SER A 370 " ideal model delta sigma weight residual 1.234 1.076 0.158 1.28e-02 6.10e+03 1.52e+02 bond pdb=" C SER A 352 " pdb=" O SER A 352 " ideal model delta sigma weight residual 1.236 1.093 0.143 1.19e-02 7.06e+03 1.44e+02 ... (remaining 20362 not shown) Histogram of bond angle deviations from ideal: 95.25 - 103.73: 310 103.73 - 112.20: 9762 112.20 - 120.67: 10467 120.67 - 129.15: 6885 129.15 - 137.62: 189 Bond angle restraints: 27613 Sorted by residual: angle pdb=" C HIS A 371 " pdb=" N PRO A 372 " pdb=" CA PRO A 372 " ideal model delta sigma weight residual 119.84 137.62 -17.78 1.25e+00 6.40e-01 2.02e+02 angle pdb=" N GLU A 378 " pdb=" CA GLU A 378 " pdb=" C GLU A 378 " ideal model delta sigma weight residual 112.72 127.03 -14.31 1.14e+00 7.69e-01 1.58e+02 angle pdb=" O VAL A 369 " pdb=" C VAL A 369 " pdb=" N SER A 370 " ideal model delta sigma weight residual 122.69 110.83 11.86 1.14e+00 7.69e-01 1.08e+02 angle pdb=" C ASN A 365 " pdb=" CA ASN A 365 " pdb=" CB ASN A 365 " ideal model delta sigma weight residual 110.26 95.25 15.01 1.50e+00 4.44e-01 1.00e+02 angle pdb=" N GLU A 378 " pdb=" CA GLU A 378 " pdb=" CB GLU A 378 " ideal model delta sigma weight residual 110.70 97.65 13.05 1.49e+00 4.50e-01 7.67e+01 ... (remaining 27608 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 10511 17.95 - 35.90: 1230 35.90 - 53.85: 338 53.85 - 71.80: 90 71.80 - 89.74: 35 Dihedral angle restraints: 12204 sinusoidal: 4947 harmonic: 7257 Sorted by residual: dihedral pdb=" CA ASN G 438 " pdb=" C ASN G 438 " pdb=" N PRO G 439 " pdb=" CA PRO G 439 " ideal model delta harmonic sigma weight residual 180.00 99.24 80.76 0 5.00e+00 4.00e-02 2.61e+02 dihedral pdb=" CA GLU F 145 " pdb=" C GLU F 145 " pdb=" N PRO F 146 " pdb=" CA PRO F 146 " ideal model delta harmonic sigma weight residual 180.00 121.06 58.94 0 5.00e+00 4.00e-02 1.39e+02 dihedral pdb=" CA SER A 332 " pdb=" C SER A 332 " pdb=" N ASP A 333 " pdb=" CA ASP A 333 " ideal model delta harmonic sigma weight residual 180.00 122.23 57.77 0 5.00e+00 4.00e-02 1.33e+02 ... (remaining 12201 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.181: 2962 0.181 - 0.361: 19 0.361 - 0.542: 4 0.542 - 0.723: 1 0.723 - 0.904: 2 Chirality restraints: 2988 Sorted by residual: chirality pdb=" CA SER A 376 " pdb=" N SER A 376 " pdb=" C SER A 376 " pdb=" CB SER A 376 " both_signs ideal model delta sigma weight residual False 2.51 1.61 0.90 2.00e-01 2.50e+01 2.04e+01 chirality pdb=" CA ASN A 350 " pdb=" N ASN A 350 " pdb=" C ASN A 350 " pdb=" CB ASN A 350 " both_signs ideal model delta sigma weight residual False 2.51 1.75 0.76 2.00e-01 2.50e+01 1.44e+01 chirality pdb=" CA GLU A 377 " pdb=" N GLU A 377 " pdb=" C GLU A 377 " pdb=" CB GLU A 377 " both_signs ideal model delta sigma weight residual False 2.51 1.87 0.64 2.00e-01 2.50e+01 1.01e+01 ... (remaining 2985 not shown) Planarity restraints: 3562 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A 336 " 0.036 2.00e-02 2.50e+03 7.52e-02 5.66e+01 pdb=" C GLU A 336 " -0.130 2.00e-02 2.50e+03 pdb=" O GLU A 336 " 0.050 2.00e-02 2.50e+03 pdb=" N CYS A 337 " 0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 373 " -0.030 2.00e-02 2.50e+03 6.08e-02 3.69e+01 pdb=" C THR A 373 " 0.105 2.00e-02 2.50e+03 pdb=" O THR A 373 " -0.040 2.00e-02 2.50e+03 pdb=" N TRP A 374 " -0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN C 247 " 0.024 2.00e-02 2.50e+03 5.05e-02 2.55e+01 pdb=" C GLN C 247 " -0.087 2.00e-02 2.50e+03 pdb=" O GLN C 247 " 0.034 2.00e-02 2.50e+03 pdb=" N ASP C 248 " 0.030 2.00e-02 2.50e+03 ... (remaining 3559 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.27: 45 2.27 - 2.99: 10466 2.99 - 3.70: 33105 3.70 - 4.42: 54880 4.42 - 5.14: 94177 Nonbonded interactions: 192673 Sorted by model distance: nonbonded pdb=" OG SER A 354 " pdb=" OD2 ASP B 67 " model vdw 1.549 2.440 nonbonded pdb=" OD2 ASP B 173 " pdb="ZN ZN B 501 " model vdw 1.810 2.230 nonbonded pdb=" NH1 ARG A 80 " pdb=" O ASN A 234 " model vdw 2.053 2.520 nonbonded pdb=" OG SER A 306 " pdb=" NH1 ARG A 310 " model vdw 2.058 2.520 nonbonded pdb=" OH TYR A1018 " pdb=" OD1 ASP A1020 " model vdw 2.075 2.440 ... (remaining 192668 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 'D' and (resid 170 through 178 or resid 180 through 329)) selection = (chain 'E' and (resid 170 through 290 or resid 294 through 329)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 10.730 Check model and map are aligned: 0.310 Set scattering table: 0.200 Process input model: 58.660 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 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 : 0.010 0.228 20367 Z= 0.627 Angle : 1.030 17.781 27613 Z= 0.604 Chirality : 0.062 0.904 2988 Planarity : 0.007 0.080 3562 Dihedral : 17.701 89.744 7500 Min Nonbonded Distance : 1.549 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.66 % Allowed : 11.80 % Favored : 87.54 % Rotamer: Outliers : 9.99 % Allowed : 20.53 % Favored : 69.48 % Cbeta Deviations : 0.34 % Peptide Plane: Cis-proline : 0.79 % Cis-general : 0.00 % Twisted Proline : 3.17 % Twisted General : 0.22 % 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: -4.49 (0.14), residues: 2415 helix: -2.31 (0.13), residues: 973 sheet: -2.91 (0.32), residues: 209 loop : -3.66 (0.14), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.004 TRP A 361 HIS 0.009 0.002 HIS B 207 PHE 0.078 0.003 PHE A 381 TYR 0.027 0.003 TYR A 891 ARG 0.016 0.001 ARG A 356 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 646 residues out of total 2241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 219 poor density : 427 time to evaluate : 2.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 142 SER cc_start: 0.5542 (OUTLIER) cc_final: 0.5184 (p) REVERT: F 360 LYS cc_start: 0.7392 (ttpp) cc_final: 0.6889 (mtmp) REVERT: F 361 LYS cc_start: 0.7674 (ttpt) cc_final: 0.7230 (mttp) REVERT: F 368 LYS cc_start: 0.7420 (ptpp) cc_final: 0.6945 (tptt) REVERT: A 40 LYS cc_start: 0.7751 (OUTLIER) cc_final: 0.7341 (mptt) REVERT: A 79 GLU cc_start: 0.7897 (pt0) cc_final: 0.7461 (mt-10) REVERT: A 346 VAL cc_start: 0.6422 (t) cc_final: 0.6162 (m) REVERT: A 374 TRP cc_start: 0.4310 (OUTLIER) cc_final: 0.3769 (t60) REVERT: A 381 PHE cc_start: 0.7073 (OUTLIER) cc_final: 0.6539 (m-80) REVERT: A 439 GLU cc_start: 0.5528 (OUTLIER) cc_final: 0.5037 (tp30) REVERT: A 446 LYS cc_start: 0.7484 (OUTLIER) cc_final: 0.7029 (ptmm) REVERT: A 527 LYS cc_start: 0.6888 (tptt) cc_final: 0.5916 (mppt) REVERT: A 603 PHE cc_start: 0.8045 (OUTLIER) cc_final: 0.7177 (t80) REVERT: A 742 GLU cc_start: 0.7548 (OUTLIER) cc_final: 0.7301 (pt0) REVERT: A 887 ASP cc_start: 0.7430 (OUTLIER) cc_final: 0.7084 (m-30) REVERT: A 992 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.7210 (tt0) REVERT: B 45 TYR cc_start: 0.6480 (OUTLIER) cc_final: 0.5939 (p90) REVERT: B 57 THR cc_start: 0.8363 (p) cc_final: 0.8011 (m) REVERT: B 275 MET cc_start: 0.8696 (ttp) cc_final: 0.7881 (mtp) REVERT: C 75 MET cc_start: 0.7304 (pp-130) cc_final: 0.6723 (ptp) REVERT: C 79 VAL cc_start: 0.7772 (OUTLIER) cc_final: 0.7564 (t) REVERT: C 83 VAL cc_start: 0.6940 (t) cc_final: 0.6514 (t) REVERT: C 197 LYS cc_start: 0.6837 (tmtt) cc_final: 0.6443 (ttpt) REVERT: C 214 LEU cc_start: 0.6968 (mt) cc_final: 0.6729 (mt) REVERT: C 248 ASP cc_start: 0.2278 (OUTLIER) cc_final: 0.1565 (t0) REVERT: C 306 ILE cc_start: 0.7501 (OUTLIER) cc_final: 0.7170 (pt) REVERT: D 261 GLN cc_start: 0.7061 (mt0) cc_final: 0.6820 (mm-40) REVERT: E 204 VAL cc_start: 0.7364 (OUTLIER) cc_final: 0.6968 (t) REVERT: E 237 ILE cc_start: 0.8341 (mt) cc_final: 0.8068 (mp) REVERT: G 438 ASN cc_start: 0.7211 (t0) cc_final: 0.6948 (t0) REVERT: G 550 PHE cc_start: 0.7528 (OUTLIER) cc_final: 0.6846 (p90) REVERT: G 565 ASP cc_start: 0.6480 (OUTLIER) cc_final: 0.6215 (m-30) outliers start: 219 outliers final: 56 residues processed: 600 average time/residue: 1.1171 time to fit residues: 771.8388 Evaluate side-chains 338 residues out of total 2241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 265 time to evaluate : 2.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 142 SER Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 185 ILE Chi-restraints excluded: chain F residue 211 THR Chi-restraints excluded: chain F residue 337 SER Chi-restraints excluded: chain F residue 345 ASP Chi-restraints excluded: chain F residue 378 VAL Chi-restraints excluded: chain A residue 40 LYS Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain A residue 354 SER Chi-restraints excluded: chain A residue 372 PRO Chi-restraints excluded: chain A residue 374 TRP Chi-restraints excluded: chain A residue 381 PHE Chi-restraints excluded: chain A residue 439 GLU Chi-restraints excluded: chain A residue 446 LYS Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 603 PHE Chi-restraints excluded: chain A residue 742 GLU Chi-restraints excluded: chain A residue 772 GLN Chi-restraints excluded: chain A residue 792 TRP Chi-restraints excluded: chain A residue 794 ASP Chi-restraints excluded: chain A residue 801 ASP Chi-restraints excluded: chain A residue 807 THR Chi-restraints excluded: chain A residue 846 THR Chi-restraints excluded: chain A residue 862 VAL Chi-restraints excluded: chain A residue 887 ASP Chi-restraints excluded: chain A residue 895 ILE Chi-restraints excluded: chain A residue 992 GLU Chi-restraints excluded: chain A residue 1050 LEU Chi-restraints excluded: chain B residue 45 TYR Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 261 ASP Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 344 SER Chi-restraints excluded: chain C residue 37 SER Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 212 TRP Chi-restraints excluded: chain C residue 248 ASP Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 306 ILE Chi-restraints excluded: chain C residue 331 ILE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 198 ILE Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 330 ASN Chi-restraints excluded: chain D residue 335 VAL Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 291 THR Chi-restraints excluded: chain E residue 300 CYS Chi-restraints excluded: chain G residue 263 ASN Chi-restraints excluded: chain G residue 279 GLU Chi-restraints excluded: chain G residue 341 LEU Chi-restraints excluded: chain G residue 342 CYS Chi-restraints excluded: chain G residue 344 TYR Chi-restraints excluded: chain G residue 397 LEU Chi-restraints excluded: chain G residue 418 VAL Chi-restraints excluded: chain G residue 472 VAL Chi-restraints excluded: chain G residue 550 PHE Chi-restraints excluded: chain G residue 565 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 205 optimal weight: 0.3980 chunk 184 optimal weight: 0.6980 chunk 102 optimal weight: 0.8980 chunk 62 optimal weight: 0.9990 chunk 124 optimal weight: 0.6980 chunk 98 optimal weight: 0.8980 chunk 190 optimal weight: 2.9990 chunk 73 optimal weight: 0.7980 chunk 115 optimal weight: 0.7980 chunk 141 optimal weight: 0.9990 chunk 220 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 116 ASN F 152 ASN ** F 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 390 ASN A 52 HIS A 109 ASN A 159 ASN A 175 ASN A 234 ASN A 241 GLN ** A 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 286 GLN A 371 HIS A 421 GLN ** A 583 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 777 GLN ** A 783 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 808 HIS A 912 ASN A 998 GLN A1040 GLN B 37 ASN B 41 ASN ** B 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 119 GLN B 125 ASN B 138 HIS B 332 GLN B 351 ASN C 21 ASN C 22 GLN C 193 ASN C 218 ASN ** C 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 362 GLN D 230 GLN ** E 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 221 ASN E 261 GLN E 303 ASN G 447 ASN G 459 HIS G 526 ASN G 529 ASN G 573 ASN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.2643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 20367 Z= 0.220 Angle : 0.696 9.474 27613 Z= 0.364 Chirality : 0.045 0.216 2988 Planarity : 0.006 0.072 3562 Dihedral : 9.041 70.722 2805 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.33 % Allowed : 8.32 % Favored : 91.35 % Rotamer: Outliers : 7.48 % Allowed : 24.95 % Favored : 67.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.79 % Cis-general : 0.00 % Twisted Proline : 3.17 % Twisted General : 0.17 % 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: -3.00 (0.15), residues: 2415 helix: -0.73 (0.16), residues: 976 sheet: -2.34 (0.33), residues: 206 loop : -3.09 (0.15), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP G 338 HIS 0.005 0.001 HIS B 207 PHE 0.024 0.002 PHE E 239 TYR 0.039 0.002 TYR C 70 ARG 0.008 0.001 ARG F 366 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 2241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 316 time to evaluate : 2.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 360 LYS cc_start: 0.7499 (ttpp) cc_final: 0.6998 (mtmt) REVERT: F 368 LYS cc_start: 0.7484 (ptpp) cc_final: 0.6980 (tptt) REVERT: F 373 VAL cc_start: 0.6967 (OUTLIER) cc_final: 0.6566 (p) REVERT: A 79 GLU cc_start: 0.7937 (pt0) cc_final: 0.7649 (mt-10) REVERT: A 182 GLU cc_start: 0.7387 (OUTLIER) cc_final: 0.6347 (tm-30) REVERT: A 226 GLN cc_start: 0.8701 (OUTLIER) cc_final: 0.8475 (mt0) REVERT: A 351 ILE cc_start: 0.7565 (mm) cc_final: 0.7152 (tt) REVERT: A 386 LYS cc_start: 0.6566 (OUTLIER) cc_final: 0.6284 (mtpp) REVERT: A 439 GLU cc_start: 0.6057 (OUTLIER) cc_final: 0.5400 (tp30) REVERT: A 527 LYS cc_start: 0.6828 (tptt) cc_final: 0.5945 (mppt) REVERT: A 619 ARG cc_start: 0.5604 (ptp-110) cc_final: 0.5219 (mtm-85) REVERT: A 795 ARG cc_start: 0.8178 (OUTLIER) cc_final: 0.7630 (mtp85) REVERT: A 871 THR cc_start: 0.7348 (t) cc_final: 0.7142 (m) REVERT: A 989 ARG cc_start: 0.7886 (mmt90) cc_final: 0.7661 (mtm180) REVERT: B 247 GLN cc_start: 0.8586 (OUTLIER) cc_final: 0.8234 (tt0) REVERT: C 75 MET cc_start: 0.7357 (pp-130) cc_final: 0.6970 (ptp) REVERT: C 197 LYS cc_start: 0.6667 (tmtt) cc_final: 0.6461 (ttpt) REVERT: C 306 ILE cc_start: 0.7887 (OUTLIER) cc_final: 0.7435 (pp) REVERT: D 215 LYS cc_start: 0.6709 (tptt) cc_final: 0.6507 (tmtm) REVERT: D 241 LYS cc_start: 0.6560 (mtmm) cc_final: 0.6000 (mtpt) REVERT: D 319 TYR cc_start: 0.6811 (m-10) cc_final: 0.6502 (m-10) REVERT: E 169 LYS cc_start: 0.7349 (OUTLIER) cc_final: 0.6957 (mttp) REVERT: G 344 TYR cc_start: 0.5059 (OUTLIER) cc_final: 0.4581 (t80) REVERT: G 550 PHE cc_start: 0.7371 (OUTLIER) cc_final: 0.7093 (p90) REVERT: G 565 ASP cc_start: 0.6535 (OUTLIER) cc_final: 0.5861 (m-30) outliers start: 164 outliers final: 61 residues processed: 445 average time/residue: 1.1362 time to fit residues: 580.9322 Evaluate side-chains 329 residues out of total 2241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 256 time to evaluate : 2.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 345 ASP Chi-restraints excluded: chain F residue 349 LYS Chi-restraints excluded: chain F residue 373 VAL Chi-restraints excluded: chain F residue 378 VAL Chi-restraints excluded: chain F residue 391 LEU Chi-restraints excluded: chain A residue 38 ASP Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 226 GLN Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 439 GLU Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 467 LYS Chi-restraints excluded: chain A residue 552 ARG Chi-restraints excluded: chain A residue 716 SER Chi-restraints excluded: chain A residue 772 GLN Chi-restraints excluded: chain A residue 774 SER Chi-restraints excluded: chain A residue 781 ILE Chi-restraints excluded: chain A residue 795 ARG Chi-restraints excluded: chain A residue 801 ASP Chi-restraints excluded: chain A residue 846 THR Chi-restraints excluded: chain A residue 862 VAL Chi-restraints excluded: chain A residue 887 ASP Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 227 ASP Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain B residue 247 GLN Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 212 TRP Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 306 ILE Chi-restraints excluded: chain C residue 331 ILE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 297 SER Chi-restraints excluded: chain D residue 330 ASN Chi-restraints excluded: chain D residue 335 VAL Chi-restraints excluded: chain E residue 169 LYS Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 300 CYS Chi-restraints excluded: chain G residue 263 ASN Chi-restraints excluded: chain G residue 341 LEU Chi-restraints excluded: chain G residue 342 CYS Chi-restraints excluded: chain G residue 344 TYR Chi-restraints excluded: chain G residue 398 LEU Chi-restraints excluded: chain G residue 418 VAL Chi-restraints excluded: chain G residue 430 SER Chi-restraints excluded: chain G residue 443 THR Chi-restraints excluded: chain G residue 458 ASP Chi-restraints excluded: chain G residue 460 VAL Chi-restraints excluded: chain G residue 472 VAL Chi-restraints excluded: chain G residue 550 PHE Chi-restraints excluded: chain G residue 565 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 122 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 183 optimal weight: 0.0970 chunk 150 optimal weight: 0.9980 chunk 60 optimal weight: 0.7980 chunk 221 optimal weight: 3.9990 chunk 238 optimal weight: 1.9990 chunk 196 optimal weight: 2.9990 chunk 219 optimal weight: 9.9990 chunk 75 optimal weight: 1.9990 chunk 177 optimal weight: 3.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 173 HIS F 364 ASN A 159 ASN ** A 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 583 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 757 ASN ** A 783 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 797 ASN A 998 GLN B 37 ASN B 125 ASN B 351 ASN C 21 ASN C 193 ASN C 236 GLN ** C 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 188 ASN ** E 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.3351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 20367 Z= 0.276 Angle : 0.709 9.602 27613 Z= 0.368 Chirality : 0.046 0.240 2988 Planarity : 0.006 0.073 3562 Dihedral : 8.106 71.257 2736 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.29 % Allowed : 9.23 % Favored : 90.48 % Rotamer: Outliers : 7.48 % Allowed : 25.50 % Favored : 67.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.79 % Cis-general : 0.00 % Twisted Proline : 3.17 % Twisted General : 0.13 % 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: -2.52 (0.16), residues: 2415 helix: -0.40 (0.16), residues: 992 sheet: -1.92 (0.36), residues: 207 loop : -2.81 (0.16), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 792 HIS 0.020 0.001 HIS A 461 PHE 0.024 0.002 PHE A 381 TYR 0.035 0.002 TYR D 272 ARG 0.008 0.001 ARG B 75 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 2241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 275 time to evaluate : 2.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 368 LYS cc_start: 0.7387 (ptpp) cc_final: 0.7073 (tptt) REVERT: F 373 VAL cc_start: 0.7075 (OUTLIER) cc_final: 0.6784 (p) REVERT: A 182 GLU cc_start: 0.7420 (OUTLIER) cc_final: 0.6244 (tm-30) REVERT: A 423 ARG cc_start: 0.7664 (OUTLIER) cc_final: 0.6729 (ptt-90) REVERT: A 527 LYS cc_start: 0.6797 (tptt) cc_final: 0.5941 (mppt) REVERT: A 970 ILE cc_start: 0.8143 (pt) cc_final: 0.7814 (pt) REVERT: B 45 TYR cc_start: 0.6614 (OUTLIER) cc_final: 0.6095 (p90) REVERT: B 57 THR cc_start: 0.8294 (OUTLIER) cc_final: 0.7864 (m) REVERT: B 74 TRP cc_start: 0.8226 (t60) cc_final: 0.7993 (t-100) REVERT: B 88 GLN cc_start: 0.8778 (OUTLIER) cc_final: 0.8410 (pt0) REVERT: C 306 ILE cc_start: 0.8148 (OUTLIER) cc_final: 0.7871 (pp) REVERT: C 398 MET cc_start: 0.8362 (ttm) cc_final: 0.7862 (tpp) REVERT: C 407 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8227 (tt) REVERT: D 246 MET cc_start: 0.7045 (pmt) cc_final: 0.6663 (pmt) REVERT: D 319 TYR cc_start: 0.7208 (m-10) cc_final: 0.6937 (m-10) REVERT: E 169 LYS cc_start: 0.7389 (OUTLIER) cc_final: 0.6913 (mttm) REVERT: E 246 MET cc_start: 0.6715 (mtm) cc_final: 0.4908 (pp-130) REVERT: G 400 LYS cc_start: 0.8051 (mtmt) cc_final: 0.7581 (ptmt) REVERT: G 449 ARG cc_start: 0.7312 (mtp-110) cc_final: 0.6971 (ttm110) REVERT: G 550 PHE cc_start: 0.7768 (OUTLIER) cc_final: 0.6949 (p90) REVERT: G 565 ASP cc_start: 0.6857 (OUTLIER) cc_final: 0.6117 (m-30) outliers start: 164 outliers final: 75 residues processed: 408 average time/residue: 1.1368 time to fit residues: 532.8076 Evaluate side-chains 333 residues out of total 2241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 247 time to evaluate : 2.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 206 ILE Chi-restraints excluded: chain F residue 345 ASP Chi-restraints excluded: chain F residue 349 LYS Chi-restraints excluded: chain F residue 373 VAL Chi-restraints excluded: chain F residue 378 VAL Chi-restraints excluded: chain F residue 391 LEU Chi-restraints excluded: chain A residue 38 ASP Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 423 ARG Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 552 ARG Chi-restraints excluded: chain A residue 584 SER Chi-restraints excluded: chain A residue 716 SER Chi-restraints excluded: chain A residue 772 GLN Chi-restraints excluded: chain A residue 774 SER Chi-restraints excluded: chain A residue 791 ILE Chi-restraints excluded: chain A residue 801 ASP Chi-restraints excluded: chain A residue 807 THR Chi-restraints excluded: chain A residue 846 THR Chi-restraints excluded: chain A residue 862 VAL Chi-restraints excluded: chain A residue 887 ASP Chi-restraints excluded: chain A residue 981 SER Chi-restraints excluded: chain A residue 1004 ASP Chi-restraints excluded: chain A residue 1009 LEU Chi-restraints excluded: chain B residue 15 ASP Chi-restraints excluded: chain B residue 45 TYR Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 88 GLN Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 227 ASP Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain B residue 261 ASP Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 51 TRP Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 212 TRP Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 306 ILE Chi-restraints excluded: chain C residue 331 ILE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 297 SER Chi-restraints excluded: chain D residue 330 ASN Chi-restraints excluded: chain D residue 335 VAL Chi-restraints excluded: chain E residue 169 LYS Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 217 SER Chi-restraints excluded: chain E residue 222 GLU Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain G residue 263 ASN Chi-restraints excluded: chain G residue 284 SER Chi-restraints excluded: chain G residue 339 MET Chi-restraints excluded: chain G residue 341 LEU Chi-restraints excluded: chain G residue 342 CYS Chi-restraints excluded: chain G residue 418 VAL Chi-restraints excluded: chain G residue 430 SER Chi-restraints excluded: chain G residue 443 THR Chi-restraints excluded: chain G residue 446 SER Chi-restraints excluded: chain G residue 458 ASP Chi-restraints excluded: chain G residue 460 VAL Chi-restraints excluded: chain G residue 472 VAL Chi-restraints excluded: chain G residue 550 PHE Chi-restraints excluded: chain G residue 565 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 218 optimal weight: 0.1980 chunk 166 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 105 optimal weight: 0.7980 chunk 148 optimal weight: 4.9990 chunk 221 optimal weight: 0.7980 chunk 234 optimal weight: 3.9990 chunk 115 optimal weight: 0.5980 chunk 210 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 364 ASN A 159 ASN A 226 GLN ** A 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 583 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 593 HIS A 783 ASN B 37 ASN B 87 HIS B 125 ASN C 21 ASN C 152 HIS ** C 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 315 ASN C 405 ASN ** D 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 303 ASN E 220 ASN E 221 ASN ** E 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 352 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 0.3850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 20367 Z= 0.227 Angle : 0.657 8.771 27613 Z= 0.341 Chirality : 0.044 0.244 2988 Planarity : 0.006 0.072 3562 Dihedral : 7.607 66.962 2726 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.24 % Favored : 91.55 % Rotamer: Outliers : 6.71 % Allowed : 26.92 % Favored : 66.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.79 % Cis-general : 0.00 % Twisted Proline : 3.17 % Twisted General : 0.13 % 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: -2.08 (0.16), residues: 2415 helix: 0.02 (0.16), residues: 988 sheet: -1.65 (0.36), residues: 205 loop : -2.63 (0.16), residues: 1222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 792 HIS 0.009 0.001 HIS A 461 PHE 0.020 0.002 PHE A1031 TYR 0.039 0.002 TYR C 70 ARG 0.010 0.000 ARG F 366 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 2241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 279 time to evaluate : 2.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 360 LYS cc_start: 0.7639 (tmmt) cc_final: 0.6804 (mtmt) REVERT: A 44 GLN cc_start: 0.7881 (OUTLIER) cc_final: 0.7424 (tt0) REVERT: A 181 SER cc_start: 0.8285 (OUTLIER) cc_final: 0.8083 (m) REVERT: A 182 GLU cc_start: 0.7473 (OUTLIER) cc_final: 0.6309 (tm-30) REVERT: A 423 ARG cc_start: 0.7506 (OUTLIER) cc_final: 0.6627 (ptt-90) REVERT: A 527 LYS cc_start: 0.6641 (tptt) cc_final: 0.5842 (mppt) REVERT: A 896 GLU cc_start: 0.7212 (OUTLIER) cc_final: 0.6835 (mt-10) REVERT: B 45 TYR cc_start: 0.6452 (OUTLIER) cc_final: 0.5934 (p90) REVERT: C 75 MET cc_start: 0.6709 (ptp) cc_final: 0.6494 (ptm) REVERT: C 86 TYR cc_start: 0.7215 (m-80) cc_final: 0.6968 (m-10) REVERT: C 93 ILE cc_start: 0.7374 (mm) cc_final: 0.7133 (mp) REVERT: C 164 GLU cc_start: 0.6464 (OUTLIER) cc_final: 0.6245 (mt-10) REVERT: C 398 MET cc_start: 0.8383 (ttm) cc_final: 0.7950 (tpp) REVERT: C 407 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8194 (tt) REVERT: D 246 MET cc_start: 0.7151 (pmt) cc_final: 0.6886 (pmt) REVERT: E 169 LYS cc_start: 0.7374 (OUTLIER) cc_final: 0.6946 (mttm) REVERT: E 216 ILE cc_start: 0.7484 (pp) cc_final: 0.6892 (mm) REVERT: E 246 MET cc_start: 0.6552 (mtm) cc_final: 0.4914 (pp-130) REVERT: G 294 ILE cc_start: 0.2369 (OUTLIER) cc_final: 0.2013 (mp) REVERT: G 352 GLN cc_start: 0.7405 (OUTLIER) cc_final: 0.7022 (tt0) REVERT: G 397 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8482 (tp) REVERT: G 400 LYS cc_start: 0.8047 (mtmt) cc_final: 0.7584 (ptmt) REVERT: G 449 ARG cc_start: 0.7408 (mtp-110) cc_final: 0.7050 (ttm110) REVERT: G 550 PHE cc_start: 0.7620 (OUTLIER) cc_final: 0.6925 (p90) REVERT: G 565 ASP cc_start: 0.6808 (OUTLIER) cc_final: 0.6154 (m-30) outliers start: 147 outliers final: 77 residues processed: 390 average time/residue: 1.2116 time to fit residues: 539.8449 Evaluate side-chains 341 residues out of total 2241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 250 time to evaluate : 2.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 132 CYS Chi-restraints excluded: chain F residue 141 LEU Chi-restraints excluded: chain F residue 163 CYS Chi-restraints excluded: chain F residue 207 SER Chi-restraints excluded: chain F residue 211 THR Chi-restraints excluded: chain F residue 345 ASP Chi-restraints excluded: chain F residue 378 VAL Chi-restraints excluded: chain F residue 391 LEU Chi-restraints excluded: chain A residue 38 ASP Chi-restraints excluded: chain A residue 44 GLN Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 423 ARG Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 516 SER Chi-restraints excluded: chain A residue 552 ARG Chi-restraints excluded: chain A residue 584 SER Chi-restraints excluded: chain A residue 716 SER Chi-restraints excluded: chain A residue 742 GLU Chi-restraints excluded: chain A residue 772 GLN Chi-restraints excluded: chain A residue 774 SER Chi-restraints excluded: chain A residue 791 ILE Chi-restraints excluded: chain A residue 801 ASP Chi-restraints excluded: chain A residue 807 THR Chi-restraints excluded: chain A residue 846 THR Chi-restraints excluded: chain A residue 862 VAL Chi-restraints excluded: chain A residue 887 ASP Chi-restraints excluded: chain A residue 896 GLU Chi-restraints excluded: chain A residue 1009 LEU Chi-restraints excluded: chain A residue 1015 GLU Chi-restraints excluded: chain B residue 15 ASP Chi-restraints excluded: chain B residue 45 TYR Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 227 ASP Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain B residue 261 ASP Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 51 TRP Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 142 ASP Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 212 TRP Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 264 ILE Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 331 ILE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 191 LYS Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 330 ASN Chi-restraints excluded: chain D residue 335 VAL Chi-restraints excluded: chain E residue 169 LYS Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain G residue 263 ASN Chi-restraints excluded: chain G residue 284 SER Chi-restraints excluded: chain G residue 294 ILE Chi-restraints excluded: chain G residue 339 MET Chi-restraints excluded: chain G residue 341 LEU Chi-restraints excluded: chain G residue 342 CYS Chi-restraints excluded: chain G residue 344 TYR Chi-restraints excluded: chain G residue 352 GLN Chi-restraints excluded: chain G residue 379 VAL Chi-restraints excluded: chain G residue 397 LEU Chi-restraints excluded: chain G residue 418 VAL Chi-restraints excluded: chain G residue 430 SER Chi-restraints excluded: chain G residue 443 THR Chi-restraints excluded: chain G residue 446 SER Chi-restraints excluded: chain G residue 472 VAL Chi-restraints excluded: chain G residue 550 PHE Chi-restraints excluded: chain G residue 565 ASP Chi-restraints excluded: chain G residue 599 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 195 optimal weight: 1.9990 chunk 133 optimal weight: 0.5980 chunk 3 optimal weight: 10.0000 chunk 174 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 200 optimal weight: 6.9990 chunk 162 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 119 optimal weight: 4.9990 chunk 210 optimal weight: 3.9990 chunk 59 optimal weight: 0.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 390 ASN A 159 ASN A 226 GLN ** A 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 583 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 593 HIS ** A 777 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 900 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 998 GLN B 37 ASN B 87 HIS B 88 GLN B 125 ASN B 369 ASN C 21 ASN C 152 HIS ** C 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 393 ASN ** D 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 325 GLN G 357 HIS G 459 HIS ** G 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.4206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 20367 Z= 0.395 Angle : 0.769 10.838 27613 Z= 0.398 Chirality : 0.049 0.278 2988 Planarity : 0.006 0.070 3562 Dihedral : 7.851 71.939 2722 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.25 % Allowed : 9.73 % Favored : 90.02 % Rotamer: Outliers : 7.53 % Allowed : 26.41 % Favored : 66.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.79 % Cis-general : 0.00 % Twisted Proline : 3.17 % Twisted General : 0.13 % 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: -2.16 (0.16), residues: 2415 helix: -0.22 (0.16), residues: 996 sheet: -1.60 (0.35), residues: 212 loop : -2.53 (0.16), residues: 1207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 792 HIS 0.008 0.001 HIS G 357 PHE 0.035 0.002 PHE A 381 TYR 0.028 0.003 TYR A 961 ARG 0.009 0.001 ARG A 754 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 2241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 269 time to evaluate : 2.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 182 GLU cc_start: 0.7519 (OUTLIER) cc_final: 0.6350 (tm-30) REVERT: A 342 ARG cc_start: 0.6315 (mtt180) cc_final: 0.5690 (mtt90) REVERT: A 423 ARG cc_start: 0.7679 (OUTLIER) cc_final: 0.6481 (ptt-90) REVERT: A 527 LYS cc_start: 0.6832 (tptt) cc_final: 0.6159 (mppt) REVERT: A 896 GLU cc_start: 0.7341 (OUTLIER) cc_final: 0.6865 (mt-10) REVERT: B 45 TYR cc_start: 0.6542 (OUTLIER) cc_final: 0.6113 (p90) REVERT: B 57 THR cc_start: 0.8324 (OUTLIER) cc_final: 0.7861 (m) REVERT: B 90 LYS cc_start: 0.8235 (ttmt) cc_final: 0.7998 (ttpt) REVERT: B 101 ASP cc_start: 0.7202 (OUTLIER) cc_final: 0.6826 (m-30) REVERT: B 323 GLU cc_start: 0.7396 (OUTLIER) cc_final: 0.7011 (tp30) REVERT: C 388 MET cc_start: 0.8161 (OUTLIER) cc_final: 0.7884 (ptt) REVERT: C 407 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8249 (tt) REVERT: D 241 LYS cc_start: 0.7055 (mtmm) cc_final: 0.6525 (mtpt) REVERT: D 246 MET cc_start: 0.7165 (OUTLIER) cc_final: 0.6846 (pmt) REVERT: E 169 LYS cc_start: 0.7325 (OUTLIER) cc_final: 0.6872 (mttm) REVERT: E 216 ILE cc_start: 0.7643 (pp) cc_final: 0.7304 (mm) REVERT: E 230 GLN cc_start: 0.7171 (OUTLIER) cc_final: 0.5928 (tp40) REVERT: E 246 MET cc_start: 0.6740 (mtm) cc_final: 0.5025 (pp-130) REVERT: E 317 ASP cc_start: 0.5013 (OUTLIER) cc_final: 0.4647 (m-30) REVERT: G 334 MET cc_start: 0.6576 (mpp) cc_final: 0.6270 (mpt) REVERT: G 400 LYS cc_start: 0.8163 (mtmt) cc_final: 0.7688 (ptmt) REVERT: G 449 ARG cc_start: 0.7448 (mtp-110) cc_final: 0.7090 (ttm110) REVERT: G 565 ASP cc_start: 0.6906 (OUTLIER) cc_final: 0.6342 (m-30) outliers start: 165 outliers final: 92 residues processed: 404 average time/residue: 1.2171 time to fit residues: 559.9220 Evaluate side-chains 360 residues out of total 2241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 254 time to evaluate : 2.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 132 CYS Chi-restraints excluded: chain F residue 141 LEU Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 192 GLN Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 207 SER Chi-restraints excluded: chain F residue 211 THR Chi-restraints excluded: chain F residue 345 ASP Chi-restraints excluded: chain F residue 349 LYS Chi-restraints excluded: chain F residue 378 VAL Chi-restraints excluded: chain F residue 391 LEU Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 423 ARG Chi-restraints excluded: chain A residue 439 GLU Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 552 ARG Chi-restraints excluded: chain A residue 584 SER Chi-restraints excluded: chain A residue 713 LYS Chi-restraints excluded: chain A residue 716 SER Chi-restraints excluded: chain A residue 742 GLU Chi-restraints excluded: chain A residue 772 GLN Chi-restraints excluded: chain A residue 791 ILE Chi-restraints excluded: chain A residue 801 ASP Chi-restraints excluded: chain A residue 807 THR Chi-restraints excluded: chain A residue 846 THR Chi-restraints excluded: chain A residue 862 VAL Chi-restraints excluded: chain A residue 872 SER Chi-restraints excluded: chain A residue 887 ASP Chi-restraints excluded: chain A residue 888 ASP Chi-restraints excluded: chain A residue 896 GLU Chi-restraints excluded: chain A residue 981 SER Chi-restraints excluded: chain A residue 1004 ASP Chi-restraints excluded: chain A residue 1015 GLU Chi-restraints excluded: chain B residue 15 ASP Chi-restraints excluded: chain B residue 45 TYR Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 58 ARG Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 227 ASP Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain B residue 261 ASP Chi-restraints excluded: chain B residue 275 MET Chi-restraints excluded: chain B residue 323 GLU Chi-restraints excluded: chain B residue 365 GLU Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 51 TRP Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 134 SER Chi-restraints excluded: chain C residue 212 TRP Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 331 ILE Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 388 MET Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 246 MET Chi-restraints excluded: chain D residue 257 LEU Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 297 SER Chi-restraints excluded: chain D residue 330 ASN Chi-restraints excluded: chain D residue 335 VAL Chi-restraints excluded: chain E residue 169 LYS Chi-restraints excluded: chain E residue 173 SER Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 222 GLU Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 230 GLN Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 300 CYS Chi-restraints excluded: chain E residue 317 ASP Chi-restraints excluded: chain G residue 263 ASN Chi-restraints excluded: chain G residue 284 SER Chi-restraints excluded: chain G residue 339 MET Chi-restraints excluded: chain G residue 342 CYS Chi-restraints excluded: chain G residue 344 TYR Chi-restraints excluded: chain G residue 379 VAL Chi-restraints excluded: chain G residue 418 VAL Chi-restraints excluded: chain G residue 430 SER Chi-restraints excluded: chain G residue 443 THR Chi-restraints excluded: chain G residue 446 SER Chi-restraints excluded: chain G residue 472 VAL Chi-restraints excluded: chain G residue 550 PHE Chi-restraints excluded: chain G residue 565 ASP Chi-restraints excluded: chain G residue 582 ASP Chi-restraints excluded: chain G residue 599 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 79 optimal weight: 0.3980 chunk 211 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 137 optimal weight: 0.3980 chunk 57 optimal weight: 0.5980 chunk 235 optimal weight: 0.7980 chunk 195 optimal weight: 5.9990 chunk 108 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 77 optimal weight: 0.3980 chunk 123 optimal weight: 0.5980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 390 ASN A 159 ASN ** A 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 583 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 593 HIS ** A 777 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 998 GLN B 37 ASN B 87 HIS B 125 ASN C 21 ASN C 152 HIS ** C 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 395 ASN ** D 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 201 ASN E 221 ASN ** E 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 459 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 moved from start: 0.4471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 20367 Z= 0.183 Angle : 0.638 9.524 27613 Z= 0.330 Chirality : 0.042 0.233 2988 Planarity : 0.005 0.071 3562 Dihedral : 7.278 64.214 2720 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.99 % Favored : 91.84 % Rotamer: Outliers : 5.75 % Allowed : 28.51 % Favored : 65.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.79 % Cis-general : 0.00 % Twisted Proline : 3.17 % Twisted General : 0.13 % 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: -1.73 (0.17), residues: 2415 helix: 0.25 (0.16), residues: 999 sheet: -1.34 (0.36), residues: 204 loop : -2.42 (0.16), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 74 HIS 0.004 0.001 HIS A 461 PHE 0.026 0.001 PHE A1031 TYR 0.028 0.001 TYR C 178 ARG 0.011 0.000 ARG F 366 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 2241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 269 time to evaluate : 2.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 368 LYS cc_start: 0.7504 (ttmp) cc_final: 0.7069 (mtmm) REVERT: F 400 ASN cc_start: 0.7141 (t0) cc_final: 0.6919 (m-40) REVERT: A 181 SER cc_start: 0.8313 (OUTLIER) cc_final: 0.8093 (m) REVERT: A 182 GLU cc_start: 0.7439 (OUTLIER) cc_final: 0.6292 (tm-30) REVERT: A 342 ARG cc_start: 0.6211 (mtt180) cc_final: 0.5643 (mtt90) REVERT: A 423 ARG cc_start: 0.7160 (OUTLIER) cc_final: 0.6277 (ptt-90) REVERT: A 552 ARG cc_start: 0.8487 (OUTLIER) cc_final: 0.7129 (ptp90) REVERT: A 554 ARG cc_start: 0.7038 (ptm-80) cc_final: 0.6731 (ptt90) REVERT: A 746 TYR cc_start: 0.7244 (m-80) cc_final: 0.6994 (m-80) REVERT: A 896 GLU cc_start: 0.7358 (OUTLIER) cc_final: 0.6853 (mt-10) REVERT: A 900 ASN cc_start: 0.5037 (OUTLIER) cc_final: 0.4789 (m-40) REVERT: B 15 ASP cc_start: 0.8192 (OUTLIER) cc_final: 0.7974 (m-30) REVERT: B 45 TYR cc_start: 0.6415 (OUTLIER) cc_final: 0.5947 (p90) REVERT: B 57 THR cc_start: 0.8202 (OUTLIER) cc_final: 0.7740 (m) REVERT: B 101 ASP cc_start: 0.6938 (OUTLIER) cc_final: 0.6526 (m-30) REVERT: C 93 ILE cc_start: 0.7467 (mm) cc_final: 0.7246 (mp) REVERT: C 175 LYS cc_start: 0.5935 (pptt) cc_final: 0.5556 (tppt) REVERT: C 388 MET cc_start: 0.7949 (OUTLIER) cc_final: 0.7648 (ptt) REVERT: C 407 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8213 (tt) REVERT: D 241 LYS cc_start: 0.6976 (mtmm) cc_final: 0.6758 (tmtt) REVERT: E 216 ILE cc_start: 0.7596 (pp) cc_final: 0.7347 (mm) REVERT: E 221 ASN cc_start: 0.8518 (p0) cc_final: 0.8124 (p0) REVERT: E 246 MET cc_start: 0.6327 (mtm) cc_final: 0.4708 (pp-130) REVERT: G 334 MET cc_start: 0.6539 (mpp) cc_final: 0.6182 (mpt) REVERT: G 400 LYS cc_start: 0.8065 (mtmt) cc_final: 0.7644 (ptmt) REVERT: G 438 ASN cc_start: 0.6579 (t0) cc_final: 0.6373 (t0) REVERT: G 449 ARG cc_start: 0.7462 (mtp-110) cc_final: 0.7109 (ttm110) REVERT: G 550 PHE cc_start: 0.7632 (OUTLIER) cc_final: 0.7074 (p90) REVERT: G 565 ASP cc_start: 0.6607 (OUTLIER) cc_final: 0.6239 (m-30) outliers start: 126 outliers final: 63 residues processed: 366 average time/residue: 1.2003 time to fit residues: 504.3095 Evaluate side-chains 328 residues out of total 2241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 251 time to evaluate : 2.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 141 LEU Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 207 SER Chi-restraints excluded: chain F residue 211 THR Chi-restraints excluded: chain F residue 345 ASP Chi-restraints excluded: chain F residue 349 LYS Chi-restraints excluded: chain F residue 391 LEU Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 423 ARG Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 552 ARG Chi-restraints excluded: chain A residue 584 SER Chi-restraints excluded: chain A residue 713 LYS Chi-restraints excluded: chain A residue 716 SER Chi-restraints excluded: chain A residue 772 GLN Chi-restraints excluded: chain A residue 801 ASP Chi-restraints excluded: chain A residue 807 THR Chi-restraints excluded: chain A residue 846 THR Chi-restraints excluded: chain A residue 862 VAL Chi-restraints excluded: chain A residue 887 ASP Chi-restraints excluded: chain A residue 896 GLU Chi-restraints excluded: chain A residue 900 ASN Chi-restraints excluded: chain A residue 1004 ASP Chi-restraints excluded: chain A residue 1009 LEU Chi-restraints excluded: chain A residue 1015 GLU Chi-restraints excluded: chain B residue 15 ASP Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 45 TYR Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 227 ASP Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain B residue 261 ASP Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 51 TRP Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 142 ASP Chi-restraints excluded: chain C residue 212 TRP Chi-restraints excluded: chain C residue 238 SER Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 331 ILE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 388 MET Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 330 ASN Chi-restraints excluded: chain D residue 335 VAL Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 215 LYS Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 294 ASP Chi-restraints excluded: chain E residue 300 CYS Chi-restraints excluded: chain G residue 263 ASN Chi-restraints excluded: chain G residue 339 MET Chi-restraints excluded: chain G residue 342 CYS Chi-restraints excluded: chain G residue 344 TYR Chi-restraints excluded: chain G residue 379 VAL Chi-restraints excluded: chain G residue 443 THR Chi-restraints excluded: chain G residue 446 SER Chi-restraints excluded: chain G residue 550 PHE Chi-restraints excluded: chain G residue 565 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 226 optimal weight: 0.9980 chunk 26 optimal weight: 0.2980 chunk 133 optimal weight: 1.9990 chunk 171 optimal weight: 5.9990 chunk 197 optimal weight: 0.8980 chunk 131 optimal weight: 4.9990 chunk 234 optimal weight: 0.1980 chunk 146 optimal weight: 1.9990 chunk 142 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 144 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 390 ASN A 159 ASN ** A 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 583 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 593 HIS ** A 777 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 998 GLN B 24 GLN B 87 HIS C 21 ASN C 152 HIS ** C 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 315 ASN ** D 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 201 ASN ** E 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 592 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 moved from start: 0.4592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 20367 Z= 0.228 Angle : 0.658 9.524 27613 Z= 0.339 Chirality : 0.044 0.342 2988 Planarity : 0.005 0.071 3562 Dihedral : 7.149 65.762 2717 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.57 % Favored : 91.26 % Rotamer: Outliers : 5.16 % Allowed : 29.20 % Favored : 65.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.79 % Cis-general : 0.00 % Twisted Proline : 3.17 % Twisted General : 0.09 % 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: -1.61 (0.17), residues: 2415 helix: 0.34 (0.17), residues: 999 sheet: -1.21 (0.36), residues: 203 loop : -2.35 (0.16), residues: 1213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 74 HIS 0.005 0.001 HIS B 207 PHE 0.024 0.002 PHE B 249 TYR 0.030 0.002 TYR A 574 ARG 0.011 0.001 ARG F 366 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 2241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 269 time to evaluate : 2.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 368 LYS cc_start: 0.7551 (ttmp) cc_final: 0.7097 (mtmm) REVERT: A 44 GLN cc_start: 0.7887 (OUTLIER) cc_final: 0.7434 (tt0) REVERT: A 182 GLU cc_start: 0.7455 (OUTLIER) cc_final: 0.6360 (tm-30) REVERT: A 342 ARG cc_start: 0.6187 (mtt180) cc_final: 0.5619 (mtt90) REVERT: A 423 ARG cc_start: 0.7220 (OUTLIER) cc_final: 0.6361 (ptt-90) REVERT: A 443 LEU cc_start: 0.6663 (OUTLIER) cc_final: 0.6365 (mt) REVERT: A 532 LYS cc_start: 0.7276 (mtpm) cc_final: 0.7054 (ttpp) REVERT: A 554 ARG cc_start: 0.7017 (ptm-80) cc_final: 0.6716 (ptt90) REVERT: A 896 GLU cc_start: 0.7139 (OUTLIER) cc_final: 0.6731 (mt-10) REVERT: B 45 TYR cc_start: 0.6470 (OUTLIER) cc_final: 0.5989 (p90) REVERT: B 57 THR cc_start: 0.8238 (OUTLIER) cc_final: 0.7758 (m) REVERT: B 101 ASP cc_start: 0.7043 (OUTLIER) cc_final: 0.6673 (m-30) REVERT: C 175 LYS cc_start: 0.5985 (pptt) cc_final: 0.5652 (tppt) REVERT: C 388 MET cc_start: 0.8000 (OUTLIER) cc_final: 0.7733 (ptt) REVERT: D 241 LYS cc_start: 0.7204 (mtmm) cc_final: 0.6906 (tmtt) REVERT: E 246 MET cc_start: 0.6489 (mtm) cc_final: 0.4845 (pp-130) REVERT: E 317 ASP cc_start: 0.4896 (OUTLIER) cc_final: 0.4616 (m-30) REVERT: G 400 LYS cc_start: 0.8064 (mtmt) cc_final: 0.7638 (ptmt) REVERT: G 449 ARG cc_start: 0.7482 (mtp-110) cc_final: 0.7120 (ttm110) REVERT: G 550 PHE cc_start: 0.7665 (OUTLIER) cc_final: 0.6800 (p90) REVERT: G 565 ASP cc_start: 0.6723 (OUTLIER) cc_final: 0.6242 (m-30) outliers start: 113 outliers final: 72 residues processed: 354 average time/residue: 1.2316 time to fit residues: 500.2409 Evaluate side-chains 336 residues out of total 2241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 252 time to evaluate : 2.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 141 LEU Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 207 SER Chi-restraints excluded: chain F residue 211 THR Chi-restraints excluded: chain F residue 345 ASP Chi-restraints excluded: chain F residue 378 VAL Chi-restraints excluded: chain F residue 391 LEU Chi-restraints excluded: chain A residue 44 GLN Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 423 ARG Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 552 ARG Chi-restraints excluded: chain A residue 584 SER Chi-restraints excluded: chain A residue 713 LYS Chi-restraints excluded: chain A residue 716 SER Chi-restraints excluded: chain A residue 772 GLN Chi-restraints excluded: chain A residue 801 ASP Chi-restraints excluded: chain A residue 807 THR Chi-restraints excluded: chain A residue 846 THR Chi-restraints excluded: chain A residue 862 VAL Chi-restraints excluded: chain A residue 887 ASP Chi-restraints excluded: chain A residue 888 ASP Chi-restraints excluded: chain A residue 896 GLU Chi-restraints excluded: chain A residue 1004 ASP Chi-restraints excluded: chain A residue 1009 LEU Chi-restraints excluded: chain A residue 1015 GLU Chi-restraints excluded: chain B residue 15 ASP Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 45 TYR Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 227 ASP Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain B residue 261 ASP Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 51 TRP Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 212 TRP Chi-restraints excluded: chain C residue 239 ASP Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 331 ILE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 388 MET Chi-restraints excluded: chain C residue 395 ASN Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 191 LYS Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 330 ASN Chi-restraints excluded: chain D residue 335 VAL Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 215 LYS Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 294 ASP Chi-restraints excluded: chain E residue 300 CYS Chi-restraints excluded: chain E residue 317 ASP Chi-restraints excluded: chain G residue 263 ASN Chi-restraints excluded: chain G residue 284 SER Chi-restraints excluded: chain G residue 339 MET Chi-restraints excluded: chain G residue 342 CYS Chi-restraints excluded: chain G residue 344 TYR Chi-restraints excluded: chain G residue 379 VAL Chi-restraints excluded: chain G residue 430 SER Chi-restraints excluded: chain G residue 443 THR Chi-restraints excluded: chain G residue 446 SER Chi-restraints excluded: chain G residue 550 PHE Chi-restraints excluded: chain G residue 565 ASP Chi-restraints excluded: chain G residue 599 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 93 optimal weight: 1.9990 chunk 139 optimal weight: 1.9990 chunk 70 optimal weight: 0.5980 chunk 46 optimal weight: 0.0010 chunk 45 optimal weight: 0.5980 chunk 148 optimal weight: 7.9990 chunk 159 optimal weight: 9.9990 chunk 115 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 184 optimal weight: 0.9990 chunk 213 optimal weight: 0.7980 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 390 ASN A 159 ASN ** A 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 583 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 593 HIS ** A 777 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 998 GLN B 24 GLN B 87 HIS C 21 ASN ** C 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 315 ASN ** D 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 201 ASN E 221 ASN ** E 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 438 ASN G 592 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.4764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 20367 Z= 0.193 Angle : 0.639 11.044 27613 Z= 0.329 Chirality : 0.043 0.380 2988 Planarity : 0.005 0.071 3562 Dihedral : 6.916 65.679 2715 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.07 % Favored : 91.76 % Rotamer: Outliers : 4.65 % Allowed : 29.93 % Favored : 65.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.79 % Cis-general : 0.00 % Twisted Proline : 3.17 % Twisted General : 0.09 % 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: -1.37 (0.17), residues: 2415 helix: 0.59 (0.17), residues: 983 sheet: -1.01 (0.37), residues: 201 loop : -2.24 (0.16), residues: 1231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 74 HIS 0.004 0.001 HIS B 36 PHE 0.025 0.001 PHE B 249 TYR 0.024 0.001 TYR D 304 ARG 0.012 0.000 ARG F 366 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 2241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 264 time to evaluate : 2.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 368 LYS cc_start: 0.7472 (ttmp) cc_final: 0.7055 (mtmm) REVERT: A 44 GLN cc_start: 0.7867 (OUTLIER) cc_final: 0.7359 (tt0) REVERT: A 182 GLU cc_start: 0.7439 (OUTLIER) cc_final: 0.6123 (tm-30) REVERT: A 423 ARG cc_start: 0.7251 (OUTLIER) cc_final: 0.6402 (ptt-90) REVERT: A 443 LEU cc_start: 0.6670 (OUTLIER) cc_final: 0.6406 (mt) REVERT: A 552 ARG cc_start: 0.8499 (OUTLIER) cc_final: 0.7319 (ptp90) REVERT: A 554 ARG cc_start: 0.7094 (ptm-80) cc_final: 0.6751 (ptt90) REVERT: B 45 TYR cc_start: 0.6375 (OUTLIER) cc_final: 0.5870 (p90) REVERT: B 57 THR cc_start: 0.8232 (OUTLIER) cc_final: 0.7751 (m) REVERT: C 68 HIS cc_start: 0.5823 (m-70) cc_final: 0.5391 (t-90) REVERT: C 77 LEU cc_start: 0.6769 (OUTLIER) cc_final: 0.6348 (pp) REVERT: C 388 MET cc_start: 0.7920 (OUTLIER) cc_final: 0.7665 (ptt) REVERT: E 216 ILE cc_start: 0.7470 (pp) cc_final: 0.7199 (mm) REVERT: E 221 ASN cc_start: 0.8242 (p0) cc_final: 0.7981 (p0) REVERT: E 246 MET cc_start: 0.6322 (mtm) cc_final: 0.4602 (pp-130) REVERT: E 270 ASP cc_start: 0.3902 (OUTLIER) cc_final: 0.2701 (p0) REVERT: G 400 LYS cc_start: 0.8059 (mtmt) cc_final: 0.7642 (ptmt) REVERT: G 449 ARG cc_start: 0.7502 (mtp-110) cc_final: 0.7118 (ttm110) REVERT: G 550 PHE cc_start: 0.7583 (OUTLIER) cc_final: 0.6975 (p90) REVERT: G 565 ASP cc_start: 0.6629 (OUTLIER) cc_final: 0.6163 (m-30) outliers start: 102 outliers final: 65 residues processed: 341 average time/residue: 1.2161 time to fit residues: 479.4998 Evaluate side-chains 326 residues out of total 2241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 249 time to evaluate : 2.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 211 THR Chi-restraints excluded: chain F residue 345 ASP Chi-restraints excluded: chain F residue 378 VAL Chi-restraints excluded: chain F residue 391 LEU Chi-restraints excluded: chain A residue 44 GLN Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 423 ARG Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 552 ARG Chi-restraints excluded: chain A residue 584 SER Chi-restraints excluded: chain A residue 713 LYS Chi-restraints excluded: chain A residue 716 SER Chi-restraints excluded: chain A residue 772 GLN Chi-restraints excluded: chain A residue 801 ASP Chi-restraints excluded: chain A residue 807 THR Chi-restraints excluded: chain A residue 846 THR Chi-restraints excluded: chain A residue 887 ASP Chi-restraints excluded: chain A residue 1004 ASP Chi-restraints excluded: chain A residue 1009 LEU Chi-restraints excluded: chain A residue 1015 GLU Chi-restraints excluded: chain B residue 15 ASP Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 45 TYR Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 227 ASP Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 261 ASP Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 51 TRP Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 212 TRP Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 264 ILE Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 384 CYS Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 388 MET Chi-restraints excluded: chain C residue 395 ASN Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain D residue 330 ASN Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 270 ASP Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 294 ASP Chi-restraints excluded: chain E residue 300 CYS Chi-restraints excluded: chain G residue 263 ASN Chi-restraints excluded: chain G residue 339 MET Chi-restraints excluded: chain G residue 342 CYS Chi-restraints excluded: chain G residue 344 TYR Chi-restraints excluded: chain G residue 348 HIS Chi-restraints excluded: chain G residue 379 VAL Chi-restraints excluded: chain G residue 430 SER Chi-restraints excluded: chain G residue 443 THR Chi-restraints excluded: chain G residue 550 PHE Chi-restraints excluded: chain G residue 565 ASP Chi-restraints excluded: chain G residue 599 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 224 optimal weight: 0.9990 chunk 204 optimal weight: 0.7980 chunk 218 optimal weight: 5.9990 chunk 131 optimal weight: 1.9990 chunk 95 optimal weight: 0.8980 chunk 171 optimal weight: 0.0070 chunk 66 optimal weight: 1.9990 chunk 197 optimal weight: 2.9990 chunk 206 optimal weight: 1.9990 chunk 217 optimal weight: 2.9990 chunk 143 optimal weight: 0.6980 overall best weight: 0.6800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 201 HIS A 159 ASN ** A 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 583 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 593 HIS ** A 777 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 998 GLN B 24 GLN B 87 HIS ** B 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 21 ASN ** C 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 315 ASN ** D 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 352 GLN G 438 ASN G 592 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.4853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 20367 Z= 0.205 Angle : 0.654 9.132 27613 Z= 0.337 Chirality : 0.044 0.369 2988 Planarity : 0.005 0.077 3562 Dihedral : 6.741 66.556 2708 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.20 % Favored : 91.68 % Rotamer: Outliers : 4.43 % Allowed : 30.38 % Favored : 65.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.79 % Cis-general : 0.00 % Twisted Proline : 3.17 % Twisted General : 0.09 % 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: -1.25 (0.17), residues: 2415 helix: 0.64 (0.17), residues: 985 sheet: -0.89 (0.37), residues: 201 loop : -2.15 (0.16), residues: 1229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 74 HIS 0.004 0.001 HIS B 36 PHE 0.029 0.001 PHE B 249 TYR 0.023 0.002 TYR A 574 ARG 0.012 0.000 ARG F 366 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 256 time to evaluate : 2.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 360 LYS cc_start: 0.7818 (tmmt) cc_final: 0.6986 (mtmt) REVERT: F 368 LYS cc_start: 0.7435 (ttmp) cc_final: 0.7067 (mtmm) REVERT: A 44 GLN cc_start: 0.7883 (OUTLIER) cc_final: 0.7391 (tt0) REVERT: A 182 GLU cc_start: 0.7431 (OUTLIER) cc_final: 0.6118 (tm-30) REVERT: A 423 ARG cc_start: 0.7233 (OUTLIER) cc_final: 0.6418 (ptt-90) REVERT: A 443 LEU cc_start: 0.6576 (OUTLIER) cc_final: 0.6161 (mt) REVERT: A 552 ARG cc_start: 0.8509 (OUTLIER) cc_final: 0.7671 (ptp90) REVERT: A 554 ARG cc_start: 0.7093 (ptm-80) cc_final: 0.6732 (ptt90) REVERT: A 1004 ASP cc_start: 0.6585 (OUTLIER) cc_final: 0.6262 (m-30) REVERT: B 45 TYR cc_start: 0.6442 (OUTLIER) cc_final: 0.5947 (p90) REVERT: B 57 THR cc_start: 0.8240 (OUTLIER) cc_final: 0.7757 (m) REVERT: C 68 HIS cc_start: 0.5849 (m-70) cc_final: 0.5472 (t-90) REVERT: C 77 LEU cc_start: 0.6899 (OUTLIER) cc_final: 0.6500 (pp) REVERT: C 388 MET cc_start: 0.7894 (OUTLIER) cc_final: 0.7671 (ptt) REVERT: E 169 LYS cc_start: 0.7387 (OUTLIER) cc_final: 0.7077 (mttm) REVERT: E 246 MET cc_start: 0.6431 (mtm) cc_final: 0.4823 (pp-130) REVERT: E 270 ASP cc_start: 0.3881 (OUTLIER) cc_final: 0.2534 (p0) REVERT: G 397 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8501 (tp) REVERT: G 400 LYS cc_start: 0.8058 (mtmt) cc_final: 0.7636 (ptmt) REVERT: G 449 ARG cc_start: 0.7504 (mtp-110) cc_final: 0.7115 (ttm110) REVERT: G 531 ARG cc_start: 0.7141 (tpt170) cc_final: 0.6593 (mtt90) REVERT: G 550 PHE cc_start: 0.7666 (OUTLIER) cc_final: 0.6940 (p90) REVERT: G 565 ASP cc_start: 0.6666 (OUTLIER) cc_final: 0.6173 (m-30) outliers start: 97 outliers final: 67 residues processed: 330 average time/residue: 1.1786 time to fit residues: 445.6292 Evaluate side-chains 329 residues out of total 2241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 247 time to evaluate : 2.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 211 THR Chi-restraints excluded: chain F residue 345 ASP Chi-restraints excluded: chain F residue 378 VAL Chi-restraints excluded: chain F residue 391 LEU Chi-restraints excluded: chain A residue 44 GLN Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 80 ARG Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 423 ARG Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 552 ARG Chi-restraints excluded: chain A residue 584 SER Chi-restraints excluded: chain A residue 713 LYS Chi-restraints excluded: chain A residue 716 SER Chi-restraints excluded: chain A residue 772 GLN Chi-restraints excluded: chain A residue 791 ILE Chi-restraints excluded: chain A residue 801 ASP Chi-restraints excluded: chain A residue 807 THR Chi-restraints excluded: chain A residue 846 THR Chi-restraints excluded: chain A residue 887 ASP Chi-restraints excluded: chain A residue 888 ASP Chi-restraints excluded: chain A residue 1004 ASP Chi-restraints excluded: chain A residue 1009 LEU Chi-restraints excluded: chain A residue 1015 GLU Chi-restraints excluded: chain B residue 15 ASP Chi-restraints excluded: chain B residue 45 TYR Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 227 ASP Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 261 ASP Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 51 TRP Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 212 TRP Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 264 ILE Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 384 CYS Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 388 MET Chi-restraints excluded: chain C residue 395 ASN Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 191 LYS Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain D residue 330 ASN Chi-restraints excluded: chain E residue 169 LYS Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 270 ASP Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 294 ASP Chi-restraints excluded: chain E residue 300 CYS Chi-restraints excluded: chain G residue 263 ASN Chi-restraints excluded: chain G residue 339 MET Chi-restraints excluded: chain G residue 342 CYS Chi-restraints excluded: chain G residue 344 TYR Chi-restraints excluded: chain G residue 348 HIS Chi-restraints excluded: chain G residue 379 VAL Chi-restraints excluded: chain G residue 397 LEU Chi-restraints excluded: chain G residue 430 SER Chi-restraints excluded: chain G residue 443 THR Chi-restraints excluded: chain G residue 550 PHE Chi-restraints excluded: chain G residue 565 ASP Chi-restraints excluded: chain G residue 599 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 230 optimal weight: 0.3980 chunk 140 optimal weight: 1.9990 chunk 109 optimal weight: 0.9990 chunk 160 optimal weight: 4.9990 chunk 242 optimal weight: 1.9990 chunk 222 optimal weight: 2.9990 chunk 192 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 148 optimal weight: 0.9990 chunk 118 optimal weight: 0.8980 chunk 153 optimal weight: 0.4980 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 ASN ** A 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 583 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 593 HIS ** A 777 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 998 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 24 GLN B 87 HIS C 21 ASN ** C 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 315 ASN ** D 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 201 ASN ** G 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 438 ASN G 592 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.4922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 20367 Z= 0.216 Angle : 0.666 10.648 27613 Z= 0.343 Chirality : 0.044 0.377 2988 Planarity : 0.005 0.078 3562 Dihedral : 6.741 67.899 2708 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.16 % Favored : 91.72 % Rotamer: Outliers : 4.52 % Allowed : 30.43 % Favored : 65.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.79 % Cis-general : 0.00 % Twisted Proline : 3.17 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.17), residues: 2415 helix: 0.70 (0.17), residues: 979 sheet: -0.89 (0.36), residues: 210 loop : -2.07 (0.17), residues: 1226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 74 HIS 0.004 0.001 HIS B 207 PHE 0.034 0.002 PHE A 889 TYR 0.030 0.002 TYR D 304 ARG 0.013 0.000 ARG F 366 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 2241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 258 time to evaluate : 2.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 360 LYS cc_start: 0.7806 (tmmt) cc_final: 0.6959 (mtmt) REVERT: F 368 LYS cc_start: 0.7482 (ttmp) cc_final: 0.7112 (mtmm) REVERT: A 44 GLN cc_start: 0.7890 (OUTLIER) cc_final: 0.7400 (tt0) REVERT: A 182 GLU cc_start: 0.7437 (OUTLIER) cc_final: 0.6127 (tm-30) REVERT: A 423 ARG cc_start: 0.7259 (OUTLIER) cc_final: 0.6451 (ptt-90) REVERT: A 443 LEU cc_start: 0.6621 (OUTLIER) cc_final: 0.6235 (mt) REVERT: A 552 ARG cc_start: 0.8504 (OUTLIER) cc_final: 0.7770 (ptp90) REVERT: A 554 ARG cc_start: 0.7088 (ptm-80) cc_final: 0.6723 (ptt90) REVERT: B 45 TYR cc_start: 0.6455 (OUTLIER) cc_final: 0.5958 (p90) REVERT: B 57 THR cc_start: 0.8226 (OUTLIER) cc_final: 0.7765 (m) REVERT: C 68 HIS cc_start: 0.5859 (m-70) cc_final: 0.5450 (t-90) REVERT: C 77 LEU cc_start: 0.6901 (OUTLIER) cc_final: 0.6513 (pp) REVERT: C 388 MET cc_start: 0.7921 (OUTLIER) cc_final: 0.7694 (ptt) REVERT: E 246 MET cc_start: 0.6341 (mtm) cc_final: 0.4596 (pp-130) REVERT: E 270 ASP cc_start: 0.3955 (OUTLIER) cc_final: 0.2744 (p0) REVERT: G 348 HIS cc_start: 0.5963 (OUTLIER) cc_final: 0.5734 (m-70) REVERT: G 397 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8500 (tp) REVERT: G 400 LYS cc_start: 0.8072 (mtmt) cc_final: 0.7618 (ptmt) REVERT: G 449 ARG cc_start: 0.7544 (mtp-110) cc_final: 0.7150 (ttm110) REVERT: G 531 ARG cc_start: 0.7189 (tpt170) cc_final: 0.6619 (mtt90) REVERT: G 550 PHE cc_start: 0.7671 (OUTLIER) cc_final: 0.6871 (p90) REVERT: G 565 ASP cc_start: 0.6589 (OUTLIER) cc_final: 0.6115 (m-30) outliers start: 99 outliers final: 74 residues processed: 334 average time/residue: 1.1491 time to fit residues: 440.7735 Evaluate side-chains 331 residues out of total 2241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 243 time to evaluate : 2.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 132 CYS Chi-restraints excluded: chain F residue 211 THR Chi-restraints excluded: chain F residue 345 ASP Chi-restraints excluded: chain F residue 378 VAL Chi-restraints excluded: chain F residue 391 LEU Chi-restraints excluded: chain A residue 44 GLN Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 80 ARG Chi-restraints excluded: chain A residue 113 ASN Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 423 ARG Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 552 ARG Chi-restraints excluded: chain A residue 584 SER Chi-restraints excluded: chain A residue 713 LYS Chi-restraints excluded: chain A residue 716 SER Chi-restraints excluded: chain A residue 772 GLN Chi-restraints excluded: chain A residue 791 ILE Chi-restraints excluded: chain A residue 801 ASP Chi-restraints excluded: chain A residue 807 THR Chi-restraints excluded: chain A residue 846 THR Chi-restraints excluded: chain A residue 887 ASP Chi-restraints excluded: chain A residue 888 ASP Chi-restraints excluded: chain A residue 900 ASN Chi-restraints excluded: chain A residue 1004 ASP Chi-restraints excluded: chain A residue 1009 LEU Chi-restraints excluded: chain A residue 1015 GLU Chi-restraints excluded: chain B residue 15 ASP Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 45 TYR Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 227 ASP Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 261 ASP Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 51 TRP Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 142 ASP Chi-restraints excluded: chain C residue 212 TRP Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 384 CYS Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 388 MET Chi-restraints excluded: chain C residue 395 ASN Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 191 LYS Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain D residue 330 ASN Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 270 ASP Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 294 ASP Chi-restraints excluded: chain E residue 300 CYS Chi-restraints excluded: chain G residue 263 ASN Chi-restraints excluded: chain G residue 284 SER Chi-restraints excluded: chain G residue 339 MET Chi-restraints excluded: chain G residue 342 CYS Chi-restraints excluded: chain G residue 344 TYR Chi-restraints excluded: chain G residue 348 HIS Chi-restraints excluded: chain G residue 379 VAL Chi-restraints excluded: chain G residue 397 LEU Chi-restraints excluded: chain G residue 430 SER Chi-restraints excluded: chain G residue 438 ASN Chi-restraints excluded: chain G residue 443 THR Chi-restraints excluded: chain G residue 550 PHE Chi-restraints excluded: chain G residue 565 ASP Chi-restraints excluded: chain G residue 599 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 205 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 177 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 193 optimal weight: 1.9990 chunk 80 optimal weight: 0.6980 chunk 198 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 169 optimal weight: 10.0000 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 ASN A 226 GLN ** A 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 583 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 593 HIS ** A 777 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 998 GLN B 24 GLN B 87 HIS C 21 ASN ** C 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 201 ASN ** G 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 438 ASN G 592 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.195873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 101)---------------| | r_work = 0.3690 r_free = 0.3690 target = 0.142449 restraints weight = 21290.549| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 1.85 r_work: 0.3471 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3352 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.4936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 20367 Z= 0.302 Angle : 0.728 14.516 27613 Z= 0.375 Chirality : 0.046 0.406 2988 Planarity : 0.006 0.076 3562 Dihedral : 6.952 76.542 2708 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.70 % Favored : 91.18 % Rotamer: Outliers : 4.65 % Allowed : 30.47 % Favored : 64.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.79 % Cis-general : 0.00 % Twisted Proline : 3.17 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.17), residues: 2415 helix: 0.47 (0.17), residues: 985 sheet: -0.92 (0.36), residues: 210 loop : -2.13 (0.16), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 74 HIS 0.006 0.001 HIS B 207 PHE 0.038 0.002 PHE A 889 TYR 0.028 0.002 TYR A 574 ARG 0.017 0.001 ARG B 75 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8524.64 seconds wall clock time: 151 minutes 48.65 seconds (9108.65 seconds total)