Starting phenix.real_space_refine on Wed Jul 24 23:33:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w9e_37366/07_2024/8w9e_37366_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w9e_37366/07_2024/8w9e_37366.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w9e_37366/07_2024/8w9e_37366.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w9e_37366/07_2024/8w9e_37366.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w9e_37366/07_2024/8w9e_37366_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w9e_37366/07_2024/8w9e_37366_neut.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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: 7 Type Number sf(0) Gaussians K 1 8.98 5 Zn 7 6.06 5 P 292 5.49 5 S 104 5.16 5 C 16810 2.51 5 N 4896 2.21 5 O 5776 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 664": "OE1" <-> "OE2" Residue "A PHE 668": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 684": "OE1" <-> "OE2" Residue "A PHE 685": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 692": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 701": "OD1" <-> "OD2" Residue "A PHE 708": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 717": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 720": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 726": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 749": "OE1" <-> "OE2" Residue "A ASP 762": "OD1" <-> "OD2" Residue "A PHE 795": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 819": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 839": "OE1" <-> "OE2" Residue "A GLU 845": "OE1" <-> "OE2" Residue "A PHE 849": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 863": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 871": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 872": "OD1" <-> "OD2" Residue "A ASP 881": "OD1" <-> "OD2" Residue "A GLU 903": "OE1" <-> "OE2" Residue "A PHE 924": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 935": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 958": "OD1" <-> "OD2" Residue "A PHE 979": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 981": "OD1" <-> "OD2" Residue "A PHE 995": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1008": "OE1" <-> "OE2" Residue "A PHE 1017": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1021": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1026": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1027": "OE1" <-> "OE2" Residue "A GLU 1030": "OE1" <-> "OE2" Residue "A TYR 1034": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1122": "OE1" <-> "OE2" Residue "A GLU 1123": "OE1" <-> "OE2" Residue "A PHE 1136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1156": "OE1" <-> "OE2" Residue "A GLU 1160": "OE1" <-> "OE2" Residue "A GLU 1166": "OE1" <-> "OE2" Residue "A PHE 1180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1185": "OD1" <-> "OD2" Residue "A ASP 1197": "OD1" <-> "OD2" Residue "A PHE 1198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1201": "OE1" <-> "OE2" Residue "A TYR 1204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1218": "OD1" <-> "OD2" Residue "A PHE 1224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1259": "OD1" <-> "OD2" Residue "A GLU 1264": "OE1" <-> "OE2" Residue "A PHE 1301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1306": "OD1" <-> "OD2" Residue "A TYR 1316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1321": "OD1" <-> "OD2" Residue "A ASP 1330": "OD1" <-> "OD2" Residue "A TYR 1337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 177": "OE1" <-> "OE2" Residue "E GLU 178": "OE1" <-> "OE2" Residue "E ASP 256": "OD1" <-> "OD2" Residue "E GLU 260": "OE1" <-> "OE2" Residue "E PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 323": "OE1" <-> "OE2" Residue "E PHE 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 359": "OE1" <-> "OE2" Residue "E PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 374": "OD1" <-> "OD2" Residue "E ASP 383": "OD1" <-> "OD2" Residue "E PHE 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 424": "NH1" <-> "NH2" Residue "E ARG 454": "NH1" <-> "NH2" Residue "E ARG 496": "NH1" <-> "NH2" Residue "E TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 507": "OE1" <-> "OE2" Residue "E TYR 549": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 550": "OD1" <-> "OD2" Residue "E PHE 551": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 556": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 571": "OE1" <-> "OE2" Residue "E ASP 575": "OD1" <-> "OD2" Residue "B GLU 4": "OE1" <-> "OE2" Residue "B PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 9": "OD1" <-> "OD2" Residue "B TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 62": "OE1" <-> "OE2" Residue "B GLU 73": "OE1" <-> "OE2" Residue "B PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 129": "OE1" <-> "OE2" Residue "B ARG 136": "NH1" <-> "NH2" Residue "B TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 195": "OE1" <-> "OE2" Residue "B PHE 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 213": "OE1" <-> "OE2" Residue "B TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 243": "OD1" <-> "OD2" Residue "B GLU 252": "OE1" <-> "OE2" Residue "B TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 325": "OE1" <-> "OE2" Residue "B TYR 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 342": "OE1" <-> "OE2" Residue "B TYR 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 368": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 370": "OD1" <-> "OD2" Residue "B GLU 381": "OE1" <-> "OE2" Residue "C TYR 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 268": "OE1" <-> "OE2" Residue "C TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 308": "OE1" <-> "OE2" Residue "C ASP 316": "OD1" <-> "OD2" Residue "C TYR 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 348": "OD1" <-> "OD2" Residue "C GLU 360": "OE1" <-> "OE2" Residue "C PHE 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 371": "OD1" <-> "OD2" Residue "C GLU 372": "OE1" <-> "OE2" Residue "C ARG 381": "NH1" <-> "NH2" Residue "C GLU 395": "OE1" <-> "OE2" Residue "D ASP 234": "OD1" <-> "OD2" Residue "D GLU 255": "OE1" <-> "OE2" Residue "D TYR 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 268": "OE1" <-> "OE2" Residue "D GLU 270": "OE1" <-> "OE2" Residue "D TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 307": "OD1" <-> "OD2" Residue "D TYR 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 360": "OE1" <-> "OE2" Residue "D PHE 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 371": "OD1" <-> "OD2" Residue "D GLU 372": "OE1" <-> "OE2" Residue "D ASP 383": "OD1" <-> "OD2" Residue "D ASP 384": "OD1" <-> "OD2" Residue "D TYR 394": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 276": "OD1" <-> "OD2" Residue "F ASP 288": "OD1" <-> "OD2" Residue "F PHE 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 323": "OE1" <-> "OE2" Residue "F PHE 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 359": "OE1" <-> "OE2" Residue "F GLU 375": "OE1" <-> "OE2" Residue "F ASP 543": "OD1" <-> "OD2" Residue "F PHE 551": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 556": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 569": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 59": "OE1" <-> "OE2" Residue "a PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 81": "OD1" <-> "OD2" Residue "a GLU 94": "OE1" <-> "OE2" Residue "a PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 63": "OE1" <-> "OE2" Residue "b TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 41": "OE1" <-> "OE2" Residue "c TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 56": "OE1" <-> "OE2" Residue "c GLU 64": "OE1" <-> "OE2" Residue "c ASP 72": "OD1" <-> "OD2" Residue "c GLU 92": "OE1" <-> "OE2" Residue "d GLU 35": "OE1" <-> "OE2" Residue "d TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 71": "OE1" <-> "OE2" Residue "d GLU 76": "OE1" <-> "OE2" Residue "d GLU 105": "OE1" <-> "OE2" Residue "e TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 50": "OE1" <-> "OE2" Residue "e TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 59": "OE1" <-> "OE2" Residue "e ASP 77": "OD1" <-> "OD2" Residue "e PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ASP 81": "OD1" <-> "OD2" Residue "e GLU 94": "OE1" <-> "OE2" Residue "e GLU 97": "OE1" <-> "OE2" Residue "e PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ASP 106": "OD1" <-> "OD2" Residue "f TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 74": "OE1" <-> "OE2" Residue "f TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 41": "OE1" <-> "OE2" Residue "g TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 56": "OE1" <-> "OE2" Residue "g GLU 64": "OE1" <-> "OE2" Residue "g ASP 72": "OD1" <-> "OD2" Residue "g GLU 92": "OE1" <-> "OE2" Residue "h GLU 35": "OE1" <-> "OE2" Residue "h TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 71": "OE1" <-> "OE2" Residue "h GLU 76": "OE1" <-> "OE2" Residue "h GLU 105": "OE1" <-> "OE2" Residue "G GLU 7": "OE1" <-> "OE2" Residue "G GLU 24": "OE1" <-> "OE2" Residue "G PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 90": "OE1" <-> "OE2" Residue "G TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 102": "OE1" <-> "OE2" Residue "G GLU 103": "OE1" <-> "OE2" Residue "G GLU 114": "OE1" <-> "OE2" Residue "G GLU 117": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 27886 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 5066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 5066 Classifications: {'peptide': 606} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 15, 'TRANS': 590} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "E" Number of atoms: 2884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2884 Classifications: {'peptide': 353} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 333} Chain breaks: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 3057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 3057 Classifications: {'peptide': 385} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 366} Chain: "C" Number of atoms: 1483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1483 Classifications: {'peptide': 183} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 175} Chain: "D" Number of atoms: 1497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1497 Classifications: {'peptide': 185} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 176} Chain: "F" Number of atoms: 1282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1282 Classifications: {'peptide': 156} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 147} Chain breaks: 1 Chain: "a" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 807 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "b" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 638 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "c" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 817 Classifications: {'peptide': 107} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "d" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 735 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "e" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 810 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "f" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 648 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "g" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 828 Classifications: {'peptide': 108} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 5, 'TRANS': 102} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "h" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 735 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "i" Number of atoms: 3011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3011 Classifications: {'DNA': 147} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 146} Chain: "j" Number of atoms: 3010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3010 Classifications: {'DNA': 147} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 146} Chain: "G" Number of atoms: 570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 570 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain breaks: 2 Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' ZN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' K': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5538 SG CYS E 263 101.457 103.747 85.536 1.00117.79 S ATOM 5555 SG CYS E 266 98.472 102.325 86.955 1.00105.03 S ATOM 5708 SG CYS E 286 102.814 101.271 87.448 1.00 96.46 S ATOM 5619 SG CYS E 275 110.324 110.355 78.330 1.00161.47 S ATOM 5640 SG CYS E 278 107.953 108.771 76.416 1.00166.22 S ATOM 5843 SG CYS E 303 110.280 106.376 76.659 1.00145.68 S ATOM 5866 SG CYS E 306 111.101 108.678 74.290 1.00146.36 S ATOM 6956 SG CYS E 440 68.269 86.757 97.346 1.00 80.51 S ATOM 6982 SG CYS E 443 65.850 83.503 97.220 1.00 83.12 S ATOM 7170 SG CYS E 466 66.498 84.995 100.330 1.00 85.78 S ATOM 6768 SG CYS E 417 59.602 86.865 107.059 1.00 90.08 S ATOM 6795 SG CYS E 420 57.427 86.765 109.770 1.00 89.58 S ATOM 7051 SG CYS E 451 61.549 86.260 110.056 1.00 70.30 S ATOM 14065 SG CYS F 263 74.355 33.528 55.854 1.00226.83 S ATOM 14235 SG CYS F 286 72.269 32.825 58.472 1.00233.15 S ATOM 14370 SG CYS F 303 71.289 45.077 55.093 1.00224.38 S Time building chain proxies: 14.29, per 1000 atoms: 0.51 Number of scatterers: 27886 At special positions: 0 Unit cell: (133.701, 185.877, 158.702, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 7 29.99 K 1 19.00 S 104 16.00 P 292 15.00 O 5776 8.00 N 4896 7.00 C 16810 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: 12.13 Conformation dependent library (CDL) restraints added in 4.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 501 " pdb="ZN ZN B 501 " - pdb=" ND1 HIS B 188 " pdb=" ZN E1000 " pdb="ZN ZN E1000 " - pdb=" ND1 HIS E 283 " pdb="ZN ZN E1000 " - pdb=" SG CYS E 263 " pdb="ZN ZN E1000 " - pdb=" SG CYS E 286 " pdb="ZN ZN E1000 " - pdb=" SG CYS E 266 " pdb=" ZN E1001 " pdb="ZN ZN E1001 " - pdb=" SG CYS E 275 " pdb="ZN ZN E1001 " - pdb=" SG CYS E 303 " pdb="ZN ZN E1001 " - pdb=" SG CYS E 278 " pdb="ZN ZN E1001 " - pdb=" SG CYS E 306 " pdb=" ZN E1002 " pdb="ZN ZN E1002 " - pdb=" SG CYS E 443 " pdb="ZN ZN E1002 " - pdb=" SG CYS E 440 " pdb="ZN ZN E1002 " - pdb=" SG CYS E 466 " pdb=" ZN E1003 " pdb="ZN ZN E1003 " - pdb=" ND1 HIS E 448 " pdb="ZN ZN E1003 " - pdb=" SG CYS E 420 " pdb="ZN ZN E1003 " - pdb=" SG CYS E 417 " pdb="ZN ZN E1003 " - pdb=" SG CYS E 451 " pdb=" ZN F1000 " pdb="ZN ZN F1000 " - pdb=" ND1 HIS F 283 " pdb="ZN ZN F1000 " - pdb=" SG CYS F 263 " pdb="ZN ZN F1000 " - pdb=" SG CYS F 286 " pdb=" ZN F1001 " pdb="ZN ZN F1001 " - pdb=" SG CYS F 303 " Number of angles added : 12 5294 Ramachandran restraints generated. 2647 Oldfield, 0 Emsley, 2647 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5114 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 21 sheets defined 59.0% alpha, 5.2% beta 147 base pairs and 271 stacking pairs defined. Time for finding SS restraints: 11.72 Creating SS restraints... Processing helix chain 'A' and resid 663 through 676 Processing helix chain 'A' and resid 678 through 694 Processing helix chain 'A' and resid 698 through 711 removed outlier: 3.581A pdb=" N PHE A 708 " --> pdb=" O GLU A 704 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N TYR A 709 " --> pdb=" O LYS A 705 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 725 Processing helix chain 'A' and resid 772 through 778 removed outlier: 3.739A pdb=" N LEU A 778 " --> pdb=" O CYS A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 840 removed outlier: 3.618A pdb=" N GLU A 805 " --> pdb=" O ASN A 801 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ILE A 810 " --> pdb=" O THR A 806 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLU A 811 " --> pdb=" O LEU A 807 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N CYS A 830 " --> pdb=" O ARG A 826 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ASN A 840 " --> pdb=" O ASN A 836 " (cutoff:3.500A) Processing helix chain 'A' and resid 842 through 849 Processing helix chain 'A' and resid 861 through 871 Processing helix chain 'A' and resid 872 through 886 Processing helix chain 'A' and resid 886 through 922 Proline residue: A 892 - end of helix removed outlier: 4.462A pdb=" N VAL A 915 " --> pdb=" O GLU A 911 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LYS A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 928 Processing helix chain 'A' and resid 944 through 964 removed outlier: 3.933A pdb=" N ILE A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE A 964 " --> pdb=" O THR A 960 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 999 removed outlier: 4.155A pdb=" N TYR A 986 " --> pdb=" O LYS A 982 " (cutoff:3.500A) Processing helix chain 'A' and resid 1003 through 1022 removed outlier: 3.517A pdb=" N PHE A1022 " --> pdb=" O ILE A1018 " (cutoff:3.500A) Processing helix chain 'A' and resid 1025 through 1039 removed outlier: 3.557A pdb=" N ASN A1039 " --> pdb=" O SER A1035 " (cutoff:3.500A) Processing helix chain 'A' and resid 1064 through 1070 Processing helix chain 'A' and resid 1070 through 1081 removed outlier: 3.765A pdb=" N ASN A1081 " --> pdb=" O LEU A1077 " (cutoff:3.500A) Processing helix chain 'A' and resid 1119 through 1127 Processing helix chain 'A' and resid 1141 through 1174 removed outlier: 3.548A pdb=" N TYR A1145 " --> pdb=" O ASN A1141 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N GLU A1166 " --> pdb=" O LYS A1162 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N ARG A1167 " --> pdb=" O GLN A1163 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N THR A1174 " --> pdb=" O LYS A1170 " (cutoff:3.500A) Processing helix chain 'A' and resid 1178 through 1184 removed outlier: 4.017A pdb=" N LEU A1184 " --> pdb=" O PHE A1180 " (cutoff:3.500A) Processing helix chain 'A' and resid 1189 through 1194 Processing helix chain 'A' and resid 1202 through 1217 Processing helix chain 'A' and resid 1220 through 1232 removed outlier: 3.619A pdb=" N PHE A1224 " --> pdb=" O GLU A1220 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR A1232 " --> pdb=" O LEU A1228 " (cutoff:3.500A) Processing helix chain 'A' and resid 1237 through 1240 Processing helix chain 'A' and resid 1241 through 1259 removed outlier: 3.743A pdb=" N THR A1246 " --> pdb=" O ILE A1242 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER A1248 " --> pdb=" O LYS A1244 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N THR A1255 " --> pdb=" O LYS A1251 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU A1256 " --> pdb=" O HIS A1252 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N MET A1257 " --> pdb=" O ALA A1253 " (cutoff:3.500A) Processing helix chain 'A' and resid 1259 through 1275 Processing helix chain 'A' and resid 1279 through 1292 removed outlier: 3.543A pdb=" N GLN A1283 " --> pdb=" O SER A1279 " (cutoff:3.500A) Processing helix chain 'A' and resid 1329 through 1343 removed outlier: 3.688A pdb=" N LEU A1343 " --> pdb=" O THR A1339 " (cutoff:3.500A) Processing helix chain 'E' and resid 303 through 313 Processing helix chain 'E' and resid 315 through 330 Processing helix chain 'E' and resid 331 through 334 Processing helix chain 'E' and resid 336 through 343 Processing helix chain 'E' and resid 344 through 346 No H-bonds generated for 'chain 'E' and resid 344 through 346' Processing helix chain 'E' and resid 354 through 359 removed outlier: 3.510A pdb=" N LYS E 358 " --> pdb=" O PRO E 354 " (cutoff:3.500A) Processing helix chain 'E' and resid 383 through 389 Processing helix chain 'E' and resid 544 through 580 removed outlier: 3.509A pdb=" N ASN E 580 " --> pdb=" O LYS E 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 55 removed outlier: 3.914A pdb=" N ALA B 48 " --> pdb=" O ARG B 44 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N HIS B 49 " --> pdb=" O ILE B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 75 Processing helix chain 'B' and resid 79 through 89 Processing helix chain 'B' and resid 93 through 98 removed outlier: 3.719A pdb=" N LYS B 98 " --> pdb=" O GLU B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 104 Processing helix chain 'B' and resid 115 through 137 Processing helix chain 'B' and resid 164 through 175 removed outlier: 3.879A pdb=" N LEU B 168 " --> pdb=" O ASN B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 197 Processing helix chain 'B' and resid 226 through 230 removed outlier: 3.589A pdb=" N LYS B 230 " --> pdb=" O GLY B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 262 Proline residue: B 253 - end of helix Processing helix chain 'B' and resid 288 through 301 removed outlier: 4.807A pdb=" N CYS B 294 " --> pdb=" O GLY B 290 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N VAL B 295 " --> pdb=" O HIS B 291 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N PHE B 301 " --> pdb=" O TYR B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 330 Processing helix chain 'B' and resid 365 through 381 Processing helix chain 'C' and resid 225 through 239 Processing helix chain 'C' and resid 253 through 269 removed outlier: 3.633A pdb=" N VAL C 257 " --> pdb=" O THR C 253 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLU C 268 " --> pdb=" O GLU C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 297 removed outlier: 3.562A pdb=" N GLN C 275 " --> pdb=" O SER C 271 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N GLY C 294 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N ASN C 295 " --> pdb=" O LYS C 291 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU C 297 " --> pdb=" O LEU C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 317 Processing helix chain 'C' and resid 321 through 325 removed outlier: 3.686A pdb=" N ARG C 324 " --> pdb=" O VAL C 321 " (cutoff:3.500A) Processing helix chain 'C' and resid 328 through 344 Proline residue: C 339 - end of helix Processing helix chain 'C' and resid 348 through 369 removed outlier: 3.632A pdb=" N HIS C 369 " --> pdb=" O TRP C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 374 removed outlier: 4.083A pdb=" N TYR C 373 " --> pdb=" O HIS C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 401 Processing helix chain 'D' and resid 225 through 241 removed outlier: 3.917A pdb=" N LYS D 229 " --> pdb=" O PRO D 225 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 266 removed outlier: 3.587A pdb=" N VAL D 257 " --> pdb=" O THR D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 269 No H-bonds generated for 'chain 'D' and resid 267 through 269' Processing helix chain 'D' and resid 271 through 293 removed outlier: 3.516A pdb=" N GLN D 275 " --> pdb=" O SER D 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 317 removed outlier: 3.555A pdb=" N GLN D 317 " --> pdb=" O SER D 313 " (cutoff:3.500A) Processing helix chain 'D' and resid 328 through 344 Proline residue: D 339 - end of helix Processing helix chain 'D' and resid 348 through 369 Processing helix chain 'D' and resid 369 through 375 removed outlier: 4.237A pdb=" N TYR D 373 " --> pdb=" O HIS D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 381 through 385 Processing helix chain 'D' and resid 391 through 399 removed outlier: 3.625A pdb=" N GLU D 395 " --> pdb=" O SER D 391 " (cutoff:3.500A) Processing helix chain 'F' and resid 303 through 313 Processing helix chain 'F' and resid 315 through 330 Processing helix chain 'F' and resid 333 through 335 No H-bonds generated for 'chain 'F' and resid 333 through 335' Processing helix chain 'F' and resid 336 through 344 removed outlier: 3.558A pdb=" N ASN F 342 " --> pdb=" O LYS F 338 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ASP F 344 " --> pdb=" O LEU F 340 " (cutoff:3.500A) Processing helix chain 'F' and resid 354 through 359 Processing helix chain 'F' and resid 544 through 577 Processing helix chain 'a' and resid 44 through 57 removed outlier: 3.520A pdb=" N SER a 57 " --> pdb=" O ARG a 53 " (cutoff:3.500A) Processing helix chain 'a' and resid 63 through 76 removed outlier: 3.636A pdb=" N PHE a 67 " --> pdb=" O ARG a 63 " (cutoff:3.500A) Processing helix chain 'a' and resid 85 through 114 removed outlier: 3.643A pdb=" N VAL a 89 " --> pdb=" O GLN a 85 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA a 114 " --> pdb=" O CYS a 110 " (cutoff:3.500A) Processing helix chain 'a' and resid 120 through 131 removed outlier: 3.570A pdb=" N ILE a 124 " --> pdb=" O MET a 120 " (cutoff:3.500A) Processing helix chain 'b' and resid 30 through 41 Processing helix chain 'b' and resid 49 through 76 removed outlier: 3.940A pdb=" N GLU b 53 " --> pdb=" O LEU b 49 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ASP b 68 " --> pdb=" O ASN b 64 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA b 76 " --> pdb=" O TYR b 72 " (cutoff:3.500A) Processing helix chain 'b' and resid 82 through 93 Processing helix chain 'c' and resid 16 through 22 Processing helix chain 'c' and resid 26 through 37 removed outlier: 3.660A pdb=" N VAL c 30 " --> pdb=" O PRO c 26 " (cutoff:3.500A) Processing helix chain 'c' and resid 45 through 73 removed outlier: 4.482A pdb=" N VAL c 49 " --> pdb=" O ALA c 45 " (cutoff:3.500A) Processing helix chain 'c' and resid 79 through 90 removed outlier: 3.624A pdb=" N ASP c 90 " --> pdb=" O ALA c 86 " (cutoff:3.500A) Processing helix chain 'c' and resid 90 through 97 Processing helix chain 'd' and resid 37 through 49 Processing helix chain 'd' and resid 55 through 84 Processing helix chain 'd' and resid 90 through 102 Processing helix chain 'd' and resid 103 through 123 removed outlier: 3.529A pdb=" N ALA d 107 " --> pdb=" O PRO d 103 " (cutoff:3.500A) Processing helix chain 'e' and resid 44 through 56 Processing helix chain 'e' and resid 63 through 79 removed outlier: 3.649A pdb=" N PHE e 67 " --> pdb=" O ARG e 63 " (cutoff:3.500A) Processing helix chain 'e' and resid 85 through 114 removed outlier: 3.748A pdb=" N VAL e 89 " --> pdb=" O GLN e 85 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA e 114 " --> pdb=" O CYS e 110 " (cutoff:3.500A) Processing helix chain 'e' and resid 120 through 132 removed outlier: 3.622A pdb=" N ILE e 124 " --> pdb=" O MET e 120 " (cutoff:3.500A) Processing helix chain 'f' and resid 25 through 29 Processing helix chain 'f' and resid 30 through 41 Processing helix chain 'f' and resid 49 through 76 removed outlier: 3.699A pdb=" N GLU f 53 " --> pdb=" O LEU f 49 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ASP f 68 " --> pdb=" O ASN f 64 " (cutoff:3.500A) Processing helix chain 'f' and resid 82 through 93 removed outlier: 3.549A pdb=" N VAL f 86 " --> pdb=" O THR f 82 " (cutoff:3.500A) Processing helix chain 'g' and resid 17 through 22 Processing helix chain 'g' and resid 26 through 37 removed outlier: 3.659A pdb=" N VAL g 30 " --> pdb=" O PRO g 26 " (cutoff:3.500A) Processing helix chain 'g' and resid 45 through 73 removed outlier: 4.481A pdb=" N VAL g 49 " --> pdb=" O ALA g 45 " (cutoff:3.500A) Processing helix chain 'g' and resid 79 through 90 removed outlier: 3.624A pdb=" N ASP g 90 " --> pdb=" O ALA g 86 " (cutoff:3.500A) Processing helix chain 'g' and resid 90 through 97 Processing helix chain 'h' and resid 37 through 49 Processing helix chain 'h' and resid 55 through 84 Processing helix chain 'h' and resid 90 through 102 Processing helix chain 'h' and resid 103 through 123 removed outlier: 3.529A pdb=" N ALA h 107 " --> pdb=" O PRO h 103 " (cutoff:3.500A) Processing helix chain 'G' and resid 101 through 122 Processing sheet with id=AA1, first strand: chain 'A' and resid 975 through 978 removed outlier: 4.115A pdb=" N MET A1300 " --> pdb=" O ILE A1317 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 975 through 978 removed outlier: 4.115A pdb=" N MET A1300 " --> pdb=" O ILE A1317 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 272 through 273 Processing sheet with id=AA4, first strand: chain 'E' and resid 365 through 366 Processing sheet with id=AA5, first strand: chain 'E' and resid 437 through 439 Processing sheet with id=AA6, first strand: chain 'E' and resid 505 through 506 removed outlier: 3.675A pdb=" N GLN E 521 " --> pdb=" O THR E 540 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 62 through 64 removed outlier: 6.575A pdb=" N ALA B 22 " --> pdb=" O VAL B 143 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N ALA B 142 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N LEU B 181 " --> pdb=" O VAL B 268 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N GLN B 270 " --> pdb=" O LEU B 181 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N ILE B 183 " --> pdb=" O GLN B 270 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N VAL B 180 " --> pdb=" O MET B 204 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N CYS B 206 " --> pdb=" O VAL B 180 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N TYR B 182 " --> pdb=" O CYS B 206 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N PHE B 208 " --> pdb=" O TYR B 182 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N ASP B 184 " --> pdb=" O PHE B 208 " (cutoff:3.500A) removed outlier: 8.680A pdb=" N LYS B 210 " --> pdb=" O ASP B 184 " (cutoff:3.500A) removed outlier: 8.291A pdb=" N VAL B 234 " --> pdb=" O VAL B 203 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N THR B 205 " --> pdb=" O VAL B 234 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N VAL B 236 " --> pdb=" O THR B 205 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N SER B 207 " --> pdb=" O VAL B 236 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N LEU B 238 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N HIS B 209 " --> pdb=" O LEU B 238 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 244 through 246 Processing sheet with id=AA9, first strand: chain 'D' and resid 244 through 246 Processing sheet with id=AB1, first strand: chain 'F' and resid 272 through 274 Processing sheet with id=AB2, first strand: chain 'F' and resid 364 through 366 Processing sheet with id=AB3, first strand: chain 'a' and resid 83 through 84 removed outlier: 6.791A pdb=" N ARG a 83 " --> pdb=" O VAL b 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'b' and resid 96 through 98 Processing sheet with id=AB5, first strand: chain 'c' and resid 42 through 43 removed outlier: 7.353A pdb=" N ARG c 42 " --> pdb=" O ILE d 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'c' and resid 77 through 78 Processing sheet with id=AB7, first strand: chain 'c' and resid 100 through 102 removed outlier: 6.514A pdb=" N THR c 101 " --> pdb=" O TYR f 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'e' and resid 83 through 84 removed outlier: 6.873A pdb=" N ARG e 83 " --> pdb=" O VAL f 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'e' and resid 118 through 119 Processing sheet with id=AC1, first strand: chain 'g' and resid 42 through 43 removed outlier: 7.090A pdb=" N ARG g 42 " --> pdb=" O ILE h 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'g' and resid 77 through 78 Processing sheet with id=AC3, first strand: chain 'G' and resid 90 through 93 removed outlier: 6.854A pdb=" N CYS G 76 " --> pdb=" O ILE G 30 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N ILE G 30 " --> pdb=" O CYS G 76 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N PHE G 78 " --> pdb=" O LEU G 28 " (cutoff:3.500A) 1146 hydrogen bonds defined for protein. 3375 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 354 hydrogen bonds 708 hydrogen bond angles 0 basepair planarities 147 basepair parallelities 271 stacking parallelities Total time for adding SS restraints: 16.81 Time building geometry restraints manager: 13.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.12 - 1.44: 13197 1.44 - 1.76: 15693 1.76 - 2.08: 158 2.08 - 2.39: 1 2.39 - 2.71: 1 Bond restraints: 29050 Sorted by residual: bond pdb=" CB TYR F 372 " pdb=" CG TYR F 372 " ideal model delta sigma weight residual 1.512 2.710 -1.198 2.20e-02 2.07e+03 2.97e+03 bond pdb=" CE3 TRP D 236 " pdb=" CZ3 TRP D 236 " ideal model delta sigma weight residual 1.382 2.260 -0.878 3.00e-02 1.11e+03 8.57e+02 bond pdb=" CE2 TRP D 236 " pdb=" CZ2 TRP D 236 " ideal model delta sigma weight residual 1.394 1.829 -0.435 2.10e-02 2.27e+03 4.30e+02 bond pdb=" CZ3 TRP D 236 " pdb=" CH2 TRP D 236 " ideal model delta sigma weight residual 1.400 1.859 -0.459 2.50e-02 1.60e+03 3.37e+02 bond pdb=" N PRO E 380 " pdb=" CA PRO E 380 " ideal model delta sigma weight residual 1.469 1.694 -0.225 1.28e-02 6.10e+03 3.10e+02 ... (remaining 29045 not shown) Histogram of bond angle deviations from ideal: 92.32 - 101.56: 298 101.56 - 110.79: 11602 110.79 - 120.02: 16526 120.02 - 129.26: 11757 129.26 - 138.49: 285 Bond angle restraints: 40468 Sorted by residual: angle pdb=" C ILE E 379 " pdb=" N PRO E 380 " pdb=" CA PRO E 380 " ideal model delta sigma weight residual 119.84 138.49 -18.65 1.25e+00 6.40e-01 2.23e+02 angle pdb=" CA TYR F 372 " pdb=" CB TYR F 372 " pdb=" CG TYR F 372 " ideal model delta sigma weight residual 113.90 137.36 -23.46 1.80e+00 3.09e-01 1.70e+02 angle pdb=" C LYS B 67 " pdb=" N PRO B 68 " pdb=" CA PRO B 68 " ideal model delta sigma weight residual 119.84 135.70 -15.86 1.25e+00 6.40e-01 1.61e+02 angle pdb=" C THR c 16 " pdb=" CA THR c 16 " pdb=" CB THR c 16 " ideal model delta sigma weight residual 111.71 92.67 19.04 2.23e+00 2.01e-01 7.29e+01 angle pdb=" N ILE E 181 " pdb=" CA ILE E 181 " pdb=" C ILE E 181 " ideal model delta sigma weight residual 113.43 104.13 9.30 1.09e+00 8.42e-01 7.28e+01 ... (remaining 40463 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 12944 17.89 - 35.78: 2063 35.78 - 53.66: 1408 53.66 - 71.55: 406 71.55 - 89.44: 31 Dihedral angle restraints: 16852 sinusoidal: 8939 harmonic: 7913 Sorted by residual: dihedral pdb=" C THR E 169 " pdb=" N THR E 169 " pdb=" CA THR E 169 " pdb=" CB THR E 169 " ideal model delta harmonic sigma weight residual -122.00 -152.25 30.25 0 2.50e+00 1.60e-01 1.46e+02 dihedral pdb=" N THR E 169 " pdb=" C THR E 169 " pdb=" CA THR E 169 " pdb=" CB THR E 169 " ideal model delta harmonic sigma weight residual 123.40 150.97 -27.57 0 2.50e+00 1.60e-01 1.22e+02 dihedral pdb=" C THR E 172 " pdb=" N THR E 172 " pdb=" CA THR E 172 " pdb=" CB THR E 172 " ideal model delta harmonic sigma weight residual -122.00 -145.09 23.09 0 2.50e+00 1.60e-01 8.53e+01 ... (remaining 16849 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.239: 4430 0.239 - 0.477: 29 0.477 - 0.716: 6 0.716 - 0.954: 2 0.954 - 1.193: 1 Chirality restraints: 4468 Sorted by residual: chirality pdb=" CA THR E 169 " pdb=" N THR E 169 " pdb=" C THR E 169 " pdb=" CB THR E 169 " both_signs ideal model delta sigma weight residual False 2.53 1.33 1.19 2.00e-01 2.50e+01 3.56e+01 chirality pdb=" CA THR E 172 " pdb=" N THR E 172 " pdb=" C THR E 172 " pdb=" CB THR E 172 " both_signs ideal model delta sigma weight residual False 2.53 1.69 0.84 2.00e-01 2.50e+01 1.75e+01 chirality pdb=" CA TYR B 32 " pdb=" N TYR B 32 " pdb=" C TYR B 32 " pdb=" CB TYR B 32 " both_signs ideal model delta sigma weight residual False 2.51 1.74 0.77 2.00e-01 2.50e+01 1.50e+01 ... (remaining 4465 not shown) Planarity restraints: 4131 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG B 20 " 0.033 2.00e-02 2.50e+03 7.02e-02 4.93e+01 pdb=" C ARG B 20 " -0.121 2.00e-02 2.50e+03 pdb=" O ARG B 20 " 0.047 2.00e-02 2.50e+03 pdb=" N VAL B 21 " 0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR g 16 " 0.027 2.00e-02 2.50e+03 5.53e-02 3.06e+01 pdb=" C THR g 16 " -0.096 2.00e-02 2.50e+03 pdb=" O THR g 16 " 0.036 2.00e-02 2.50e+03 pdb=" N ARG g 17 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE E 379 " -0.029 2.00e-02 2.50e+03 5.18e-02 2.68e+01 pdb=" C ILE E 379 " 0.090 2.00e-02 2.50e+03 pdb=" O ILE E 379 " -0.032 2.00e-02 2.50e+03 pdb=" N PRO E 380 " -0.029 2.00e-02 2.50e+03 ... (remaining 4128 not shown) Histogram of nonbonded interaction distances: 1.01 - 1.84: 12 1.84 - 2.66: 852 2.66 - 3.49: 42895 3.49 - 4.31: 86742 4.31 - 5.14: 143286 Nonbonded interactions: 273787 Sorted by model distance: nonbonded pdb=" CD1 TRP E 187 " pdb=" OE1 GLN B 72 " model vdw 1.013 3.260 nonbonded pdb=" CB SER E 179 " pdb=" OE2 GLU B 129 " model vdw 1.135 3.440 nonbonded pdb=" CG2 THR E 169 " pdb=" CB MET B 53 " model vdw 1.327 3.860 nonbonded pdb=" OE2 GLU A 918 " pdb=" CA LEU E 128 " model vdw 1.410 3.470 nonbonded pdb=" OE2 GLU A 918 " pdb=" CB LEU E 128 " model vdw 1.555 3.440 ... (remaining 273782 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 'C' selection = (chain 'D' and resid 219 through 401) } ncs_group { reference = (chain 'a' and resid 38 through 134) selection = (chain 'e' and resid 38 through 134) } ncs_group { reference = (chain 'b' and resid 23 through 101) selection = (chain 'f' and resid 23 through 101) } ncs_group { reference = chain 'c' selection = (chain 'g' and resid 12 through 118) } ncs_group { reference = chain 'd' selection = chain 'h' } ncs_group { reference = (chain 'i' and (resid -73 through -1 or resid 1 through 73)) selection = (chain 'j' and (resid -73 through -1 or resid 1 through 73)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 1.000 Check model and map are aligned: 0.200 Set scattering table: 0.250 Process input model: 92.220 Find NCS groups from input model: 1.060 Set up NCS constraints: 0.120 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: 0.000 Load rotamer database and sin/cos tables:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 98.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5522 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 : 0.013 1.198 29050 Z= 0.796 Angle : 0.972 23.459 40468 Z= 0.603 Chirality : 0.063 1.193 4468 Planarity : 0.007 0.108 4131 Dihedral : 23.116 89.440 11738 Min Nonbonded Distance : 1.013 Molprobity Statistics. All-atom Clashscore : 14.93 Ramachandran Plot: Outliers : 0.64 % Allowed : 5.82 % Favored : 93.54 % Rotamer: Outliers : 3.59 % Allowed : 7.76 % Favored : 88.66 % Cbeta Deviations : 0.66 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.23 % 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: -2.40 (0.14), residues: 2647 helix: -0.73 (0.12), residues: 1508 sheet: -1.72 (0.45), residues: 106 loop : -2.86 (0.16), residues: 1033 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.005 TRP G 31 HIS 0.009 0.002 HIS G 18 PHE 0.033 0.002 PHE A1301 TYR 0.053 0.002 TYR G 100 ARG 0.010 0.001 ARG h 33 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5294 Ramachandran restraints generated. 2647 Oldfield, 0 Emsley, 2647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5294 Ramachandran restraints generated. 2647 Oldfield, 0 Emsley, 2647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 2405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 387 time to evaluate : 2.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 800 LYS cc_start: 0.0373 (mmpt) cc_final: -0.0153 (ttmt) REVERT: A 998 HIS cc_start: 0.4273 (t-170) cc_final: 0.3973 (t-170) REVERT: A 1009 ARG cc_start: 0.3927 (mtp180) cc_final: 0.3449 (tpt90) REVERT: A 1164 MET cc_start: 0.0791 (mtm) cc_final: 0.0040 (tpp) REVERT: A 1209 ARG cc_start: 0.2884 (ttp-170) cc_final: 0.0811 (tmm-80) REVERT: A 1286 TYR cc_start: 0.1359 (t80) cc_final: 0.1009 (m-80) REVERT: A 1290 VAL cc_start: 0.1613 (t) cc_final: 0.0823 (p) REVERT: E 105 ASP cc_start: 0.1790 (OUTLIER) cc_final: 0.1551 (t0) REVERT: E 316 MET cc_start: 0.0241 (mmp) cc_final: -0.0341 (mtm) REVERT: E 350 GLN cc_start: 0.2243 (pt0) cc_final: 0.1325 (mm-40) REVERT: E 523 ILE cc_start: 0.3386 (pt) cc_final: 0.3148 (tp) REVERT: E 557 LYS cc_start: 0.1253 (pptt) cc_final: 0.0910 (tppt) REVERT: B 163 LEU cc_start: 0.0472 (tp) cc_final: -0.0159 (tp) REVERT: D 227 LYS cc_start: -0.0452 (tttt) cc_final: -0.0683 (tttp) REVERT: D 296 MET cc_start: 0.2181 (ttp) cc_final: 0.1595 (tmm) REVERT: F 331 ASN cc_start: 0.3576 (t0) cc_final: 0.3004 (p0) REVERT: F 559 LYS cc_start: 0.1437 (mtpt) cc_final: 0.0871 (tptp) REVERT: F 560 MET cc_start: 0.1275 (mmp) cc_final: 0.1064 (tmm) REVERT: a 76 GLN cc_start: 0.7918 (tp40) cc_final: 0.7170 (mt0) REVERT: c 110 ASN cc_start: 0.8091 (t0) cc_final: 0.7545 (p0) REVERT: d 91 SER cc_start: 0.8212 (OUTLIER) cc_final: 0.7920 (t) outliers start: 86 outliers final: 25 residues processed: 455 average time/residue: 0.4928 time to fit residues: 328.3421 Evaluate side-chains 224 residues out of total 2405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 197 time to evaluate : 2.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain E residue 187 TRP Chi-restraints excluded: chain E residue 389 THR Chi-restraints excluded: chain a residue 87 SER Chi-restraints excluded: chain b residue 50 ILE Chi-restraints excluded: chain b residue 82 THR Chi-restraints excluded: chain b residue 93 GLN Chi-restraints excluded: chain c residue 18 SER Chi-restraints excluded: chain c residue 59 THR Chi-restraints excluded: chain c residue 100 VAL Chi-restraints excluded: chain d residue 52 THR Chi-restraints excluded: chain d residue 55 SER Chi-restraints excluded: chain d residue 91 SER Chi-restraints excluded: chain d residue 115 THR Chi-restraints excluded: chain f residue 21 VAL Chi-restraints excluded: chain f residue 22 LEU Chi-restraints excluded: chain f residue 50 ILE Chi-restraints excluded: chain f residue 92 ARG Chi-restraints excluded: chain g residue 59 THR Chi-restraints excluded: chain g residue 76 THR Chi-restraints excluded: chain g residue 100 VAL Chi-restraints excluded: chain h residue 55 SER Chi-restraints excluded: chain h residue 91 SER Chi-restraints excluded: chain h residue 115 THR Chi-restraints excluded: chain h residue 123 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 244 optimal weight: 2.9990 chunk 219 optimal weight: 2.9990 chunk 121 optimal weight: 20.0000 chunk 75 optimal weight: 0.6980 chunk 148 optimal weight: 3.9990 chunk 117 optimal weight: 10.0000 chunk 227 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 138 optimal weight: 20.0000 chunk 169 optimal weight: 0.1980 chunk 263 optimal weight: 6.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 663 ASN A 798 HIS A 857 HIS A 884 HIS A 974 GLN A1039 ASN A1081 ASN A1127 GLN A1234 ASN A1293 HIS E 355 ASN ** E 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 376 ASN E 385 GLN E 433 ASN ** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 177 HIS C 389 ASN F 259 ASN F 302 HIS F 329 GLN F 331 ASN a 39 HIS b 93 GLN c 31 HIS d 109 HIS e 125 GLN f 75 HIS f 93 GLN g 31 HIS ** h 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 109 HIS Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5693 moved from start: 0.2687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 1.197 29050 Z= 0.673 Angle : 0.668 23.264 40468 Z= 0.378 Chirality : 0.040 0.362 4468 Planarity : 0.005 0.128 4131 Dihedral : 25.835 84.529 6278 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.68 % Favored : 95.09 % Rotamer: Outliers : 2.38 % Allowed : 12.84 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.16), residues: 2647 helix: 0.87 (0.13), residues: 1524 sheet: -0.99 (0.49), residues: 104 loop : -2.23 (0.17), residues: 1019 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP D 236 HIS 0.022 0.001 HIS B 188 PHE 0.020 0.002 PHE B 301 TYR 0.024 0.002 TYR E 514 ARG 0.006 0.001 ARG B 136 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5294 Ramachandran restraints generated. 2647 Oldfield, 0 Emsley, 2647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5294 Ramachandran restraints generated. 2647 Oldfield, 0 Emsley, 2647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 219 time to evaluate : 2.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 998 HIS cc_start: 0.4153 (t-170) cc_final: 0.3808 (t-170) REVERT: A 1129 ILE cc_start: 0.2861 (OUTLIER) cc_final: 0.2320 (tt) REVERT: A 1164 MET cc_start: 0.0658 (mtm) cc_final: -0.0514 (tpp) REVERT: A 1209 ARG cc_start: 0.3285 (ttp-170) cc_final: 0.1241 (tmm-80) REVERT: A 1286 TYR cc_start: 0.1683 (t80) cc_final: 0.0931 (t80) REVERT: E 316 MET cc_start: -0.0071 (mmp) cc_final: -0.0552 (mtt) REVERT: E 350 GLN cc_start: 0.2574 (pt0) cc_final: 0.1547 (mm-40) REVERT: E 507 GLU cc_start: 0.3121 (mt-10) cc_final: 0.2715 (pp20) REVERT: E 557 LYS cc_start: 0.1530 (pptt) cc_final: 0.1037 (tppt) REVERT: D 227 LYS cc_start: -0.0600 (tttt) cc_final: -0.0810 (tttm) REVERT: D 296 MET cc_start: 0.2610 (ttp) cc_final: 0.1581 (tmm) REVERT: D 310 LEU cc_start: 0.2292 (OUTLIER) cc_final: 0.1738 (tt) REVERT: F 326 PHE cc_start: 0.2261 (t80) cc_final: 0.2034 (m-10) REVERT: F 553 ASP cc_start: 0.3715 (OUTLIER) cc_final: 0.3127 (t0) REVERT: c 110 ASN cc_start: 0.8102 (t0) cc_final: 0.7650 (p0) outliers start: 57 outliers final: 25 residues processed: 265 average time/residue: 0.4155 time to fit residues: 172.4679 Evaluate side-chains 176 residues out of total 2405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 148 time to evaluate : 2.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 712 SER Chi-restraints excluded: chain A residue 871 TYR Chi-restraints excluded: chain A residue 1129 ILE Chi-restraints excluded: chain A residue 1207 VAL Chi-restraints excluded: chain A residue 1301 PHE Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 389 THR Chi-restraints excluded: chain E residue 430 HIS Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain C residue 336 SER Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 382 SER Chi-restraints excluded: chain F residue 553 ASP Chi-restraints excluded: chain c residue 59 THR Chi-restraints excluded: chain c residue 72 ASP Chi-restraints excluded: chain c residue 100 VAL Chi-restraints excluded: chain d residue 52 THR Chi-restraints excluded: chain d residue 55 SER Chi-restraints excluded: chain f residue 21 VAL Chi-restraints excluded: chain f residue 52 GLU Chi-restraints excluded: chain g residue 18 SER Chi-restraints excluded: chain g residue 59 THR Chi-restraints excluded: chain g residue 100 VAL Chi-restraints excluded: chain h residue 52 THR Chi-restraints excluded: chain h residue 115 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 146 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 219 optimal weight: 0.9990 chunk 179 optimal weight: 8.9990 chunk 72 optimal weight: 7.9990 chunk 263 optimal weight: 7.9990 chunk 285 optimal weight: 20.0000 chunk 234 optimal weight: 0.1980 chunk 261 optimal weight: 10.0000 chunk 89 optimal weight: 5.9990 chunk 211 optimal weight: 9.9990 overall best weight: 2.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 779 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 974 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1143 ASN A1234 ASN A1254 HIS E 302 HIS E 371 GLN ** E 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 305 GLN ** C 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 267 GLN ** D 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 259 ASN a 76 GLN c 24 GLN h 63 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5811 moved from start: 0.4006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 1.199 29050 Z= 0.678 Angle : 0.659 23.287 40468 Z= 0.371 Chirality : 0.040 0.249 4468 Planarity : 0.005 0.113 4131 Dihedral : 25.768 84.640 6251 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.95 % Favored : 94.82 % Rotamer: Outliers : 2.67 % Allowed : 15.30 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.16), residues: 2647 helix: 1.16 (0.13), residues: 1532 sheet: -0.72 (0.48), residues: 109 loop : -1.96 (0.18), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP D 236 HIS 0.010 0.001 HIS A 930 PHE 0.025 0.002 PHE E 282 TYR 0.023 0.002 TYR F 372 ARG 0.004 0.001 ARG g 35 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5294 Ramachandran restraints generated. 2647 Oldfield, 0 Emsley, 2647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5294 Ramachandran restraints generated. 2647 Oldfield, 0 Emsley, 2647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 176 time to evaluate : 2.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 709 TYR cc_start: -0.1294 (m-80) cc_final: -0.1533 (m-80) REVERT: A 881 ASP cc_start: 0.2602 (OUTLIER) cc_final: 0.1420 (m-30) REVERT: A 998 HIS cc_start: 0.4434 (t-170) cc_final: 0.4122 (t-170) REVERT: A 1129 ILE cc_start: 0.2868 (OUTLIER) cc_final: 0.2430 (tt) REVERT: A 1164 MET cc_start: 0.0244 (mtm) cc_final: -0.0204 (ttp) REVERT: A 1209 ARG cc_start: 0.3513 (ttp-170) cc_final: 0.1215 (tmm-80) REVERT: A 1228 LEU cc_start: 0.3575 (OUTLIER) cc_final: 0.3270 (mt) REVERT: E 316 MET cc_start: -0.0083 (mmp) cc_final: -0.0292 (mtm) REVERT: E 350 GLN cc_start: 0.2613 (pt0) cc_final: 0.1441 (mm-40) REVERT: E 507 GLU cc_start: 0.3477 (mt-10) cc_final: 0.2799 (pp20) REVERT: E 557 LYS cc_start: 0.1788 (pptt) cc_final: 0.1316 (ptmt) REVERT: E 562 GLN cc_start: -0.0350 (tm-30) cc_final: -0.0681 (pp30) REVERT: B 108 ASP cc_start: 0.2424 (m-30) cc_final: 0.2215 (p0) REVERT: B 280 ARG cc_start: 0.4166 (OUTLIER) cc_final: 0.3380 (mtm-85) REVERT: B 301 PHE cc_start: 0.3337 (m-80) cc_final: 0.3057 (t80) REVERT: B 315 MET cc_start: 0.2370 (OUTLIER) cc_final: 0.2080 (mmp) REVERT: D 227 LYS cc_start: -0.0257 (tttt) cc_final: -0.0505 (mttt) REVERT: D 296 MET cc_start: 0.2751 (ttp) cc_final: 0.2432 (tmm) REVERT: D 310 LEU cc_start: 0.2290 (OUTLIER) cc_final: 0.1817 (tt) REVERT: F 560 MET cc_start: 0.1424 (OUTLIER) cc_final: 0.0648 (tpt) REVERT: a 133 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.7467 (mt-10) REVERT: c 110 ASN cc_start: 0.8099 (t0) cc_final: 0.7637 (p0) outliers start: 64 outliers final: 28 residues processed: 231 average time/residue: 0.4171 time to fit residues: 152.3313 Evaluate side-chains 174 residues out of total 2405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 138 time to evaluate : 4.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 712 SER Chi-restraints excluded: chain A residue 871 TYR Chi-restraints excluded: chain A residue 881 ASP Chi-restraints excluded: chain A residue 1129 ILE Chi-restraints excluded: chain A residue 1228 LEU Chi-restraints excluded: chain A residue 1292 SER Chi-restraints excluded: chain A residue 1305 PHE Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 123 ILE Chi-restraints excluded: chain E residue 389 THR Chi-restraints excluded: chain E residue 430 HIS Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 280 ARG Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 315 MET Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 336 SER Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 368 MET Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 382 SER Chi-restraints excluded: chain F residue 560 MET Chi-restraints excluded: chain a residue 71 VAL Chi-restraints excluded: chain a residue 87 SER Chi-restraints excluded: chain a residue 133 GLU Chi-restraints excluded: chain c residue 40 SER Chi-restraints excluded: chain c residue 59 THR Chi-restraints excluded: chain c residue 72 ASP Chi-restraints excluded: chain d residue 52 THR Chi-restraints excluded: chain d residue 55 SER Chi-restraints excluded: chain f residue 21 VAL Chi-restraints excluded: chain f residue 52 GLU Chi-restraints excluded: chain g residue 18 SER Chi-restraints excluded: chain h residue 52 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 260 optimal weight: 10.0000 chunk 198 optimal weight: 2.9990 chunk 136 optimal weight: 20.0000 chunk 29 optimal weight: 10.0000 chunk 125 optimal weight: 4.9990 chunk 177 optimal weight: 6.9990 chunk 264 optimal weight: 8.9990 chunk 280 optimal weight: 7.9990 chunk 138 optimal weight: 3.9990 chunk 250 optimal weight: 0.9990 chunk 75 optimal weight: 0.0000 overall best weight: 2.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 690 ASN ** A 779 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 974 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 371 GLN ** E 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 364 ASN ** C 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 259 ASN F 568 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5833 moved from start: 0.4696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 1.200 29050 Z= 0.669 Angle : 0.623 23.407 40468 Z= 0.351 Chirality : 0.039 0.243 4468 Planarity : 0.005 0.103 4131 Dihedral : 25.641 89.835 6247 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.27 % Favored : 95.58 % Rotamer: Outliers : 2.50 % Allowed : 16.68 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.16), residues: 2647 helix: 1.36 (0.13), residues: 1535 sheet: -0.43 (0.52), residues: 101 loop : -1.82 (0.18), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP D 236 HIS 0.005 0.001 HIS B 43 PHE 0.024 0.002 PHE A1305 TYR 0.029 0.002 TYR F 556 ARG 0.007 0.000 ARG A1302 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5294 Ramachandran restraints generated. 2647 Oldfield, 0 Emsley, 2647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5294 Ramachandran restraints generated. 2647 Oldfield, 0 Emsley, 2647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 2405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 163 time to evaluate : 2.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 765 MET cc_start: -0.0126 (mmm) cc_final: -0.0986 (mtp) REVERT: A 1129 ILE cc_start: 0.2719 (OUTLIER) cc_final: 0.2325 (tt) REVERT: A 1164 MET cc_start: 0.0245 (mtm) cc_final: -0.0173 (ttp) REVERT: A 1209 ARG cc_start: 0.3560 (ttp-170) cc_final: 0.1264 (tmm-80) REVERT: A 1247 GLN cc_start: 0.6158 (tt0) cc_final: 0.5929 (tt0) REVERT: A 1317 ILE cc_start: 0.0790 (OUTLIER) cc_final: 0.0568 (mt) REVERT: E 507 GLU cc_start: 0.3457 (mt-10) cc_final: 0.2773 (pp20) REVERT: E 557 LYS cc_start: 0.1936 (pptt) cc_final: 0.1600 (ptmt) REVERT: B 280 ARG cc_start: 0.3855 (OUTLIER) cc_final: 0.3533 (mtm180) REVERT: B 315 MET cc_start: 0.2381 (OUTLIER) cc_final: 0.1440 (mmp) REVERT: D 227 LYS cc_start: -0.0038 (tttt) cc_final: -0.0337 (mtmt) REVERT: D 310 LEU cc_start: 0.2188 (OUTLIER) cc_final: 0.1706 (tt) REVERT: F 560 MET cc_start: 0.1415 (OUTLIER) cc_final: -0.0054 (tpt) REVERT: a 133 GLU cc_start: 0.7617 (OUTLIER) cc_final: 0.7383 (mt-10) REVERT: c 41 GLU cc_start: 0.7315 (tm-30) cc_final: 0.7006 (tm-30) REVERT: c 110 ASN cc_start: 0.8044 (t0) cc_final: 0.7724 (p0) outliers start: 60 outliers final: 34 residues processed: 214 average time/residue: 0.3966 time to fit residues: 136.5933 Evaluate side-chains 176 residues out of total 2405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 135 time to evaluate : 2.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 712 SER Chi-restraints excluded: chain A residue 871 TYR Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 1129 ILE Chi-restraints excluded: chain A residue 1159 LEU Chi-restraints excluded: chain A residue 1179 THR Chi-restraints excluded: chain A residue 1208 LEU Chi-restraints excluded: chain A residue 1277 THR Chi-restraints excluded: chain A residue 1317 ILE Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 123 ILE Chi-restraints excluded: chain E residue 430 HIS Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 280 ARG Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 315 MET Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 336 SER Chi-restraints excluded: chain C residue 366 LEU Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 368 MET Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain D residue 262 GLU Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 382 SER Chi-restraints excluded: chain F residue 560 MET Chi-restraints excluded: chain a residue 87 SER Chi-restraints excluded: chain a residue 133 GLU Chi-restraints excluded: chain c residue 18 SER Chi-restraints excluded: chain c residue 40 SER Chi-restraints excluded: chain c residue 59 THR Chi-restraints excluded: chain c residue 72 ASP Chi-restraints excluded: chain d residue 55 SER Chi-restraints excluded: chain d residue 106 LEU Chi-restraints excluded: chain e residue 123 ASP Chi-restraints excluded: chain f residue 21 VAL Chi-restraints excluded: chain g residue 18 SER Chi-restraints excluded: chain h residue 55 SER Chi-restraints excluded: chain h residue 63 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 233 optimal weight: 0.6980 chunk 159 optimal weight: 9.9990 chunk 4 optimal weight: 30.0000 chunk 208 optimal weight: 0.8980 chunk 115 optimal weight: 20.0000 chunk 239 optimal weight: 0.0270 chunk 193 optimal weight: 0.8980 chunk 0 optimal weight: 30.0000 chunk 143 optimal weight: 0.9990 chunk 251 optimal weight: 0.7980 chunk 70 optimal weight: 5.9990 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 779 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 785 HIS ** A 974 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 313 ASN E 469 HIS ** E 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 295 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5755 moved from start: 0.4999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 1.198 29050 Z= 0.649 Angle : 0.569 23.251 40468 Z= 0.324 Chirality : 0.036 0.157 4468 Planarity : 0.004 0.089 4131 Dihedral : 25.310 87.209 6245 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.08 % Favored : 95.81 % Rotamer: Outliers : 1.75 % Allowed : 18.18 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.76 (0.16), residues: 2647 helix: 1.80 (0.13), residues: 1530 sheet: -0.57 (0.57), residues: 89 loop : -1.47 (0.19), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP D 236 HIS 0.004 0.001 HIS A 815 PHE 0.026 0.001 PHE F 336 TYR 0.028 0.001 TYR F 556 ARG 0.005 0.000 ARG g 35 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5294 Ramachandran restraints generated. 2647 Oldfield, 0 Emsley, 2647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5294 Ramachandran restraints generated. 2647 Oldfield, 0 Emsley, 2647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 2405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 171 time to evaluate : 2.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 765 MET cc_start: -0.0091 (mmm) cc_final: -0.0883 (mtp) REVERT: A 1063 MET cc_start: 0.0288 (tpt) cc_final: -0.1056 (pmm) REVERT: A 1129 ILE cc_start: 0.2761 (OUTLIER) cc_final: 0.2394 (tt) REVERT: A 1209 ARG cc_start: 0.3439 (ttp-170) cc_final: 0.1317 (tmm-80) REVERT: E 310 ILE cc_start: 0.1180 (mm) cc_final: 0.0867 (mt) REVERT: E 507 GLU cc_start: 0.3418 (mt-10) cc_final: 0.2941 (pp20) REVERT: E 557 LYS cc_start: 0.2338 (pptt) cc_final: 0.2063 (ptmt) REVERT: B 280 ARG cc_start: 0.3826 (OUTLIER) cc_final: 0.3324 (mtt180) REVERT: B 315 MET cc_start: 0.2684 (mmp) cc_final: 0.2326 (mmp) REVERT: B 373 MET cc_start: 0.0149 (mmm) cc_final: -0.0402 (ttm) REVERT: C 381 ARG cc_start: 0.1357 (ptp90) cc_final: 0.0499 (ttp80) REVERT: D 227 LYS cc_start: -0.0159 (tttt) cc_final: -0.0464 (mttt) REVERT: D 310 LEU cc_start: 0.1740 (OUTLIER) cc_final: 0.1514 (tt) REVERT: F 560 MET cc_start: 0.1907 (ptp) cc_final: 0.0436 (tpt) REVERT: c 41 GLU cc_start: 0.7272 (tm-30) cc_final: 0.7012 (tm-30) REVERT: c 75 LYS cc_start: 0.8094 (mttm) cc_final: 0.7729 (mtpp) REVERT: c 110 ASN cc_start: 0.8039 (t0) cc_final: 0.7792 (p0) outliers start: 42 outliers final: 20 residues processed: 208 average time/residue: 0.4209 time to fit residues: 137.8949 Evaluate side-chains 168 residues out of total 2405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 145 time to evaluate : 2.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 871 TYR Chi-restraints excluded: chain A residue 1129 ILE Chi-restraints excluded: chain A residue 1166 GLU Chi-restraints excluded: chain A residue 1199 VAL Chi-restraints excluded: chain A residue 1292 SER Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 383 ASP Chi-restraints excluded: chain E residue 430 HIS Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 280 ARG Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain D residue 262 GLU Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain a residue 65 LEU Chi-restraints excluded: chain c residue 40 SER Chi-restraints excluded: chain e residue 123 ASP Chi-restraints excluded: chain f residue 21 VAL Chi-restraints excluded: chain f residue 92 ARG Chi-restraints excluded: chain h residue 52 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 94 optimal weight: 6.9990 chunk 252 optimal weight: 0.0870 chunk 55 optimal weight: 2.9990 chunk 164 optimal weight: 5.9990 chunk 69 optimal weight: 9.9990 chunk 280 optimal weight: 10.0000 chunk 232 optimal weight: 0.7980 chunk 129 optimal weight: 2.9990 chunk 23 optimal weight: 6.9990 chunk 92 optimal weight: 20.0000 chunk 147 optimal weight: 7.9990 overall best weight: 2.5764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 779 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 974 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 516 ASN ** E 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 294 ASN c 73 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5860 moved from start: 0.5500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 1.201 29050 Z= 0.669 Angle : 0.610 23.510 40468 Z= 0.345 Chirality : 0.038 0.153 4468 Planarity : 0.004 0.079 4131 Dihedral : 25.520 87.591 6243 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.53 % Favored : 95.39 % Rotamer: Outliers : 2.34 % Allowed : 18.81 % Favored : 78.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.65 (0.16), residues: 2647 helix: 1.66 (0.13), residues: 1530 sheet: -0.56 (0.57), residues: 89 loop : -1.44 (0.19), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP D 236 HIS 0.006 0.001 HIS B 43 PHE 0.056 0.002 PHE E 567 TYR 0.025 0.002 TYR F 372 ARG 0.003 0.000 ARG A1009 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5294 Ramachandran restraints generated. 2647 Oldfield, 0 Emsley, 2647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5294 Ramachandran restraints generated. 2647 Oldfield, 0 Emsley, 2647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 2405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 157 time to evaluate : 2.469 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 765 MET cc_start: -0.0461 (mmm) cc_final: -0.1180 (mtp) REVERT: A 884 HIS cc_start: 0.1797 (m90) cc_final: 0.0128 (p-80) REVERT: A 1063 MET cc_start: 0.0497 (tpt) cc_final: -0.0968 (pmm) REVERT: A 1129 ILE cc_start: 0.2635 (OUTLIER) cc_final: 0.2266 (tt) REVERT: A 1209 ARG cc_start: 0.3460 (ttp-170) cc_final: 0.1292 (tmm-80) REVERT: A 1247 GLN cc_start: 0.5837 (tt0) cc_final: 0.5478 (tt0) REVERT: E 175 MET cc_start: 0.1540 (mpp) cc_final: -0.0170 (mmt) REVERT: E 310 ILE cc_start: 0.1010 (mm) cc_final: 0.0759 (mt) REVERT: E 356 TYR cc_start: 0.1129 (OUTLIER) cc_final: 0.0151 (m-10) REVERT: E 507 GLU cc_start: 0.4410 (mt-10) cc_final: 0.3548 (pp20) REVERT: E 542 ILE cc_start: 0.1361 (OUTLIER) cc_final: 0.1043 (mp) REVERT: E 557 LYS cc_start: 0.2506 (pptt) cc_final: 0.2107 (ptmt) REVERT: B 315 MET cc_start: 0.2584 (mmp) cc_final: 0.2245 (mmp) REVERT: B 373 MET cc_start: 0.0086 (mmm) cc_final: -0.0134 (ttm) REVERT: F 560 MET cc_start: 0.1785 (ptp) cc_final: 0.0245 (tpt) REVERT: c 41 GLU cc_start: 0.7292 (tm-30) cc_final: 0.7005 (tm-30) REVERT: c 110 ASN cc_start: 0.7999 (t0) cc_final: 0.7700 (p0) outliers start: 56 outliers final: 32 residues processed: 208 average time/residue: 0.3941 time to fit residues: 131.6455 Evaluate side-chains 174 residues out of total 2405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 139 time to evaluate : 2.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 871 TYR Chi-restraints excluded: chain A residue 881 ASP Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain A residue 1038 GLN Chi-restraints excluded: chain A residue 1129 ILE Chi-restraints excluded: chain A residue 1159 LEU Chi-restraints excluded: chain A residue 1166 GLU Chi-restraints excluded: chain A residue 1199 VAL Chi-restraints excluded: chain A residue 1292 SER Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 356 TYR Chi-restraints excluded: chain E residue 383 ASP Chi-restraints excluded: chain E residue 430 HIS Chi-restraints excluded: chain E residue 542 ILE Chi-restraints excluded: chain B residue 44 ARG Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain a residue 65 LEU Chi-restraints excluded: chain a residue 71 VAL Chi-restraints excluded: chain a residue 87 SER Chi-restraints excluded: chain c residue 18 SER Chi-restraints excluded: chain c residue 72 ASP Chi-restraints excluded: chain d residue 91 SER Chi-restraints excluded: chain e residue 80 THR Chi-restraints excluded: chain e residue 123 ASP Chi-restraints excluded: chain f residue 21 VAL Chi-restraints excluded: chain f residue 92 ARG Chi-restraints excluded: chain h residue 55 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 270 optimal weight: 10.0000 chunk 31 optimal weight: 3.9990 chunk 159 optimal weight: 6.9990 chunk 204 optimal weight: 1.9990 chunk 158 optimal weight: 7.9990 chunk 236 optimal weight: 4.9990 chunk 156 optimal weight: 6.9990 chunk 279 optimal weight: 10.0000 chunk 174 optimal weight: 0.9990 chunk 170 optimal weight: 10.0000 chunk 129 optimal weight: 10.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 779 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 974 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1131 GLN E 516 ASN ** C 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 330 HIS F 314 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5925 moved from start: 0.6320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 1.202 29050 Z= 0.692 Angle : 0.678 23.816 40468 Z= 0.377 Chirality : 0.041 0.252 4468 Planarity : 0.005 0.060 4131 Dihedral : 25.792 85.501 6243 Min Nonbonded Distance : 1.783 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.95 % Favored : 94.94 % Rotamer: Outliers : 2.75 % Allowed : 19.22 % Favored : 78.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.17 (0.16), residues: 2647 helix: 1.26 (0.13), residues: 1539 sheet: -1.07 (0.52), residues: 100 loop : -1.60 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.003 TRP D 236 HIS 0.009 0.001 HIS B 43 PHE 0.054 0.002 PHE E 567 TYR 0.027 0.002 TYR F 372 ARG 0.004 0.001 ARG E 564 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5294 Ramachandran restraints generated. 2647 Oldfield, 0 Emsley, 2647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5294 Ramachandran restraints generated. 2647 Oldfield, 0 Emsley, 2647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 2405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 141 time to evaluate : 2.646 Fit side-chains REVERT: A 765 MET cc_start: -0.0505 (mmm) cc_final: -0.0871 (mtt) REVERT: A 874 GLU cc_start: 0.0361 (OUTLIER) cc_final: -0.0220 (tp30) REVERT: A 884 HIS cc_start: 0.1789 (m90) cc_final: 0.0212 (p-80) REVERT: A 1063 MET cc_start: 0.0348 (tpt) cc_final: -0.1181 (pmm) REVERT: A 1129 ILE cc_start: 0.2060 (OUTLIER) cc_final: 0.1575 (tp) REVERT: A 1139 PHE cc_start: 0.0605 (m-80) cc_final: 0.0080 (m-10) REVERT: A 1209 ARG cc_start: 0.3657 (ttp-110) cc_final: 0.1321 (tmm-80) REVERT: A 1215 ILE cc_start: -0.0240 (OUTLIER) cc_final: -0.1017 (tp) REVERT: E 107 LYS cc_start: -0.0173 (mttp) cc_final: -0.0511 (mtmt) REVERT: E 175 MET cc_start: 0.1435 (mpp) cc_final: -0.0084 (mmt) REVERT: E 310 ILE cc_start: 0.0748 (mm) cc_final: 0.0494 (mt) REVERT: E 507 GLU cc_start: 0.4139 (mt-10) cc_final: 0.3418 (pp20) REVERT: E 542 ILE cc_start: 0.1482 (OUTLIER) cc_final: 0.1139 (mp) REVERT: B 315 MET cc_start: 0.2570 (mmp) cc_final: 0.2317 (mmp) REVERT: C 381 ARG cc_start: 0.1962 (ptp90) cc_final: 0.1002 (ttp80) REVERT: D 347 MET cc_start: -0.0757 (mtt) cc_final: -0.1172 (mtp) REVERT: F 560 MET cc_start: 0.1973 (ptp) cc_final: 0.0426 (tpt) REVERT: c 110 ASN cc_start: 0.8062 (t0) cc_final: 0.7612 (p0) outliers start: 66 outliers final: 41 residues processed: 201 average time/residue: 0.4046 time to fit residues: 131.0787 Evaluate side-chains 171 residues out of total 2405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 126 time to evaluate : 2.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 751 PHE Chi-restraints excluded: chain A residue 871 TYR Chi-restraints excluded: chain A residue 874 GLU Chi-restraints excluded: chain A residue 881 ASP Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain A residue 1038 GLN Chi-restraints excluded: chain A residue 1129 ILE Chi-restraints excluded: chain A residue 1159 LEU Chi-restraints excluded: chain A residue 1166 GLU Chi-restraints excluded: chain A residue 1199 VAL Chi-restraints excluded: chain A residue 1208 LEU Chi-restraints excluded: chain A residue 1215 ILE Chi-restraints excluded: chain A residue 1218 ASP Chi-restraints excluded: chain A residue 1277 THR Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 123 ILE Chi-restraints excluded: chain E residue 272 PHE Chi-restraints excluded: chain E residue 356 TYR Chi-restraints excluded: chain E residue 383 ASP Chi-restraints excluded: chain E residue 430 HIS Chi-restraints excluded: chain E residue 450 ASP Chi-restraints excluded: chain E residue 542 ILE Chi-restraints excluded: chain B residue 44 ARG Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 261 TRP Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain D residue 316 ASP Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 382 SER Chi-restraints excluded: chain a residue 65 LEU Chi-restraints excluded: chain a residue 71 VAL Chi-restraints excluded: chain a residue 87 SER Chi-restraints excluded: chain c residue 18 SER Chi-restraints excluded: chain d residue 91 SER Chi-restraints excluded: chain e residue 76 GLN Chi-restraints excluded: chain e residue 80 THR Chi-restraints excluded: chain f residue 21 VAL Chi-restraints excluded: chain f residue 92 ARG Chi-restraints excluded: chain h residue 55 SER Chi-restraints excluded: chain h residue 63 ASN Chi-restraints excluded: chain h residue 91 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 172 optimal weight: 8.9990 chunk 111 optimal weight: 6.9990 chunk 166 optimal weight: 3.9990 chunk 84 optimal weight: 9.9990 chunk 54 optimal weight: 5.9990 chunk 177 optimal weight: 6.9990 chunk 190 optimal weight: 2.9990 chunk 138 optimal weight: 3.9990 chunk 26 optimal weight: 8.9990 chunk 219 optimal weight: 0.9990 chunk 254 optimal weight: 0.1980 overall best weight: 2.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 779 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 974 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 516 ASN ** B 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 223 GLN ** C 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5892 moved from start: 0.6506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 1.200 29050 Z= 0.664 Angle : 0.605 23.748 40468 Z= 0.342 Chirality : 0.038 0.263 4468 Planarity : 0.004 0.076 4131 Dihedral : 25.590 86.519 6243 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.42 % Favored : 95.50 % Rotamer: Outliers : 1.79 % Allowed : 20.52 % Favored : 77.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.49 (0.16), residues: 2647 helix: 1.55 (0.13), residues: 1544 sheet: -1.13 (0.53), residues: 102 loop : -1.52 (0.19), residues: 1001 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP D 236 HIS 0.006 0.001 HIS B 43 PHE 0.054 0.002 PHE E 567 TYR 0.029 0.001 TYR A 682 ARG 0.004 0.000 ARG A1009 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5294 Ramachandran restraints generated. 2647 Oldfield, 0 Emsley, 2647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5294 Ramachandran restraints generated. 2647 Oldfield, 0 Emsley, 2647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 2405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 151 time to evaluate : 2.493 Fit side-chains REVERT: A 765 MET cc_start: -0.0461 (mmm) cc_final: -0.0704 (mtt) REVERT: A 874 GLU cc_start: 0.0050 (OUTLIER) cc_final: -0.0418 (tp30) REVERT: A 1016 TYR cc_start: 0.3315 (m-80) cc_final: 0.2912 (m-80) REVERT: A 1129 ILE cc_start: 0.2137 (OUTLIER) cc_final: 0.1645 (tp) REVERT: A 1139 PHE cc_start: 0.1043 (m-80) cc_final: 0.0460 (m-10) REVERT: A 1209 ARG cc_start: 0.3384 (ttp-110) cc_final: 0.1429 (tmm-80) REVERT: A 1215 ILE cc_start: -0.0191 (OUTLIER) cc_final: -0.0925 (tp) REVERT: E 107 LYS cc_start: 0.0037 (mttp) cc_final: -0.0216 (mtmt) REVERT: E 175 MET cc_start: 0.1321 (mpp) cc_final: 0.0147 (mmt) REVERT: E 310 ILE cc_start: 0.0743 (mm) cc_final: 0.0542 (mt) REVERT: E 507 GLU cc_start: 0.4203 (mt-10) cc_final: 0.3315 (tm-30) REVERT: E 542 ILE cc_start: 0.1253 (OUTLIER) cc_final: 0.0913 (mp) REVERT: E 550 ASP cc_start: 0.1470 (m-30) cc_final: 0.0490 (t70) REVERT: c 110 ASN cc_start: 0.8007 (t0) cc_final: 0.7682 (p0) outliers start: 43 outliers final: 32 residues processed: 192 average time/residue: 0.3920 time to fit residues: 121.5000 Evaluate side-chains 175 residues out of total 2405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 139 time to evaluate : 2.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 751 PHE Chi-restraints excluded: chain A residue 871 TYR Chi-restraints excluded: chain A residue 874 GLU Chi-restraints excluded: chain A residue 881 ASP Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 1129 ILE Chi-restraints excluded: chain A residue 1159 LEU Chi-restraints excluded: chain A residue 1199 VAL Chi-restraints excluded: chain A residue 1208 LEU Chi-restraints excluded: chain A residue 1215 ILE Chi-restraints excluded: chain A residue 1218 ASP Chi-restraints excluded: chain A residue 1277 THR Chi-restraints excluded: chain E residue 123 ILE Chi-restraints excluded: chain E residue 383 ASP Chi-restraints excluded: chain E residue 450 ASP Chi-restraints excluded: chain E residue 542 ILE Chi-restraints excluded: chain B residue 44 ARG Chi-restraints excluded: chain B residue 72 GLN Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 261 TRP Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain D residue 316 ASP Chi-restraints excluded: chain D residue 382 SER Chi-restraints excluded: chain a residue 65 LEU Chi-restraints excluded: chain a residue 87 SER Chi-restraints excluded: chain c residue 18 SER Chi-restraints excluded: chain d residue 91 SER Chi-restraints excluded: chain e residue 76 GLN Chi-restraints excluded: chain e residue 123 ASP Chi-restraints excluded: chain f residue 21 VAL Chi-restraints excluded: chain f residue 92 ARG Chi-restraints excluded: chain h residue 55 SER Chi-restraints excluded: chain h residue 63 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 267 optimal weight: 10.0000 chunk 244 optimal weight: 0.9990 chunk 260 optimal weight: 10.0000 chunk 156 optimal weight: 2.9990 chunk 113 optimal weight: 7.9990 chunk 204 optimal weight: 1.9990 chunk 79 optimal weight: 0.0370 chunk 235 optimal weight: 0.8980 chunk 246 optimal weight: 0.9990 chunk 259 optimal weight: 10.0000 chunk 171 optimal weight: 6.9990 overall best weight: 0.9864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 779 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 974 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 516 ASN B 231 ASN ** C 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5834 moved from start: 0.6628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 1.199 29050 Z= 0.650 Angle : 0.577 23.541 40468 Z= 0.326 Chirality : 0.037 0.237 4468 Planarity : 0.004 0.064 4131 Dihedral : 25.345 88.407 6242 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.00 % Favored : 95.96 % Rotamer: Outliers : 1.38 % Allowed : 20.93 % Favored : 77.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.17), residues: 2647 helix: 1.89 (0.13), residues: 1536 sheet: -1.19 (0.55), residues: 97 loop : -1.37 (0.19), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP D 236 HIS 0.004 0.001 HIS B 43 PHE 0.057 0.001 PHE E 567 TYR 0.024 0.001 TYR F 372 ARG 0.005 0.000 ARG g 35 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5294 Ramachandran restraints generated. 2647 Oldfield, 0 Emsley, 2647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5294 Ramachandran restraints generated. 2647 Oldfield, 0 Emsley, 2647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 2405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 148 time to evaluate : 2.768 Fit side-chains revert: symmetry clash REVERT: A 765 MET cc_start: -0.0496 (mmm) cc_final: -0.0736 (mtt) REVERT: A 884 HIS cc_start: 0.2282 (m90) cc_final: 0.1607 (m90) REVERT: A 1016 TYR cc_start: 0.3560 (m-80) cc_final: 0.3125 (m-80) REVERT: A 1063 MET cc_start: 0.0004 (tpt) cc_final: -0.0404 (tpp) REVERT: A 1129 ILE cc_start: 0.2523 (OUTLIER) cc_final: 0.2076 (tp) REVERT: A 1209 ARG cc_start: 0.3275 (ttp-110) cc_final: 0.1340 (tmm-80) REVERT: A 1215 ILE cc_start: -0.0188 (OUTLIER) cc_final: -0.1011 (tp) REVERT: E 107 LYS cc_start: 0.0038 (mttp) cc_final: -0.0250 (mtmt) REVERT: E 175 MET cc_start: 0.1494 (mpp) cc_final: 0.0318 (mmt) REVERT: E 310 ILE cc_start: 0.1020 (mm) cc_final: 0.0813 (mt) REVERT: E 507 GLU cc_start: 0.4296 (mt-10) cc_final: 0.3542 (pp20) REVERT: E 542 ILE cc_start: 0.1305 (OUTLIER) cc_final: 0.0968 (mp) REVERT: E 550 ASP cc_start: 0.1693 (m-30) cc_final: 0.0699 (t70) REVERT: E 557 LYS cc_start: 0.1926 (pptt) cc_final: 0.1553 (ptpt) REVERT: B 315 MET cc_start: 0.1851 (mmp) cc_final: 0.1615 (mmm) REVERT: C 241 LYS cc_start: 0.2664 (pptt) cc_final: 0.2434 (tptm) REVERT: c 41 GLU cc_start: 0.7341 (tm-30) cc_final: 0.7095 (tm-30) REVERT: c 110 ASN cc_start: 0.7999 (t0) cc_final: 0.7745 (p0) outliers start: 33 outliers final: 24 residues processed: 179 average time/residue: 0.3934 time to fit residues: 113.5951 Evaluate side-chains 167 residues out of total 2405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 140 time to evaluate : 2.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 751 PHE Chi-restraints excluded: chain A residue 871 TYR Chi-restraints excluded: chain A residue 881 ASP Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 1129 ILE Chi-restraints excluded: chain A residue 1159 LEU Chi-restraints excluded: chain A residue 1199 VAL Chi-restraints excluded: chain A residue 1215 ILE Chi-restraints excluded: chain A residue 1277 THR Chi-restraints excluded: chain E residue 272 PHE Chi-restraints excluded: chain E residue 356 TYR Chi-restraints excluded: chain E residue 383 ASP Chi-restraints excluded: chain E residue 542 ILE Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 261 TRP Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain D residue 382 SER Chi-restraints excluded: chain a residue 65 LEU Chi-restraints excluded: chain d residue 106 LEU Chi-restraints excluded: chain e residue 80 THR Chi-restraints excluded: chain e residue 123 ASP Chi-restraints excluded: chain f residue 21 VAL Chi-restraints excluded: chain f residue 92 ARG Chi-restraints excluded: chain h residue 55 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 275 optimal weight: 10.0000 chunk 168 optimal weight: 20.0000 chunk 130 optimal weight: 1.9990 chunk 191 optimal weight: 6.9990 chunk 288 optimal weight: 5.9990 chunk 265 optimal weight: 8.9990 chunk 230 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 chunk 177 optimal weight: 0.0770 chunk 141 optimal weight: 20.0000 chunk 182 optimal weight: 5.9990 overall best weight: 3.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 779 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 150 HIS ** C 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5925 moved from start: 0.6911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 1.201 29050 Z= 0.680 Angle : 0.641 23.818 40468 Z= 0.359 Chirality : 0.039 0.205 4468 Planarity : 0.004 0.055 4131 Dihedral : 25.631 86.301 6242 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.36 % Favored : 94.60 % Rotamer: Outliers : 1.63 % Allowed : 20.81 % Favored : 77.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.16), residues: 2647 helix: 1.55 (0.13), residues: 1542 sheet: -1.13 (0.55), residues: 102 loop : -1.46 (0.19), residues: 1003 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP D 236 HIS 0.009 0.001 HIS B 43 PHE 0.057 0.002 PHE E 567 TYR 0.027 0.002 TYR F 372 ARG 0.004 0.000 ARG g 35 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5294 Ramachandran restraints generated. 2647 Oldfield, 0 Emsley, 2647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5294 Ramachandran restraints generated. 2647 Oldfield, 0 Emsley, 2647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 2405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 129 time to evaluate : 2.765 Fit side-chains revert: symmetry clash REVERT: A 765 MET cc_start: -0.0376 (mmm) cc_final: -0.0666 (mtt) REVERT: A 874 GLU cc_start: 0.0220 (OUTLIER) cc_final: -0.0329 (tp30) REVERT: A 884 HIS cc_start: 0.2277 (m90) cc_final: 0.1570 (m90) REVERT: A 1016 TYR cc_start: 0.3638 (m-80) cc_final: 0.3254 (m-80) REVERT: A 1129 ILE cc_start: 0.1935 (OUTLIER) cc_final: 0.1481 (tp) REVERT: A 1209 ARG cc_start: 0.3559 (ttp-110) cc_final: 0.1244 (tmm-80) REVERT: A 1215 ILE cc_start: 0.0003 (OUTLIER) cc_final: -0.0940 (tp) REVERT: E 107 LYS cc_start: 0.0105 (mttp) cc_final: -0.0200 (mtmt) REVERT: E 175 MET cc_start: 0.1500 (mpp) cc_final: 0.0310 (mmt) REVERT: E 507 GLU cc_start: 0.4419 (mt-10) cc_final: 0.3684 (pp20) REVERT: E 542 ILE cc_start: 0.1516 (OUTLIER) cc_final: 0.1153 (mp) REVERT: B 373 MET cc_start: -0.0052 (ttp) cc_final: -0.0886 (mmm) REVERT: c 110 ASN cc_start: 0.7993 (t0) cc_final: 0.7673 (p0) REVERT: f 92 ARG cc_start: 0.7817 (OUTLIER) cc_final: 0.7586 (ptm-80) REVERT: g 41 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7699 (mm-30) outliers start: 39 outliers final: 26 residues processed: 167 average time/residue: 0.4066 time to fit residues: 109.3389 Evaluate side-chains 158 residues out of total 2405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 126 time to evaluate : 2.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 751 PHE Chi-restraints excluded: chain A residue 871 TYR Chi-restraints excluded: chain A residue 874 GLU Chi-restraints excluded: chain A residue 881 ASP Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 993 ASP Chi-restraints excluded: chain A residue 1129 ILE Chi-restraints excluded: chain A residue 1159 LEU Chi-restraints excluded: chain A residue 1199 VAL Chi-restraints excluded: chain A residue 1215 ILE Chi-restraints excluded: chain E residue 272 PHE Chi-restraints excluded: chain E residue 356 TYR Chi-restraints excluded: chain E residue 383 ASP Chi-restraints excluded: chain E residue 542 ILE Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 72 GLN Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 261 TRP Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain D residue 382 SER Chi-restraints excluded: chain a residue 65 LEU Chi-restraints excluded: chain c residue 18 SER Chi-restraints excluded: chain d residue 106 LEU Chi-restraints excluded: chain e residue 123 ASP Chi-restraints excluded: chain f residue 21 VAL Chi-restraints excluded: chain f residue 92 ARG Chi-restraints excluded: chain g residue 41 GLU Chi-restraints excluded: chain h residue 55 SER Chi-restraints excluded: chain h residue 63 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 245 optimal weight: 0.9980 chunk 70 optimal weight: 0.5980 chunk 212 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 63 optimal weight: 5.9990 chunk 230 optimal weight: 0.5980 chunk 96 optimal weight: 20.0000 chunk 236 optimal weight: 0.9980 chunk 29 optimal weight: 6.9990 chunk 42 optimal weight: 20.0000 chunk 202 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 779 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 974 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 433 ASN E 516 ASN ** B 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 364 ASN ** C 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4758 r_free = 0.4758 target = 0.189363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4545 r_free = 0.4545 target = 0.173134 restraints weight = 70356.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4536 r_free = 0.4536 target = 0.172566 restraints weight = 121437.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4523 r_free = 0.4523 target = 0.171565 restraints weight = 115722.523| |-----------------------------------------------------------------------------| r_work (final): 0.4518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5306 moved from start: 0.6965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 1.199 29050 Z= 0.649 Angle : 0.577 23.640 40468 Z= 0.326 Chirality : 0.036 0.173 4468 Planarity : 0.004 0.044 4131 Dihedral : 25.303 89.241 6242 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.93 % Favored : 96.03 % Rotamer: Outliers : 1.33 % Allowed : 21.10 % Favored : 77.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.17), residues: 2647 helix: 1.89 (0.13), residues: 1541 sheet: -1.20 (0.55), residues: 97 loop : -1.30 (0.19), residues: 1009 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP D 236 HIS 0.004 0.001 HIS B 43 PHE 0.060 0.001 PHE E 567 TYR 0.023 0.001 TYR F 372 ARG 0.006 0.000 ARG g 35 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4281.02 seconds wall clock time: 78 minutes 39.47 seconds (4719.47 seconds total)