Starting phenix.real_space_refine on Fri Aug 9 23:06:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w9d_37365/08_2024/8w9d_37365_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w9d_37365/08_2024/8w9d_37365.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w9d_37365/08_2024/8w9d_37365.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w9d_37365/08_2024/8w9d_37365.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w9d_37365/08_2024/8w9d_37365_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w9d_37365/08_2024/8w9d_37365_neut.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 2 8.98 5 Zn 7 6.06 5 P 292 5.49 5 S 104 5.16 5 C 16874 2.51 5 N 4918 2.21 5 O 5793 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 668": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 675": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 682": "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 698": "OD1" <-> "OD2" Residue "A GLU 715": "OE1" <-> "OE2" Residue "A PHE 717": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 720": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 723": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 726": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 749": "OE1" <-> "OE2" Residue "A TYR 755": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 772": "OD1" <-> "OD2" Residue "A GLU 776": "OE1" <-> "OE2" Residue "A ASP 780": "OD1" <-> "OD2" Residue "A GLU 781": "OE1" <-> "OE2" Residue "A PHE 795": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 804": "OE1" <-> "OE2" Residue "A GLU 805": "OE1" <-> "OE2" Residue "A GLU 813": "OE1" <-> "OE2" Residue "A GLU 816": "OE1" <-> "OE2" Residue "A PHE 819": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 832": "OE1" <-> "OE2" Residue "A GLU 839": "OE1" <-> "OE2" Residue "A PHE 849": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 872": "OD1" <-> "OD2" Residue "A GLU 878": "OE1" <-> "OE2" Residue "A GLU 904": "OE1" <-> "OE2" Residue "A GLU 920": "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 ASP 978": "OD1" <-> "OD2" Residue "A ASP 981": "OD1" <-> "OD2" Residue "A PHE 995": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1006": "OD1" <-> "OD2" Residue "A GLU 1008": "OE1" <-> "OE2" Residue "A ASP 1012": "OD1" <-> "OD2" Residue "A TYR 1016": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1017": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1026": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1067": "OD1" <-> "OD2" Residue "A TYR 1074": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1122": "OE1" <-> "OE2" Residue "A PHE 1136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1156": "OE1" <-> "OE2" Residue "A GLU 1166": "OE1" <-> "OE2" Residue "A GLU 1171": "OE1" <-> "OE2" Residue "A PHE 1180": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 TYR 1232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1264": "OE1" <-> "OE2" Residue "A PHE 1269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1298": "OE1" <-> "OE2" Residue "A PHE 1301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1320": "OD1" <-> "OD2" Residue "A ASP 1330": "OD1" <-> "OD2" Residue "A GLU 1331": "OE1" <-> "OE2" Residue "A ASP 1332": "OD1" <-> "OD2" Residue "A TYR 1336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1337": "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 PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 258": "OE1" <-> "OE2" Residue "E GLU 260": "OE1" <-> "OE2" Residue "E PHE 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 344": "OD1" <-> "OD2" Residue "E PHE 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 359": "OE1" <-> "OE2" Residue "E TYR 372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 375": "OE1" <-> "OE2" Residue "E TYR 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 424": "NH1" <-> "NH2" Residue "E TYR 442": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 454": "NH1" <-> "NH2" Residue "E PHE 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 496": "NH1" <-> "NH2" Residue "E TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 514": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 551": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 553": "OD1" <-> "OD2" Residue "E TYR 556": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 569": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 575": "OD1" <-> "OD2" Residue "B PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 20": "NH1" <-> "NH2" Residue "B TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 73": "OE1" <-> "OE2" Residue "B PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 80": "OD1" <-> "OD2" Residue "B TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 84": "OD1" <-> "OD2" Residue "B PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 108": "OD1" <-> "OD2" 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 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 172": "OE1" <-> "OE2" Residue "B TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 184": "OD1" <-> "OD2" Residue "B ASP 186": "OD1" <-> "OD2" Residue "B GLU 195": "OE1" <-> "OE2" Residue "B TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 252": "OE1" <-> "OE2" Residue "B TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 289": "OE1" <-> "OE2" Residue "B TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 367": "OE1" <-> "OE2" Residue "B TYR 368": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 370": "OD1" <-> "OD2" Residue "B GLU 381": "OE1" <-> "OE2" Residue "B TYR 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 237": "OE1" <-> "OE2" Residue "C TYR 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 251": "OD1" <-> "OD2" Residue "C TYR 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 262": "OE1" <-> "OE2" Residue "C GLU 264": "OE1" <-> "OE2" Residue "C GLU 268": "OE1" <-> "OE2" Residue "C TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 290": "OD1" <-> "OD2" Residue "C GLU 302": "OE1" <-> "OE2" Residue "C TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 307": "OD1" <-> "OD2" Residue "C ASP 316": "OD1" <-> "OD2" Residue "C GLU 340": "OE1" <-> "OE2" Residue "C GLU 360": "OE1" <-> "OE2" Residue "C ASP 361": "OD1" <-> "OD2" Residue "C PHE 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 372": "OE1" <-> "OE2" Residue "C ARG 381": "NH1" <-> "NH2" Residue "C TYR 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 395": "OE1" <-> "OE2" Residue "D ASP 235": "OD1" <-> "OD2" Residue "D ASP 251": "OD1" <-> "OD2" Residue "D GLU 255": "OE1" <-> "OE2" Residue "D TYR 261": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 ASP 290": "OD1" <-> "OD2" Residue "D TYR 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 340": "OE1" <-> "OE2" Residue "D GLU 360": "OE1" <-> "OE2" Residue "D PHE 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 372": "OE1" <-> "OE2" Residue "D TYR 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 376": "OD1" <-> "OD2" Residue "D ASP 378": "OD1" <-> "OD2" Residue "D ASP 383": "OD1" <-> "OD2" Residue "D ASP 384": "OD1" <-> "OD2" Residue "D GLU 395": "OE1" <-> "OE2" Residue "F PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 258": "OE1" <-> "OE2" Residue "F ASP 261": "OD1" <-> "OD2" Residue "F PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 276": "OD1" <-> "OD2" Residue "F ASP 288": "OD1" <-> "OD2" Residue "F PHE 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 344": "OD1" <-> "OD2" Residue "F PHE 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 374": "OD1" <-> "OD2" Residue "F GLU 375": "OE1" <-> "OE2" Residue "F TYR 556": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 569": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 571": "OE1" <-> "OE2" Residue "F ASP 575": "OD1" <-> "OD2" Residue "a TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 59": "OE1" <-> "OE2" Residue "a ASP 77": "OD1" <-> "OD2" 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 "a ASP 123": "OD1" <-> "OD2" Residue "a GLU 133": "OE1" <-> "OE2" Residue "b ARG 23": "NH1" <-> "NH2" Residue "b TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 63": "OE1" <-> "OE2" Residue "b ASP 68": "OD1" <-> "OD2" Residue "b TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 74": "OE1" <-> "OE2" Residue "b TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 91": "OE1" <-> "OE2" Residue "d ARG 31": "NH1" <-> "NH2" 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 TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ASP 106": "OD1" <-> "OD2" Residue "e ASP 123": "OD1" <-> "OD2" Residue "f TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 63": "OE1" <-> "OE2" Residue "f ASP 68": "OD1" <-> "OD2" Residue "f TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 74": "OE1" <-> "OE2" Residue "f TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 56": "OE1" <-> "OE2" Residue "g ASP 72": "OD1" <-> "OD2" Residue "h TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ASP 68": "OD1" <-> "OD2" Residue "h PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 76": "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-5409/modules/chem_data/mon_lib" Total number of atoms: 27990 Number of models: 1 Model: "" Number of chains: 21 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: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "b" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "c" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 812 Classifications: {'peptide': 106} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 5, 'TRANS': 100} 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: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 744 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "e" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 857 Classifications: {'peptide': 104} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 99} Chain breaks: 1 Chain: "f" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} 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: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 744 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} 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: "H" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 29 Classifications: {'peptide': 5} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'TRANS': 4} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'UNK:plan-1': 4} Unresolved non-hydrogen planarities: 4 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: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' K': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "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 95.945 97.988 84.400 1.00 41.65 S ATOM 5555 SG CYS E 266 93.206 96.692 86.613 1.00 37.12 S ATOM 5708 SG CYS E 286 96.717 95.119 87.251 1.00 32.48 S ATOM 5619 SG CYS E 275 104.117 103.028 76.035 1.00 75.04 S ATOM 5640 SG CYS E 278 101.718 102.280 74.106 1.00 80.64 S ATOM 5843 SG CYS E 303 103.082 99.150 74.710 1.00 77.29 S ATOM 5866 SG CYS E 306 103.956 101.507 71.469 1.00 87.59 S ATOM 6956 SG CYS E 440 62.238 85.587 102.105 1.00 43.56 S ATOM 6982 SG CYS E 443 59.142 83.263 101.859 1.00 42.11 S ATOM 6768 SG CYS E 417 55.505 87.436 112.700 1.00 31.16 S ATOM 6795 SG CYS E 420 53.328 87.794 115.635 1.00 34.53 S ATOM 7051 SG CYS E 451 57.329 87.185 116.091 1.00 35.06 S ATOM 14146 SG CYS F 275 50.062 45.721 55.986 1.00189.31 S ATOM 14370 SG CYS F 303 51.124 42.019 59.711 1.00186.67 S Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N LEU b 22 " occ=0.00 ... (6 atoms not shown) pdb=" CD2 LEU b 22 " occ=0.00 residue: pdb=" N ARG b 23 " occ=0.00 ... (9 atoms not shown) pdb=" NH2 ARG b 23 " occ=0.00 Time building chain proxies: 14.51, per 1000 atoms: 0.52 Number of scatterers: 27990 At special positions: 0 Unit cell: (142.397, 200.008, 159.789, 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 2 19.00 S 104 16.00 P 292 15.00 O 5793 8.00 N 4918 7.00 C 16874 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: 12.98 Conformation dependent library (CDL) restraints added in 3.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B1000 " pdb="ZN ZN B1000 " - 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 266 " pdb="ZN ZN E1000 " - pdb=" SG CYS E 286 " pdb=" ZN E1001 " pdb="ZN ZN E1001 " - pdb=" SG CYS E 303 " pdb="ZN ZN E1001 " - pdb=" SG CYS E 306 " pdb="ZN ZN E1001 " - pdb=" SG CYS E 278 " pdb="ZN ZN E1001 " - pdb=" SG CYS E 275 " pdb=" ZN E1002 " pdb="ZN ZN E1002 " - pdb=" SG CYS E 443 " pdb="ZN ZN E1002 " - pdb=" NE2 HIS E 469 " pdb="ZN ZN E1002 " - pdb=" SG CYS E 440 " pdb=" ZN E1003 " pdb="ZN ZN E1003 " - pdb=" SG CYS E 417 " pdb="ZN ZN E1003 " - pdb=" SG CYS E 420 " pdb="ZN ZN E1003 " - pdb=" SG CYS E 451 " pdb="ZN ZN E1003 " - pdb=" ND1 HIS E 448 " pdb=" ZN F1000 " pdb="ZN ZN F1000 " - pdb=" ND1 HIS F 283 " pdb=" ZN F1001 " pdb="ZN ZN F1001 " - pdb=" SG CYS F 303 " pdb="ZN ZN F1001 " - pdb=" SG CYS F 275 " Number of angles added : 12 5308 Ramachandran restraints generated. 2654 Oldfield, 0 Emsley, 2654 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5140 Finding SS restraints... Secondary structure from input PDB file: 109 helices and 22 sheets defined 58.4% alpha, 5.0% beta 147 base pairs and 276 stacking pairs defined. Time for finding SS restraints: 11.91 Creating SS restraints... Processing helix chain 'A' and resid 664 through 677 removed outlier: 3.721A pdb=" N GLY A 677 " --> pdb=" O LYS A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 679 through 694 Processing helix chain 'A' and resid 698 through 708 removed outlier: 3.728A pdb=" N PHE A 708 " --> pdb=" O GLU A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 724 Processing helix chain 'A' and resid 771 through 778 removed outlier: 3.529A pdb=" N GLU A 776 " --> pdb=" O ASP A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 839 removed outlier: 3.899A pdb=" N CYS A 830 " --> pdb=" O ARG A 826 " (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 924 removed outlier: 4.003A pdb=" N THR A 890 " --> pdb=" O HIS A 886 " (cutoff:3.500A) Proline residue: A 892 - end of helix removed outlier: 4.569A pdb=" N VAL A 915 " --> pdb=" O GLU A 911 " (cutoff:3.500A) Processing helix chain 'A' and resid 925 through 929 removed outlier: 4.042A pdb=" N ASP A 929 " --> pdb=" O LYS A 926 " (cutoff:3.500A) Processing helix chain 'A' and resid 934 through 943 removed outlier: 4.194A pdb=" N LYS A 940 " --> pdb=" O LYS A 936 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LYS A 941 " --> pdb=" O GLN A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 944 through 964 removed outlier: 4.005A pdb=" N ILE A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 983 through 999 Processing helix chain 'A' and resid 1003 through 1022 removed outlier: 3.577A pdb=" N PHE A1022 " --> pdb=" O ILE A1018 " (cutoff:3.500A) Processing helix chain 'A' and resid 1025 through 1038 Processing helix chain 'A' and resid 1065 through 1070 removed outlier: 3.626A pdb=" N HIS A1070 " --> pdb=" O LEU A1066 " (cutoff:3.500A) Processing helix chain 'A' and resid 1070 through 1081 removed outlier: 4.102A pdb=" N TYR A1074 " --> pdb=" O HIS A1070 " (cutoff:3.500A) Processing helix chain 'A' and resid 1119 through 1127 removed outlier: 3.766A pdb=" N GLN A1127 " --> pdb=" O GLU A1123 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1174 removed outlier: 4.778A pdb=" N GLU A1166 " --> pdb=" O LYS A1162 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N ARG A1167 " --> pdb=" O GLN A1163 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR A1174 " --> pdb=" O LYS A1170 " (cutoff:3.500A) Processing helix chain 'A' and resid 1178 through 1183 Processing helix chain 'A' and resid 1202 through 1216 Processing helix chain 'A' and resid 1220 through 1232 removed outlier: 3.913A pdb=" N TYR A1232 " --> pdb=" O LEU A1228 " (cutoff:3.500A) Processing helix chain 'A' and resid 1236 through 1240 removed outlier: 3.840A pdb=" N LEU A1239 " --> pdb=" O ALA A1236 " (cutoff:3.500A) Processing helix chain 'A' and resid 1241 through 1259 removed outlier: 3.867A pdb=" N THR A1246 " --> pdb=" O ILE A1242 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N MET A1257 " --> pdb=" O ALA A1253 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASP A1259 " --> pdb=" O THR A1255 " (cutoff:3.500A) Processing helix chain 'A' and resid 1260 through 1275 Processing helix chain 'A' and resid 1279 through 1294 removed outlier: 3.890A pdb=" N HIS A1293 " --> pdb=" O GLN A1289 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N MET A1294 " --> pdb=" O VAL A1290 " (cutoff:3.500A) Processing helix chain 'A' and resid 1329 through 1341 Processing helix chain 'E' and resid 303 through 312 Processing helix chain 'E' and resid 315 through 330 removed outlier: 3.515A pdb=" N LEU E 319 " --> pdb=" O SER E 315 " (cutoff:3.500A) Processing helix chain 'E' and resid 333 through 335 No H-bonds generated for 'chain 'E' and resid 333 through 335' 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 Processing helix chain 'E' and resid 381 through 390 Processing helix chain 'E' and resid 430 through 434 removed outlier: 3.792A pdb=" N SER E 434 " --> pdb=" O PRO E 431 " (cutoff:3.500A) Processing helix chain 'E' and resid 543 through 579 Processing helix chain 'B' and resid 28 through 32 removed outlier: 3.680A pdb=" N TYR B 32 " --> pdb=" O VAL B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 55 Processing helix chain 'B' and resid 56 through 60 removed outlier: 3.667A pdb=" N LYS B 59 " --> pdb=" O GLY B 56 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS B 60 " --> pdb=" O LEU B 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 56 through 60' Processing helix chain 'B' and resid 79 through 89 Processing helix chain 'B' and resid 92 through 97 removed outlier: 4.324A pdb=" N GLU B 95 " --> pdb=" O ASP B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 104 Processing helix chain 'B' and resid 115 through 136 removed outlier: 3.597A pdb=" N ASN B 135 " --> pdb=" O ALA B 131 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG B 136 " --> pdb=" O ALA B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 174 removed outlier: 3.846A 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: 3.775A 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: 4.745A pdb=" N CYS B 294 " --> pdb=" O GLY B 290 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N VAL B 295 " --> pdb=" O HIS B 291 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N PHE B 301 " --> pdb=" O TYR B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 330 removed outlier: 3.660A pdb=" N VAL B 318 " --> pdb=" O THR B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 348 removed outlier: 3.546A pdb=" N TYR B 347 " --> pdb=" O TYR B 344 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLY B 348 " --> pdb=" O GLU B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 381 Processing helix chain 'C' and resid 225 through 240 Processing helix chain 'C' and resid 253 through 266 Processing helix chain 'C' and resid 271 through 297 removed outlier: 3.758A pdb=" N GLN C 275 " --> pdb=" O SER C 271 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N GLY C 294 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N ASN C 295 " --> pdb=" O LYS C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 316 removed outlier: 3.892A pdb=" N ASP C 316 " --> pdb=" O LYS C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 325 Processing helix chain 'C' and resid 327 through 344 removed outlier: 3.890A pdb=" N LEU C 331 " --> pdb=" O GLY C 327 " (cutoff:3.500A) Proline residue: C 339 - end of helix Processing helix chain 'C' and resid 349 through 374 removed outlier: 5.264A pdb=" N ASP C 371 " --> pdb=" O LEU C 367 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N GLU C 372 " --> pdb=" O MET C 368 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N TYR C 373 " --> pdb=" O HIS C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 399 Processing helix chain 'D' and resid 225 through 241 removed outlier: 3.563A pdb=" N LYS D 241 " --> pdb=" O GLU D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 266 Processing helix chain 'D' and resid 271 through 292 removed outlier: 3.635A pdb=" N GLN D 275 " --> pdb=" O SER D 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 292 through 297 Processing helix chain 'D' and resid 302 through 316 Processing helix chain 'D' and resid 321 through 325 Processing helix chain 'D' and resid 327 through 344 removed outlier: 3.686A pdb=" N LEU D 331 " --> pdb=" O GLY D 327 " (cutoff:3.500A) Proline residue: D 339 - end of helix Processing helix chain 'D' and resid 348 through 369 Processing helix chain 'D' and resid 369 through 374 removed outlier: 4.400A pdb=" N TYR D 373 " --> pdb=" O HIS D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 391 through 399 removed outlier: 3.587A pdb=" N GLU D 395 " --> pdb=" O SER D 391 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N LEU D 399 " --> pdb=" O GLU D 395 " (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: 3.930A pdb=" N ASN F 342 " --> pdb=" O LYS F 338 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ILE F 343 " --> pdb=" O LEU F 339 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ASP F 344 " --> pdb=" O LEU F 340 " (cutoff:3.500A) Processing helix chain 'F' and resid 357 through 361 removed outlier: 3.848A pdb=" N THR F 360 " --> pdb=" O ILE F 357 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE F 361 " --> pdb=" O LYS F 358 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 357 through 361' Processing helix chain 'F' and resid 544 through 576 Processing helix chain 'a' and resid 44 through 57 removed outlier: 3.568A pdb=" N SER a 57 " --> pdb=" O ARG a 53 " (cutoff:3.500A) Processing helix chain 'a' and resid 63 through 76 removed outlier: 3.530A pdb=" N PHE a 67 " --> pdb=" O ARG a 63 " (cutoff:3.500A) Processing helix chain 'a' and resid 85 through 114 removed outlier: 3.529A pdb=" N VAL a 89 " --> pdb=" O GLN a 85 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA a 114 " --> pdb=" O CYS a 110 " (cutoff:3.500A) Processing helix chain 'a' and resid 120 through 131 removed outlier: 3.523A pdb=" N ILE a 124 " --> pdb=" O MET a 120 " (cutoff:3.500A) Processing helix chain 'b' and resid 30 through 42 Processing helix chain 'b' and resid 49 through 76 removed outlier: 3.967A pdb=" N GLU b 53 " --> pdb=" O LEU b 49 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ASP b 68 " --> pdb=" O ASN b 64 " (cutoff:3.500A) Processing helix chain 'b' and resid 82 through 92 removed outlier: 3.582A pdb=" N VAL b 86 " --> pdb=" O THR b 82 " (cutoff:3.500A) Processing helix chain 'c' and resid 16 through 22 Processing helix chain 'c' and resid 26 through 36 removed outlier: 3.542A pdb=" N VAL c 30 " --> pdb=" O PRO c 26 " (cutoff:3.500A) Processing helix chain 'c' and resid 46 through 72 Processing helix chain 'c' and resid 79 through 90 removed outlier: 3.618A 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 56 through 84 Processing helix chain 'd' and resid 90 through 102 Processing helix chain 'd' and resid 104 through 124 removed outlier: 3.728A pdb=" N LYS d 108 " --> pdb=" O GLY d 104 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA d 124 " --> pdb=" O LYS d 120 " (cutoff:3.500A) Processing helix chain 'e' and resid 44 through 57 Processing helix chain 'e' and resid 63 through 79 removed outlier: 3.579A pdb=" N PHE e 67 " --> pdb=" O ARG e 63 " (cutoff:3.500A) Processing helix chain 'e' and resid 85 through 114 removed outlier: 3.559A pdb=" N VAL e 89 " --> pdb=" O GLN e 85 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ALA e 114 " --> pdb=" O CYS e 110 " (cutoff:3.500A) Processing helix chain 'e' and resid 120 through 131 removed outlier: 3.597A pdb=" N ILE e 124 " --> pdb=" O MET e 120 " (cutoff:3.500A) Processing helix chain 'f' and resid 30 through 42 Processing helix chain 'f' and resid 49 through 76 removed outlier: 3.967A pdb=" N GLU f 53 " --> pdb=" O LEU f 49 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ASP f 68 " --> pdb=" O ASN f 64 " (cutoff:3.500A) Processing helix chain 'f' and resid 82 through 92 removed outlier: 3.581A pdb=" N VAL f 86 " --> pdb=" O THR f 82 " (cutoff:3.500A) Processing helix chain 'g' and resid 16 through 22 Processing helix chain 'g' and resid 26 through 37 Processing helix chain 'g' and resid 45 through 72 removed outlier: 4.487A pdb=" N VAL g 49 " --> pdb=" O ALA g 45 " (cutoff:3.500A) Processing helix chain 'g' and resid 79 through 89 Processing helix chain 'g' and resid 91 through 97 Processing helix chain 'h' and resid 37 through 49 Processing helix chain 'h' and resid 55 through 84 removed outlier: 4.034A pdb=" N ASN h 84 " --> pdb=" O LEU h 80 " (cutoff:3.500A) Processing helix chain 'h' and resid 90 through 102 Processing helix chain 'h' and resid 103 through 123 Processing helix chain 'G' and resid 101 through 122 Processing sheet with id=AA1, first strand: chain 'A' and resid 756 through 757 Processing sheet with id=AA2, first strand: chain 'A' and resid 975 through 978 removed outlier: 4.215A pdb=" N MET A1300 " --> pdb=" O ILE A1317 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 177 through 179 removed outlier: 3.695A pdb=" N GLU E 177 " --> pdb=" O ILE B 63 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ARG B 65 " --> pdb=" O GLU E 177 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER E 179 " --> pdb=" O ARG B 65 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU B 62 " --> pdb=" O VAL B 21 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ALA B 22 " --> pdb=" O VAL B 143 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N VAL B 267 " --> pdb=" O MET B 306 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N VAL B 308 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N LEU B 269 " --> pdb=" O VAL B 308 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N LEU B 181 " --> pdb=" O VAL B 268 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N GLN B 270 " --> pdb=" O LEU B 181 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ILE B 183 " --> pdb=" O GLN B 270 " (cutoff:3.500A) removed outlier: 8.211A pdb=" N VAL B 234 " --> pdb=" O VAL B 203 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N THR B 205 " --> pdb=" O VAL B 234 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N VAL B 236 " --> pdb=" O THR B 205 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N SER B 207 " --> pdb=" O VAL B 236 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N LEU B 238 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N HIS B 209 " --> pdb=" O LEU B 238 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 273 through 274 Processing sheet with id=AA5, first strand: chain 'E' and resid 365 through 366 Processing sheet with id=AA6, first strand: chain 'E' and resid 437 through 439 Processing sheet with id=AA7, first strand: chain 'E' and resid 505 through 506 removed outlier: 6.649A pdb=" N TYR E 506 " --> pdb=" O GLN E 541 " (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: 7.231A 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 'a' and resid 118 through 119 removed outlier: 3.614A pdb=" N ILE a 119 " --> pdb=" O ARG b 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'b' and resid 96 through 98 removed outlier: 6.511A pdb=" N THR b 96 " --> pdb=" O THR g 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'c' and resid 42 through 43 removed outlier: 7.215A pdb=" N ARG c 42 " --> pdb=" O ILE d 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'c' and resid 77 through 78 removed outlier: 3.566A pdb=" N ILE c 78 " --> pdb=" O GLY d 53 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'c' and resid 100 through 102 removed outlier: 6.585A pdb=" N THR c 101 " --> pdb=" O TYR f 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'e' and resid 83 through 84 removed outlier: 6.741A pdb=" N ARG e 83 " --> pdb=" O VAL f 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'e' and resid 118 through 119 Processing sheet with id=AC2, first strand: chain 'g' and resid 42 through 43 removed outlier: 7.423A pdb=" N ARG g 42 " --> pdb=" O ILE h 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'g' and resid 77 through 78 removed outlier: 3.605A pdb=" N ILE g 78 " --> pdb=" O GLY h 53 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'G' and resid 90 through 93 removed outlier: 6.852A pdb=" N CYS G 76 " --> pdb=" O ILE G 30 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N ILE G 30 " --> pdb=" O CYS G 76 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N PHE G 78 " --> pdb=" O LEU G 28 " (cutoff:3.500A) 1128 hydrogen bonds defined for protein. 3327 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 354 hydrogen bonds 708 hydrogen bond angles 0 basepair planarities 147 basepair parallelities 276 stacking parallelities Total time for adding SS restraints: 17.52 Time building geometry restraints manager: 14.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.01 - 1.17: 61 1.17 - 1.33: 5887 1.33 - 1.49: 11926 1.49 - 1.66: 11118 1.66 - 1.82: 159 Bond restraints: 29151 Sorted by residual: bond pdb=" C GLU A 920 " pdb=" O GLU A 920 " ideal model delta sigma weight residual 1.237 1.006 0.231 1.19e-02 7.06e+03 3.76e+02 bond pdb=" N PRO E 380 " pdb=" CA PRO E 380 " ideal model delta sigma weight residual 1.466 1.691 -0.225 1.21e-02 6.83e+03 3.46e+02 bond pdb=" C PRO B 42 " pdb=" O PRO B 42 " ideal model delta sigma weight residual 1.236 1.012 0.225 1.36e-02 5.41e+03 2.73e+02 bond pdb=" C PRO B 68 " pdb=" O PRO B 68 " ideal model delta sigma weight residual 1.234 1.048 0.186 1.14e-02 7.69e+03 2.66e+02 bond pdb=" C SER B 158 " pdb=" O SER B 158 " ideal model delta sigma weight residual 1.234 1.038 0.196 1.22e-02 6.72e+03 2.57e+02 ... (remaining 29146 not shown) Histogram of bond angle deviations from ideal: 90.15 - 100.52: 148 100.52 - 110.89: 12244 110.89 - 121.27: 21063 121.27 - 131.64: 7015 131.64 - 142.01: 128 Bond angle restraints: 40598 Sorted by residual: angle pdb=" C ARG E 384 " pdb=" CA ARG E 384 " pdb=" CB ARG E 384 " ideal model delta sigma weight residual 109.65 142.01 -32.36 1.74e+00 3.30e-01 3.46e+02 angle pdb=" O ILE E 379 " pdb=" C ILE E 379 " pdb=" N PRO E 380 " ideal model delta sigma weight residual 121.10 102.94 18.16 1.14e+00 7.69e-01 2.54e+02 angle pdb=" C ARG B 136 " pdb=" N GLY B 137 " pdb=" CA GLY B 137 " ideal model delta sigma weight residual 121.51 139.52 -18.01 1.52e+00 4.33e-01 1.40e+02 angle pdb=" CA ILE E 379 " pdb=" C ILE E 379 " pdb=" N PRO E 380 " ideal model delta sigma weight residual 118.88 135.17 -16.29 1.54e+00 4.22e-01 1.12e+02 angle pdb=" C GLU B 129 " pdb=" CA GLU B 129 " pdb=" CB GLU B 129 " ideal model delta sigma weight residual 110.85 92.93 17.92 1.70e+00 3.46e-01 1.11e+02 ... (remaining 40593 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.74: 12687 18.74 - 37.48: 2295 37.48 - 56.22: 1609 56.22 - 74.96: 293 74.96 - 93.70: 35 Dihedral angle restraints: 16919 sinusoidal: 8968 harmonic: 7951 Sorted by residual: dihedral pdb=" C ARG E 384 " pdb=" N ARG E 384 " pdb=" CA ARG E 384 " pdb=" CB ARG E 384 " ideal model delta harmonic sigma weight residual -122.60 -155.40 32.80 0 2.50e+00 1.60e-01 1.72e+02 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 -152.24 30.24 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 123.40 151.01 -27.61 0 2.50e+00 1.60e-01 1.22e+02 ... (remaining 16916 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.239: 4431 0.239 - 0.477: 38 0.477 - 0.716: 9 0.716 - 0.954: 3 0.954 - 1.193: 3 Chirality restraints: 4484 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 ARG E 384 " pdb=" N ARG E 384 " pdb=" C ARG E 384 " pdb=" CB ARG E 384 " both_signs ideal model delta sigma weight residual False 2.51 1.35 1.16 2.00e-01 2.50e+01 3.35e+01 chirality pdb=" CA TYR B 313 " pdb=" N TYR B 313 " pdb=" C TYR B 313 " pdb=" CB TYR B 313 " both_signs ideal model delta sigma weight residual False 2.51 1.51 1.00 2.00e-01 2.50e+01 2.49e+01 ... (remaining 4481 not shown) Planarity restraints: 4146 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN B 135 " 0.042 2.00e-02 2.50e+03 8.02e-02 6.44e+01 pdb=" C ASN B 135 " -0.139 2.00e-02 2.50e+03 pdb=" O ASN B 135 " 0.050 2.00e-02 2.50e+03 pdb=" N ARG B 136 " 0.047 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 70 " 0.033 2.00e-02 2.50e+03 6.80e-02 4.63e+01 pdb=" C THR B 70 " -0.118 2.00e-02 2.50e+03 pdb=" O THR B 70 " 0.046 2.00e-02 2.50e+03 pdb=" N LYS B 71 " 0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 132 " 0.030 2.00e-02 2.50e+03 6.33e-02 4.01e+01 pdb=" C ALA B 132 " -0.109 2.00e-02 2.50e+03 pdb=" O ALA B 132 " 0.042 2.00e-02 2.50e+03 pdb=" N ARG B 133 " 0.037 2.00e-02 2.50e+03 ... (remaining 4143 not shown) Histogram of nonbonded interaction distances: 1.49 - 2.22: 19 2.22 - 2.95: 12204 2.95 - 3.68: 48048 3.68 - 4.41: 84775 4.41 - 5.14: 133386 Nonbonded interactions: 278432 Sorted by model distance: nonbonded pdb=" CG2 THR E 169 " pdb=" CB MET B 53 " model vdw 1.489 3.860 nonbonded pdb=" NH1 ARG d 31 " pdb=" OP1 DA j 51 " model vdw 1.593 3.120 nonbonded pdb=" OE2 GLU E 178 " pdb=" NH1 ARG B 65 " model vdw 1.674 3.120 nonbonded pdb=" OG1 THR E 184 " pdb=" OE2 GLU B 73 " model vdw 1.685 3.040 nonbonded pdb=" OD1 ASP B 184 " pdb=" K K B1001 " model vdw 1.873 2.850 ... (remaining 278427 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'C' selection = (chain 'D' and resid 219 through 401) } ncs_group { reference = chain 'a' selection = (chain 'e' and resid 38 through 134) } ncs_group { reference = chain 'b' selection = chain 'f' } ncs_group { reference = chain 'c' selection = (chain 'g' and resid 13 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=0.00 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: 1.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.120 Check model and map are aligned: 0.180 Set scattering table: 0.280 Process input model: 95.590 Find NCS groups from input model: 0.650 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 102.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5936 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.231 29151 Z= 0.648 Angle : 1.130 32.365 40598 Z= 0.718 Chirality : 0.072 1.193 4484 Planarity : 0.007 0.118 4146 Dihedral : 24.445 93.697 11779 Min Nonbonded Distance : 1.489 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.68 % Allowed : 4.90 % Favored : 94.42 % Rotamer: Outliers : 8.35 % Allowed : 22.48 % Favored : 69.17 % Cbeta Deviations : 1.87 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % 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: -2.31 (0.14), residues: 2654 helix: -0.77 (0.12), residues: 1482 sheet: -1.35 (0.47), residues: 113 loop : -2.61 (0.16), residues: 1059 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.005 TRP E 301 HIS 0.009 0.001 HIS G 80 PHE 0.048 0.002 PHE E 387 TYR 0.063 0.002 TYR B 176 ARG 0.013 0.001 ARG A 917 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5308 Ramachandran restraints generated. 2654 Oldfield, 0 Emsley, 2654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5308 Ramachandran restraints generated. 2654 Oldfield, 0 Emsley, 2654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 806 residues out of total 2414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 201 poor density : 605 time to evaluate : 2.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 691 LEU cc_start: 0.7374 (mt) cc_final: 0.6941 (tt) REVERT: A 702 LEU cc_start: 0.7861 (OUTLIER) cc_final: 0.7298 (tp) REVERT: A 837 LYS cc_start: 0.5000 (OUTLIER) cc_final: 0.4742 (mptp) REVERT: A 867 ILE cc_start: 0.7426 (mt) cc_final: 0.6604 (mm) REVERT: A 934 THR cc_start: 0.6454 (OUTLIER) cc_final: 0.5852 (t) REVERT: A 1069 LEU cc_start: -0.1619 (OUTLIER) cc_final: -0.2657 (mt) REVERT: A 1261 LYS cc_start: 0.5672 (mmtt) cc_final: 0.5441 (mmtp) REVERT: A 1286 TYR cc_start: 0.5571 (t80) cc_final: 0.5350 (t80) REVERT: E 105 ASP cc_start: -0.4256 (OUTLIER) cc_final: -0.4793 (t70) REVERT: E 318 THR cc_start: 0.4647 (p) cc_final: 0.4290 (m) REVERT: E 386 LEU cc_start: 0.4935 (OUTLIER) cc_final: 0.4573 (tp) REVERT: E 468 LEU cc_start: 0.5290 (mt) cc_final: 0.5079 (mt) REVERT: E 491 VAL cc_start: 0.7166 (OUTLIER) cc_final: 0.6410 (p) REVERT: E 569 PHE cc_start: 0.3812 (t80) cc_final: 0.3255 (t80) REVERT: B 40 MET cc_start: 0.4180 (OUTLIER) cc_final: 0.3900 (tpt) REVERT: B 74 MET cc_start: 0.5258 (mtt) cc_final: 0.5056 (mtt) REVERT: C 364 VAL cc_start: 0.7964 (m) cc_final: 0.7621 (p) REVERT: D 217 THR cc_start: 0.2408 (OUTLIER) cc_final: 0.1761 (t) REVERT: D 325 ILE cc_start: 0.4032 (OUTLIER) cc_final: 0.3274 (mp) REVERT: D 337 VAL cc_start: 0.6224 (OUTLIER) cc_final: 0.5569 (t) REVERT: D 345 THR cc_start: 0.6046 (OUTLIER) cc_final: 0.5759 (t) REVERT: D 353 GLN cc_start: 0.8450 (tt0) cc_final: 0.8026 (mt0) REVERT: F 546 SER cc_start: 0.7318 (t) cc_final: 0.7036 (p) REVERT: F 556 TYR cc_start: 0.4570 (t80) cc_final: 0.3804 (t80) REVERT: a 120 MET cc_start: 0.7471 (mtt) cc_final: 0.6944 (mtt) REVERT: b 80 THR cc_start: 0.7435 (OUTLIER) cc_final: 0.7155 (t) REVERT: b 88 TYR cc_start: 0.7865 (m-10) cc_final: 0.6764 (m-80) REVERT: d 87 SER cc_start: 0.7037 (OUTLIER) cc_final: 0.6814 (t) REVERT: G 22 MET cc_start: 0.0044 (mtm) cc_final: -0.1046 (tpp) outliers start: 201 outliers final: 26 residues processed: 751 average time/residue: 0.4318 time to fit residues: 488.4243 Evaluate side-chains 290 residues out of total 2414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 250 time to evaluate : 2.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 763 THR Chi-restraints excluded: chain A residue 767 CYS Chi-restraints excluded: chain A residue 828 ILE Chi-restraints excluded: chain A residue 837 LYS Chi-restraints excluded: chain A residue 878 GLU Chi-restraints excluded: chain A residue 934 THR Chi-restraints excluded: chain A residue 1069 LEU Chi-restraints excluded: chain A residue 1153 THR Chi-restraints excluded: chain A residue 1337 TYR Chi-restraints excluded: chain A residue 1339 THR Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain E residue 114 PRO Chi-restraints excluded: chain E residue 386 LEU Chi-restraints excluded: chain E residue 437 ILE Chi-restraints excluded: chain E residue 491 VAL Chi-restraints excluded: chain E residue 492 TRP Chi-restraints excluded: chain B residue 40 MET Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain D residue 325 ILE Chi-restraints excluded: chain D residue 337 VAL Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain F residue 264 SER Chi-restraints excluded: chain F residue 304 ASN Chi-restraints excluded: chain F residue 346 HIS Chi-restraints excluded: chain b residue 50 ILE Chi-restraints excluded: chain b residue 80 THR Chi-restraints excluded: chain c residue 108 LEU Chi-restraints excluded: chain d residue 33 ARG Chi-restraints excluded: chain d residue 87 SER Chi-restraints excluded: chain d residue 123 SER Chi-restraints excluded: chain f residue 21 VAL Chi-restraints excluded: chain f residue 22 LEU Chi-restraints excluded: chain g residue 11 ARG Chi-restraints excluded: chain h residue 63 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 245 optimal weight: 2.9990 chunk 220 optimal weight: 7.9990 chunk 122 optimal weight: 9.9990 chunk 75 optimal weight: 0.0370 chunk 148 optimal weight: 9.9990 chunk 117 optimal weight: 7.9990 chunk 228 optimal weight: 2.9990 chunk 88 optimal weight: 0.0270 chunk 138 optimal weight: 5.9990 chunk 169 optimal weight: 20.0000 chunk 264 optimal weight: 7.9990 overall best weight: 2.4122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 663 ASN ** A 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 722 ASN A 930 HIS A1038 GLN A1216 ASN A1289 GLN E 342 ASN E 346 HIS E 376 ASN E 406 HIS E 495 GLN E 503 GLN E 510 GLN ** E 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 541 GLN ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 291 HIS B 364 ASN C 330 HIS D 275 GLN D 277 GLN ** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 350 GLN D 358 GLN F 259 ASN F 283 HIS F 294 ASN F 329 GLN F 332 ASN F 350 GLN F 568 GLN a 39 HIS b 75 HIS c 38 ASN c 112 GLN d 49 HIS e 5 GLN e 76 GLN e 125 GLN g 73 ASN h 47 GLN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6196 moved from start: 0.3582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 29151 Z= 0.243 Angle : 0.723 10.549 40598 Z= 0.396 Chirality : 0.042 0.528 4484 Planarity : 0.005 0.100 4146 Dihedral : 25.991 82.560 6326 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.48 % Favored : 95.37 % Rotamer: Outliers : 4.69 % Allowed : 23.68 % Favored : 71.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.16 % 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: -0.79 (0.16), residues: 2654 helix: 0.51 (0.13), residues: 1505 sheet: -0.93 (0.51), residues: 102 loop : -2.03 (0.17), residues: 1047 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP C 236 HIS 0.012 0.001 HIS A1252 PHE 0.043 0.002 PHE B 377 TYR 0.022 0.002 TYR C 306 ARG 0.007 0.001 ARG B 133 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5308 Ramachandran restraints generated. 2654 Oldfield, 0 Emsley, 2654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5308 Ramachandran restraints generated. 2654 Oldfield, 0 Emsley, 2654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 2414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 284 time to evaluate : 2.919 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: A 1004 ASN cc_start: 0.6468 (m-40) cc_final: 0.6073 (t0) REVERT: A 1068 ILE cc_start: 0.3446 (mt) cc_final: 0.3097 (tp) REVERT: A 1069 LEU cc_start: -0.2204 (OUTLIER) cc_final: -0.2655 (mt) REVERT: A 1325 LYS cc_start: -0.3661 (OUTLIER) cc_final: -0.3901 (tppt) REVERT: E 390 SER cc_start: 0.4018 (OUTLIER) cc_final: 0.3609 (t) REVERT: E 512 ILE cc_start: 0.4740 (OUTLIER) cc_final: 0.4492 (mm) REVERT: C 228 LEU cc_start: 0.5665 (mt) cc_final: 0.5412 (mp) REVERT: C 364 VAL cc_start: 0.8186 (m) cc_final: 0.7982 (p) REVERT: D 296 MET cc_start: 0.7477 (tmm) cc_final: 0.7082 (tmm) REVERT: D 303 ARG cc_start: 0.4017 (mtm180) cc_final: 0.3485 (mtm180) REVERT: D 353 GLN cc_start: 0.8283 (tt0) cc_final: 0.7958 (mt0) REVERT: D 355 LEU cc_start: 0.6944 (OUTLIER) cc_final: 0.6541 (mt) REVERT: D 362 PHE cc_start: 0.5607 (t80) cc_final: 0.5346 (t80) REVERT: b 44 LYS cc_start: 0.8785 (tmtt) cc_final: 0.8188 (tttm) REVERT: d 62 MET cc_start: 0.7470 (OUTLIER) cc_final: 0.7246 (mpp) REVERT: d 89 ILE cc_start: 0.6659 (mm) cc_final: 0.6329 (mm) REVERT: h 90 THR cc_start: 0.7509 (OUTLIER) cc_final: 0.7123 (p) REVERT: h 93 GLU cc_start: 0.8150 (mp0) cc_final: 0.7881 (mp0) REVERT: G 22 MET cc_start: -0.0587 (mtm) cc_final: -0.1115 (tpp) outliers start: 113 outliers final: 46 residues processed: 373 average time/residue: 0.3822 time to fit residues: 228.3669 Evaluate side-chains 261 residues out of total 2414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 208 time to evaluate : 2.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 676 ILE Chi-restraints excluded: chain A residue 679 LYS Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 767 CYS Chi-restraints excluded: chain A residue 828 ILE Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 880 ILE Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 934 THR Chi-restraints excluded: chain A residue 1069 LEU Chi-restraints excluded: chain A residue 1250 VAL Chi-restraints excluded: chain A residue 1325 LYS Chi-restraints excluded: chain A residue 1337 TYR Chi-restraints excluded: chain A residue 1339 THR Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain E residue 280 LYS Chi-restraints excluded: chain E residue 375 GLU Chi-restraints excluded: chain E residue 386 LEU Chi-restraints excluded: chain E residue 390 SER Chi-restraints excluded: chain E residue 395 ILE Chi-restraints excluded: chain E residue 415 LEU Chi-restraints excluded: chain E residue 492 TRP Chi-restraints excluded: chain E residue 512 ILE Chi-restraints excluded: chain B residue 40 MET Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 263 HIS Chi-restraints excluded: chain D residue 341 LEU Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain F residue 277 THR Chi-restraints excluded: chain a residue 71 VAL Chi-restraints excluded: chain a residue 80 THR Chi-restraints excluded: chain a residue 96 CYS Chi-restraints excluded: chain a residue 103 LEU Chi-restraints excluded: chain b residue 50 ILE Chi-restraints excluded: chain c residue 43 VAL Chi-restraints excluded: chain c residue 49 VAL Chi-restraints excluded: chain c residue 114 VAL Chi-restraints excluded: chain d residue 42 TYR Chi-restraints excluded: chain d residue 62 MET Chi-restraints excluded: chain d residue 80 LEU Chi-restraints excluded: chain e residue 86 SER Chi-restraints excluded: chain e residue 87 SER Chi-restraints excluded: chain f residue 49 LEU Chi-restraints excluded: chain g residue 114 VAL Chi-restraints excluded: chain h residue 90 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 146 optimal weight: 3.9990 chunk 82 optimal weight: 0.9980 chunk 219 optimal weight: 5.9990 chunk 179 optimal weight: 20.0000 chunk 72 optimal weight: 0.2980 chunk 264 optimal weight: 10.0000 chunk 285 optimal weight: 0.8980 chunk 235 optimal weight: 2.9990 chunk 262 optimal weight: 10.0000 chunk 90 optimal weight: 9.9990 chunk 212 optimal weight: 0.0270 overall best weight: 1.0440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: