Starting phenix.real_space_refine on Sat Mar 23 16:49:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9v_34583/03_2024/8h9v_34583_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9v_34583/03_2024/8h9v_34583.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9v_34583/03_2024/8h9v_34583.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9v_34583/03_2024/8h9v_34583.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9v_34583/03_2024/8h9v_34583_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9v_34583/03_2024/8h9v_34583_updated.pdb" } resolution = 3.02 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= 0.009 sd= 1.076 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 13 5.49 5 Mg 5 5.21 5 S 158 5.16 5 C 24212 2.51 5 N 6427 2.21 5 O 7106 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "4 PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ARG 38": "NH1" <-> "NH2" Residue "4 PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ARG 38": "NH1" <-> "NH2" Residue "5 PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ARG 38": "NH1" <-> "NH2" Residue "6 PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ARG 38": "NH1" <-> "NH2" Residue "7 PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ARG 38": "NH1" <-> "NH2" Residue "2 PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 38": "NH1" <-> "NH2" Residue "3 PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 113": "OE1" <-> "OE2" Residue "H GLU 118": "OE1" <-> "OE2" Residue "H GLU 125": "OE1" <-> "OE2" Residue "H GLU 130": "OE1" <-> "OE2" Residue "H GLU 136": "OE1" <-> "OE2" Residue "H GLU 139": "OE1" <-> "OE2" Residue "I TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 36": "OE1" <-> "OE2" Residue "K TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 19": "OE1" <-> "OE2" Residue "K TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 80": "OD1" <-> "OD2" Residue "K TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 142": "OE1" <-> "OE2" Residue "K ASP 156": "OD1" <-> "OD2" Residue "K TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 169": "OE1" <-> "OE2" Residue "M ASP 11": "OD1" <-> "OD2" Residue "M PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 90": "OD1" <-> "OD2" Residue "M GLU 92": "OE1" <-> "OE2" Residue "M ASP 96": "OD1" <-> "OD2" Residue "M PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 128": "OD1" <-> "OD2" Residue "M GLU 158": "OE1" <-> "OE2" Residue "N PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 203": "OE1" <-> "OE2" Residue "N PHE 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 33": "OD1" <-> "OD2" Residue "R ARG 45": "NH1" <-> "NH2" Residue "R TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 87": "OE1" <-> "OE2" Residue "R TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 38": "OE1" <-> "OE2" Residue "L PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 26": "OE1" <-> "OE2" Residue "A PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 102": "OE1" <-> "OE2" Residue "A GLU 165": "OE1" <-> "OE2" Residue "A ARG 171": "NH1" <-> "NH2" Residue "A TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 224": "OD1" <-> "OD2" Residue "A TYR 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 259": "OD1" <-> "OD2" Residue "A TYR 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 292": "OE1" <-> "OE2" Residue "A TYR 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 439": "OE1" <-> "OE2" Residue "A GLU 440": "OE1" <-> "OE2" Residue "A ASP 454": "OD1" <-> "OD2" Residue "A PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 465": "OE1" <-> "OE2" Residue "A PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 486": "OD1" <-> "OD2" Residue "A ASP 494": "OD1" <-> "OD2" Residue "A PHE 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 50": "OE1" <-> "OE2" Residue "B PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 102": "OE1" <-> "OE2" Residue "B ASP 109": "OD1" <-> "OD2" Residue "B GLU 165": "OE1" <-> "OE2" Residue "B TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 255": "OE1" <-> "OE2" Residue "B TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 328": "OE1" <-> "OE2" Residue "B TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 355": "OE1" <-> "OE2" Residue "B PHE 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 373": "NH1" <-> "NH2" Residue "B TYR 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 411": "OD1" <-> "OD2" Residue "B GLU 440": "OE1" <-> "OE2" Residue "B TYR 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 30": "NH1" <-> "NH2" Residue "C GLU 54": "OE1" <-> "OE2" Residue "C PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 67": "OE1" <-> "OE2" Residue "C ASP 69": "OD1" <-> "OD2" Residue "C ASP 79": "OD1" <-> "OD2" Residue "C GLU 102": "OE1" <-> "OE2" Residue "C GLU 165": "OE1" <-> "OE2" Residue "C TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 255": "OE1" <-> "OE2" Residue "C TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 292": "OE1" <-> "OE2" Residue "C TYR 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 373": "NH1" <-> "NH2" Residue "C TYR 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 426": "OE1" <-> "OE2" Residue "C GLU 440": "OE1" <-> "OE2" Residue "C TYR 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 486": "OD1" <-> "OD2" Residue "C PHE 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 45": "OE1" <-> "OE2" Residue "E GLU 70": "OE1" <-> "OE2" Residue "E GLU 107": "OE1" <-> "OE2" Residue "E PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 171": "OE1" <-> "OE2" Residue "E GLU 191": "OE1" <-> "OE2" Residue "E TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 213": "OD1" <-> "OD2" Residue "E GLU 227": "OE1" <-> "OE2" Residue "E GLU 244": "OE1" <-> "OE2" Residue "E TYR 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 253": "OD1" <-> "OD2" Residue "E PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 270": "OE1" <-> "OE2" Residue "E GLU 297": "OE1" <-> "OE2" Residue "E TYR 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 344": "OE1" <-> "OE2" Residue "E ARG 359": "NH1" <-> "NH2" Residue "E TYR 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 383": "OD1" <-> "OD2" Residue "E TYR 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 403": "OD1" <-> "OD2" Residue "E ARG 411": "NH1" <-> "NH2" Residue "E PHE 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 425": "OE1" <-> "OE2" Residue "E PHE 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 451": "OE1" <-> "OE2" Residue "E GLU 468": "OE1" <-> "OE2" Residue "F PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 29": "OD1" <-> "OD2" Residue "F ARG 74": "NH1" <-> "NH2" Residue "F GLU 92": "OE1" <-> "OE2" Residue "F GLU 103": "OE1" <-> "OE2" Residue "F ARG 108": "NH1" <-> "NH2" Residue "F PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 132": "OE1" <-> "OE2" Residue "F PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 171": "OE1" <-> "OE2" Residue "F GLU 191": "OE1" <-> "OE2" Residue "F ARG 192": "NH1" <-> "NH2" Residue "F GLU 195": "OE1" <-> "OE2" Residue "F TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 232": "NH1" <-> "NH2" Residue "F GLU 244": "OE1" <-> "OE2" Residue "F ARG 247": "NH1" <-> "NH2" Residue "F ASP 253": "OD1" <-> "OD2" Residue "F PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 263": "NH1" <-> "NH2" Residue "F PHE 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 322": "OD1" <-> "OD2" Residue "F PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 397": "OD1" <-> "OD2" Residue "F PHE 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 451": "OE1" <-> "OE2" Residue "F PHE 460": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 461": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 468": "OE1" <-> "OE2" Residue "D GLU 40": "OE1" <-> "OE2" Residue "D ASP 80": "OD1" <-> "OD2" Residue "D PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 194": "NH1" <-> "NH2" Residue "D PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 362": "OD1" <-> "OD2" Residue "D ASP 372": "OD1" <-> "OD2" Residue "D PHE 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 461": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 53": "OE1" <-> "OE2" Residue "G GLU 61": "OE1" <-> "OE2" Residue "G GLU 92": "OE1" <-> "OE2" Residue "G ASP 110": "OD1" <-> "OD2" Residue "G ASP 122": "OD1" <-> "OD2" Residue "G PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 156": "OD1" <-> "OD2" Residue "G TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 244": "OD1" <-> "OD2" Residue "G PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 261": "OE1" <-> "OE2" Residue "O TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 38": "OE1" <-> "OE2" Residue "O ASP 71": "OD1" <-> "OD2" Residue "O PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 133": "OE1" <-> "OE2" Residue "O GLU 151": "OE1" <-> "OE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 37921 Number of models: 1 Model: "" Number of chains: 32 Chain: "4" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 534 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "5" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 534 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "6" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 534 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "7" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 534 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "8" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 534 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "1" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 534 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "2" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 534 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "3" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 534 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "H" Number of atoms: 975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 975 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 4, 'TRANS': 127} Chain: "I" Number of atoms: 354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 354 Classifications: {'peptide': 45} Link IDs: {'TRANS': 44} Chain: "K" Number of atoms: 1573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1573 Classifications: {'peptide': 198} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 6, 'TRANS': 191} Chain breaks: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "M" Number of atoms: 1259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1259 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 144} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "N" Number of atoms: 1718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1718 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 208} Chain: "P" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 344 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 2, 'TRANS': 38} Chain: "Q" Number of atoms: 422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 422 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 8, 'TRANS': 42} Chain: "R" Number of atoms: 621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 621 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 71} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "S" Number of atoms: 605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 605 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 72} Chain: "T" Number of atoms: 346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 346 Classifications: {'peptide': 44} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 39} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 549 Classifications: {'peptide': 67} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 62} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "A" Number of atoms: 3706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3706 Classifications: {'peptide': 486} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 467} Chain: "B" Number of atoms: 3639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 477, 3639 Classifications: {'peptide': 477} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 458} Chain breaks: 1 Chain: "C" Number of atoms: 3587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3587 Classifications: {'peptide': 470} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 451} Chain breaks: 1 Chain: "E" Number of atoms: 3458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3458 Classifications: {'peptide': 456} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 430} Chain breaks: 1 Chain: "F" Number of atoms: 3529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3529 Classifications: {'peptide': 466} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 440} Chain: "D" Number of atoms: 3272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3272 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 410} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "G" Number of atoms: 2103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2103 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 5, 'TRANS': 265} Chain: "O" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1437 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 8, 'TRANS': 178} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 18.28, per 1000 atoms: 0.48 Number of scatterers: 37921 At special positions: 0 Unit cell: (150.38, 141.62, 249.66, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 158 16.00 P 13 15.00 Mg 5 11.99 O 7106 8.00 N 6427 7.00 C 24212 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: 14.94 Conformation dependent library (CDL) restraints added in 6.6 seconds 9770 Ramachandran restraints generated. 4885 Oldfield, 0 Emsley, 4885 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9036 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 179 helices and 25 sheets defined 53.1% alpha, 9.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.12 Creating SS restraints... Processing helix chain '4' and resid 2 through 38 removed outlier: 3.868A pdb=" N GLY 4 17 " --> pdb=" O ALA 4 13 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N VAL 4 18 " --> pdb=" O ALA 4 14 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N ALA 4 19 " --> pdb=" O THR 4 15 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N GLY 4 20 " --> pdb=" O VAL 4 16 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N SER 4 21 " --> pdb=" O GLY 4 17 " (cutoff:3.500A) Processing helix chain '4' and resid 40 through 72 removed outlier: 5.220A pdb=" N GLN 4 44 " --> pdb=" O SER 4 41 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N GLU 4 58 " --> pdb=" O ALA 4 55 " (cutoff:3.500A) Processing helix chain '5' and resid 2 through 38 removed outlier: 3.868A pdb=" N GLY 5 17 " --> pdb=" O ALA 5 13 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N VAL 5 18 " --> pdb=" O ALA 5 14 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N ALA 5 19 " --> pdb=" O THR 5 15 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N GLY 5 20 " --> pdb=" O VAL 5 16 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N SER 5 21 " --> pdb=" O GLY 5 17 " (cutoff:3.500A) Processing helix chain '5' and resid 40 through 72 removed outlier: 5.214A pdb=" N GLN 5 44 " --> pdb=" O SER 5 41 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N GLU 5 58 " --> pdb=" O ALA 5 55 " (cutoff:3.500A) Processing helix chain '6' and resid 2 through 38 removed outlier: 3.868A pdb=" N GLY 6 17 " --> pdb=" O ALA 6 13 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N VAL 6 18 " --> pdb=" O ALA 6 14 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N ALA 6 19 " --> pdb=" O THR 6 15 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N GLY 6 20 " --> pdb=" O VAL 6 16 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N SER 6 21 " --> pdb=" O GLY 6 17 " (cutoff:3.500A) Processing helix chain '6' and resid 40 through 72 removed outlier: 5.201A pdb=" N GLN 6 44 " --> pdb=" O SER 6 41 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N GLU 6 58 " --> pdb=" O ALA 6 55 " (cutoff:3.500A) Processing helix chain '7' and resid 2 through 38 removed outlier: 3.868A pdb=" N GLY 7 17 " --> pdb=" O ALA 7 13 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N VAL 7 18 " --> pdb=" O ALA 7 14 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N ALA 7 19 " --> pdb=" O THR 7 15 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N GLY 7 20 " --> pdb=" O VAL 7 16 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N SER 7 21 " --> pdb=" O GLY 7 17 " (cutoff:3.500A) Processing helix chain '7' and resid 40 through 72 removed outlier: 5.198A pdb=" N GLN 7 44 " --> pdb=" O SER 7 41 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N GLU 7 58 " --> pdb=" O ALA 7 55 " (cutoff:3.500A) Processing helix chain '8' and resid 2 through 38 removed outlier: 3.868A pdb=" N GLY 8 17 " --> pdb=" O ALA 8 13 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N VAL 8 18 " --> pdb=" O ALA 8 14 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N ALA 8 19 " --> pdb=" O THR 8 15 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N GLY 8 20 " --> pdb=" O VAL 8 16 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N SER 8 21 " --> pdb=" O GLY 8 17 " (cutoff:3.500A) Processing helix chain '8' and resid 40 through 72 removed outlier: 5.216A pdb=" N GLN 8 44 " --> pdb=" O SER 8 41 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N GLU 8 58 " --> pdb=" O ALA 8 55 " (cutoff:3.500A) Processing helix chain '1' and resid 2 through 38 removed outlier: 3.868A pdb=" N GLY 1 17 " --> pdb=" O ALA 1 13 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N VAL 1 18 " --> pdb=" O ALA 1 14 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N ALA 1 19 " --> pdb=" O THR 1 15 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N GLY 1 20 " --> pdb=" O VAL 1 16 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N SER 1 21 " --> pdb=" O GLY 1 17 " (cutoff:3.500A) Processing helix chain '1' and resid 40 through 72 removed outlier: 5.209A pdb=" N GLN 1 44 " --> pdb=" O SER 1 41 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N GLU 1 58 " --> pdb=" O ALA 1 55 " (cutoff:3.500A) Processing helix chain '2' and resid 2 through 38 removed outlier: 3.868A pdb=" N GLY 2 17 " --> pdb=" O ALA 2 13 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N VAL 2 18 " --> pdb=" O ALA 2 14 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N ALA 2 19 " --> pdb=" O THR 2 15 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N GLY 2 20 " --> pdb=" O VAL 2 16 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N SER 2 21 " --> pdb=" O GLY 2 17 " (cutoff:3.500A) Processing helix chain '2' and resid 40 through 72 removed outlier: 5.208A pdb=" N GLN 2 44 " --> pdb=" O SER 2 41 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N GLU 2 58 " --> pdb=" O ALA 2 55 " (cutoff:3.500A) Processing helix chain '3' and resid 2 through 38 removed outlier: 3.867A pdb=" N GLY 3 17 " --> pdb=" O ALA 3 13 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N VAL 3 18 " --> pdb=" O ALA 3 14 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N ALA 3 19 " --> pdb=" O THR 3 15 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N GLY 3 20 " --> pdb=" O VAL 3 16 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N SER 3 21 " --> pdb=" O GLY 3 17 " (cutoff:3.500A) Processing helix chain '3' and resid 40 through 72 removed outlier: 5.226A pdb=" N GLN 3 44 " --> pdb=" O SER 3 41 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N GLU 3 58 " --> pdb=" O ALA 3 55 " (cutoff:3.500A) Processing helix chain 'H' and resid 100 through 102 No H-bonds generated for 'chain 'H' and resid 100 through 102' Processing helix chain 'H' and resid 105 through 121 Processing helix chain 'H' and resid 125 through 145 Processing helix chain 'I' and resid 4 through 8 Processing helix chain 'I' and resid 12 through 25 Processing helix chain 'I' and resid 29 through 39 removed outlier: 4.643A pdb=" N ALA I 33 " --> pdb=" O THR I 29 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N ASN I 34 " --> pdb=" O GLU I 30 " (cutoff:3.500A) Processing helix chain 'K' and resid 19 through 29 Proline residue: K 27 - end of helix Processing helix chain 'K' and resid 33 through 47 Processing helix chain 'K' and resid 55 through 96 Proline residue: K 76 - end of helix Processing helix chain 'K' and resid 99 through 183 removed outlier: 3.627A pdb=" N HIS K 103 " --> pdb=" O ALA K 99 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N HIS K 122 " --> pdb=" O VAL K 118 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N TYR K 123 " --> pdb=" O GLN K 119 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N LEU K 124 " --> pdb=" O LYS K 120 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N PHE K 125 " --> pdb=" O ARG K 121 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASP K 126 " --> pdb=" O HIS K 122 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASN K 175 " --> pdb=" O GLU K 171 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL K 177 " --> pdb=" O MET K 173 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLU K 178 " --> pdb=" O ILE K 174 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL K 182 " --> pdb=" O GLU K 178 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N GLN K 183 " --> pdb=" O LYS K 179 " (cutoff:3.500A) Processing helix chain 'K' and resid 195 through 207 Processing helix chain 'M' and resid 13 through 18 removed outlier: 3.639A pdb=" N ILE M 18 " --> pdb=" O ALA M 14 " (cutoff:3.500A) Processing helix chain 'M' and resid 21 through 42 removed outlier: 3.948A pdb=" N LYS M 24 " --> pdb=" O GLN M 21 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N ALA M 25 " --> pdb=" O ASN M 22 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ILE M 26 " --> pdb=" O GLN M 23 " (cutoff:3.500A) Processing helix chain 'M' and resid 54 through 57 No H-bonds generated for 'chain 'M' and resid 54 through 57' Processing helix chain 'M' and resid 65 through 74 Processing helix chain 'M' and resid 86 through 122 Processing helix chain 'M' and resid 127 through 129 No H-bonds generated for 'chain 'M' and resid 127 through 129' Processing helix chain 'M' and resid 132 through 138 Processing helix chain 'N' and resid 7 through 9 No H-bonds generated for 'chain 'N' and resid 7 through 9' Processing helix chain 'N' and resid 20 through 30 Proline residue: N 27 - end of helix removed outlier: 4.010A pdb=" N LEU N 30 " --> pdb=" O PHE N 26 " (cutoff:3.500A) Processing helix chain 'N' and resid 41 through 60 removed outlier: 3.591A pdb=" N THR N 59 " --> pdb=" O LYS N 55 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N MET N 60 " --> pdb=" O GLN N 56 " (cutoff:3.500A) Processing helix chain 'N' and resid 65 through 87 removed outlier: 4.195A pdb=" N LEU N 70 " --> pdb=" O THR N 67 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N VAL N 73 " --> pdb=" O LEU N 70 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N ILE N 79 " --> pdb=" O ILE N 76 " (cutoff:3.500A) Processing helix chain 'N' and resid 94 through 96 No H-bonds generated for 'chain 'N' and resid 94 through 96' Processing helix chain 'N' and resid 98 through 118 Proline residue: N 107 - end of helix Processing helix chain 'N' and resid 121 through 127 Processing helix chain 'N' and resid 135 through 181 Proline residue: N 139 - end of helix removed outlier: 4.181A pdb=" N ILE N 144 " --> pdb=" O LEU N 141 " (cutoff:3.500A) Proline residue: N 153 - end of helix removed outlier: 4.632A pdb=" N ALA N 162 " --> pdb=" O ARG N 159 " (cutoff:3.500A) Processing helix chain 'N' and resid 186 through 224 Processing helix chain 'P' and resid 5 through 8 No H-bonds generated for 'chain 'P' and resid 5 through 8' Processing helix chain 'P' and resid 10 through 18 removed outlier: 3.577A pdb=" N LYS P 14 " --> pdb=" O TRP P 10 " (cutoff:3.500A) Proline residue: P 15 - end of helix Processing helix chain 'P' and resid 22 through 40 Processing helix chain 'Q' and resid 2 through 4 No H-bonds generated for 'chain 'Q' and resid 2 through 4' Processing helix chain 'Q' and resid 6 through 8 No H-bonds generated for 'chain 'Q' and resid 6 through 8' Processing helix chain 'Q' and resid 10 through 21 Proline residue: Q 15 - end of helix removed outlier: 3.524A pdb=" N PHE Q 21 " --> pdb=" O LEU Q 17 " (cutoff:3.500A) Processing helix chain 'Q' and resid 23 through 29 Processing helix chain 'R' and resid 26 through 31 Processing helix chain 'R' and resid 36 through 54 Processing helix chain 'R' and resid 63 through 87 removed outlier: 4.761A pdb=" N VAL R 68 " --> pdb=" O GLY R 64 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N PHE R 79 " --> pdb=" O PHE R 75 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N LYS R 82 " --> pdb=" O SER R 78 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N HIS R 83 " --> pdb=" O PHE R 79 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N HIS R 86 " --> pdb=" O LYS R 82 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N GLU R 87 " --> pdb=" O HIS R 83 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 36 removed outlier: 4.229A pdb=" N VAL S 35 " --> pdb=" O TYR S 31 " (cutoff:3.500A) Processing helix chain 'S' and resid 45 through 61 Processing helix chain 'S' and resid 63 through 66 Processing helix chain 'S' and resid 69 through 93 Processing helix chain 'T' and resid 9 through 44 Proline residue: T 35 - end of helix Processing helix chain 'L' and resid 41 through 54 Processing helix chain 'L' and resid 68 through 82 removed outlier: 4.379A pdb=" N ARG L 73 " --> pdb=" O GLN L 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 103 No H-bonds generated for 'chain 'A' and resid 101 through 103' Processing helix chain 'A' and resid 151 through 156 Processing helix chain 'A' and resid 175 through 190 removed outlier: 3.809A pdb=" N GLN A 186 " --> pdb=" O THR A 182 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N LYS A 187 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N ARG A 188 " --> pdb=" O ILE A 184 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N PHE A 189 " --> pdb=" O ASN A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 221 Processing helix chain 'A' and resid 226 through 228 No H-bonds generated for 'chain 'A' and resid 226 through 228' Processing helix chain 'A' and resid 240 through 260 Proline residue: A 247 - end of helix removed outlier: 3.775A pdb=" N PHE A 257 " --> pdb=" O MET A 253 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASN A 260 " --> pdb=" O TYR A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 284 Processing helix chain 'A' and resid 291 through 293 No H-bonds generated for 'chain 'A' and resid 291 through 293' Processing helix chain 'A' and resid 298 through 308 removed outlier: 4.419A pdb=" N ARG A 308 " --> pdb=" O ARG A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 345 Processing helix chain 'A' and resid 354 through 358 Processing helix chain 'A' and resid 375 through 378 Processing helix chain 'A' and resid 381 through 398 removed outlier: 4.260A pdb=" N THR A 389 " --> pdb=" O GLN A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 403 No H-bonds generated for 'chain 'A' and resid 401 through 403' Processing helix chain 'A' and resid 407 through 409 No H-bonds generated for 'chain 'A' and resid 407 through 409' Processing helix chain 'A' and resid 412 through 428 Processing helix chain 'A' and resid 438 through 449 Processing helix chain 'A' and resid 458 through 475 removed outlier: 5.405A pdb=" N THR A 462 " --> pdb=" O SER A 459 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N PHE A 468 " --> pdb=" O GLU A 465 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N GLN A 475 " --> pdb=" O VAL A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 486 Processing helix chain 'A' and resid 491 through 507 Processing helix chain 'B' and resid 79 through 81 No H-bonds generated for 'chain 'B' and resid 79 through 81' Processing helix chain 'B' and resid 101 through 103 No H-bonds generated for 'chain 'B' and resid 101 through 103' Processing helix chain 'B' and resid 151 through 156 Processing helix chain 'B' and resid 175 through 187 removed outlier: 4.371A pdb=" N LYS B 187 " --> pdb=" O ILE B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 222 Processing helix chain 'B' and resid 240 through 260 Proline residue: B 247 - end of helix removed outlier: 3.976A pdb=" N PHE B 257 " --> pdb=" O MET B 253 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASN B 260 " --> pdb=" O TYR B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 283 Processing helix chain 'B' and resid 291 through 293 No H-bonds generated for 'chain 'B' and resid 291 through 293' Processing helix chain 'B' and resid 298 through 306 removed outlier: 4.014A pdb=" N HIS B 302 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LEU B 305 " --> pdb=" O LEU B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 316 No H-bonds generated for 'chain 'B' and resid 314 through 316' Processing helix chain 'B' and resid 337 through 345 Processing helix chain 'B' and resid 355 through 358 No H-bonds generated for 'chain 'B' and resid 355 through 358' Processing helix chain 'B' and resid 381 through 400 removed outlier: 4.404A pdb=" N THR B 389 " --> pdb=" O GLN B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 428 Processing helix chain 'B' and resid 438 through 449 Processing helix chain 'B' and resid 458 through 475 removed outlier: 4.405A pdb=" N THR B 462 " --> pdb=" O PRO B 458 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N LYS B 463 " --> pdb=" O SER B 459 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 486 Processing helix chain 'B' and resid 491 through 506 Processing helix chain 'C' and resid 79 through 81 No H-bonds generated for 'chain 'C' and resid 79 through 81' Processing helix chain 'C' and resid 101 through 103 No H-bonds generated for 'chain 'C' and resid 101 through 103' Processing helix chain 'C' and resid 151 through 156 Processing helix chain 'C' and resid 175 through 190 removed outlier: 3.705A pdb=" N GLN C 186 " --> pdb=" O THR C 182 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N LYS C 187 " --> pdb=" O ILE C 183 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N ARG C 188 " --> pdb=" O ILE C 184 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N PHE C 189 " --> pdb=" O ASN C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 222 Processing helix chain 'C' and resid 240 through 259 Proline residue: C 247 - end of helix removed outlier: 4.152A pdb=" N PHE C 257 " --> pdb=" O MET C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 284 Processing helix chain 'C' and resid 291 through 293 No H-bonds generated for 'chain 'C' and resid 291 through 293' Processing helix chain 'C' and resid 298 through 308 removed outlier: 3.940A pdb=" N LEU C 305 " --> pdb=" O LEU C 301 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N ARG C 308 " --> pdb=" O ARG C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 345 Processing helix chain 'C' and resid 355 through 358 No H-bonds generated for 'chain 'C' and resid 355 through 358' Processing helix chain 'C' and resid 375 through 378 Processing helix chain 'C' and resid 381 through 400 removed outlier: 4.254A pdb=" N THR C 389 " --> pdb=" O GLN C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 419 through 428 Processing helix chain 'C' and resid 438 through 449 Processing helix chain 'C' and resid 461 through 475 Processing helix chain 'C' and resid 477 through 486 Processing helix chain 'C' and resid 491 through 506 Processing helix chain 'E' and resid 91 through 93 No H-bonds generated for 'chain 'E' and resid 91 through 93' Processing helix chain 'E' and resid 126 through 128 No H-bonds generated for 'chain 'E' and resid 126 through 128' Processing helix chain 'E' and resid 141 through 146 Processing helix chain 'E' and resid 165 through 179 Processing helix chain 'E' and resid 193 through 205 Processing helix chain 'E' and resid 229 through 248 removed outlier: 4.930A pdb=" N ALA E 236 " --> pdb=" O ARG E 232 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N LEU E 237 " --> pdb=" O ALA E 233 " (cutoff:3.500A) Processing helix chain 'E' and resid 262 through 274 Processing helix chain 'E' and resid 288 through 298 removed outlier: 4.648A pdb=" N ARG E 298 " --> pdb=" O THR E 294 " (cutoff:3.500A) Processing helix chain 'E' and resid 316 through 318 No H-bonds generated for 'chain 'E' and resid 316 through 318' Processing helix chain 'E' and resid 323 through 331 removed outlier: 3.982A pdb=" N ALA E 330 " --> pdb=" O ALA E 326 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N HIS E 331 " --> pdb=" O THR E 327 " (cutoff:3.500A) Processing helix chain 'E' and resid 341 through 344 No H-bonds generated for 'chain 'E' and resid 341 through 344' Processing helix chain 'E' and resid 363 through 390 removed outlier: 7.399A pdb=" N SER E 368 " --> pdb=" O ASN E 364 " (cutoff:3.500A) removed outlier: 8.740A pdb=" N GLU E 369 " --> pdb=" O ILE E 365 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N HIS E 370 " --> pdb=" O VAL E 366 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ILE E 390 " --> pdb=" O SER E 386 " (cutoff:3.500A) Processing helix chain 'E' and resid 403 through 417 Processing helix chain 'E' and resid 422 through 428 removed outlier: 5.098A pdb=" N VAL E 426 " --> pdb=" O VAL E 423 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N THR E 428 " --> pdb=" O GLU E 425 " (cutoff:3.500A) Processing helix chain 'E' and resid 437 through 449 Processing helix chain 'E' and resid 457 through 460 Processing helix chain 'E' and resid 466 through 474 Processing helix chain 'F' and resid 91 through 93 No H-bonds generated for 'chain 'F' and resid 91 through 93' Processing helix chain 'F' and resid 141 through 146 Processing helix chain 'F' and resid 165 through 175 Processing helix chain 'F' and resid 193 through 205 Processing helix chain 'F' and resid 229 through 248 removed outlier: 4.797A pdb=" N ALA F 236 " --> pdb=" O ARG F 232 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N LEU F 237 " --> pdb=" O ALA F 233 " (cutoff:3.500A) Processing helix chain 'F' and resid 262 through 272 Processing helix chain 'F' and resid 288 through 296 Processing helix chain 'F' and resid 316 through 318 No H-bonds generated for 'chain 'F' and resid 316 through 318' Processing helix chain 'F' and resid 323 through 331 removed outlier: 4.803A pdb=" N ALA F 330 " --> pdb=" O ALA F 326 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N HIS F 331 " --> pdb=" O THR F 327 " (cutoff:3.500A) Processing helix chain 'F' and resid 340 through 345 removed outlier: 3.804A pdb=" N LEU F 345 " --> pdb=" O ALA F 341 " (cutoff:3.500A) Processing helix chain 'F' and resid 368 through 393 removed outlier: 4.912A pdb=" N ASP F 389 " --> pdb=" O LYS F 385 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N ILE F 390 " --> pdb=" O SER F 386 " (cutoff:3.500A) Processing helix chain 'F' and resid 401 through 417 Processing helix chain 'F' and resid 437 through 448 Processing helix chain 'F' and resid 457 through 459 No H-bonds generated for 'chain 'F' and resid 457 through 459' Processing helix chain 'F' and resid 466 through 475 Processing helix chain 'D' and resid 91 through 93 No H-bonds generated for 'chain 'D' and resid 91 through 93' Processing helix chain 'D' and resid 126 through 128 No H-bonds generated for 'chain 'D' and resid 126 through 128' Processing helix chain 'D' and resid 166 through 178 Processing helix chain 'D' and resid 193 through 206 Processing helix chain 'D' and resid 229 through 250 removed outlier: 5.268A pdb=" N ALA D 236 " --> pdb=" O ARG D 232 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N LEU D 237 " --> pdb=" O ALA D 233 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLY D 239 " --> pdb=" O VAL D 235 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N PHE D 246 " --> pdb=" O VAL D 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 275 Processing helix chain 'D' and resid 292 through 298 removed outlier: 3.901A pdb=" N ARG D 298 " --> pdb=" O THR D 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 340 through 344 Processing helix chain 'D' and resid 368 through 387 Processing helix chain 'D' and resid 404 through 416 Processing helix chain 'D' and resid 422 through 424 No H-bonds generated for 'chain 'D' and resid 422 through 424' Processing helix chain 'D' and resid 437 through 449 removed outlier: 3.501A pdb=" N ALA D 449 " --> pdb=" O GLN D 445 " (cutoff:3.500A) Processing helix chain 'D' and resid 457 through 459 No H-bonds generated for 'chain 'D' and resid 457 through 459' Processing helix chain 'D' and resid 466 through 476 Processing helix chain 'G' and resid 3 through 31 Processing helix chain 'G' and resid 36 through 55 Proline residue: G 40 - end of helix removed outlier: 4.447A pdb=" N LEU G 51 " --> pdb=" O GLY G 47 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N TYR G 52 " --> pdb=" O SER G 48 " (cutoff:3.500A) Processing helix chain 'G' and resid 81 through 99 removed outlier: 3.654A pdb=" N ALA G 99 " --> pdb=" O THR G 95 " (cutoff:3.500A) Processing helix chain 'G' and resid 110 through 117 Processing helix chain 'G' and resid 138 through 149 Processing helix chain 'G' and resid 181 through 186 Processing helix chain 'G' and resid 188 through 192 removed outlier: 3.952A pdb=" N ILE G 192 " --> pdb=" O SER G 189 " (cutoff:3.500A) Processing helix chain 'G' and resid 198 through 269 removed outlier: 3.791A pdb=" N THR G 222 " --> pdb=" O LYS G 218 " (cutoff:3.500A) Processing helix chain 'O' and resid 13 through 27 Processing helix chain 'O' and resid 32 through 47 Processing helix chain 'O' and resid 49 through 54 Processing helix chain 'O' and resid 62 through 76 removed outlier: 4.039A pdb=" N LYS O 75 " --> pdb=" O ASP O 71 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N GLU O 76 " --> pdb=" O ILE O 72 " (cutoff:3.500A) Processing helix chain 'O' and resid 80 through 90 Processing helix chain 'O' and resid 98 through 112 Processing helix chain 'O' and resid 128 through 140 Processing helix chain 'O' and resid 156 through 158 No H-bonds generated for 'chain 'O' and resid 156 through 158' Processing helix chain 'O' and resid 175 through 186 Processing sheet with id= A, first strand: chain 'H' and resid 17 through 22 Processing sheet with id= B, first strand: chain 'H' and resid 43 through 48 removed outlier: 6.882A pdb=" N HIS H 66 " --> pdb=" O ARG H 34 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N VAL H 36 " --> pdb=" O VAL H 64 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N VAL H 64 " --> pdb=" O VAL H 36 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N VAL H 38 " --> pdb=" O LEU H 62 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N LEU H 62 " --> pdb=" O VAL H 38 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 29 through 33 removed outlier: 6.488A pdb=" N ARG A 40 " --> pdb=" O LEU A 32 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N VAL A 74 " --> pdb=" O SER A 63 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N SER A 63 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLU A 51 " --> pdb=" O SER A 63 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 96 through 99 removed outlier: 4.165A pdb=" N THR A 125 " --> pdb=" O VAL A 99 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 349 through 351 removed outlier: 7.078A pdb=" N LEU A 166 " --> pdb=" O ILE A 350 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 229 through 234 removed outlier: 6.715A pdb=" N CYS A 201 " --> pdb=" O ILE A 230 " (cutoff:3.500A) removed outlier: 8.215A pdb=" N VAL A 232 " --> pdb=" O CYS A 201 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N TYR A 203 " --> pdb=" O VAL A 232 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N ALA A 234 " --> pdb=" O TYR A 203 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N ALA A 205 " --> pdb=" O ALA A 234 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N SER A 320 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N ILE A 266 " --> pdb=" O SER A 320 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N THR A 322 " --> pdb=" O ILE A 266 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N TYR A 268 " --> pdb=" O THR A 322 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 28 through 30 removed outlier: 6.406A pdb=" N GLY B 72 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N LEU B 66 " --> pdb=" O ASN B 70 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N ASN B 70 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N HIS B 42 " --> pdb=" O VAL B 31 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N VAL B 31 " --> pdb=" O HIS B 42 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 96 through 99 removed outlier: 4.355A pdb=" N THR B 125 " --> pdb=" O VAL B 99 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 349 through 352 removed outlier: 6.875A pdb=" N LEU B 166 " --> pdb=" O ILE B 350 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N LEU B 352 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ILE B 168 " --> pdb=" O LEU B 352 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.820A pdb=" N CYS B 201 " --> pdb=" O ILE B 230 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N VAL B 232 " --> pdb=" O CYS B 201 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N TYR B 203 " --> pdb=" O VAL B 232 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N ALA B 234 " --> pdb=" O TYR B 203 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N ALA B 205 " --> pdb=" O ALA B 234 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N SER B 320 " --> pdb=" O ALA B 264 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N ILE B 266 " --> pdb=" O SER B 320 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N THR B 322 " --> pdb=" O ILE B 266 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N TYR B 268 " --> pdb=" O THR B 322 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 87 through 89 removed outlier: 6.660A pdb=" N ARG C 40 " --> pdb=" O LEU C 32 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ILE C 34 " --> pdb=" O ILE C 38 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ILE C 38 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL C 74 " --> pdb=" O SER C 63 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N SER C 63 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLU C 51 " --> pdb=" O SER C 63 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 96 through 99 removed outlier: 4.349A pdb=" N THR C 125 " --> pdb=" O VAL C 99 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 167 through 169 Processing sheet with id= N, first strand: chain 'C' and resid 229 through 234 removed outlier: 8.990A pdb=" N ILE C 230 " --> pdb=" O LEU C 199 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N CYS C 201 " --> pdb=" O ILE C 230 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N VAL C 232 " --> pdb=" O CYS C 201 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N TYR C 203 " --> pdb=" O VAL C 232 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N ALA C 234 " --> pdb=" O TYR C 203 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N ALA C 205 " --> pdb=" O ALA C 234 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N HIS C 263 " --> pdb=" O TYR C 200 " (cutoff:3.500A) removed outlier: 8.146A pdb=" N ILE C 202 " --> pdb=" O HIS C 263 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N LEU C 265 " --> pdb=" O ILE C 202 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N VAL C 204 " --> pdb=" O LEU C 265 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ILE C 267 " --> pdb=" O VAL C 204 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N ILE C 206 " --> pdb=" O ILE C 267 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N ASP C 269 " --> pdb=" O ILE C 206 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N SER C 320 " --> pdb=" O ALA C 264 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N ILE C 266 " --> pdb=" O SER C 320 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N THR C 322 " --> pdb=" O ILE C 266 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N TYR C 268 " --> pdb=" O THR C 322 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'E' and resid 13 through 15 removed outlier: 6.693A pdb=" N ARG E 62 " --> pdb=" O ALA E 53 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N HIS E 55 " --> pdb=" O THR E 60 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N THR E 60 " --> pdb=" O HIS E 55 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N GLN E 27 " --> pdb=" O ILE E 16 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N ILE E 16 " --> pdb=" O GLN E 27 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 86 through 89 removed outlier: 4.124A pdb=" N GLN E 115 " --> pdb=" O VAL E 89 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 218 through 224 removed outlier: 6.700A pdb=" N SER E 184 " --> pdb=" O ALA E 219 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N VAL E 221 " --> pdb=" O SER E 184 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N PHE E 186 " --> pdb=" O VAL E 221 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N GLY E 223 " --> pdb=" O PHE E 186 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N GLY E 188 " --> pdb=" O GLY E 223 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N VAL E 185 " --> pdb=" O ASP E 253 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N LEU E 255 " --> pdb=" O VAL E 185 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N ALA E 187 " --> pdb=" O LEU E 255 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N PHE E 257 " --> pdb=" O ALA E 187 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VAL E 189 " --> pdb=" O PHE E 257 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N SER E 306 " --> pdb=" O VAL E 254 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N LEU E 256 " --> pdb=" O SER E 306 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N THR E 308 " --> pdb=" O LEU E 256 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N ILE E 258 " --> pdb=" O THR E 308 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N VAL E 310 " --> pdb=" O ILE E 258 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N GLY E 156 " --> pdb=" O ASP E 333 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N THR E 335 " --> pdb=" O GLY E 156 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'F' and resid 13 through 15 removed outlier: 6.625A pdb=" N ARG F 62 " --> pdb=" O ALA F 53 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N HIS F 55 " --> pdb=" O THR F 60 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N THR F 60 " --> pdb=" O HIS F 55 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N GLN F 27 " --> pdb=" O ILE F 16 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N ILE F 16 " --> pdb=" O GLN F 27 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'F' and resid 86 through 89 removed outlier: 4.282A pdb=" N GLN F 115 " --> pdb=" O VAL F 89 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'F' and resid 334 through 337 removed outlier: 7.459A pdb=" N ILE F 155 " --> pdb=" O ILE F 307 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N SER F 309 " --> pdb=" O ILE F 155 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N LEU F 157 " --> pdb=" O SER F 309 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N GLN F 311 " --> pdb=" O LEU F 157 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N GLY F 159 " --> pdb=" O GLN F 311 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N ILE F 313 " --> pdb=" O GLY F 159 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ALA F 219 " --> pdb=" O PHE F 186 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N GLY F 188 " --> pdb=" O ALA F 219 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N VAL F 221 " --> pdb=" O GLY F 188 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'D' and resid 77 through 79 removed outlier: 6.315A pdb=" N ASP D 25 " --> pdb=" O VAL D 17 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N VAL D 19 " --> pdb=" O VAL D 23 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N VAL D 23 " --> pdb=" O VAL D 19 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N ILE D 64 " --> pdb=" O VAL D 52 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N VAL D 52 " --> pdb=" O ILE D 64 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'D' and resid 86 through 89 removed outlier: 3.966A pdb=" N GLN D 115 " --> pdb=" O VAL D 89 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'D' and resid 154 through 156 removed outlier: 8.802A pdb=" N ILE D 155 " --> pdb=" O ILE D 307 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N SER D 309 " --> pdb=" O ILE D 155 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY D 223 " --> pdb=" O GLY D 188 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'G' and resid 171 through 179 removed outlier: 5.294A pdb=" N ASN G 163 " --> pdb=" O VAL G 71 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N VAL G 126 " --> pdb=" O GLY G 107 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'O' and resid 147 through 150 1991 hydrogen bonds defined for protein. 4992 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 14.16 Time building geometry restraints manager: 16.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 11867 1.33 - 1.46: 6263 1.46 - 1.58: 20098 1.58 - 1.70: 21 1.70 - 1.82: 297 Bond restraints: 38546 Sorted by residual: bond pdb=" C6 ATP A 601 " pdb=" N6 ATP A 601 " ideal model delta sigma weight residual 1.337 1.461 -0.124 1.10e-02 8.26e+03 1.27e+02 bond pdb=" C6 ATP C 601 " pdb=" N6 ATP C 601 " ideal model delta sigma weight residual 1.337 1.456 -0.119 1.10e-02 8.26e+03 1.18e+02 bond pdb=" C6 ATP B 601 " pdb=" N6 ATP B 601 " ideal model delta sigma weight residual 1.337 1.455 -0.118 1.10e-02 8.26e+03 1.15e+02 bond pdb=" C4 ATP C 601 " pdb=" N9 ATP C 601 " ideal model delta sigma weight residual 1.374 1.279 0.095 1.00e-02 1.00e+04 9.02e+01 bond pdb=" C4 ATP B 601 " pdb=" N9 ATP B 601 " ideal model delta sigma weight residual 1.374 1.280 0.094 1.00e-02 1.00e+04 8.92e+01 ... (remaining 38541 not shown) Histogram of bond angle deviations from ideal: 98.36 - 106.24: 921 106.24 - 114.13: 23221 114.13 - 122.02: 21457 122.02 - 129.90: 6433 129.90 - 137.79: 119 Bond angle restraints: 52151 Sorted by residual: angle pdb=" PB ATP B 601 " pdb=" O3B ATP B 601 " pdb=" PG ATP B 601 " ideal model delta sigma weight residual 139.87 121.81 18.06 1.00e+00 1.00e+00 3.26e+02 angle pdb=" PB ATP A 601 " pdb=" O3B ATP A 601 " pdb=" PG ATP A 601 " ideal model delta sigma weight residual 139.87 121.85 18.02 1.00e+00 1.00e+00 3.25e+02 angle pdb=" PA ATP B 601 " pdb=" O3A ATP B 601 " pdb=" PB ATP B 601 " ideal model delta sigma weight residual 136.83 121.14 15.69 1.00e+00 1.00e+00 2.46e+02 angle pdb=" PB ATP C 601 " pdb=" O3B ATP C 601 " pdb=" PG ATP C 601 " ideal model delta sigma weight residual 139.87 125.69 14.18 1.00e+00 1.00e+00 2.01e+02 angle pdb=" PA ATP A 601 " pdb=" O3A ATP A 601 " pdb=" PB ATP A 601 " ideal model delta sigma weight residual 136.83 122.90 13.93 1.00e+00 1.00e+00 1.94e+02 ... (remaining 52146 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.05: 22519 29.05 - 58.10: 731 58.10 - 87.16: 104 87.16 - 116.21: 6 116.21 - 145.26: 2 Dihedral angle restraints: 23362 sinusoidal: 9242 harmonic: 14120 Sorted by residual: dihedral pdb=" O1B ADP D 501 " pdb=" O3A ADP D 501 " pdb=" PB ADP D 501 " pdb=" PA ADP D 501 " ideal model delta sinusoidal sigma weight residual 300.00 154.74 145.26 1 2.00e+01 2.50e-03 4.37e+01 dihedral pdb=" O2A ADP D 501 " pdb=" O3A ADP D 501 " pdb=" PA ADP D 501 " pdb=" PB ADP D 501 " ideal model delta sinusoidal sigma weight residual -60.00 59.26 -119.25 1 2.00e+01 2.50e-03 3.57e+01 dihedral pdb=" C5' ADP D 501 " pdb=" O5' ADP D 501 " pdb=" PA ADP D 501 " pdb=" O2A ADP D 501 " ideal model delta sinusoidal sigma weight residual -60.00 47.78 -107.77 1 2.00e+01 2.50e-03 3.13e+01 ... (remaining 23359 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 4345 0.048 - 0.096: 1373 0.096 - 0.143: 339 0.143 - 0.191: 17 0.191 - 0.239: 4 Chirality restraints: 6078 Sorted by residual: chirality pdb=" C2' ATP B 601 " pdb=" C1' ATP B 601 " pdb=" C3' ATP B 601 " pdb=" O2' ATP B 601 " both_signs ideal model delta sigma weight residual False -2.68 -2.44 -0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" C2' ATP C 601 " pdb=" C1' ATP C 601 " pdb=" C3' ATP C 601 " pdb=" O2' ATP C 601 " both_signs ideal model delta sigma weight residual False -2.68 -2.45 -0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" C2' ATP A 601 " pdb=" C1' ATP A 601 " pdb=" C3' ATP A 601 " pdb=" O2' ATP A 601 " both_signs ideal model delta sigma weight residual False -2.68 -2.46 -0.22 2.00e-01 2.50e+01 1.25e+00 ... (remaining 6075 not shown) Planarity restraints: 6644 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP Q 51 " -0.013 2.00e-02 2.50e+03 2.05e-02 1.05e+01 pdb=" CG TRP Q 51 " 0.031 2.00e-02 2.50e+03 pdb=" CD1 TRP Q 51 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TRP Q 51 " -0.022 2.00e-02 2.50e+03 pdb=" NE1 TRP Q 51 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP Q 51 " -0.008 2.00e-02 2.50e+03 pdb=" CE3 TRP Q 51 " -0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP Q 51 " 0.026 2.00e-02 2.50e+03 pdb=" CZ3 TRP Q 51 " 0.027 2.00e-02 2.50e+03 pdb=" CH2 TRP Q 51 " -0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS Q 49 " -0.041 5.00e-02 4.00e+02 6.19e-02 6.13e+00 pdb=" N PRO Q 50 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO Q 50 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO Q 50 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE E 140 " -0.011 2.00e-02 2.50e+03 2.12e-02 4.48e+00 pdb=" C ILE E 140 " 0.037 2.00e-02 2.50e+03 pdb=" O ILE E 140 " -0.014 2.00e-02 2.50e+03 pdb=" N LYS E 141 " -0.012 2.00e-02 2.50e+03 ... (remaining 6641 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 4866 2.74 - 3.28: 41164 3.28 - 3.82: 63015 3.82 - 4.36: 78662 4.36 - 4.90: 130648 Nonbonded interactions: 318355 Sorted by model distance: nonbonded pdb=" O THR H 122 " pdb=" NH2 ARG H 128 " model vdw 2.196 2.520 nonbonded pdb=" OE1 GLU B 307 " pdb=" OG1 THR F 193 " model vdw 2.203 2.440 nonbonded pdb=" O ARG H 134 " pdb=" ND2 ASN H 138 " model vdw 2.206 2.520 nonbonded pdb=" O VAL G 168 " pdb=" OG SER G 226 " model vdw 2.210 2.440 nonbonded pdb=" NE ARG D 411 " pdb=" OE2 GLU D 457 " model vdw 2.212 2.520 ... (remaining 318350 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 '1' selection = chain '2' selection = chain '3' selection = chain '4' selection = chain '5' selection = chain '6' selection = chain '7' selection = chain '8' } ncs_group { reference = (chain 'A' and (resid 24 through 401 or resid 417 through 508 or resid 601 throu \ gh 602)) selection = (chain 'B' and (resid 24 through 401 or resid 417 through 508 or resid 601 throu \ gh 602)) selection = chain 'C' } ncs_group { reference = (chain 'D' and resid 12 through 475) selection = (chain 'E' and (resid 12 through 160 or resid 162 through 312 or resid 332 throu \ gh 389 or (resid 404 and (name N or name CA or name C or name O or name CB )) or \ resid 405 through 475)) selection = (chain 'F' and (resid 12 through 160 or resid 162 through 312 or resid 332 throu \ gh 389 or (resid 404 and (name N or name CA or name C or name O or name CB )) or \ resid 405 through 475)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.750 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: 0.040 Extract box with map and model: 30.300 Check model and map are aligned: 0.670 Set scattering table: 0.320 Process input model: 97.240 Find NCS groups from input model: 2.280 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 142.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 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 : 0.009 0.145 38546 Z= 0.578 Angle : 0.785 18.063 52151 Z= 0.476 Chirality : 0.047 0.239 6078 Planarity : 0.004 0.065 6644 Dihedral : 14.502 145.261 14326 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.02 % Favored : 93.96 % Rotamer: Outliers : 0.08 % Allowed : 5.16 % Favored : 94.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.50 % Cis-general : 0.11 % 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: -3.18 (0.10), residues: 4885 helix: -1.70 (0.09), residues: 2624 sheet: -2.50 (0.18), residues: 575 loop : -2.33 (0.14), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP Q 51 HIS 0.005 0.001 HIS K 172 PHE 0.021 0.002 PHE H 45 TYR 0.024 0.002 TYR D 284 ARG 0.005 0.000 ARG C 30 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9770 Ramachandran restraints generated. 4885 Oldfield, 0 Emsley, 4885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9770 Ramachandran restraints generated. 4885 Oldfield, 0 Emsley, 4885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 895 residues out of total 4012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 892 time to evaluate : 4.203 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: 2 39 ASN cc_start: 0.7811 (t0) cc_final: 0.7601 (t0) REVERT: 2 60 MET cc_start: 0.7962 (mmm) cc_final: 0.7704 (mmm) REVERT: H 111 ASN cc_start: 0.8382 (m110) cc_final: 0.8179 (m-40) REVERT: I 13 ILE cc_start: 0.8701 (mm) cc_final: 0.8438 (mm) REVERT: I 28 LYS cc_start: 0.6946 (mtpp) cc_final: 0.6705 (mttt) REVERT: M 51 ILE cc_start: 0.8219 (pt) cc_final: 0.7920 (mt) REVERT: N 145 GLU cc_start: 0.8065 (mm-30) cc_final: 0.7832 (tp30) REVERT: S 70 LYS cc_start: 0.7077 (tptt) cc_final: 0.6841 (tptt) REVERT: T 16 TYR cc_start: 0.7287 (m-80) cc_final: 0.7008 (m-80) REVERT: L 74 GLU cc_start: 0.8517 (tm-30) cc_final: 0.8302 (tm-30) REVERT: A 416 GLN cc_start: 0.8116 (tm-30) cc_final: 0.7893 (tm-30) REVERT: A 463 LYS cc_start: 0.8854 (mtpt) cc_final: 0.8558 (mtpt) REVERT: B 226 MET cc_start: 0.8212 (mmm) cc_final: 0.7801 (tpt) REVERT: C 373 ARG cc_start: 0.8189 (OUTLIER) cc_final: 0.7757 (mtt90) REVERT: E 347 ILE cc_start: 0.9213 (mm) cc_final: 0.8896 (mm) REVERT: E 458 GLN cc_start: 0.7938 (mm110) cc_final: 0.7496 (tp40) REVERT: D 62 ARG cc_start: 0.7928 (ttm170) cc_final: 0.7665 (ttm-80) REVERT: D 296 GLN cc_start: 0.8209 (mm-40) cc_final: 0.7917 (tt0) REVERT: D 297 GLU cc_start: 0.8246 (tp30) cc_final: 0.8042 (tp30) REVERT: D 433 LYS cc_start: 0.6790 (mmtm) cc_final: 0.6275 (mptt) REVERT: D 460 PHE cc_start: 0.6993 (m-10) cc_final: 0.6720 (m-10) REVERT: D 467 GLU cc_start: 0.7216 (tt0) cc_final: 0.6702 (mp0) REVERT: G 75 ARG cc_start: 0.7949 (mtp85) cc_final: 0.7652 (ttt180) REVERT: G 104 MET cc_start: 0.6501 (tpp) cc_final: 0.5924 (tpt) REVERT: O 163 ILE cc_start: 0.8444 (mm) cc_final: 0.8206 (tp) outliers start: 3 outliers final: 0 residues processed: 894 average time/residue: 0.5318 time to fit residues: 742.4394 Evaluate side-chains 639 residues out of total 4012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 638 time to evaluate : 4.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 373 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 407 optimal weight: 7.9990 chunk 366 optimal weight: 0.9990 chunk 203 optimal weight: 5.9990 chunk 125 optimal weight: 4.9990 chunk 246 optimal weight: 1.9990 chunk 195 optimal weight: 1.9990 chunk 378 optimal weight: 0.8980 chunk 146 optimal weight: 5.9990 chunk 230 optimal weight: 0.9980 chunk 281 optimal weight: 0.9990 chunk 438 optimal weight: 0.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 45 GLN 6 45 GLN 8 44 GLN 1 45 GLN 2 45 GLN H 111 ASN ** H 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 102 GLN ** K 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 130 ASN ** K 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 180 HIS M 34 ASN N 46 GLN N 47 GLN N 101 ASN N 185 ASN Q 32 ASN R 83 HIS S 57 ASN T 31 ASN L 84 ASN A 208 GLN A 349 GLN A 385 GLN A 415 GLN A 432 GLN B 65 ASN B 475 GLN C 78 ASN C 208 GLN C 385 GLN E 210 ASN E 224 GLN E 388 GLN F 133 GLN F 175 ASN F 197 ASN F 249 GLN F 252 GLN D 197 ASN D 378 GLN D 382 GLN D 419 GLN G 120 HIS G 163 ASN ** G 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 57 ASN O 84 ASN Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 38546 Z= 0.188 Angle : 0.591 14.151 52151 Z= 0.297 Chirality : 0.042 0.216 6078 Planarity : 0.004 0.044 6644 Dihedral : 6.841 124.917 5440 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.93 % Allowed : 11.97 % Favored : 86.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.50 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.12), residues: 4885 helix: -0.12 (0.10), residues: 2594 sheet: -1.98 (0.20), residues: 530 loop : -1.55 (0.14), residues: 1761 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP M 53 HIS 0.006 0.001 HIS K 158 PHE 0.032 0.001 PHE T 20 TYR 0.021 0.001 TYR D 371 ARG 0.011 0.000 ARG K 166 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9770 Ramachandran restraints generated. 4885 Oldfield, 0 Emsley, 4885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9770 Ramachandran restraints generated. 4885 Oldfield, 0 Emsley, 4885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 842 residues out of total 4012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 765 time to evaluate : 4.369 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: 4 75 MET cc_start: 0.7860 (mtp) cc_final: 0.6682 (mmt) REVERT: 1 69 PHE cc_start: 0.8516 (m-80) cc_final: 0.8169 (m-80) REVERT: 1 73 PHE cc_start: 0.7590 (m-80) cc_final: 0.6703 (m-80) REVERT: K 166 ARG cc_start: 0.8632 (ttm110) cc_final: 0.8427 (ptp-170) REVERT: M 128 ASP cc_start: 0.7828 (p0) cc_final: 0.7296 (p0) REVERT: N 56 GLN cc_start: 0.7579 (tt0) cc_final: 0.7360 (tt0) REVERT: N 152 GLN cc_start: 0.8149 (mt0) cc_final: 0.7843 (mp10) REVERT: S 70 LYS cc_start: 0.7063 (tptt) cc_final: 0.6831 (tptt) REVERT: A 45 ARG cc_start: 0.8171 (ttp80) cc_final: 0.7897 (ttp-110) REVERT: A 416 GLN cc_start: 0.8145 (tm-30) cc_final: 0.7940 (tm-30) REVERT: B 80 LYS cc_start: 0.9259 (OUTLIER) cc_final: 0.9046 (ptpt) REVERT: B 226 MET cc_start: 0.8108 (mmm) cc_final: 0.7859 (tpt) REVERT: B 415 GLN cc_start: 0.7561 (mt0) cc_final: 0.7321 (mt0) REVERT: B 477 GLN cc_start: 0.7698 (mm-40) cc_final: 0.7142 (tm-30) REVERT: E 347 ILE cc_start: 0.9188 (mm) cc_final: 0.8927 (mm) REVERT: E 384 TYR cc_start: 0.8601 (t80) cc_final: 0.8154 (t80) REVERT: E 458 GLN cc_start: 0.7889 (mm110) cc_final: 0.7423 (tp40) REVERT: D 62 ARG cc_start: 0.7822 (ttm170) cc_final: 0.7575 (ttm-80) REVERT: D 101 ILE cc_start: 0.8815 (OUTLIER) cc_final: 0.8560 (mt) REVERT: D 225 MET cc_start: 0.8936 (mtm) cc_final: 0.8718 (mtm) REVERT: D 263 ARG cc_start: 0.8192 (mmt-90) cc_final: 0.7805 (mpt180) REVERT: D 371 TYR cc_start: 0.8026 (t80) cc_final: 0.7787 (t80) REVERT: D 433 LYS cc_start: 0.6783 (mmtm) cc_final: 0.6286 (mptt) REVERT: D 460 PHE cc_start: 0.6978 (m-10) cc_final: 0.6748 (m-10) REVERT: D 467 GLU cc_start: 0.7170 (tt0) cc_final: 0.6752 (mp0) REVERT: G 104 MET cc_start: 0.6571 (tpp) cc_final: 0.5986 (tpt) REVERT: O 163 ILE cc_start: 0.8542 (mm) cc_final: 0.8283 (tp) outliers start: 77 outliers final: 42 residues processed: 796 average time/residue: 0.5259 time to fit residues: 670.1833 Evaluate side-chains 691 residues out of total 4012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 647 time to evaluate : 4.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 4 residue 18 VAL Chi-restraints excluded: chain 4 residue 41 SER Chi-restraints excluded: chain 5 residue 28 VAL Chi-restraints excluded: chain 5 residue 54 PHE Chi-restraints excluded: chain 5 residue 62 LEU Chi-restraints excluded: chain 6 residue 16 VAL Chi-restraints excluded: chain 6 residue 18 VAL Chi-restraints excluded: chain 6 residue 66 MET Chi-restraints excluded: chain 7 residue 31 SER Chi-restraints excluded: chain 1 residue 18 VAL Chi-restraints excluded: chain 1 residue 33 ILE Chi-restraints excluded: chain 1 residue 71 ILE Chi-restraints excluded: chain 2 residue 28 VAL Chi-restraints excluded: chain 3 residue 9 ILE Chi-restraints excluded: chain K residue 98 GLN Chi-restraints excluded: chain M residue 33 TRP Chi-restraints excluded: chain N residue 81 THR Chi-restraints excluded: chain P residue 5 ILE Chi-restraints excluded: chain P residue 25 TRP Chi-restraints excluded: chain Q residue 7 THR Chi-restraints excluded: chain Q residue 42 MET Chi-restraints excluded: chain S residue 50 GLN Chi-restraints excluded: chain S residue 52 LEU Chi-restraints excluded: chain S residue 83 LEU Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 92 THR Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 358 TYR Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain B residue 436 MET Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain E residue 37 ASN Chi-restraints excluded: chain E residue 333 ASP Chi-restraints excluded: chain F residue 169 ILE Chi-restraints excluded: chain F residue 292 MET Chi-restraints excluded: chain F residue 389 ASP Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain G residue 78 CYS Chi-restraints excluded: chain G residue 247 THR Chi-restraints excluded: chain O residue 120 VAL Chi-restraints excluded: chain O residue 155 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 243 optimal weight: 0.0370 chunk 136 optimal weight: 0.7980 chunk 365 optimal weight: 1.9990 chunk 298 optimal weight: 10.0000 chunk 120 optimal weight: 8.9990 chunk 439 optimal weight: 0.9990 chunk 474 optimal weight: 9.9990 chunk 391 optimal weight: 6.9990 chunk 435 optimal weight: 2.9990 chunk 149 optimal weight: 0.2980 chunk 352 optimal weight: 0.6980 overall best weight: 0.5660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 35 GLN ** H 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 127 HIS R 83 HIS T 31 ASN B 379 GLN B 416 GLN E 174 ASN F 331 HIS ** D 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 296 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.2109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 38546 Z= 0.163 Angle : 0.563 10.495 52151 Z= 0.282 Chirality : 0.041 0.176 6078 Planarity : 0.004 0.046 6644 Dihedral : 6.275 113.551 5436 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.00 % Allowed : 13.95 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.50 % Cis-general : 0.11 % 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: -0.62 (0.12), residues: 4885 helix: 0.45 (0.10), residues: 2604 sheet: -1.58 (0.21), residues: 530 loop : -1.22 (0.15), residues: 1751 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP M 53 HIS 0.014 0.001 HIS K 158 PHE 0.019 0.001 PHE 3 54 TYR 0.020 0.001 TYR C 397 ARG 0.008 0.000 ARG G 133 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9770 Ramachandran restraints generated. 4885 Oldfield, 0 Emsley, 4885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9770 Ramachandran restraints generated. 4885 Oldfield, 0 Emsley, 4885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 813 residues out of total 4012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 733 time to evaluate : 4.602 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: 4 75 MET cc_start: 0.7779 (mtp) cc_final: 0.6866 (mmt) REVERT: 5 60 MET cc_start: 0.8271 (mmm) cc_final: 0.7809 (mmt) REVERT: 1 69 PHE cc_start: 0.8489 (m-80) cc_final: 0.8207 (m-80) REVERT: 1 73 PHE cc_start: 0.7683 (m-80) cc_final: 0.6978 (m-80) REVERT: H 59 ARG cc_start: 0.7747 (OUTLIER) cc_final: 0.7223 (ptt90) REVERT: H 136 GLU cc_start: 0.8297 (mt-10) cc_final: 0.8050 (mt-10) REVERT: I 34 ASN cc_start: 0.6817 (t0) cc_final: 0.6485 (m110) REVERT: M 128 ASP cc_start: 0.7706 (p0) cc_final: 0.7176 (p0) REVERT: N 152 GLN cc_start: 0.7878 (mt0) cc_final: 0.7490 (mt0) REVERT: P 5 ILE cc_start: 0.7614 (OUTLIER) cc_final: 0.7397 (mm) REVERT: T 21 LEU cc_start: 0.8848 (mt) cc_final: 0.8475 (tt) REVERT: T 41 ARG cc_start: 0.8657 (ptt-90) cc_final: 0.8408 (ptt-90) REVERT: L 81 MET cc_start: 0.8735 (ppp) cc_final: 0.8520 (ppp) REVERT: L 87 MET cc_start: 0.6458 (tpt) cc_final: 0.6226 (mmm) REVERT: A 416 GLN cc_start: 0.8182 (tm-30) cc_final: 0.7974 (tm-30) REVERT: A 463 LYS cc_start: 0.8850 (mtpt) cc_final: 0.8545 (mtpp) REVERT: B 80 LYS cc_start: 0.9249 (OUTLIER) cc_final: 0.9019 (ptpt) REVERT: B 477 GLN cc_start: 0.7674 (mm-40) cc_final: 0.7125 (tm-30) REVERT: E 347 ILE cc_start: 0.9187 (mm) cc_final: 0.8929 (mm) REVERT: E 384 TYR cc_start: 0.8585 (t80) cc_final: 0.8151 (t80) REVERT: E 458 GLN cc_start: 0.7873 (mm110) cc_final: 0.7355 (tp40) REVERT: F 174 ASN cc_start: 0.8377 (t0) cc_final: 0.7942 (t0) REVERT: D 62 ARG cc_start: 0.7834 (ttm170) cc_final: 0.7594 (ttm-80) REVERT: D 260 ASN cc_start: 0.7370 (OUTLIER) cc_final: 0.7071 (m-40) REVERT: D 433 LYS cc_start: 0.6859 (mmtm) cc_final: 0.6361 (mptt) REVERT: D 460 PHE cc_start: 0.6973 (m-10) cc_final: 0.6726 (m-10) REVERT: D 467 GLU cc_start: 0.7055 (tt0) cc_final: 0.6681 (mp0) REVERT: G 25 MET cc_start: 0.7525 (mmm) cc_final: 0.7311 (mmt) REVERT: G 104 MET cc_start: 0.6583 (tpp) cc_final: 0.5972 (tpt) REVERT: O 113 ARG cc_start: 0.6429 (mtm180) cc_final: 0.6197 (mtm180) REVERT: O 163 ILE cc_start: 0.8619 (mm) cc_final: 0.8355 (tp) outliers start: 80 outliers final: 52 residues processed: 768 average time/residue: 0.5062 time to fit residues: 627.9093 Evaluate side-chains 713 residues out of total 4012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 657 time to evaluate : 4.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 4 residue 18 VAL Chi-restraints excluded: chain 4 residue 62 LEU Chi-restraints excluded: chain 5 residue 16 VAL Chi-restraints excluded: chain 5 residue 21 SER Chi-restraints excluded: chain 5 residue 28 VAL Chi-restraints excluded: chain 5 residue 54 PHE Chi-restraints excluded: chain 5 residue 62 LEU Chi-restraints excluded: chain 6 residue 58 GLU Chi-restraints excluded: chain 6 residue 62 LEU Chi-restraints excluded: chain 7 residue 31 SER Chi-restraints excluded: chain 8 residue 65 LEU Chi-restraints excluded: chain 1 residue 18 VAL Chi-restraints excluded: chain 1 residue 31 SER Chi-restraints excluded: chain 1 residue 33 ILE Chi-restraints excluded: chain 1 residue 71 ILE Chi-restraints excluded: chain 1 residue 72 LEU Chi-restraints excluded: chain 2 residue 16 VAL Chi-restraints excluded: chain H residue 59 ARG Chi-restraints excluded: chain M residue 33 TRP Chi-restraints excluded: chain N residue 10 ILE Chi-restraints excluded: chain N residue 39 ASN Chi-restraints excluded: chain N residue 185 ASN Chi-restraints excluded: chain N residue 206 VAL Chi-restraints excluded: chain P residue 5 ILE Chi-restraints excluded: chain P residue 42 ASP Chi-restraints excluded: chain Q residue 47 TYR Chi-restraints excluded: chain S residue 50 GLN Chi-restraints excluded: chain S residue 83 LEU Chi-restraints excluded: chain L residue 92 THR Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 358 TYR Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain B residue 379 GLN Chi-restraints excluded: chain B residue 393 GLU Chi-restraints excluded: chain B residue 436 MET Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain E residue 37 ASN Chi-restraints excluded: chain E residue 225 MET Chi-restraints excluded: chain E residue 255 LEU Chi-restraints excluded: chain F residue 169 ILE Chi-restraints excluded: chain F residue 292 MET Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 260 ASN Chi-restraints excluded: chain D residue 364 ASN Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain G residue 78 CYS Chi-restraints excluded: chain G residue 123 GLN Chi-restraints excluded: chain G residue 140 ASP Chi-restraints excluded: chain O residue 5 VAL Chi-restraints excluded: chain O residue 118 CYS Chi-restraints excluded: chain O residue 120 VAL Chi-restraints excluded: chain O residue 155 ASP Chi-restraints excluded: chain O residue 166 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 434 optimal weight: 0.6980 chunk 330 optimal weight: 7.9990 chunk 228 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 209 optimal weight: 0.9990 chunk 295 optimal weight: 5.9990 chunk 440 optimal weight: 3.9990 chunk 466 optimal weight: 0.9990 chunk 230 optimal weight: 3.9990 chunk 417 optimal weight: 6.9990 chunk 125 optimal weight: 4.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 8 44 GLN ** H 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 136 ASN N 101 ASN R 83 HIS ** L 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 46 ASN A 208 GLN A 432 GLN B 379 GLN C 471 HIS E 174 ASN E 311 GLN F 296 GLN ** D 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 285 GLN G 163 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 38546 Z= 0.244 Angle : 0.577 9.973 52151 Z= 0.288 Chirality : 0.042 0.185 6078 Planarity : 0.004 0.041 6644 Dihedral : 6.136 108.697 5436 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.75 % Allowed : 15.65 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.50 % Cis-general : 0.11 % 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: -0.36 (0.12), residues: 4885 helix: 0.63 (0.10), residues: 2603 sheet: -1.41 (0.21), residues: 538 loop : -1.05 (0.15), residues: 1744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 176 HIS 0.011 0.001 HIS K 158 PHE 0.020 0.001 PHE L 76 TYR 0.025 0.001 TYR C 397 ARG 0.010 0.000 ARG L 73 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9770 Ramachandran restraints generated. 4885 Oldfield, 0 Emsley, 4885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9770 Ramachandran restraints generated. 4885 Oldfield, 0 Emsley, 4885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 782 residues out of total 4012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 672 time to evaluate : 4.152 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: 4 70 LEU cc_start: 0.7884 (tt) cc_final: 0.7674 (tt) REVERT: 4 75 MET cc_start: 0.7859 (mtp) cc_final: 0.6975 (mmt) REVERT: 6 32 LEU cc_start: 0.7754 (OUTLIER) cc_final: 0.7502 (tt) REVERT: 1 69 PHE cc_start: 0.8507 (m-80) cc_final: 0.8218 (m-80) REVERT: 1 73 PHE cc_start: 0.7754 (m-80) cc_final: 0.6993 (m-80) REVERT: H 59 ARG cc_start: 0.7782 (OUTLIER) cc_final: 0.7244 (ptt90) REVERT: I 34 ASN cc_start: 0.6865 (t0) cc_final: 0.6543 (m110) REVERT: K 156 ASP cc_start: 0.8955 (m-30) cc_final: 0.8589 (p0) REVERT: M 128 ASP cc_start: 0.7721 (p0) cc_final: 0.7147 (p0) REVERT: T 21 LEU cc_start: 0.8857 (mt) cc_final: 0.8489 (tt) REVERT: T 40 GLU cc_start: 0.9134 (tp30) cc_final: 0.8710 (tp30) REVERT: L 74 GLU cc_start: 0.8473 (tm-30) cc_final: 0.8232 (pp20) REVERT: L 87 MET cc_start: 0.6615 (tpt) cc_final: 0.6330 (mmm) REVERT: A 416 GLN cc_start: 0.8187 (tm-30) cc_final: 0.7953 (tm-30) REVERT: A 463 LYS cc_start: 0.8853 (mtpt) cc_final: 0.8561 (mtpp) REVERT: B 80 LYS cc_start: 0.9272 (OUTLIER) cc_final: 0.9019 (ptpt) REVERT: B 477 GLN cc_start: 0.7700 (mm-40) cc_final: 0.7095 (tm-30) REVERT: E 347 ILE cc_start: 0.9229 (mm) cc_final: 0.8897 (mm) REVERT: E 384 TYR cc_start: 0.8589 (t80) cc_final: 0.8121 (t80) REVERT: E 427 PHE cc_start: 0.7781 (t80) cc_final: 0.7559 (t80) REVERT: E 458 GLN cc_start: 0.7884 (mm110) cc_final: 0.7361 (tp40) REVERT: D 62 ARG cc_start: 0.7878 (ttm170) cc_final: 0.7639 (ttm-80) REVERT: D 260 ASN cc_start: 0.7457 (OUTLIER) cc_final: 0.7093 (m-40) REVERT: D 384 TYR cc_start: 0.5317 (t80) cc_final: 0.5064 (t80) REVERT: D 433 LYS cc_start: 0.6911 (mmtm) cc_final: 0.6387 (mptt) REVERT: D 460 PHE cc_start: 0.6987 (m-10) cc_final: 0.6741 (m-10) REVERT: D 467 GLU cc_start: 0.7118 (tt0) cc_final: 0.6708 (mp0) REVERT: G 104 MET cc_start: 0.6620 (tpp) cc_final: 0.5993 (tpt) REVERT: O 163 ILE cc_start: 0.8646 (mm) cc_final: 0.8365 (tp) outliers start: 110 outliers final: 75 residues processed: 727 average time/residue: 0.4926 time to fit residues: 577.3375 Evaluate side-chains 708 residues out of total 4012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 629 time to evaluate : 4.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 4 residue 18 VAL Chi-restraints excluded: chain 4 residue 41 SER Chi-restraints excluded: chain 4 residue 62 LEU Chi-restraints excluded: chain 5 residue 16 VAL Chi-restraints excluded: chain 5 residue 21 SER Chi-restraints excluded: chain 5 residue 28 VAL Chi-restraints excluded: chain 5 residue 62 LEU Chi-restraints excluded: chain 6 residue 18 VAL Chi-restraints excluded: chain 6 residue 32 LEU Chi-restraints excluded: chain 6 residue 58 GLU Chi-restraints excluded: chain 6 residue 62 LEU Chi-restraints excluded: chain 7 residue 31 SER Chi-restraints excluded: chain 7 residue 33 ILE Chi-restraints excluded: chain 8 residue 27 THR Chi-restraints excluded: chain 8 residue 65 LEU Chi-restraints excluded: chain 1 residue 18 VAL Chi-restraints excluded: chain 1 residue 31 SER Chi-restraints excluded: chain 1 residue 32 LEU Chi-restraints excluded: chain 1 residue 33 ILE Chi-restraints excluded: chain 1 residue 71 ILE Chi-restraints excluded: chain 1 residue 72 LEU Chi-restraints excluded: chain 2 residue 16 VAL Chi-restraints excluded: chain 2 residue 28 VAL Chi-restraints excluded: chain 3 residue 65 LEU Chi-restraints excluded: chain H residue 59 ARG Chi-restraints excluded: chain H residue 81 SER Chi-restraints excluded: chain M residue 33 TRP Chi-restraints excluded: chain N residue 37 LEU Chi-restraints excluded: chain N residue 39 ASN Chi-restraints excluded: chain N residue 81 THR Chi-restraints excluded: chain N residue 144 ILE Chi-restraints excluded: chain N residue 185 ASN Chi-restraints excluded: chain N residue 206 VAL Chi-restraints excluded: chain P residue 5 ILE Chi-restraints excluded: chain P residue 42 ASP Chi-restraints excluded: chain Q residue 47 TYR Chi-restraints excluded: chain R residue 76 SER Chi-restraints excluded: chain S residue 50 GLN Chi-restraints excluded: chain S residue 52 LEU Chi-restraints excluded: chain S residue 83 LEU Chi-restraints excluded: chain L residue 92 THR Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 358 TYR Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain B residue 379 GLN Chi-restraints excluded: chain B residue 393 GLU Chi-restraints excluded: chain B residue 436 MET Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 335 SER Chi-restraints excluded: chain E residue 37 ASN Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 225 MET Chi-restraints excluded: chain E residue 255 LEU Chi-restraints excluded: chain E residue 333 ASP Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 169 ILE Chi-restraints excluded: chain F residue 240 LEU Chi-restraints excluded: chain F residue 292 MET Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 87 ILE Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 260 ASN Chi-restraints excluded: chain D residue 364 ASN Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 466 ILE Chi-restraints excluded: chain G residue 16 ILE Chi-restraints excluded: chain G residue 78 CYS Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 247 THR Chi-restraints excluded: chain O residue 51 VAL Chi-restraints excluded: chain O residue 118 CYS Chi-restraints excluded: chain O residue 120 VAL Chi-restraints excluded: chain O residue 166 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 388 optimal weight: 3.9990 chunk 265 optimal weight: 7.9990 chunk 6 optimal weight: 5.9990 chunk 347 optimal weight: 8.9990 chunk 192 optimal weight: 0.9990 chunk 398 optimal weight: 1.9990 chunk 322 optimal weight: 0.7980 chunk 0 optimal weight: 20.0000 chunk 238 optimal weight: 5.9990 chunk 419 optimal weight: 6.9990 chunk 117 optimal weight: 4.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 136 ASN ** N 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 83 HIS ** L 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 208 GLN B 379 GLN E 174 ASN ** D 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.2305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 38546 Z= 0.299 Angle : 0.601 11.736 52151 Z= 0.301 Chirality : 0.043 0.214 6078 Planarity : 0.004 0.043 6644 Dihedral : 6.148 109.392 5436 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.78 % Allowed : 16.70 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.50 % Cis-general : 0.11 % 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: -0.24 (0.12), residues: 4885 helix: 0.68 (0.10), residues: 2615 sheet: -1.35 (0.21), residues: 544 loop : -0.92 (0.15), residues: 1726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP M 53 HIS 0.007 0.001 HIS K 158 PHE 0.020 0.001 PHE 4 29 TYR 0.027 0.001 TYR C 397 ARG 0.009 0.000 ARG G 133 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9770 Ramachandran restraints generated. 4885 Oldfield, 0 Emsley, 4885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9770 Ramachandran restraints generated. 4885 Oldfield, 0 Emsley, 4885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 766 residues out of total 4012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 655 time to evaluate : 4.330 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: symmetry clash REVERT: 4 75 MET cc_start: 0.7814 (mtp) cc_final: 0.7009 (mmt) REVERT: 1 69 PHE cc_start: 0.8507 (m-80) cc_final: 0.8301 (m-80) REVERT: H 59 ARG cc_start: 0.7805 (OUTLIER) cc_final: 0.7260 (ptt90) REVERT: I 34 ASN cc_start: 0.6908 (t0) cc_final: 0.6584 (m110) REVERT: K 156 ASP cc_start: 0.8950 (m-30) cc_final: 0.8608 (p0) REVERT: M 128 ASP cc_start: 0.7749 (p0) cc_final: 0.7165 (p0) REVERT: T 21 LEU cc_start: 0.8825 (mt) cc_final: 0.8487 (tt) REVERT: T 40 GLU cc_start: 0.9129 (tp30) cc_final: 0.8729 (tp30) REVERT: L 87 MET cc_start: 0.6718 (tpt) cc_final: 0.6472 (mmm) REVERT: A 416 GLN cc_start: 0.8277 (tm-30) cc_final: 0.8027 (tm-30) REVERT: A 463 LYS cc_start: 0.8862 (mtpt) cc_final: 0.8572 (mtpp) REVERT: B 477 GLN cc_start: 0.7688 (mm-40) cc_final: 0.7084 (tm-30) REVERT: C 455 LYS cc_start: 0.7758 (mtpt) cc_final: 0.7442 (mttp) REVERT: E 347 ILE cc_start: 0.9250 (mm) cc_final: 0.8921 (mm) REVERT: E 384 TYR cc_start: 0.8604 (t80) cc_final: 0.8119 (t80) REVERT: E 458 GLN cc_start: 0.7910 (mm110) cc_final: 0.7380 (tp40) REVERT: D 62 ARG cc_start: 0.7888 (ttm170) cc_final: 0.7648 (ttm-80) REVERT: D 260 ASN cc_start: 0.7460 (m-40) cc_final: 0.7087 (m-40) REVERT: D 263 ARG cc_start: 0.8084 (mmt-90) cc_final: 0.7778 (mpt180) REVERT: D 433 LYS cc_start: 0.6956 (mmtm) cc_final: 0.6466 (mptt) REVERT: D 460 PHE cc_start: 0.6967 (m-10) cc_final: 0.6722 (m-10) REVERT: D 467 GLU cc_start: 0.7141 (tt0) cc_final: 0.6643 (mp0) REVERT: G 25 MET cc_start: 0.7746 (mmm) cc_final: 0.7485 (mmt) REVERT: G 104 MET cc_start: 0.6637 (tpp) cc_final: 0.6028 (tpt) REVERT: O 163 ILE cc_start: 0.8629 (mm) cc_final: 0.8324 (tp) outliers start: 111 outliers final: 82 residues processed: 719 average time/residue: 0.5091 time to fit residues: 592.3620 Evaluate side-chains 696 residues out of total 4012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 613 time to evaluate : 4.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 4 residue 18 VAL Chi-restraints excluded: chain 4 residue 41 SER Chi-restraints excluded: chain 4 residue 62 LEU Chi-restraints excluded: chain 4 residue 64 CYS Chi-restraints excluded: chain 5 residue 16 VAL Chi-restraints excluded: chain 5 residue 21 SER Chi-restraints excluded: chain 5 residue 28 VAL Chi-restraints excluded: chain 5 residue 62 LEU Chi-restraints excluded: chain 6 residue 18 VAL Chi-restraints excluded: chain 6 residue 58 GLU Chi-restraints excluded: chain 6 residue 62 LEU Chi-restraints excluded: chain 7 residue 31 SER Chi-restraints excluded: chain 7 residue 33 ILE Chi-restraints excluded: chain 8 residue 27 THR Chi-restraints excluded: chain 8 residue 65 LEU Chi-restraints excluded: chain 1 residue 18 VAL Chi-restraints excluded: chain 1 residue 31 SER Chi-restraints excluded: chain 1 residue 32 LEU Chi-restraints excluded: chain 1 residue 33 ILE Chi-restraints excluded: chain 1 residue 71 ILE Chi-restraints excluded: chain 1 residue 72 LEU Chi-restraints excluded: chain 2 residue 16 VAL Chi-restraints excluded: chain 2 residue 28 VAL Chi-restraints excluded: chain 3 residue 64 CYS Chi-restraints excluded: chain 3 residue 65 LEU Chi-restraints excluded: chain 3 residue 70 LEU Chi-restraints excluded: chain H residue 59 ARG Chi-restraints excluded: chain H residue 81 SER Chi-restraints excluded: chain M residue 9 THR Chi-restraints excluded: chain M residue 33 TRP Chi-restraints excluded: chain M residue 131 THR Chi-restraints excluded: chain N residue 37 LEU Chi-restraints excluded: chain N residue 39 ASN Chi-restraints excluded: chain N residue 81 THR Chi-restraints excluded: chain N residue 144 ILE Chi-restraints excluded: chain N residue 174 ILE Chi-restraints excluded: chain N residue 185 ASN Chi-restraints excluded: chain N residue 206 VAL Chi-restraints excluded: chain P residue 5 ILE Chi-restraints excluded: chain Q residue 42 MET Chi-restraints excluded: chain Q residue 47 TYR Chi-restraints excluded: chain R residue 65 ILE Chi-restraints excluded: chain R residue 76 SER Chi-restraints excluded: chain S residue 50 GLN Chi-restraints excluded: chain S residue 83 LEU Chi-restraints excluded: chain T residue 38 GLU Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 358 TYR Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain B residue 393 GLU Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 335 SER Chi-restraints excluded: chain E residue 37 ASN Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 333 ASP Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 169 ILE Chi-restraints excluded: chain F residue 240 LEU Chi-restraints excluded: chain F residue 292 MET Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 87 ILE Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 284 TYR Chi-restraints excluded: chain D residue 300 THR Chi-restraints excluded: chain D residue 364 ASN Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 466 ILE Chi-restraints excluded: chain G residue 16 ILE Chi-restraints excluded: chain G residue 78 CYS Chi-restraints excluded: chain G residue 247 THR Chi-restraints excluded: chain O residue 5 VAL Chi-restraints excluded: chain O residue 51 VAL Chi-restraints excluded: chain O residue 120 VAL Chi-restraints excluded: chain O residue 155 ASP Chi-restraints excluded: chain O residue 166 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 157 optimal weight: 0.9990 chunk 420 optimal weight: 0.9990 chunk 92 optimal weight: 0.0980 chunk 274 optimal weight: 0.9990 chunk 115 optimal weight: 0.3980 chunk 467 optimal weight: 5.9990 chunk 387 optimal weight: 9.9990 chunk 216 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 154 optimal weight: 8.9990 chunk 245 optimal weight: 5.9990 overall best weight: 0.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 103 HIS ** K 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 136 ASN ** N 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 432 GLN E 174 ASN ** D 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 112 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 38546 Z= 0.156 Angle : 0.560 11.191 52151 Z= 0.278 Chirality : 0.042 0.217 6078 Planarity : 0.004 0.046 6644 Dihedral : 5.771 102.494 5436 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.18 % Allowed : 17.53 % Favored : 80.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.50 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.12), residues: 4885 helix: 0.94 (0.10), residues: 2599 sheet: -1.06 (0.22), residues: 520 loop : -0.80 (0.15), residues: 1766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP M 53 HIS 0.006 0.001 HIS K 158 PHE 0.017 0.001 PHE L 76 TYR 0.021 0.001 TYR C 397 ARG 0.011 0.000 ARG G 133 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9770 Ramachandran restraints generated. 4885 Oldfield, 0 Emsley, 4885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9770 Ramachandran restraints generated. 4885 Oldfield, 0 Emsley, 4885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 777 residues out of total 4012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 690 time to evaluate : 4.664 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: symmetry clash REVERT: 4 75 MET cc_start: 0.7796 (mtp) cc_final: 0.6968 (mmt) REVERT: 5 60 MET cc_start: 0.8092 (mmm) cc_final: 0.7739 (mmt) REVERT: 1 69 PHE cc_start: 0.8455 (m-80) cc_final: 0.8145 (m-80) REVERT: 1 73 PHE cc_start: 0.7831 (m-80) cc_final: 0.7029 (m-80) REVERT: H 59 ARG cc_start: 0.7708 (OUTLIER) cc_final: 0.7213 (ptt90) REVERT: I 34 ASN cc_start: 0.6800 (t0) cc_final: 0.6528 (m110) REVERT: K 156 ASP cc_start: 0.8952 (m-30) cc_final: 0.8622 (p0) REVERT: M 128 ASP cc_start: 0.7656 (p0) cc_final: 0.7034 (p0) REVERT: N 152 GLN cc_start: 0.7989 (mt0) cc_final: 0.7676 (mt0) REVERT: S 54 LYS cc_start: 0.9162 (mtmm) cc_final: 0.8887 (mtmm) REVERT: S 57 ASN cc_start: 0.9118 (m110) cc_final: 0.8830 (p0) REVERT: S 90 GLU cc_start: 0.8170 (tm-30) cc_final: 0.7913 (tm-30) REVERT: T 21 LEU cc_start: 0.8778 (mt) cc_final: 0.8470 (tp) REVERT: L 74 GLU cc_start: 0.8579 (pp20) cc_final: 0.8159 (pp20) REVERT: A 226 MET cc_start: 0.8213 (mmm) cc_final: 0.8005 (mmm) REVERT: A 416 GLN cc_start: 0.8287 (tm-30) cc_final: 0.8054 (tm-30) REVERT: A 463 LYS cc_start: 0.8831 (mtpt) cc_final: 0.8550 (mtpp) REVERT: B 477 GLN cc_start: 0.7633 (mm-40) cc_final: 0.7068 (tm-30) REVERT: C 455 LYS cc_start: 0.7708 (mtpt) cc_final: 0.7400 (mttp) REVERT: E 291 ASP cc_start: 0.7462 (m-30) cc_final: 0.7098 (m-30) REVERT: E 347 ILE cc_start: 0.9200 (mm) cc_final: 0.8854 (mm) REVERT: E 384 TYR cc_start: 0.8585 (t80) cc_final: 0.8046 (t80) REVERT: E 458 GLN cc_start: 0.7859 (mm110) cc_final: 0.7277 (tp40) REVERT: F 398 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7094 (mp0) REVERT: D 62 ARG cc_start: 0.7887 (ttm170) cc_final: 0.7590 (ttm-80) REVERT: D 263 ARG cc_start: 0.7924 (mmt-90) cc_final: 0.7690 (mpt180) REVERT: D 433 LYS cc_start: 0.6910 (mmtm) cc_final: 0.6440 (mptt) REVERT: D 460 PHE cc_start: 0.6932 (m-10) cc_final: 0.6726 (m-10) REVERT: D 467 GLU cc_start: 0.7073 (tt0) cc_final: 0.6686 (mp0) REVERT: G 104 MET cc_start: 0.6693 (tpp) cc_final: 0.6102 (tpt) REVERT: O 113 ARG cc_start: 0.6514 (ptp-170) cc_final: 0.6145 (ptp-110) REVERT: O 163 ILE cc_start: 0.8664 (mm) cc_final: 0.8374 (tp) outliers start: 87 outliers final: 56 residues processed: 733 average time/residue: 0.5008 time to fit residues: 592.4841 Evaluate side-chains 691 residues out of total 4012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 633 time to evaluate : 4.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 4 residue 18 VAL Chi-restraints excluded: chain 5 residue 21 SER Chi-restraints excluded: chain 5 residue 28 VAL Chi-restraints excluded: chain 5 residue 62 LEU Chi-restraints excluded: chain 6 residue 58 GLU Chi-restraints excluded: chain 6 residue 62 LEU Chi-restraints excluded: chain 7 residue 31 SER Chi-restraints excluded: chain 1 residue 18 VAL Chi-restraints excluded: chain 1 residue 31 SER Chi-restraints excluded: chain 1 residue 33 ILE Chi-restraints excluded: chain 2 residue 16 VAL Chi-restraints excluded: chain 3 residue 64 CYS Chi-restraints excluded: chain H residue 59 ARG Chi-restraints excluded: chain K residue 41 LEU Chi-restraints excluded: chain M residue 33 TRP Chi-restraints excluded: chain N residue 10 ILE Chi-restraints excluded: chain N residue 37 LEU Chi-restraints excluded: chain N residue 39 ASN Chi-restraints excluded: chain N residue 138 ILE Chi-restraints excluded: chain N residue 144 ILE Chi-restraints excluded: chain N residue 185 ASN Chi-restraints excluded: chain P residue 5 ILE Chi-restraints excluded: chain Q residue 47 TYR Chi-restraints excluded: chain R residue 65 ILE Chi-restraints excluded: chain R residue 76 SER Chi-restraints excluded: chain S residue 50 GLN Chi-restraints excluded: chain S residue 83 LEU Chi-restraints excluded: chain T residue 38 GLU Chi-restraints excluded: chain L residue 92 THR Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 358 TYR Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain B residue 393 GLU Chi-restraints excluded: chain B residue 502 THR Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 42 HIS Chi-restraints excluded: chain C residue 335 SER Chi-restraints excluded: chain E residue 37 ASN Chi-restraints excluded: chain E residue 255 LEU Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 169 ILE Chi-restraints excluded: chain F residue 240 LEU Chi-restraints excluded: chain F residue 398 GLU Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 260 ASN Chi-restraints excluded: chain D residue 284 TYR Chi-restraints excluded: chain D residue 364 ASN Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain G residue 16 ILE Chi-restraints excluded: chain G residue 78 CYS Chi-restraints excluded: chain O residue 5 VAL Chi-restraints excluded: chain O residue 51 VAL Chi-restraints excluded: chain O residue 120 VAL Chi-restraints excluded: chain O residue 166 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 450 optimal weight: 3.9990 chunk 52 optimal weight: 0.9990 chunk 266 optimal weight: 10.0000 chunk 341 optimal weight: 1.9990 chunk 264 optimal weight: 0.4980 chunk 393 optimal weight: 0.0060 chunk 260 optimal weight: 5.9990 chunk 465 optimal weight: 9.9990 chunk 291 optimal weight: 0.9990 chunk 283 optimal weight: 0.4980 chunk 214 optimal weight: 6.9990 overall best weight: 0.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 80 GLN A 208 GLN ** A 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 174 ASN F 174 ASN ** D 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.2829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 38546 Z= 0.156 Angle : 0.577 12.752 52151 Z= 0.283 Chirality : 0.042 0.216 6078 Planarity : 0.004 0.062 6644 Dihedral : 5.520 92.108 5436 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.15 % Allowed : 18.51 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.50 % Cis-general : 0.11 % 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: 0.27 (0.12), residues: 4885 helix: 1.04 (0.10), residues: 2602 sheet: -0.88 (0.21), residues: 538 loop : -0.68 (0.15), residues: 1745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP P 10 HIS 0.005 0.001 HIS C 476 PHE 0.025 0.001 PHE T 20 TYR 0.021 0.001 TYR C 397 ARG 0.016 0.000 ARG T 36 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9770 Ramachandran restraints generated. 4885 Oldfield, 0 Emsley, 4885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9770 Ramachandran restraints generated. 4885 Oldfield, 0 Emsley, 4885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 766 residues out of total 4012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 680 time to evaluate : 3.996 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: 4 75 MET cc_start: 0.8059 (mtp) cc_final: 0.6795 (mmt) REVERT: 1 69 PHE cc_start: 0.8450 (m-80) cc_final: 0.8118 (m-80) REVERT: 1 73 PHE cc_start: 0.7723 (m-80) cc_final: 0.7016 (m-80) REVERT: 3 7 LYS cc_start: 0.8344 (mtmt) cc_final: 0.8101 (ttpp) REVERT: H 59 ARG cc_start: 0.7724 (OUTLIER) cc_final: 0.7230 (ptt90) REVERT: I 34 ASN cc_start: 0.6756 (t0) cc_final: 0.6516 (m110) REVERT: K 156 ASP cc_start: 0.8931 (m-30) cc_final: 0.8587 (p0) REVERT: K 165 MET cc_start: 0.8305 (mmp) cc_final: 0.8068 (mmp) REVERT: M 128 ASP cc_start: 0.7611 (p0) cc_final: 0.6980 (p0) REVERT: Q 12 MET cc_start: 0.8195 (mmt) cc_final: 0.7715 (mmt) REVERT: R 20 VAL cc_start: 0.8728 (t) cc_final: 0.8504 (p) REVERT: S 57 ASN cc_start: 0.9112 (m110) cc_final: 0.8825 (p0) REVERT: S 90 GLU cc_start: 0.8197 (tm-30) cc_final: 0.7931 (tm-30) REVERT: T 21 LEU cc_start: 0.8796 (mt) cc_final: 0.8518 (tt) REVERT: L 74 GLU cc_start: 0.8628 (pp20) cc_final: 0.8197 (pp20) REVERT: L 87 MET cc_start: 0.6376 (tpt) cc_final: 0.6101 (mmm) REVERT: A 416 GLN cc_start: 0.8305 (tm-30) cc_final: 0.8076 (tm-30) REVERT: B 475 GLN cc_start: 0.7596 (mp10) cc_final: 0.6953 (mp10) REVERT: B 477 GLN cc_start: 0.7623 (mm-40) cc_final: 0.7162 (tm-30) REVERT: C 455 LYS cc_start: 0.7684 (mtpt) cc_final: 0.7380 (mttp) REVERT: E 291 ASP cc_start: 0.7430 (m-30) cc_final: 0.7081 (m-30) REVERT: E 347 ILE cc_start: 0.9186 (mm) cc_final: 0.8863 (mm) REVERT: E 458 GLN cc_start: 0.7817 (mm110) cc_final: 0.7241 (tp40) REVERT: F 174 ASN cc_start: 0.8277 (t0) cc_final: 0.7853 (t0) REVERT: D 62 ARG cc_start: 0.7885 (ttm170) cc_final: 0.7597 (ttm-80) REVERT: D 433 LYS cc_start: 0.6896 (mmtm) cc_final: 0.6466 (mptt) REVERT: D 452 TYR cc_start: 0.7170 (m-80) cc_final: 0.6957 (m-80) REVERT: D 467 GLU cc_start: 0.6978 (tt0) cc_final: 0.6619 (mp0) REVERT: O 113 ARG cc_start: 0.6520 (ptp-170) cc_final: 0.6189 (ptp-110) REVERT: O 163 ILE cc_start: 0.8673 (mm) cc_final: 0.8387 (tp) REVERT: O 180 GLN cc_start: 0.9246 (mm-40) cc_final: 0.8900 (mm-40) outliers start: 86 outliers final: 60 residues processed: 728 average time/residue: 0.5018 time to fit residues: 591.3028 Evaluate side-chains 698 residues out of total 4012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 637 time to evaluate : 3.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 4 residue 18 VAL Chi-restraints excluded: chain 5 residue 21 SER Chi-restraints excluded: chain 5 residue 28 VAL Chi-restraints excluded: chain 5 residue 62 LEU Chi-restraints excluded: chain 6 residue 58 GLU Chi-restraints excluded: chain 6 residue 62 LEU Chi-restraints excluded: chain 7 residue 31 SER Chi-restraints excluded: chain 8 residue 65 LEU Chi-restraints excluded: chain 1 residue 18 VAL Chi-restraints excluded: chain 1 residue 31 SER Chi-restraints excluded: chain 1 residue 32 LEU Chi-restraints excluded: chain 2 residue 16 VAL Chi-restraints excluded: chain 2 residue 28 VAL Chi-restraints excluded: chain 3 residue 64 CYS Chi-restraints excluded: chain H residue 59 ARG Chi-restraints excluded: chain K residue 41 LEU Chi-restraints excluded: chain M residue 33 TRP Chi-restraints excluded: chain N residue 37 LEU Chi-restraints excluded: chain N residue 39 ASN Chi-restraints excluded: chain N residue 81 THR Chi-restraints excluded: chain N residue 138 ILE Chi-restraints excluded: chain N residue 185 ASN Chi-restraints excluded: chain P residue 5 ILE Chi-restraints excluded: chain P residue 17 TYR Chi-restraints excluded: chain P residue 42 ASP Chi-restraints excluded: chain Q residue 47 TYR Chi-restraints excluded: chain R residue 76 SER Chi-restraints excluded: chain S residue 50 GLN Chi-restraints excluded: chain S residue 83 LEU Chi-restraints excluded: chain T residue 38 GLU Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 358 TYR Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain B residue 393 GLU Chi-restraints excluded: chain B residue 502 THR Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 42 HIS Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 335 SER Chi-restraints excluded: chain E residue 37 ASN Chi-restraints excluded: chain E residue 101 ILE Chi-restraints excluded: chain E residue 333 ASP Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 169 ILE Chi-restraints excluded: chain F residue 240 LEU Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 260 ASN Chi-restraints excluded: chain D residue 284 TYR Chi-restraints excluded: chain D residue 339 SER Chi-restraints excluded: chain D residue 364 ASN Chi-restraints excluded: chain G residue 16 ILE Chi-restraints excluded: chain G residue 78 CYS Chi-restraints excluded: chain G residue 140 ASP Chi-restraints excluded: chain O residue 5 VAL Chi-restraints excluded: chain O residue 51 VAL Chi-restraints excluded: chain O residue 120 VAL Chi-restraints excluded: chain O residue 166 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 288 optimal weight: 0.9990 chunk 185 optimal weight: 2.9990 chunk 278 optimal weight: 3.9990 chunk 140 optimal weight: 4.9990 chunk 91 optimal weight: 0.0980 chunk 90 optimal weight: 2.9990 chunk 295 optimal weight: 8.9990 chunk 317 optimal weight: 1.9990 chunk 230 optimal weight: 4.9990 chunk 43 optimal weight: 4.9990 chunk 365 optimal weight: 2.9990 overall best weight: 1.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 432 GLN E 174 ASN ** D 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.2838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 38546 Z= 0.239 Angle : 0.611 15.759 52151 Z= 0.300 Chirality : 0.043 0.214 6078 Planarity : 0.004 0.054 6644 Dihedral : 5.526 89.118 5436 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.74 % Favored : 97.24 % Rotamer: Outliers : 2.08 % Allowed : 19.43 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.50 % Cis-general : 0.11 % 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: 0.27 (0.12), residues: 4885 helix: 1.09 (0.11), residues: 2568 sheet: -0.87 (0.21), residues: 535 loop : -0.72 (0.15), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP P 10 HIS 0.006 0.001 HIS C 476 PHE 0.023 0.001 PHE D 460 TYR 0.036 0.001 TYR E 384 ARG 0.012 0.000 ARG G 133 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9770 Ramachandran restraints generated. 4885 Oldfield, 0 Emsley, 4885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9770 Ramachandran restraints generated. 4885 Oldfield, 0 Emsley, 4885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 727 residues out of total 4012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 644 time to evaluate : 4.311 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: symmetry clash REVERT: 1 69 PHE cc_start: 0.8456 (m-80) cc_final: 0.8115 (m-80) REVERT: 1 73 PHE cc_start: 0.7829 (m-80) cc_final: 0.7126 (m-80) REVERT: H 59 ARG cc_start: 0.7759 (OUTLIER) cc_final: 0.7252 (ptt90) REVERT: I 34 ASN cc_start: 0.6781 (t0) cc_final: 0.6519 (m110) REVERT: K 156 ASP cc_start: 0.8935 (m-30) cc_final: 0.8608 (p0) REVERT: K 165 MET cc_start: 0.8356 (mmp) cc_final: 0.8062 (mmp) REVERT: K 173 MET cc_start: 0.7145 (OUTLIER) cc_final: 0.6799 (mmp) REVERT: M 128 ASP cc_start: 0.7668 (p0) cc_final: 0.7032 (p0) REVERT: N 152 GLN cc_start: 0.8016 (mt0) cc_final: 0.7770 (mt0) REVERT: Q 12 MET cc_start: 0.8254 (mmt) cc_final: 0.7769 (mmt) REVERT: R 20 VAL cc_start: 0.8735 (t) cc_final: 0.8508 (p) REVERT: S 57 ASN cc_start: 0.9101 (m110) cc_final: 0.8873 (p0) REVERT: S 84 MET cc_start: 0.8713 (tpp) cc_final: 0.8194 (tmm) REVERT: S 90 GLU cc_start: 0.8219 (tm-30) cc_final: 0.7926 (tm-30) REVERT: T 21 LEU cc_start: 0.8778 (mt) cc_final: 0.8501 (tt) REVERT: L 74 GLU cc_start: 0.8606 (pp20) cc_final: 0.8208 (pp20) REVERT: L 87 MET cc_start: 0.6434 (tpt) cc_final: 0.6200 (mmm) REVERT: A 54 GLU cc_start: 0.7358 (OUTLIER) cc_final: 0.6949 (tm-30) REVERT: A 416 GLN cc_start: 0.8317 (tm-30) cc_final: 0.8077 (tm-30) REVERT: B 415 GLN cc_start: 0.7723 (mt0) cc_final: 0.7473 (mt0) REVERT: B 475 GLN cc_start: 0.7620 (mp10) cc_final: 0.6945 (mp10) REVERT: B 477 GLN cc_start: 0.7638 (mm-40) cc_final: 0.7166 (tm-30) REVERT: C 455 LYS cc_start: 0.7705 (mtpt) cc_final: 0.7400 (mttp) REVERT: E 291 ASP cc_start: 0.7469 (m-30) cc_final: 0.7123 (m-30) REVERT: E 347 ILE cc_start: 0.9210 (mm) cc_final: 0.8894 (mm) REVERT: E 458 GLN cc_start: 0.7871 (mm110) cc_final: 0.7288 (tp40) REVERT: F 398 GLU cc_start: 0.7922 (OUTLIER) cc_final: 0.7078 (mp0) REVERT: D 62 ARG cc_start: 0.7887 (ttm170) cc_final: 0.7594 (ttm-80) REVERT: D 433 LYS cc_start: 0.6957 (mmtm) cc_final: 0.6508 (mptt) REVERT: D 467 GLU cc_start: 0.7068 (tt0) cc_final: 0.6663 (mp0) REVERT: G 104 MET cc_start: 0.6565 (tpp) cc_final: 0.5786 (tpt) REVERT: O 113 ARG cc_start: 0.6509 (ptp-170) cc_final: 0.6166 (ptp-110) REVERT: O 163 ILE cc_start: 0.8700 (mm) cc_final: 0.8403 (tp) REVERT: O 180 GLN cc_start: 0.9226 (mm-40) cc_final: 0.8889 (mm-40) outliers start: 83 outliers final: 65 residues processed: 689 average time/residue: 0.5138 time to fit residues: 572.0778 Evaluate side-chains 690 residues out of total 4012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 621 time to evaluate : 4.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 4 residue 18 VAL Chi-restraints excluded: chain 5 residue 21 SER Chi-restraints excluded: chain 5 residue 28 VAL Chi-restraints excluded: chain 5 residue 62 LEU Chi-restraints excluded: chain 6 residue 58 GLU Chi-restraints excluded: chain 6 residue 62 LEU Chi-restraints excluded: chain 7 residue 31 SER Chi-restraints excluded: chain 7 residue 33 ILE Chi-restraints excluded: chain 1 residue 18 VAL Chi-restraints excluded: chain 1 residue 31 SER Chi-restraints excluded: chain 1 residue 32 LEU Chi-restraints excluded: chain 1 residue 33 ILE Chi-restraints excluded: chain 2 residue 16 VAL Chi-restraints excluded: chain 2 residue 28 VAL Chi-restraints excluded: chain 3 residue 64 CYS Chi-restraints excluded: chain 3 residue 65 LEU Chi-restraints excluded: chain H residue 59 ARG Chi-restraints excluded: chain K residue 41 LEU Chi-restraints excluded: chain K residue 173 MET Chi-restraints excluded: chain M residue 33 TRP Chi-restraints excluded: chain N residue 37 LEU Chi-restraints excluded: chain N residue 39 ASN Chi-restraints excluded: chain N residue 81 THR Chi-restraints excluded: chain N residue 138 ILE Chi-restraints excluded: chain N residue 185 ASN Chi-restraints excluded: chain P residue 5 ILE Chi-restraints excluded: chain P residue 17 TYR Chi-restraints excluded: chain P residue 42 ASP Chi-restraints excluded: chain Q residue 47 TYR Chi-restraints excluded: chain R residue 65 ILE Chi-restraints excluded: chain R residue 76 SER Chi-restraints excluded: chain S residue 50 GLN Chi-restraints excluded: chain S residue 54 LYS Chi-restraints excluded: chain S residue 83 LEU Chi-restraints excluded: chain A residue 54 GLU Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 358 TYR Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain B residue 393 GLU Chi-restraints excluded: chain B residue 436 MET Chi-restraints excluded: chain B residue 502 THR Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 335 SER Chi-restraints excluded: chain C residue 505 LEU Chi-restraints excluded: chain E residue 37 ASN Chi-restraints excluded: chain E residue 101 ILE Chi-restraints excluded: chain E residue 333 ASP Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 169 ILE Chi-restraints excluded: chain F residue 240 LEU Chi-restraints excluded: chain F residue 398 GLU Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 339 SER Chi-restraints excluded: chain D residue 385 LYS Chi-restraints excluded: chain D residue 466 ILE Chi-restraints excluded: chain G residue 16 ILE Chi-restraints excluded: chain G residue 78 CYS Chi-restraints excluded: chain G residue 140 ASP Chi-restraints excluded: chain O residue 5 VAL Chi-restraints excluded: chain O residue 51 VAL Chi-restraints excluded: chain O residue 120 VAL Chi-restraints excluded: chain O residue 166 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 423 optimal weight: 0.9990 chunk 445 optimal weight: 0.0050 chunk 406 optimal weight: 7.9990 chunk 433 optimal weight: 10.0000 chunk 261 optimal weight: 0.0970 chunk 188 optimal weight: 0.9990 chunk 340 optimal weight: 3.9990 chunk 133 optimal weight: 1.9990 chunk 392 optimal weight: 1.9990 chunk 410 optimal weight: 6.9990 chunk 432 optimal weight: 4.9990 overall best weight: 0.8198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 285 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.2999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 38546 Z= 0.171 Angle : 0.597 14.879 52151 Z= 0.292 Chirality : 0.042 0.213 6078 Planarity : 0.004 0.057 6644 Dihedral : 5.348 88.429 5436 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.78 % Favored : 97.20 % Rotamer: Outliers : 2.10 % Allowed : 19.73 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.50 % Cis-general : 0.11 % 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: 0.39 (0.12), residues: 4885 helix: 1.18 (0.11), residues: 2568 sheet: -0.78 (0.22), residues: 529 loop : -0.67 (0.15), residues: 1788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP P 10 HIS 0.006 0.001 HIS C 476 PHE 0.028 0.001 PHE T 20 TYR 0.030 0.001 TYR T 32 ARG 0.014 0.000 ARG G 133 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9770 Ramachandran restraints generated. 4885 Oldfield, 0 Emsley, 4885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9770 Ramachandran restraints generated. 4885 Oldfield, 0 Emsley, 4885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 758 residues out of total 4012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 674 time to evaluate : 4.208 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 69 PHE cc_start: 0.8417 (m-80) cc_final: 0.8069 (m-80) REVERT: 1 73 PHE cc_start: 0.7770 (m-80) cc_final: 0.7117 (m-80) REVERT: H 59 ARG cc_start: 0.7720 (OUTLIER) cc_final: 0.7233 (ptt90) REVERT: K 156 ASP cc_start: 0.8901 (m-30) cc_final: 0.8584 (p0) REVERT: K 165 MET cc_start: 0.8319 (mmp) cc_final: 0.8041 (mmp) REVERT: K 173 MET cc_start: 0.7245 (OUTLIER) cc_final: 0.6931 (mmp) REVERT: M 128 ASP cc_start: 0.7621 (p0) cc_final: 0.6959 (p0) REVERT: R 20 VAL cc_start: 0.8699 (t) cc_final: 0.8485 (p) REVERT: S 57 ASN cc_start: 0.9101 (m110) cc_final: 0.8840 (p0) REVERT: S 84 MET cc_start: 0.8702 (tpp) cc_final: 0.8210 (tmm) REVERT: S 90 GLU cc_start: 0.8218 (tm-30) cc_final: 0.7911 (tm-30) REVERT: T 21 LEU cc_start: 0.8765 (mt) cc_final: 0.8493 (tt) REVERT: L 74 GLU cc_start: 0.8598 (pp20) cc_final: 0.8226 (pp20) REVERT: L 87 MET cc_start: 0.6508 (tpt) cc_final: 0.6215 (mmm) REVERT: A 54 GLU cc_start: 0.7343 (OUTLIER) cc_final: 0.7038 (tm-30) REVERT: A 416 GLN cc_start: 0.8309 (tm-30) cc_final: 0.8076 (tm-30) REVERT: B 415 GLN cc_start: 0.7718 (mt0) cc_final: 0.7269 (mm-40) REVERT: B 475 GLN cc_start: 0.7571 (mp10) cc_final: 0.6943 (mp10) REVERT: B 477 GLN cc_start: 0.7630 (mm-40) cc_final: 0.7207 (tm-30) REVERT: C 455 LYS cc_start: 0.7686 (mtpt) cc_final: 0.7375 (mttp) REVERT: E 291 ASP cc_start: 0.7392 (m-30) cc_final: 0.7037 (m-30) REVERT: E 347 ILE cc_start: 0.9181 (mm) cc_final: 0.8884 (mm) REVERT: E 458 GLN cc_start: 0.7854 (mm110) cc_final: 0.7265 (tp40) REVERT: F 398 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7046 (mp0) REVERT: D 62 ARG cc_start: 0.7883 (ttm170) cc_final: 0.7596 (ttm-80) REVERT: D 129 MET cc_start: 0.8856 (mmt) cc_final: 0.8606 (mmm) REVERT: D 433 LYS cc_start: 0.6926 (mmtm) cc_final: 0.6280 (mppt) REVERT: D 467 GLU cc_start: 0.6992 (tt0) cc_final: 0.6609 (mp0) REVERT: G 104 MET cc_start: 0.6598 (tpp) cc_final: 0.5792 (tpt) REVERT: G 201 LEU cc_start: 0.8380 (mt) cc_final: 0.7853 (mt) REVERT: O 113 ARG cc_start: 0.6571 (ptp-170) cc_final: 0.6228 (ptp-110) REVERT: O 163 ILE cc_start: 0.8706 (mm) cc_final: 0.8422 (tp) REVERT: O 180 GLN cc_start: 0.9229 (mm-40) cc_final: 0.8895 (mm-40) outliers start: 84 outliers final: 69 residues processed: 713 average time/residue: 0.5027 time to fit residues: 579.5279 Evaluate side-chains 710 residues out of total 4012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 637 time to evaluate : 5.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 4 residue 18 VAL Chi-restraints excluded: chain 5 residue 21 SER Chi-restraints excluded: chain 5 residue 28 VAL Chi-restraints excluded: chain 5 residue 62 LEU Chi-restraints excluded: chain 6 residue 58 GLU Chi-restraints excluded: chain 6 residue 62 LEU Chi-restraints excluded: chain 7 residue 31 SER Chi-restraints excluded: chain 7 residue 33 ILE Chi-restraints excluded: chain 1 residue 18 VAL Chi-restraints excluded: chain 1 residue 31 SER Chi-restraints excluded: chain 1 residue 32 LEU Chi-restraints excluded: chain 1 residue 33 ILE Chi-restraints excluded: chain 2 residue 16 VAL Chi-restraints excluded: chain 2 residue 28 VAL Chi-restraints excluded: chain 3 residue 64 CYS Chi-restraints excluded: chain 3 residue 65 LEU Chi-restraints excluded: chain H residue 59 ARG Chi-restraints excluded: chain K residue 173 MET Chi-restraints excluded: chain M residue 33 TRP Chi-restraints excluded: chain N residue 37 LEU Chi-restraints excluded: chain N residue 39 ASN Chi-restraints excluded: chain N residue 81 THR Chi-restraints excluded: chain N residue 138 ILE Chi-restraints excluded: chain N residue 185 ASN Chi-restraints excluded: chain N residue 203 GLU Chi-restraints excluded: chain N residue 206 VAL Chi-restraints excluded: chain P residue 5 ILE Chi-restraints excluded: chain P residue 17 TYR Chi-restraints excluded: chain P residue 42 ASP Chi-restraints excluded: chain Q residue 47 TYR Chi-restraints excluded: chain R residue 65 ILE Chi-restraints excluded: chain R residue 76 SER Chi-restraints excluded: chain S residue 50 GLN Chi-restraints excluded: chain S residue 54 LYS Chi-restraints excluded: chain S residue 67 LEU Chi-restraints excluded: chain S residue 83 LEU Chi-restraints excluded: chain T residue 38 GLU Chi-restraints excluded: chain A residue 54 GLU Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 358 TYR Chi-restraints excluded: chain A residue 390 MET Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain B residue 393 GLU Chi-restraints excluded: chain B residue 436 MET Chi-restraints excluded: chain B residue 502 THR Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 270 ASP Chi-restraints excluded: chain C residue 335 SER Chi-restraints excluded: chain C residue 505 LEU Chi-restraints excluded: chain E residue 37 ASN Chi-restraints excluded: chain E residue 101 ILE Chi-restraints excluded: chain E residue 255 LEU Chi-restraints excluded: chain E residue 333 ASP Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 169 ILE Chi-restraints excluded: chain F residue 240 LEU Chi-restraints excluded: chain F residue 398 GLU Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 339 SER Chi-restraints excluded: chain D residue 385 LYS Chi-restraints excluded: chain D residue 466 ILE Chi-restraints excluded: chain G residue 16 ILE Chi-restraints excluded: chain G residue 78 CYS Chi-restraints excluded: chain G residue 140 ASP Chi-restraints excluded: chain O residue 5 VAL Chi-restraints excluded: chain O residue 51 VAL Chi-restraints excluded: chain O residue 120 VAL Chi-restraints excluded: chain O residue 166 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 284 optimal weight: 2.9990 chunk 458 optimal weight: 2.9990 chunk 279 optimal weight: 1.9990 chunk 217 optimal weight: 0.0770 chunk 318 optimal weight: 0.1980 chunk 481 optimal weight: 0.8980 chunk 442 optimal weight: 2.9990 chunk 383 optimal weight: 6.9990 chunk 39 optimal weight: 0.7980 chunk 295 optimal weight: 1.9990 chunk 234 optimal weight: 1.9990 overall best weight: 0.7940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.3121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 38546 Z= 0.172 Angle : 0.610 14.256 52151 Z= 0.297 Chirality : 0.042 0.237 6078 Planarity : 0.004 0.060 6644 Dihedral : 5.266 88.247 5436 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.95 % Allowed : 20.14 % Favored : 77.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.50 % Cis-general : 0.11 % 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: 0.43 (0.12), residues: 4885 helix: 1.16 (0.11), residues: 2584 sheet: -0.68 (0.21), residues: 546 loop : -0.59 (0.16), residues: 1755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP P 10 HIS 0.006 0.001 HIS C 476 PHE 0.029 0.001 PHE D 262 TYR 0.040 0.001 TYR T 32 ARG 0.014 0.000 ARG G 133 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9770 Ramachandran restraints generated. 4885 Oldfield, 0 Emsley, 4885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9770 Ramachandran restraints generated. 4885 Oldfield, 0 Emsley, 4885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 751 residues out of total 4012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 673 time to evaluate : 6.152 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 69 PHE cc_start: 0.8389 (m-80) cc_final: 0.8030 (m-80) REVERT: 1 73 PHE cc_start: 0.7697 (m-80) cc_final: 0.7067 (m-80) REVERT: H 59 ARG cc_start: 0.7732 (OUTLIER) cc_final: 0.7228 (ptt90) REVERT: I 34 ASN cc_start: 0.6692 (t0) cc_final: 0.6440 (m110) REVERT: K 165 MET cc_start: 0.8345 (mmp) cc_final: 0.8028 (mmp) REVERT: K 173 MET cc_start: 0.7256 (OUTLIER) cc_final: 0.6927 (mmp) REVERT: S 54 LYS cc_start: 0.9211 (OUTLIER) cc_final: 0.9007 (pttp) REVERT: S 84 MET cc_start: 0.8680 (tpp) cc_final: 0.8246 (tmm) REVERT: S 90 GLU cc_start: 0.8266 (tm-30) cc_final: 0.7945 (tm-30) REVERT: T 21 LEU cc_start: 0.8769 (mt) cc_final: 0.8492 (tp) REVERT: L 74 GLU cc_start: 0.8590 (pp20) cc_final: 0.8227 (pp20) REVERT: L 87 MET cc_start: 0.6452 (tpt) cc_final: 0.6216 (mmm) REVERT: A 416 GLN cc_start: 0.8323 (tm-30) cc_final: 0.8089 (tm-30) REVERT: B 415 GLN cc_start: 0.7727 (mt0) cc_final: 0.7269 (mm-40) REVERT: B 475 GLN cc_start: 0.7559 (mp10) cc_final: 0.6946 (mp10) REVERT: B 477 GLN cc_start: 0.7628 (mm-40) cc_final: 0.7221 (tm-30) REVERT: E 291 ASP cc_start: 0.7354 (m-30) cc_final: 0.7011 (m-30) REVERT: E 347 ILE cc_start: 0.9176 (mm) cc_final: 0.8885 (mm) REVERT: E 458 GLN cc_start: 0.7845 (mm110) cc_final: 0.7242 (tp40) REVERT: F 174 ASN cc_start: 0.8241 (t0) cc_final: 0.7793 (t0) REVERT: F 398 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.7000 (mp0) REVERT: D 62 ARG cc_start: 0.7879 (ttm170) cc_final: 0.7600 (ttm-80) REVERT: D 295 MET cc_start: 0.8532 (tmm) cc_final: 0.8277 (tmm) REVERT: D 433 LYS cc_start: 0.6897 (mmtm) cc_final: 0.6248 (mppt) REVERT: D 467 GLU cc_start: 0.6981 (tt0) cc_final: 0.6606 (mp0) REVERT: G 66 HIS cc_start: 0.7725 (t70) cc_final: 0.7469 (t-90) REVERT: G 104 MET cc_start: 0.6614 (tpp) cc_final: 0.5802 (tpt) REVERT: G 201 LEU cc_start: 0.8351 (mt) cc_final: 0.7807 (mt) REVERT: O 113 ARG cc_start: 0.6602 (ptp-170) cc_final: 0.6277 (ptp-110) REVERT: O 163 ILE cc_start: 0.8735 (mm) cc_final: 0.8443 (tp) REVERT: O 180 GLN cc_start: 0.9234 (mm-40) cc_final: 0.8904 (mm-40) outliers start: 78 outliers final: 65 residues processed: 709 average time/residue: 0.5177 time to fit residues: 597.7116 Evaluate side-chains 716 residues out of total 4012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 647 time to evaluate : 4.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 4 residue 18 VAL Chi-restraints excluded: chain 5 residue 21 SER Chi-restraints excluded: chain 5 residue 28 VAL Chi-restraints excluded: chain 5 residue 62 LEU Chi-restraints excluded: chain 6 residue 58 GLU Chi-restraints excluded: chain 6 residue 62 LEU Chi-restraints excluded: chain 7 residue 31 SER Chi-restraints excluded: chain 7 residue 33 ILE Chi-restraints excluded: chain 1 residue 18 VAL Chi-restraints excluded: chain 1 residue 31 SER Chi-restraints excluded: chain 1 residue 32 LEU Chi-restraints excluded: chain 1 residue 33 ILE Chi-restraints excluded: chain 2 residue 28 VAL Chi-restraints excluded: chain 3 residue 65 LEU Chi-restraints excluded: chain H residue 59 ARG Chi-restraints excluded: chain K residue 173 MET Chi-restraints excluded: chain M residue 33 TRP Chi-restraints excluded: chain M residue 68 ASP Chi-restraints excluded: chain M residue 131 THR Chi-restraints excluded: chain N residue 37 LEU Chi-restraints excluded: chain N residue 39 ASN Chi-restraints excluded: chain N residue 81 THR Chi-restraints excluded: chain N residue 138 ILE Chi-restraints excluded: chain N residue 185 ASN Chi-restraints excluded: chain N residue 206 VAL Chi-restraints excluded: chain P residue 5 ILE Chi-restraints excluded: chain P residue 17 TYR Chi-restraints excluded: chain P residue 42 ASP Chi-restraints excluded: chain Q residue 47 TYR Chi-restraints excluded: chain R residue 65 ILE Chi-restraints excluded: chain R residue 76 SER Chi-restraints excluded: chain S residue 50 GLN Chi-restraints excluded: chain S residue 54 LYS Chi-restraints excluded: chain S residue 67 LEU Chi-restraints excluded: chain S residue 83 LEU Chi-restraints excluded: chain T residue 38 GLU Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 358 TYR Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain B residue 393 GLU Chi-restraints excluded: chain B residue 436 MET Chi-restraints excluded: chain B residue 502 THR Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 79 ASP Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 270 ASP Chi-restraints excluded: chain C residue 335 SER Chi-restraints excluded: chain C residue 505 LEU Chi-restraints excluded: chain E residue 37 ASN Chi-restraints excluded: chain E residue 101 ILE Chi-restraints excluded: chain E residue 333 ASP Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 169 ILE Chi-restraints excluded: chain F residue 240 LEU Chi-restraints excluded: chain F residue 398 GLU Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 339 SER Chi-restraints excluded: chain D residue 466 ILE Chi-restraints excluded: chain G residue 16 ILE Chi-restraints excluded: chain G residue 78 CYS Chi-restraints excluded: chain G residue 140 ASP Chi-restraints excluded: chain O residue 4 LEU Chi-restraints excluded: chain O residue 5 VAL Chi-restraints excluded: chain O residue 51 VAL Chi-restraints excluded: chain O residue 120 VAL Chi-restraints excluded: chain O residue 166 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 61.13 > 50: distance: 50 - 77: 4.410 distance: 54 - 86: 13.515 distance: 64 - 95: 12.387 distance: 73 - 103: 12.496 distance: 77 - 78: 5.366 distance: 78 - 79: 6.248 distance: 78 - 81: 8.575 distance: 79 - 80: 12.815 distance: 79 - 86: 6.794 distance: 81 - 82: 7.468 distance: 82 - 83: 8.355 distance: 84 - 85: 9.106 distance: 86 - 87: 5.618 distance: 87 - 90: 6.721 distance: 88 - 89: 8.003 distance: 88 - 95: 7.606 distance: 90 - 91: 7.172 distance: 91 - 92: 7.282 distance: 92 - 93: 3.919 distance: 92 - 94: 4.685 distance: 95 - 96: 10.525 distance: 96 - 97: 9.887 distance: 96 - 99: 7.464 distance: 97 - 98: 13.869 distance: 97 - 103: 7.569 distance: 99 - 100: 18.841 distance: 100 - 101: 11.691 distance: 103 - 104: 5.784 distance: 104 - 105: 6.627 distance: 105 - 106: 6.055 distance: 105 - 114: 7.603 distance: 107 - 108: 5.097 distance: 108 - 109: 4.710 distance: 108 - 110: 4.981 distance: 109 - 111: 17.284 distance: 110 - 112: 9.870 distance: 111 - 113: 8.160 distance: 112 - 113: 13.023 distance: 114 - 115: 21.413 distance: 115 - 116: 10.811 distance: 116 - 117: 19.553 distance: 116 - 118: 7.100 distance: 118 - 119: 4.710 distance: 119 - 120: 6.062 distance: 119 - 122: 8.241 distance: 120 - 121: 10.005 distance: 120 - 126: 21.339 distance: 122 - 123: 15.494 distance: 123 - 124: 6.551 distance: 123 - 125: 18.430 distance: 126 - 127: 11.022 distance: 127 - 128: 12.658 distance: 127 - 130: 9.279 distance: 128 - 129: 46.877 distance: 128 - 131: 13.339 distance: 131 - 132: 5.496 distance: 132 - 133: 8.349 distance: 132 - 135: 10.956 distance: 133 - 134: 25.761 distance: 133 - 139: 45.113 distance: 135 - 136: 6.853 distance: 136 - 137: 11.670 distance: 136 - 138: 4.500 distance: 139 - 140: 19.293 distance: 140 - 141: 20.277 distance: 140 - 143: 6.340 distance: 141 - 142: 15.297 distance: 141 - 147: 7.245 distance: 143 - 144: 31.111 distance: 144 - 145: 12.566 distance: 145 - 146: 31.418 distance: 147 - 148: 14.455 distance: 148 - 149: 3.738 distance: 148 - 151: 19.655 distance: 149 - 150: 4.182 distance: 149 - 155: 3.461 distance: 151 - 152: 14.480 distance: 152 - 153: 11.510 distance: 152 - 154: 13.173