Starting phenix.real_space_refine on Sat Mar 23 22:13:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9s_34580/03_2024/8h9s_34580_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9s_34580/03_2024/8h9s_34580.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9s_34580/03_2024/8h9s_34580.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9s_34580/03_2024/8h9s_34580.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9s_34580/03_2024/8h9s_34580_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9s_34580/03_2024/8h9s_34580_updated.pdb" } resolution = 2.53 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= 0.003 sd= 1.095 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 18 5.49 5 Mg 5 5.21 5 S 161 5.16 5 C 24846 2.51 5 N 6576 2.21 5 O 7324 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "K TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 83": "OD1" <-> "OD2" Residue "K TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 150": "OE1" <-> "OE2" Residue "K TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 17": "OE1" <-> "OE2" Residue "M ASP 68": "OD1" <-> "OD2" Residue "M PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 90": "OD1" <-> "OD2" Residue "M PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 137": "OE1" <-> "OE2" Residue "M PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 24": "OD1" <-> "OD2" Residue "A GLU 50": "OE1" <-> "OE2" Residue "A ASP 96": "OD1" <-> "OD2" Residue "A GLU 102": "OE1" <-> "OE2" Residue "A GLU 165": "OE1" <-> "OE2" Residue "A ARG 171": "NH1" <-> "NH2" Residue "A ASP 191": "OD1" <-> "OD2" Residue "A ASP 194": "OD1" <-> "OD2" Residue "A TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 255": "OE1" <-> "OE2" Residue "A TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 GLU 328": "OE1" <-> "OE2" Residue "A PHE 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 399": "OE1" <-> "OE2" Residue "A ASP 411": "OD1" <-> "OD2" Residue "A GLU 439": "OE1" <-> "OE2" Residue "A GLU 440": "OE1" <-> "OE2" Residue "A PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 36": "OD1" <-> "OD2" Residue "B GLU 50": "OE1" <-> "OE2" Residue "B GLU 102": "OE1" <-> "OE2" Residue "B GLU 165": "OE1" <-> "OE2" Residue "B GLU 195": "OE1" <-> "OE2" Residue "B TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 228": "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 ASP 314": "OD1" <-> "OD2" Residue "B TYR 337": "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 GLU 426": "OE1" <-> "OE2" Residue "B GLU 439": "OE1" <-> "OE2" Residue "B GLU 440": "OE1" <-> "OE2" Residue "B ASP 454": "OD1" <-> "OD2" 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 15": "NH1" <-> "NH2" Residue "C ARG 30": "NH1" <-> "NH2" Residue "C GLU 67": "OE1" <-> "OE2" Residue "C GLU 102": "OE1" <-> "OE2" Residue "C GLU 144": "OE1" <-> "OE2" Residue "C GLU 165": "OE1" <-> "OE2" Residue "C ASP 181": "OD1" <-> "OD2" Residue "C ASP 191": "OD1" <-> "OD2" Residue "C TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 224": "OD1" <-> "OD2" Residue "C TYR 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 255": "OE1" <-> "OE2" Residue "C TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 270": "OD1" <-> "OD2" Residue "C TYR 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 292": "OE1" <-> "OE2" Residue "C PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 307": "OE1" <-> "OE2" Residue "C PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 355": "OE1" <-> "OE2" Residue "C TYR 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 440": "OE1" <-> "OE2" Residue "C PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 494": "OD1" <-> "OD2" Residue "C GLU 499": "OE1" <-> "OE2" Residue "C PHE 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 29": "OD1" <-> "OD2" Residue "E GLU 103": "OE1" <-> "OE2" Residue "E GLU 107": "OE1" <-> "OE2" Residue "E PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 125": "OE1" <-> "OE2" 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 195": "OE1" <-> "OE2" Residue "E TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 202": "OE1" <-> "OE2" Residue "E GLU 205": "OE1" <-> "OE2" 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 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 TYR 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 322": "OD1" <-> "OD2" Residue "E ARG 359": "NH1" <-> "NH2" Residue "E TYR 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 411": "NH1" <-> "NH2" Residue "E PHE 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 425": "OE1" <-> "OE2" Residue "E GLU 451": "OE1" <-> "OE2" Residue "E ASP 453": "OD1" <-> "OD2" Residue "E TYR 461": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 468": "OE1" <-> "OE2" Residue "E ASP 474": "OD1" <-> "OD2" Residue "F PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 30": "OE1" <-> "OE2" Residue "F GLU 45": "OE1" <-> "OE2" 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 GLU 122": "OE1" <-> "OE2" Residue "F PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 GLU 202": "OE1" <-> "OE2" Residue "F GLU 205": "OE1" <-> "OE2" Residue "F TYR 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 227": "OE1" <-> "OE2" Residue "F ARG 232": "NH1" <-> "NH2" 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 318": "OD1" <-> "OD2" Residue "F PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 369": "OE1" <-> "OE2" Residue "F TYR 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 383": "OD1" <-> "OD2" Residue "F TYR 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 389": "OD1" <-> "OD2" Residue "F GLU 398": "OE1" <-> "OE2" Residue "F GLU 401": "OE1" <-> "OE2" Residue "F PHE 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 425": "OE1" <-> "OE2" 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 PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 30": "OE1" <-> "OE2" Residue "D GLU 40": "OE1" <-> "OE2" Residue "D GLU 58": "OE1" <-> "OE2" Residue "D GLU 103": "OE1" <-> "OE2" Residue "D PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 125": "OE1" <-> "OE2" Residue "D PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 128": "OE1" <-> "OE2" Residue "D PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 171": "OE1" <-> "OE2" Residue "D GLU 195": "OE1" <-> "OE2" Residue "D ASP 198": "OD1" <-> "OD2" Residue "D ASP 213": "OD1" <-> "OD2" Residue "D TYR 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 244": "OE1" <-> "OE2" Residue "D PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 247": "NH1" <-> "NH2" Residue "D ASP 248": "OD1" <-> "OD2" Residue "D GLU 250": "OE1" <-> "OE2" Residue "D PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 277": "NH1" <-> "NH2" Residue "D TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 291": "OD1" <-> "OD2" Residue "D GLU 297": "OE1" <-> "OE2" Residue "D TYR 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 340": "NH1" <-> "NH2" Residue "D TYR 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 401": "OE1" <-> "OE2" Residue "D PHE 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 425": "OE1" <-> "OE2" Residue "D GLU 439": "OE1" <-> "OE2" Residue "D GLU 451": "OE1" <-> "OE2" Residue "D TYR 461": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 467": "OE1" <-> "OE2" Residue "D GLU 468": "OE1" <-> "OE2" Residue "D GLU 478": "OE1" <-> "OE2" Residue "G GLU 37": "OE1" <-> "OE2" Residue "G ASP 62": "OD1" <-> "OD2" Residue "G GLU 92": "OE1" <-> "OE2" Residue "G PHE 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 195": "OD1" <-> "OD2" Residue "G GLU 241": "OE1" <-> "OE2" Residue "G ASP 244": "OD1" <-> "OD2" Residue "G PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 261": "OE1" <-> "OE2" Residue "J ARG 16": "NH1" <-> "NH2" Residue "J PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 29": "OE1" <-> "OE2" Residue "J ARG 32": "NH1" <-> "NH2" Residue "J TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 35": "NH1" <-> "NH2" Residue "J ARG 39": "NH1" <-> "NH2" Residue "O TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 15": "OE1" <-> "OE2" Residue "O TYR 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 38": "OE1" <-> "OE2" Residue "O TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 91": "OE1" <-> "OE2" Residue "O PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 133": "OE1" <-> "OE2" Residue "O PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 155": "OD1" <-> "OD2" Residue "O TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ARG 38": "NH1" <-> "NH2" Residue "1 PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ASP 1": "OD1" <-> "OD2" Residue "2 ASP 3": "OD1" <-> "OD2" Residue "2 ARG 38": "NH1" <-> "NH2" Residue "2 ARG 38": "NH1" <-> "NH2" Residue "2 PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ASP 1": "OD1" <-> "OD2" Residue "3 PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 38": "NH1" <-> "NH2" Residue "3 ARG 38": "NH1" <-> "NH2" Residue "3 TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ARG 38": "NH1" <-> "NH2" Residue "4 GLU 58": "OE1" <-> "OE2" Residue "4 PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ASP 1": "OD1" <-> "OD2" Residue "5 ARG 38": "NH1" <-> "NH2" Residue "5 TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ASP 1": "OD1" <-> "OD2" Residue "6 ARG 38": "NH1" <-> "NH2" Residue "6 TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 GLU 58": "OE1" <-> "OE2" Residue "6 PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ARG 38": "NH1" <-> "NH2" Residue "7 TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 GLU 58": "OE1" <-> "OE2" Residue "7 PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 ARG 38": "NH1" <-> "NH2" Residue "8 TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 113": "OE1" <-> "OE2" Residue "H GLU 118": "OE1" <-> "OE2" Residue "H GLU 130": "OE1" <-> "OE2" Residue "I TYR 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 203": "OE1" <-> "OE2" Residue "Q TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 24": "OE1" <-> "OE2" Residue "R ARG 45": "NH1" <-> "NH2" 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 GLU 36": "OE1" <-> "OE2" Residue "S GLU 44": "OE1" <-> "OE2" Residue "S PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 71": "OE1" <-> "OE2" Residue "S ASP 101": "OD1" <-> "OD2" Residue "T PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 38": "OE1" <-> "OE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 38930 Number of models: 1 Model: "" Number of chains: 36 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: "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: "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: "A" Number of atoms: 3830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 503, 3830 Classifications: {'peptide': 503} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 484} Chain breaks: 1 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: 3714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 487, 3714 Classifications: {'peptide': 487} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 468} 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: 3562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3562 Classifications: {'peptide': 470} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 444} 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: "J" Number of atoms: 270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 270 Classifications: {'peptide': 35} Link IDs: {'TRANS': 34} 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: "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: 542 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 75, 534 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Conformer: "B" Number of residues, atoms: 75, 534 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} bond proxies already assigned to first conformer: 534 Chain: "3" Number of atoms: 542 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 75, 534 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Conformer: "B" Number of residues, atoms: 75, 534 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} bond proxies already assigned to first conformer: 534 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: "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: "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: 655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 655 Classifications: {'peptide': 78} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 75} 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: "K" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 72 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 28 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} Chain: "Q" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'3PH': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 21 Chain: "R" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 51 Time building chain proxies: 20.16, per 1000 atoms: 0.52 Number of scatterers: 38930 At special positions: 0 Unit cell: (143.08, 132.86, 246.01, 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 161 16.00 P 18 15.00 Mg 5 11.99 O 7324 8.00 N 6576 7.00 C 24846 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: 16.24 Conformation dependent library (CDL) restraints added in 7.5 seconds 10000 Ramachandran restraints generated. 5000 Oldfield, 0 Emsley, 5000 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9244 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 197 helices and 26 sheets defined 53.8% alpha, 9.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.41 Creating SS restraints... 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 183 Proline residue: K 76 - end of helix removed outlier: 3.528A pdb=" N SER K 100 " --> pdb=" O ALA K 96 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N HIS K 122 " --> pdb=" O VAL K 118 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N TYR K 123 " --> pdb=" O GLN K 119 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N LEU K 124 " --> pdb=" O LYS K 120 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N PHE K 125 " --> pdb=" O ARG K 121 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL K 182 " --> pdb=" O GLU K 178 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLN K 183 " --> pdb=" O LYS K 179 " (cutoff:3.500A) Processing helix chain 'K' and resid 194 through 207 Processing helix chain 'L' and resid 41 through 54 Processing helix chain 'L' and resid 69 through 82 removed outlier: 4.079A pdb=" N ARG L 73 " --> pdb=" O GLN L 69 " (cutoff:3.500A) Processing helix chain 'M' and resid 24 through 42 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 132 through 138 Processing helix chain 'M' and resid 140 through 142 No H-bonds generated for 'chain 'M' and resid 140 through 142' Processing helix chain 'M' and resid 157 through 159 No H-bonds generated for 'chain 'M' and resid 157 through 159' Processing helix chain 'A' and resid 9 through 17 Processing helix chain 'A' and resid 79 through 81 No H-bonds generated for 'chain 'A' and resid 79 through 81' 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 191 removed outlier: 3.798A pdb=" N GLN A 186 " --> pdb=" O THR A 182 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N LYS A 187 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N ARG A 188 " --> pdb=" O ILE A 184 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N PHE A 189 " --> pdb=" O ASN A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 222 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: 3.898A pdb=" N PHE A 257 " --> pdb=" O MET A 253 " (cutoff:3.500A) removed outlier: 3.580A 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: 4.345A pdb=" N ARG A 308 " --> pdb=" O ARG A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 316 No H-bonds generated for 'chain 'A' and resid 314 through 316' 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 403 removed outlier: 4.144A pdb=" N THR A 389 " --> pdb=" O GLN A 385 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N ALA A 402 " --> pdb=" O ARG A 398 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N PHE A 403 " --> pdb=" O GLU A 399 " (cutoff:3.500A) 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 427 Processing helix chain 'A' and resid 438 through 449 Processing helix chain 'A' and resid 458 through 475 removed outlier: 4.422A pdb=" N THR A 462 " --> pdb=" O PRO A 458 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N LYS A 463 " --> pdb=" O SER A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 486 Processing helix chain 'A' and resid 491 through 506 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 190 removed outlier: 4.248A pdb=" N LYS B 187 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N ARG B 188 " --> pdb=" O ILE B 184 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N PHE B 189 " --> pdb=" O ASN B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 197 No H-bonds generated for 'chain 'B' and resid 195 through 197' 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: 3.945A pdb=" N PHE B 257 " --> pdb=" O MET B 253 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASN B 260 " --> pdb=" O TYR B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 285 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: 3.760A pdb=" N HIS B 302 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 4.017A 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 354 through 358 Processing helix chain 'B' and resid 376 through 378 No H-bonds generated for 'chain 'B' and resid 376 through 378' Processing helix chain 'B' and resid 381 through 400 removed outlier: 4.403A pdb=" N THR B 389 " --> pdb=" O GLN B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 427 Processing helix chain 'B' and resid 438 through 449 Processing helix chain 'B' and resid 458 through 475 removed outlier: 4.585A pdb=" N THR B 462 " --> pdb=" O PRO B 458 " (cutoff:3.500A) removed outlier: 5.379A 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: 3.741A pdb=" N GLN C 186 " --> pdb=" O THR C 182 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N LYS C 187 " --> pdb=" O ILE C 183 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N ARG C 188 " --> pdb=" O ILE C 184 " (cutoff:3.500A) removed outlier: 4.870A 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 226 through 228 No H-bonds generated for 'chain 'C' and resid 226 through 228' Processing helix chain 'C' and resid 240 through 260 Proline residue: C 247 - end of helix removed outlier: 4.033A pdb=" N PHE C 257 " --> pdb=" O MET C 253 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASN C 260 " --> pdb=" O TYR C 256 " (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 306 removed outlier: 3.816A pdb=" N LEU C 305 " --> pdb=" O LEU C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 316 No H-bonds generated for 'chain 'C' and resid 314 through 316' Processing helix chain 'C' and resid 337 through 345 Processing helix chain 'C' and resid 354 through 358 Processing helix chain 'C' and resid 375 through 378 Processing helix chain 'C' and resid 381 through 400 removed outlier: 4.043A pdb=" N THR C 389 " --> pdb=" O GLN C 385 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL C 400 " --> pdb=" O GLN C 396 " (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 507 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: 4.878A pdb=" N ALA E 236 " --> pdb=" O ARG E 232 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N LEU E 237 " --> pdb=" O ALA E 233 " (cutoff:3.500A) Processing helix chain 'E' and resid 261 through 274 Processing helix chain 'E' and resid 281 through 283 No H-bonds generated for 'chain 'E' and resid 281 through 283' Processing helix chain 'E' and resid 288 through 298 removed outlier: 4.446A 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 329 Processing helix chain 'E' and resid 340 through 343 No H-bonds generated for 'chain 'E' and resid 340 through 343' Processing helix chain 'E' and resid 363 through 366 No H-bonds generated for 'chain 'E' and resid 363 through 366' Processing helix chain 'E' and resid 368 through 390 removed outlier: 3.640A 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: 5.251A pdb=" N VAL E 426 " --> pdb=" O VAL E 423 " (cutoff:3.500A) removed outlier: 3.749A 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 459 No H-bonds generated for 'chain 'E' and resid 457 through 459' 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 126 through 128 No H-bonds generated for 'chain 'F' and resid 126 through 128' Processing helix chain 'F' and resid 141 through 146 Processing helix chain 'F' and resid 165 through 176 Processing helix chain 'F' and resid 193 through 205 Processing helix chain 'F' and resid 229 through 248 removed outlier: 4.953A pdb=" N ALA F 236 " --> pdb=" O ARG F 232 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N LEU F 237 " --> pdb=" O ALA F 233 " (cutoff:3.500A) Processing helix chain 'F' and resid 261 through 272 removed outlier: 3.839A pdb=" N THR F 265 " --> pdb=" O ILE F 261 " (cutoff:3.500A) Processing helix chain 'F' and resid 281 through 283 No H-bonds generated for 'chain 'F' and resid 281 through 283' Processing helix chain 'F' and resid 288 through 298 removed outlier: 4.220A pdb=" N ARG F 298 " --> pdb=" O THR F 294 " (cutoff:3.500A) 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: 4.519A pdb=" N ALA F 330 " --> pdb=" O ALA F 326 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N HIS F 331 " --> pdb=" O THR F 327 " (cutoff:3.500A) Processing helix chain 'F' and resid 340 through 344 Processing helix chain 'F' and resid 363 through 366 No H-bonds generated for 'chain 'F' and resid 363 through 366' Processing helix chain 'F' and resid 368 through 393 removed outlier: 4.596A pdb=" N ASP F 389 " --> pdb=" O LYS F 385 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N ILE F 390 " --> pdb=" O SER F 386 " (cutoff:3.500A) Processing helix chain 'F' and resid 396 through 398 No H-bonds generated for 'chain 'F' and resid 396 through 398' Processing helix chain 'F' and resid 401 through 417 Processing helix chain 'F' and resid 437 through 449 Processing helix chain 'F' and resid 457 through 460 Processing helix chain 'F' and resid 466 through 476 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 141 through 146 Processing helix chain 'D' and resid 165 through 178 Processing helix chain 'D' and resid 193 through 205 Processing helix chain 'D' and resid 229 through 248 removed outlier: 4.859A pdb=" N ALA D 236 " --> pdb=" O ARG D 232 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N LEU D 237 " --> pdb=" O ALA D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 275 removed outlier: 3.768A pdb=" N THR D 265 " --> pdb=" O ILE D 261 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL D 271 " --> pdb=" O ALA D 267 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ALA D 273 " --> pdb=" O SER D 269 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N LEU D 274 " --> pdb=" O GLU D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 283 No H-bonds generated for 'chain 'D' and resid 281 through 283' Processing helix chain 'D' and resid 288 through 298 removed outlier: 4.347A pdb=" N ARG D 298 " --> pdb=" O THR D 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 316 through 318 No H-bonds generated for 'chain 'D' and resid 316 through 318' Processing helix chain 'D' and resid 323 through 331 removed outlier: 4.510A pdb=" N ALA D 330 " --> pdb=" O ALA D 326 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N HIS D 331 " --> pdb=" O THR D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 340 through 344 Processing helix chain 'D' and resid 368 through 394 removed outlier: 4.130A pdb=" N ASP D 389 " --> pdb=" O LYS D 385 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ILE D 390 " --> pdb=" O SER D 386 " (cutoff:3.500A) Processing helix chain 'D' and resid 396 through 398 No H-bonds generated for 'chain 'D' and resid 396 through 398' Processing helix chain 'D' and resid 401 through 417 Processing helix chain 'D' and resid 422 through 428 removed outlier: 3.552A pdb=" N GLU D 425 " --> pdb=" O GLN D 422 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N VAL D 426 " --> pdb=" O VAL D 423 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N THR D 428 " --> pdb=" O GLU D 425 " (cutoff:3.500A) Processing helix chain 'D' and resid 437 through 449 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 479 Processing helix chain 'G' and resid 3 through 47 removed outlier: 3.575A pdb=" N ARG G 33 " --> pdb=" O ALA G 29 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N LYS G 39 " --> pdb=" O GLU G 35 " (cutoff:3.500A) Proline residue: G 40 - end of helix Processing helix chain 'G' and resid 50 through 54 Processing helix chain 'G' and resid 81 through 99 removed outlier: 3.675A pdb=" N ALA G 99 " --> pdb=" O THR G 95 " (cutoff:3.500A) Processing helix chain 'G' and resid 110 through 116 Processing helix chain 'G' and resid 138 through 149 Processing helix chain 'G' and resid 181 through 185 Processing helix chain 'G' and resid 188 through 192 removed outlier: 3.541A pdb=" N SER G 191 " --> pdb=" O ASP G 188 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ILE G 192 " --> pdb=" O SER G 189 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 188 through 192' Processing helix chain 'G' and resid 198 through 270 removed outlier: 3.780A pdb=" N THR G 222 " --> pdb=" O LYS G 218 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 17 No H-bonds generated for 'chain 'J' and resid 14 through 17' Processing helix chain 'J' and resid 21 through 43 removed outlier: 3.620A pdb=" N ARG J 25 " --> pdb=" O ALA J 21 " (cutoff:3.500A) Processing helix chain 'O' and resid 13 through 28 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 74 Processing helix chain 'O' and resid 80 through 92 Processing helix chain 'O' and resid 95 through 112 removed outlier: 4.578A pdb=" N GLN O 99 " --> pdb=" O SER O 96 " (cutoff:3.500A) Processing helix chain 'O' and resid 128 through 141 removed outlier: 3.960A pdb=" N SER O 140 " --> pdb=" O THR O 136 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N PHE O 141 " --> pdb=" O VAL O 137 " (cutoff:3.500A) 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 187 Processing helix chain '1' and resid 3 through 38 removed outlier: 3.938A pdb=" N VAL 1 16 " --> pdb=" O GLY 1 12 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N GLY 1 17 " --> pdb=" O ALA 1 13 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N VAL 1 18 " --> pdb=" O ALA 1 14 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N ALA 1 19 " --> pdb=" O THR 1 15 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N GLY 1 20 " --> pdb=" O VAL 1 16 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N SER 1 21 " --> pdb=" O GLY 1 17 " (cutoff:3.500A) Processing helix chain '1' and resid 40 through 72 removed outlier: 3.701A pdb=" N LYS 1 43 " --> pdb=" O PRO 1 40 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N GLN 1 44 " --> pdb=" O SER 1 41 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N LEU 1 46 " --> pdb=" O LYS 1 43 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N GLU 1 58 " --> pdb=" O ALA 1 55 " (cutoff:3.500A) Processing helix chain '2' and resid 3 through 38 removed outlier: 4.172A pdb=" N GLY 2 17 " --> pdb=" O ALA 2 13 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N VAL 2 18 " --> pdb=" O ALA 2 14 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N ALA 2 19 " --> pdb=" O THR 2 15 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N GLY 2 20 " --> pdb=" O VAL 2 16 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N SER 2 21 " --> pdb=" O GLY 2 17 " (cutoff:3.500A) Processing helix chain '2' and resid 40 through 72 removed outlier: 3.801A pdb=" N LYS 2 43 " --> pdb=" O PRO 2 40 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N GLN 2 44 " --> pdb=" O SER 2 41 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LEU 2 46 " --> pdb=" O LYS 2 43 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N GLU 2 58 " --> pdb=" O ALA 2 55 " (cutoff:3.500A) Processing helix chain '3' and resid 3 through 38 removed outlier: 4.009A pdb=" N GLY 3 17 " --> pdb=" O ALA 3 13 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N VAL 3 18 " --> pdb=" O ALA 3 14 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N ALA 3 19 " --> pdb=" O THR 3 15 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N GLY 3 20 " --> pdb=" O VAL 3 16 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N SER 3 21 " --> pdb=" O GLY 3 17 " (cutoff:3.500A) Processing helix chain '3' and resid 40 through 72 removed outlier: 5.267A pdb=" N GLN 3 44 " --> pdb=" O SER 3 41 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LEU 3 46 " --> pdb=" O LYS 3 43 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N GLU 3 58 " --> pdb=" O ALA 3 55 " (cutoff:3.500A) Processing helix chain '4' and resid 2 through 38 removed outlier: 4.252A pdb=" N GLY 4 17 " --> pdb=" O ALA 4 13 " (cutoff:3.500A) removed outlier: 4.875A 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: 4.912A pdb=" N GLY 4 20 " --> pdb=" O VAL 4 16 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N SER 4 21 " --> pdb=" O GLY 4 17 " (cutoff:3.500A) Processing helix chain '4' and resid 43 through 72 removed outlier: 3.794A pdb=" N CYS 4 64 " --> pdb=" O MET 4 60 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N VAL 4 67 " --> pdb=" O PHE 4 63 " (cutoff:3.500A) Processing helix chain '5' and resid 2 through 38 removed outlier: 4.197A pdb=" N GLY 5 17 " --> pdb=" O ALA 5 13 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N VAL 5 18 " --> pdb=" O ALA 5 14 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N ALA 5 19 " --> pdb=" O THR 5 15 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N GLY 5 20 " --> pdb=" O VAL 5 16 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N SER 5 21 " --> pdb=" O GLY 5 17 " (cutoff:3.500A) Processing helix chain '5' and resid 43 through 72 removed outlier: 3.687A pdb=" N GLU 5 58 " --> pdb=" O PHE 5 54 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA 5 59 " --> pdb=" O ALA 5 55 " (cutoff:3.500A) Processing helix chain '6' and resid 2 through 38 removed outlier: 3.967A pdb=" N GLY 6 17 " --> pdb=" O ALA 6 13 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N VAL 6 18 " --> pdb=" O ALA 6 14 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N ALA 6 19 " --> pdb=" O THR 6 15 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N GLY 6 20 " --> pdb=" O VAL 6 16 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N SER 6 21 " --> pdb=" O GLY 6 17 " (cutoff:3.500A) Processing helix chain '6' and resid 43 through 72 Processing helix chain '7' and resid 2 through 38 removed outlier: 4.235A pdb=" N GLY 7 17 " --> pdb=" O ALA 7 13 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N VAL 7 18 " --> pdb=" O ALA 7 14 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N ALA 7 19 " --> pdb=" O THR 7 15 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N GLY 7 20 " --> pdb=" O VAL 7 16 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N SER 7 21 " --> pdb=" O GLY 7 17 " (cutoff:3.500A) Processing helix chain '7' and resid 40 through 72 removed outlier: 4.921A pdb=" N GLN 7 44 " --> pdb=" O SER 7 41 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LEU 7 46 " --> pdb=" O LYS 7 43 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N GLU 7 58 " --> pdb=" O ALA 7 55 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LEU 7 72 " --> pdb=" O PHE 7 69 " (cutoff:3.500A) Processing helix chain '8' and resid 2 through 38 removed outlier: 3.997A pdb=" N GLY 8 17 " --> pdb=" O ALA 8 13 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N VAL 8 18 " --> pdb=" O ALA 8 14 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N ALA 8 19 " --> pdb=" O THR 8 15 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N GLY 8 20 " --> pdb=" O VAL 8 16 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N SER 8 21 " --> pdb=" O GLY 8 17 " (cutoff:3.500A) Processing helix chain '8' and resid 40 through 72 removed outlier: 3.642A pdb=" N LYS 8 43 " --> pdb=" O PRO 8 40 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N GLN 8 44 " --> pdb=" O SER 8 41 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N GLU 8 58 " --> pdb=" O ALA 8 55 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N LEU 8 72 " --> pdb=" O PHE 8 69 " (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 126 through 145 Processing helix chain 'I' and resid 4 through 7 No H-bonds generated for 'chain 'I' and resid 4 through 7' Processing helix chain 'I' and resid 12 through 25 Processing helix chain 'I' and resid 29 through 38 removed outlier: 4.340A pdb=" N ALA I 33 " --> pdb=" O THR I 29 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N ASN I 34 " --> pdb=" O GLU I 30 " (cutoff:3.500A) 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 19 through 25 Processing helix chain 'N' and resid 27 through 30 Processing helix chain 'N' and resid 41 through 58 Processing helix chain 'N' and resid 65 through 87 removed outlier: 4.570A pdb=" N LEU N 70 " --> pdb=" O THR N 67 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL N 73 " --> pdb=" O LEU N 70 " (cutoff:3.500A) removed outlier: 3.539A 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 126 Processing helix chain 'N' and resid 135 through 137 No H-bonds generated for 'chain 'N' and resid 135 through 137' Processing helix chain 'N' and resid 140 through 180 removed outlier: 3.525A pdb=" N GLU N 145 " --> pdb=" O LEU N 141 " (cutoff:3.500A) Proline residue: N 153 - end of helix removed outlier: 3.524A pdb=" N ASN N 163 " --> pdb=" O ARG N 159 " (cutoff:3.500A) Processing helix chain 'N' and resid 186 through 225 removed outlier: 3.750A pdb=" N ASN N 225 " --> pdb=" O TYR N 221 " (cutoff:3.500A) Processing helix chain 'P' and resid 10 through 18 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 21 removed outlier: 3.695A pdb=" N TRP Q 9 " --> pdb=" O THR Q 6 " (cutoff:3.500A) Proline residue: Q 10 - end of helix removed outlier: 4.548A pdb=" N THR Q 14 " --> pdb=" O THR Q 11 " (cutoff:3.500A) Proline residue: Q 15 - end of helix removed outlier: 4.105A pdb=" N LEU Q 20 " --> pdb=" O LEU Q 17 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N PHE Q 21 " --> pdb=" O LEU Q 18 " (cutoff:3.500A) Processing helix chain 'Q' and resid 23 through 29 Processing helix chain 'R' and resid 27 through 31 Processing helix chain 'R' and resid 36 through 54 Processing helix chain 'R' and resid 62 through 79 removed outlier: 4.760A pdb=" N MET R 67 " --> pdb=" O GLY R 64 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N PHE R 79 " --> pdb=" O SER R 76 " (cutoff:3.500A) Processing helix chain 'R' and resid 81 through 86 removed outlier: 4.919A pdb=" N HIS R 86 " --> pdb=" O LYS R 82 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 36 removed outlier: 4.546A pdb=" N VAL S 35 " --> pdb=" O TYR S 31 " (cutoff:3.500A) Processing helix chain 'S' and resid 45 through 60 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 43 Proline residue: T 35 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 28 through 30 removed outlier: 3.945A pdb=" N GLU A 51 " --> pdb=" O SER A 63 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N GLY A 72 " --> pdb=" O LEU A 64 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N HIS A 42 " --> pdb=" O VAL A 31 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N VAL A 31 " --> pdb=" O HIS A 42 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 96 through 99 removed outlier: 4.086A pdb=" N THR A 125 " --> pdb=" O VAL A 99 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 349 through 352 removed outlier: 6.364A pdb=" N LEU A 166 " --> pdb=" O ILE A 350 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N LEU A 352 " --> pdb=" O LEU A 166 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N ILE A 168 " --> pdb=" O LEU A 352 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 229 through 234 removed outlier: 8.756A pdb=" N ILE A 230 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N CYS A 201 " --> pdb=" O ILE A 230 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N VAL A 232 " --> pdb=" O CYS A 201 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N TYR A 203 " --> pdb=" O VAL A 232 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N ALA A 234 " --> pdb=" O TYR A 203 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ALA A 205 " --> pdb=" O ALA A 234 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N HIS A 263 " --> pdb=" O TYR A 200 " (cutoff:3.500A) removed outlier: 8.146A pdb=" N ILE A 202 " --> pdb=" O HIS A 263 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N LEU A 265 " --> pdb=" O ILE A 202 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N VAL A 204 " --> pdb=" O LEU A 265 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N ILE A 267 " --> pdb=" O VAL A 204 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N ILE A 206 " --> pdb=" O ILE A 267 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ASP A 269 " --> pdb=" O ILE A 206 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N SER A 320 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 8.078A pdb=" N ILE A 266 " --> pdb=" O SER A 320 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N THR A 322 " --> pdb=" O ILE A 266 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N TYR A 268 " --> pdb=" O THR A 322 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N LEU A 324 " --> pdb=" O TYR A 268 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'B' and resid 28 through 30 removed outlier: 4.592A pdb=" N LYS B 60 " --> pdb=" O PHE B 76 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N GLY B 72 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N HIS B 42 " --> pdb=" O VAL B 31 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N VAL B 31 " --> pdb=" O HIS B 42 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 96 through 99 removed outlier: 4.181A pdb=" N THR B 125 " --> pdb=" O VAL B 99 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 107 through 109 removed outlier: 8.217A pdb=" N VAL B 108 " --> pdb=" O THR B 229 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N VAL B 231 " --> pdb=" O VAL B 108 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N CYS B 201 " --> pdb=" O ILE B 230 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N VAL B 232 " --> pdb=" O CYS B 201 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N TYR B 203 " --> pdb=" O VAL B 232 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N ALA B 234 " --> pdb=" O TYR B 203 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N ALA B 205 " --> pdb=" O ALA B 234 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N SER B 320 " --> pdb=" O ALA B 264 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N ILE B 266 " --> pdb=" O SER B 320 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N THR B 322 " --> pdb=" O ILE B 266 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N TYR B 268 " --> pdb=" O THR B 322 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N LEU B 324 " --> pdb=" O TYR B 268 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 349 through 352 removed outlier: 6.752A pdb=" N LEU B 166 " --> pdb=" O ILE B 350 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N LEU B 352 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ILE B 168 " --> pdb=" O LEU B 352 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 28 through 30 removed outlier: 3.983A pdb=" N GLU C 51 " --> pdb=" O SER C 63 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N GLY C 72 " --> pdb=" O LEU C 64 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N HIS C 42 " --> pdb=" O VAL C 31 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N VAL C 31 " --> pdb=" O HIS C 42 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 96 through 99 removed outlier: 4.072A pdb=" N THR C 125 " --> pdb=" O VAL C 99 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 349 through 351 removed outlier: 6.727A pdb=" N LEU C 166 " --> pdb=" O ILE C 350 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 229 through 234 removed outlier: 8.744A pdb=" N ILE C 230 " --> pdb=" O LEU C 199 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N CYS C 201 " --> pdb=" O ILE C 230 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N VAL C 232 " --> pdb=" O CYS C 201 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N TYR C 203 " --> pdb=" O VAL C 232 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N ALA C 234 " --> pdb=" O TYR C 203 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N ALA C 205 " --> pdb=" O ALA C 234 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N HIS C 263 " --> pdb=" O TYR C 200 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N ILE C 202 " --> pdb=" O HIS C 263 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N LEU C 265 " --> pdb=" O ILE C 202 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N VAL C 204 " --> pdb=" O LEU C 265 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ILE C 267 " --> pdb=" O VAL C 204 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N ILE C 206 " --> pdb=" O ILE C 267 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ASP C 269 " --> pdb=" O ILE C 206 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N SER C 320 " --> pdb=" O ALA C 264 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N ILE C 266 " --> pdb=" O SER C 320 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N THR C 322 " --> pdb=" O ILE C 266 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N TYR C 268 " --> pdb=" O THR C 322 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N LEU C 324 " --> pdb=" O TYR C 268 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'E' and resid 13 through 15 removed outlier: 6.775A pdb=" N ARG E 62 " --> pdb=" O ALA E 53 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N HIS E 55 " --> pdb=" O THR E 60 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N THR E 60 " --> pdb=" O HIS E 55 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N GLN E 27 " --> pdb=" O ILE E 16 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N ILE E 16 " --> pdb=" O GLN E 27 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 86 through 89 removed outlier: 4.225A pdb=" N GLN E 115 " --> pdb=" O VAL E 89 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 334 through 337 removed outlier: 8.433A pdb=" N ILE E 155 " --> pdb=" O ILE E 307 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N SER E 309 " --> pdb=" O ILE E 155 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N LEU E 157 " --> pdb=" O SER E 309 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N GLN E 311 " --> pdb=" O LEU E 157 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'F' and resid 13 through 15 removed outlier: 6.762A pdb=" N ARG F 62 " --> pdb=" O ALA F 53 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N HIS F 55 " --> pdb=" O THR F 60 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N THR F 60 " --> pdb=" O HIS F 55 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA F 18 " --> pdb=" O ASP F 25 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N GLN F 27 " --> pdb=" O ILE F 16 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N ILE F 16 " --> pdb=" O GLN F 27 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'F' and resid 86 through 89 removed outlier: 4.234A pdb=" N GLN F 115 " --> pdb=" O VAL F 89 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'F' and resid 334 through 337 removed outlier: 7.501A pdb=" N ILE F 155 " --> pdb=" O ILE F 307 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N SER F 309 " --> pdb=" O ILE F 155 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N LEU F 157 " --> pdb=" O SER F 309 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N GLN F 311 " --> pdb=" O LEU F 157 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N GLY F 159 " --> pdb=" O GLN F 311 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N ILE F 313 " --> pdb=" O GLY F 159 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N TYR F 183 " --> pdb=" O LEU F 255 " (cutoff:3.500A) removed outlier: 8.346A pdb=" N PHE F 257 " --> pdb=" O TYR F 183 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N VAL F 185 " --> pdb=" O PHE F 257 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N ASP F 259 " --> pdb=" O VAL F 185 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ALA F 187 " --> pdb=" O ASP F 259 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 13 through 15 removed outlier: 6.724A pdb=" N ARG D 62 " --> pdb=" O ALA D 53 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N HIS D 55 " --> pdb=" O THR D 60 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N THR D 60 " --> pdb=" O HIS D 55 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N GLN D 27 " --> pdb=" O ILE D 16 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N ILE D 16 " --> pdb=" O GLN D 27 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 86 through 89 removed outlier: 4.250A pdb=" N GLN D 115 " --> pdb=" O VAL D 89 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'D' and resid 312 through 314 removed outlier: 5.958A pdb=" N LEU D 157 " --> pdb=" O ILE D 313 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N THR D 336 " --> pdb=" O PHE D 158 " (cutoff:3.500A) No H-bonds generated for sheet with id= U Processing sheet with id= V, first strand: chain 'D' and resid 218 through 223 removed outlier: 7.080A pdb=" N SER D 184 " --> pdb=" O ALA D 219 " (cutoff:3.500A) removed outlier: 8.580A pdb=" N VAL D 221 " --> pdb=" O SER D 184 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N PHE D 186 " --> pdb=" O VAL D 221 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N GLY D 223 " --> pdb=" O PHE D 186 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N GLY D 188 " --> pdb=" O GLY D 223 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N SER D 306 " --> pdb=" O VAL D 254 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N LEU D 256 " --> pdb=" O SER D 306 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N THR D 308 " --> pdb=" O LEU D 256 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N ILE D 258 " --> pdb=" O THR D 308 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N VAL D 310 " --> pdb=" O ILE D 258 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'G' and resid 171 through 179 removed outlier: 5.074A pdb=" N ASN G 163 " --> pdb=" O VAL G 71 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N GLU G 102 " --> pdb=" O HIS G 66 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N LEU G 68 " --> pdb=" O GLU G 102 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N MET G 104 " --> pdb=" O LEU G 68 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N GLY G 70 " --> pdb=" O MET G 104 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N VAL G 106 " --> pdb=" O GLY G 70 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N VAL G 126 " --> pdb=" O GLY G 107 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'O' and resid 147 through 151 removed outlier: 3.704A pdb=" N VAL O 120 " --> pdb=" O GLU O 151 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'H' and resid 54 through 57 removed outlier: 6.152A pdb=" N SER H 17 " --> pdb=" O VAL H 90 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N LEU H 92 " --> pdb=" O SER H 17 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N THR H 19 " --> pdb=" O LEU H 92 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N ALA H 94 " --> pdb=" O THR H 19 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ALA H 21 " --> pdb=" O ALA H 94 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N SER H 22 " --> pdb=" O VAL H 26 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N VAL H 26 " --> pdb=" O SER H 22 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'H' and resid 43 through 47 removed outlier: 6.827A pdb=" N HIS H 66 " --> pdb=" O ARG H 34 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N VAL H 36 " --> pdb=" O VAL H 64 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N VAL H 64 " --> pdb=" O VAL H 36 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N VAL H 38 " --> pdb=" O LEU H 62 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N LEU H 62 " --> pdb=" O VAL H 38 " (cutoff:3.500A) 2029 hydrogen bonds defined for protein. 5473 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: 15.86 Time building geometry restraints manager: 17.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 6504 1.30 - 1.43: 9341 1.43 - 1.56: 23387 1.56 - 1.68: 30 1.68 - 1.81: 303 Bond restraints: 39565 Sorted by residual: bond pdb=" C6 ATP B 601 " pdb=" N6 ATP B 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 1.460 -0.123 1.10e-02 8.26e+03 1.25e+02 bond pdb=" C6 ATP A 601 " pdb=" N6 ATP A 601 " ideal model delta sigma weight residual 1.337 1.458 -0.121 1.10e-02 8.26e+03 1.21e+02 bond pdb=" C4 ATP A 601 " pdb=" N9 ATP A 601 " ideal model delta sigma weight residual 1.374 1.287 0.087 1.00e-02 1.00e+04 7.56e+01 bond pdb=" C8 ATP C 601 " pdb=" N9 ATP C 601 " ideal model delta sigma weight residual 1.370 1.266 0.104 1.20e-02 6.94e+03 7.55e+01 ... (remaining 39560 not shown) Histogram of bond angle deviations from ideal: 98.64 - 106.39: 988 106.39 - 114.14: 23438 114.14 - 121.90: 21610 121.90 - 129.65: 7348 129.65 - 137.41: 122 Bond angle restraints: 53506 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 139.87 122.94 16.93 1.00e+00 1.00e+00 2.87e+02 angle pdb=" PB ATP A 601 " pdb=" O3B ATP A 601 " pdb=" PG ATP A 601 " ideal model delta sigma weight residual 139.87 123.70 16.17 1.00e+00 1.00e+00 2.61e+02 angle pdb=" PB ATP C 601 " pdb=" O3B ATP C 601 " pdb=" PG ATP C 601 " ideal model delta sigma weight residual 139.87 124.72 15.15 1.00e+00 1.00e+00 2.30e+02 angle pdb=" PA ATP C 601 " pdb=" O3A ATP C 601 " pdb=" PB ATP C 601 " ideal model delta sigma weight residual 136.83 125.06 11.77 1.00e+00 1.00e+00 1.38e+02 angle pdb=" N ILE 1 71 " pdb=" CA ILE 1 71 " pdb=" C ILE 1 71 " ideal model delta sigma weight residual 113.71 102.64 11.07 9.50e-01 1.11e+00 1.36e+02 ... (remaining 53501 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.95: 23514 35.95 - 71.89: 477 71.89 - 107.84: 48 107.84 - 143.78: 1 143.78 - 179.73: 2 Dihedral angle restraints: 24042 sinusoidal: 9596 harmonic: 14446 Sorted by residual: dihedral pdb=" O1B ADP F 501 " pdb=" O3A ADP F 501 " pdb=" PB ADP F 501 " pdb=" PA ADP F 501 " ideal model delta sinusoidal sigma weight residual 300.00 129.43 170.57 1 2.00e+01 2.50e-03 4.77e+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 83.39 -143.39 1 2.00e+01 2.50e-03 4.33e+01 dihedral pdb=" O2A ADP F 501 " pdb=" O3A ADP F 501 " pdb=" PA ADP F 501 " pdb=" PB ADP F 501 " ideal model delta sinusoidal sigma weight residual -60.00 43.78 -103.78 1 2.00e+01 2.50e-03 2.97e+01 ... (remaining 24039 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 5133 0.056 - 0.113: 936 0.113 - 0.169: 138 0.169 - 0.226: 6 0.226 - 0.282: 3 Chirality restraints: 6216 Sorted by residual: chirality pdb=" CA ILE 1 71 " pdb=" N ILE 1 71 " pdb=" C ILE 1 71 " pdb=" CB ILE 1 71 " both_signs ideal model delta sigma weight residual False 2.43 2.72 -0.28 2.00e-01 2.50e+01 1.99e+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 -2.43 -0.25 2.00e-01 2.50e+01 1.51e+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 -2.44 -0.24 2.00e-01 2.50e+01 1.39e+00 ... (remaining 6213 not shown) Planarity restraints: 6813 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN D 174 " -0.011 2.00e-02 2.50e+03 2.20e-02 4.82e+00 pdb=" C ASN D 174 " 0.038 2.00e-02 2.50e+03 pdb=" O ASN D 174 " -0.014 2.00e-02 2.50e+03 pdb=" N ASN D 175 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR N 93 " 0.035 5.00e-02 4.00e+02 5.31e-02 4.51e+00 pdb=" N PRO N 94 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO N 94 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO N 94 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE 3 54 " 0.010 2.00e-02 2.50e+03 2.01e-02 4.03e+00 pdb=" C PHE 3 54 " -0.035 2.00e-02 2.50e+03 pdb=" O PHE 3 54 " 0.013 2.00e-02 2.50e+03 pdb=" N ALA 3 55 " 0.012 2.00e-02 2.50e+03 ... (remaining 6810 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.50: 175 2.50 - 3.10: 28848 3.10 - 3.70: 59397 3.70 - 4.30: 93363 4.30 - 4.90: 151673 Nonbonded interactions: 333456 Sorted by model distance: nonbonded pdb=" OG1 THR A 176 " pdb="MG MG A 602 " model vdw 1.895 2.170 nonbonded pdb=" OG1 THR F 166 " pdb="MG MG F 502 " model vdw 1.937 2.170 nonbonded pdb=" OG1 THR B 176 " pdb="MG MG B 602 " model vdw 1.940 2.170 nonbonded pdb=" OG1 THR C 176 " pdb="MG MG C 602 " model vdw 2.016 2.170 nonbonded pdb=" O1B ATP C 601 " pdb="MG MG C 602 " model vdw 2.038 2.170 ... (remaining 333451 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' and (resid 1 through 37 or resid 39 through 75)) selection = (chain '2' and (resid 1 through 37 or resid 39 through 75)) selection = (chain '3' and (resid 1 through 37 or resid 39 through 75)) selection = (chain '4' and (resid 1 through 37 or resid 39 through 75)) selection = (chain '5' and (resid 1 through 37 or resid 39 through 75)) selection = (chain '6' and (resid 1 through 37 or resid 39 through 75)) selection = (chain '7' and (resid 1 through 37 or resid 39 through 75)) selection = (chain '8' and (resid 1 through 37 or resid 39 through 75)) } 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' and (resid 24 through 508 or resid 601 through 602)) } ncs_group { reference = (chain 'D' and (resid 12 through 391 or resid 400 through 475)) selection = chain 'E' selection = (chain 'F' and (resid 12 through 391 or resid 400 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=0.50 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: 8.670 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: 0.020 Extract box with map and model: 30.020 Check model and map are aligned: 0.570 Set scattering table: 0.340 Process input model: 102.630 Find NCS groups from input model: 2.620 Set up NCS constraints: 0.210 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:11.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 156.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 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 : 0.006 0.145 39565 Z= 0.421 Angle : 0.689 16.929 53506 Z= 0.424 Chirality : 0.045 0.282 6216 Planarity : 0.004 0.053 6813 Dihedral : 15.014 179.728 14798 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.92 % Favored : 97.02 % Rotamer: Outliers : 0.05 % Allowed : 3.97 % Favored : 95.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (0.10), residues: 5000 helix: -1.08 (0.09), residues: 2702 sheet: -1.06 (0.20), residues: 578 loop : -1.83 (0.13), residues: 1720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP P 10 HIS 0.004 0.001 HIS H 51 PHE 0.023 0.002 PHE 8 29 TYR 0.016 0.001 TYR G 193 ARG 0.005 0.000 ARG T 41 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10000 Ramachandran restraints generated. 5000 Oldfield, 0 Emsley, 5000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10000 Ramachandran restraints generated. 5000 Oldfield, 0 Emsley, 5000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 670 residues out of total 4096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 669 time to evaluate : 4.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 359 LYS cc_start: 0.8125 (mttt) cc_final: 0.7919 (mttm) REVERT: A 488 LYS cc_start: 0.8564 (pttt) cc_final: 0.8354 (ptpt) REVERT: B 195 GLU cc_start: 0.6836 (tp30) cc_final: 0.6391 (tp30) REVERT: N 36 TYR cc_start: 0.6522 (m-10) cc_final: 0.6303 (m-10) REVERT: R 32 ARG cc_start: 0.7817 (mmp-170) cc_final: 0.6529 (mmp-170) outliers start: 1 outliers final: 0 residues processed: 670 average time/residue: 1.7448 time to fit residues: 1384.5395 Evaluate side-chains 528 residues out of total 4096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 528 time to evaluate : 4.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 416 optimal weight: 2.9990 chunk 373 optimal weight: 0.8980 chunk 207 optimal weight: 0.9990 chunk 127 optimal weight: 6.9990 chunk 252 optimal weight: 4.9990 chunk 199 optimal weight: 0.0170 chunk 386 optimal weight: 0.9990 chunk 149 optimal weight: 7.9990 chunk 234 optimal weight: 3.9990 chunk 287 optimal weight: 5.9990 chunk 447 optimal weight: 0.4980 overall best weight: 0.6822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 88 GLN K 183 GLN L 80 GLN M 23 GLN M 136 ASN A 396 GLN A 416 GLN A 432 GLN A 503 ASN B 70 ASN B 492 GLN B 503 ASN C 208 GLN C 432 GLN C 466 ASN C 503 ASN ** E 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 180 HIS F 249 GLN F 331 HIS F 422 GLN F 458 GLN D 201 HIS ** D 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 266 GLN ** G 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 163 ASN G 182 ASN O 99 GLN H 15 GLN H 85 ASN N 4 ASN N 46 GLN N 47 GLN N 61 HIS S 75 ASN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.0991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 39565 Z= 0.165 Angle : 0.504 7.199 53506 Z= 0.264 Chirality : 0.041 0.155 6216 Planarity : 0.004 0.061 6813 Dihedral : 8.429 147.184 5695 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.14 % Favored : 97.80 % Rotamer: Outliers : 1.91 % Allowed : 10.51 % Favored : 87.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.12 % 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: -0.47 (0.11), residues: 5000 helix: 0.33 (0.10), residues: 2716 sheet: -0.61 (0.21), residues: 569 loop : -1.08 (0.14), residues: 1715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 28 HIS 0.003 0.001 HIS B 476 PHE 0.022 0.001 PHE C 464 TYR 0.013 0.001 TYR S 100 ARG 0.007 0.000 ARG C 381 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10000 Ramachandran restraints generated. 5000 Oldfield, 0 Emsley, 5000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10000 Ramachandran restraints generated. 5000 Oldfield, 0 Emsley, 5000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 646 residues out of total 4096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 569 time to evaluate : 4.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 MET cc_start: 0.6960 (mtm) cc_final: 0.6745 (mmt) REVERT: A 101 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7585 (mt-10) REVERT: A 170 ASP cc_start: 0.7573 (OUTLIER) cc_final: 0.7306 (m-30) REVERT: A 390 MET cc_start: 0.8456 (ttt) cc_final: 0.8203 (ttt) REVERT: B 195 GLU cc_start: 0.6814 (tp30) cc_final: 0.6505 (tp30) REVERT: E 112 LYS cc_start: 0.8196 (OUTLIER) cc_final: 0.7924 (mtpt) REVERT: E 249 GLN cc_start: 0.7958 (OUTLIER) cc_final: 0.7399 (mp10) REVERT: D 132 GLU cc_start: 0.7567 (OUTLIER) cc_final: 0.7033 (mp0) REVERT: D 470 VAL cc_start: 0.8064 (m) cc_final: 0.7831 (t) REVERT: R 32 ARG cc_start: 0.7692 (mmp-170) cc_final: 0.6558 (mmp-170) outliers start: 77 outliers final: 21 residues processed: 602 average time/residue: 1.6135 time to fit residues: 1162.9283 Evaluate side-chains 553 residues out of total 4096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 527 time to evaluate : 4.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain M residue 83 ASP Chi-restraints excluded: chain M residue 107 SER Chi-restraints excluded: chain M residue 112 VAL Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain C residue 54 GLU Chi-restraints excluded: chain C residue 132 LYS Chi-restraints excluded: chain E residue 112 LYS Chi-restraints excluded: chain E residue 249 GLN Chi-restraints excluded: chain E residue 340 ARG Chi-restraints excluded: chain F residue 205 GLU Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 115 GLN Chi-restraints excluded: chain D residue 132 GLU Chi-restraints excluded: chain D residue 344 GLU Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain G residue 169 ILE Chi-restraints excluded: chain O residue 107 THR Chi-restraints excluded: chain 1 residue 21 SER Chi-restraints excluded: chain 7 residue 72 LEU Chi-restraints excluded: chain I residue 29 THR Chi-restraints excluded: chain P residue 28 MET Chi-restraints excluded: chain R residue 30 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 248 optimal weight: 3.9990 chunk 138 optimal weight: 9.9990 chunk 372 optimal weight: 6.9990 chunk 304 optimal weight: 0.9990 chunk 123 optimal weight: 5.9990 chunk 448 optimal weight: 1.9990 chunk 484 optimal weight: 6.9990 chunk 399 optimal weight: 5.9990 chunk 444 optimal weight: 4.9990 chunk 152 optimal weight: 10.0000 chunk 359 optimal weight: 9.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 158 HIS ** L 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 432 GLN A 492 GLN B 78 ASN ** B 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 492 GLN C 503 ASN E 445 GLN F 224 GLN F 458 GLN D 201 HIS G 163 ASN G 182 ASN N 4 ASN N 56 GLN N 172 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.0986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.081 39565 Z= 0.469 Angle : 0.613 9.470 53506 Z= 0.318 Chirality : 0.047 0.185 6216 Planarity : 0.005 0.057 6813 Dihedral : 8.656 151.731 5695 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.94 % Favored : 97.02 % Rotamer: Outliers : 2.47 % Allowed : 12.35 % Favored : 85.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.12 % 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: -0.26 (0.12), residues: 5000 helix: 0.47 (0.10), residues: 2726 sheet: -0.49 (0.21), residues: 576 loop : -0.95 (0.14), residues: 1698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP R 28 HIS 0.006 0.001 HIS H 51 PHE 0.034 0.002 PHE H 45 TYR 0.018 0.002 TYR G 193 ARG 0.005 0.000 ARG C 381 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10000 Ramachandran restraints generated. 5000 Oldfield, 0 Emsley, 5000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10000 Ramachandran restraints generated. 5000 Oldfield, 0 Emsley, 5000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 653 residues out of total 4096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 553 time to evaluate : 5.365 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 78 LEU cc_start: 0.8102 (tp) cc_final: 0.7827 (tp) REVERT: A 101 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7580 (mt-10) REVERT: A 411 ASP cc_start: 0.7576 (OUTLIER) cc_final: 0.7369 (p0) REVERT: B 54 GLU cc_start: 0.7361 (OUTLIER) cc_final: 0.6805 (tm-30) REVERT: B 195 GLU cc_start: 0.6853 (tp30) cc_final: 0.6544 (tp30) REVERT: E 112 LYS cc_start: 0.8250 (OUTLIER) cc_final: 0.7952 (mtpt) REVERT: E 249 GLN cc_start: 0.8107 (OUTLIER) cc_final: 0.7502 (mp10) REVERT: F 422 GLN cc_start: 0.7390 (OUTLIER) cc_final: 0.7055 (mt0) REVERT: D 132 GLU cc_start: 0.7629 (OUTLIER) cc_final: 0.7109 (mp0) REVERT: D 470 VAL cc_start: 0.8079 (OUTLIER) cc_final: 0.7833 (t) REVERT: O 146 GLN cc_start: 0.7432 (mm-40) cc_final: 0.7208 (mm-40) REVERT: R 32 ARG cc_start: 0.7758 (mmp-170) cc_final: 0.6608 (mmp-170) outliers start: 100 outliers final: 41 residues processed: 600 average time/residue: 1.6364 time to fit residues: 1177.3855 Evaluate side-chains 580 residues out of total 4096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 531 time to evaluate : 4.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 104 ILE Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain L residue 55 GLN Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain M residue 83 ASP Chi-restraints excluded: chain M residue 107 SER Chi-restraints excluded: chain M residue 112 VAL Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 349 GLN Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain C residue 54 GLU Chi-restraints excluded: chain C residue 124 LYS Chi-restraints excluded: chain C residue 132 LYS Chi-restraints excluded: chain E residue 112 LYS Chi-restraints excluded: chain E residue 225 MET Chi-restraints excluded: chain E residue 249 GLN Chi-restraints excluded: chain E residue 294 THR Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain E residue 340 ARG Chi-restraints excluded: chain F residue 205 GLU Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 422 GLN Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 115 GLN Chi-restraints excluded: chain D residue 132 GLU Chi-restraints excluded: chain D residue 292 MET Chi-restraints excluded: chain D residue 344 GLU Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain G residue 169 ILE Chi-restraints excluded: chain G residue 197 ASP Chi-restraints excluded: chain O residue 107 THR Chi-restraints excluded: chain 1 residue 21 SER Chi-restraints excluded: chain 2 residue 41 SER Chi-restraints excluded: chain 7 residue 72 LEU Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain I residue 29 THR Chi-restraints excluded: chain I residue 39 SER Chi-restraints excluded: chain N residue 39 ASN Chi-restraints excluded: chain N residue 151 ILE Chi-restraints excluded: chain P residue 6 ILE Chi-restraints excluded: chain R residue 30 LEU Chi-restraints excluded: chain R residue 74 LEU Chi-restraints excluded: chain S residue 30 TRP Chi-restraints excluded: chain T residue 28 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 443 optimal weight: 8.9990 chunk 337 optimal weight: 2.9990 chunk 232 optimal weight: 0.9990 chunk 49 optimal weight: 0.4980 chunk 214 optimal weight: 1.9990 chunk 301 optimal weight: 0.9980 chunk 450 optimal weight: 0.9980 chunk 476 optimal weight: 5.9990 chunk 235 optimal weight: 0.7980 chunk 426 optimal weight: 1.9990 chunk 128 optimal weight: 10.0000 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 158 HIS A 416 GLN B 492 GLN C 503 ASN F 458 GLN ** D 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 364 ASN ** G 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 163 ASN G 182 ASN 7 45 GLN H 15 GLN N 4 ASN N 56 GLN N 163 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.1252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 39565 Z= 0.169 Angle : 0.501 7.705 53506 Z= 0.260 Chirality : 0.041 0.162 6216 Planarity : 0.004 0.048 6813 Dihedral : 7.966 147.617 5695 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.96 % Favored : 98.00 % Rotamer: Outliers : 2.25 % Allowed : 14.23 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.12 % 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: 0.35 (0.12), residues: 5000 helix: 0.98 (0.10), residues: 2727 sheet: -0.31 (0.21), residues: 570 loop : -0.67 (0.15), residues: 1703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 28 HIS 0.002 0.001 HIS K 172 PHE 0.018 0.001 PHE C 464 TYR 0.021 0.001 TYR T 32 ARG 0.008 0.000 ARG G 33 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10000 Ramachandran restraints generated. 5000 Oldfield, 0 Emsley, 5000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10000 Ramachandran restraints generated. 5000 Oldfield, 0 Emsley, 5000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 646 residues out of total 4096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 555 time to evaluate : 3.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 55 GLN cc_start: 0.7034 (OUTLIER) cc_final: 0.5765 (pm20) REVERT: L 78 LEU cc_start: 0.8013 (tp) cc_final: 0.7791 (tp) REVERT: A 170 ASP cc_start: 0.7579 (OUTLIER) cc_final: 0.7327 (m-30) REVERT: A 381 ARG cc_start: 0.7305 (OUTLIER) cc_final: 0.6544 (mtp85) REVERT: B 195 GLU cc_start: 0.6822 (tp30) cc_final: 0.6492 (tp30) REVERT: E 112 LYS cc_start: 0.8174 (OUTLIER) cc_final: 0.7897 (mtpt) REVERT: E 249 GLN cc_start: 0.8007 (OUTLIER) cc_final: 0.7441 (mp10) REVERT: F 422 GLN cc_start: 0.7274 (OUTLIER) cc_final: 0.6951 (mt0) REVERT: D 132 GLU cc_start: 0.7590 (OUTLIER) cc_final: 0.7063 (mp0) REVERT: D 470 VAL cc_start: 0.8019 (m) cc_final: 0.7785 (t) REVERT: R 32 ARG cc_start: 0.7483 (mmp-170) cc_final: 0.6580 (mtp-110) outliers start: 91 outliers final: 33 residues processed: 601 average time/residue: 1.6176 time to fit residues: 1173.5636 Evaluate side-chains 571 residues out of total 4096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 531 time to evaluate : 4.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 55 GLN Chi-restraints excluded: chain L residue 71 LEU Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain M residue 107 SER Chi-restraints excluded: chain M residue 112 VAL Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 196 LYS Chi-restraints excluded: chain A residue 349 GLN Chi-restraints excluded: chain A residue 381 ARG Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain C residue 54 GLU Chi-restraints excluded: chain C residue 124 LYS Chi-restraints excluded: chain C residue 132 LYS Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 497 LEU Chi-restraints excluded: chain E residue 112 LYS Chi-restraints excluded: chain E residue 249 GLN Chi-restraints excluded: chain E residue 340 ARG Chi-restraints excluded: chain F residue 134 GLU Chi-restraints excluded: chain F residue 422 GLN Chi-restraints excluded: chain F residue 470 VAL Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 115 GLN Chi-restraints excluded: chain D residue 132 GLU Chi-restraints excluded: chain D residue 292 MET Chi-restraints excluded: chain D residue 344 GLU Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain G residue 35 GLU Chi-restraints excluded: chain G residue 169 ILE Chi-restraints excluded: chain O residue 107 THR Chi-restraints excluded: chain 2 residue 41 SER Chi-restraints excluded: chain 7 residue 72 LEU Chi-restraints excluded: chain H residue 32 ASN Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain I residue 29 THR Chi-restraints excluded: chain N residue 52 LEU Chi-restraints excluded: chain N residue 151 ILE Chi-restraints excluded: chain N residue 199 LEU Chi-restraints excluded: chain P residue 28 MET Chi-restraints excluded: chain S residue 30 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 396 optimal weight: 5.9990 chunk 270 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 chunk 354 optimal weight: 10.0000 chunk 196 optimal weight: 5.9990 chunk 406 optimal weight: 8.9990 chunk 329 optimal weight: 0.5980 chunk 0 optimal weight: 6.9990 chunk 243 optimal weight: 3.9990 chunk 427 optimal weight: 3.9990 chunk 120 optimal weight: 4.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 80 GLN A 432 GLN A 492 GLN B 492 GLN C 503 ASN E 445 GLN F 27 GLN F 42 GLN F 458 GLN D 364 ASN G 182 ASN H 15 GLN N 4 ASN N 56 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.1174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.080 39565 Z= 0.461 Angle : 0.618 9.528 53506 Z= 0.319 Chirality : 0.047 0.187 6216 Planarity : 0.005 0.055 6813 Dihedral : 8.436 148.906 5695 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.80 % Favored : 97.16 % Rotamer: Outliers : 2.82 % Allowed : 14.70 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.12 % 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: 0.20 (0.12), residues: 5000 helix: 0.87 (0.10), residues: 2678 sheet: -0.33 (0.21), residues: 576 loop : -0.73 (0.14), residues: 1746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP R 28 HIS 0.006 0.001 HIS H 51 PHE 0.035 0.002 PHE H 45 TYR 0.018 0.002 TYR G 193 ARG 0.010 0.001 ARG G 33 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10000 Ramachandran restraints generated. 5000 Oldfield, 0 Emsley, 5000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10000 Ramachandran restraints generated. 5000 Oldfield, 0 Emsley, 5000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 656 residues out of total 4096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 542 time to evaluate : 4.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 78 LEU cc_start: 0.8048 (tp) cc_final: 0.7814 (tp) REVERT: A 101 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.7570 (mt-10) REVERT: A 411 ASP cc_start: 0.7575 (OUTLIER) cc_final: 0.7349 (p0) REVERT: B 26 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7412 (mt-10) REVERT: B 54 GLU cc_start: 0.7346 (OUTLIER) cc_final: 0.6804 (tm-30) REVERT: B 195 GLU cc_start: 0.6860 (tp30) cc_final: 0.6560 (tp30) REVERT: E 112 LYS cc_start: 0.8240 (OUTLIER) cc_final: 0.7917 (mtpt) REVERT: E 249 GLN cc_start: 0.8117 (OUTLIER) cc_final: 0.7451 (mp10) REVERT: F 15 ARG cc_start: 0.7741 (OUTLIER) cc_final: 0.7356 (ptm-80) REVERT: F 422 GLN cc_start: 0.7377 (OUTLIER) cc_final: 0.7059 (mt0) REVERT: D 132 GLU cc_start: 0.7616 (OUTLIER) cc_final: 0.7089 (mp0) REVERT: D 318 ASP cc_start: 0.8390 (OUTLIER) cc_final: 0.7935 (m-30) REVERT: D 470 VAL cc_start: 0.8055 (m) cc_final: 0.7813 (t) REVERT: G 56 ASP cc_start: 0.6965 (OUTLIER) cc_final: 0.6677 (m-30) REVERT: G 166 ARG cc_start: 0.7512 (OUTLIER) cc_final: 0.7000 (mtp85) REVERT: O 146 GLN cc_start: 0.7710 (mm-40) cc_final: 0.7303 (mm-40) REVERT: R 19 GLU cc_start: 0.3831 (OUTLIER) cc_final: 0.2832 (mm-30) REVERT: R 32 ARG cc_start: 0.7617 (mmp-170) cc_final: 0.6678 (mtp-110) outliers start: 114 outliers final: 50 residues processed: 603 average time/residue: 1.6106 time to fit residues: 1165.2760 Evaluate side-chains 591 residues out of total 4096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 528 time to evaluate : 4.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 55 GLN Chi-restraints excluded: chain L residue 74 GLU Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain M residue 107 SER Chi-restraints excluded: chain M residue 112 VAL Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 349 GLN Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 143 ARG Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 502 THR Chi-restraints excluded: chain C residue 54 GLU Chi-restraints excluded: chain C residue 124 LYS Chi-restraints excluded: chain C residue 132 LYS Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 497 LEU Chi-restraints excluded: chain E residue 112 LYS Chi-restraints excluded: chain E residue 249 GLN Chi-restraints excluded: chain E residue 266 GLN Chi-restraints excluded: chain E residue 294 THR Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain E residue 340 ARG Chi-restraints excluded: chain E residue 355 ASP Chi-restraints excluded: chain F residue 15 ARG Chi-restraints excluded: chain F residue 134 GLU Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 422 GLN Chi-restraints excluded: chain F residue 470 VAL Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 127 MET Chi-restraints excluded: chain D residue 132 GLU Chi-restraints excluded: chain D residue 318 ASP Chi-restraints excluded: chain D residue 344 GLU Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain G residue 35 GLU Chi-restraints excluded: chain G residue 56 ASP Chi-restraints excluded: chain G residue 166 ARG Chi-restraints excluded: chain G residue 169 ILE Chi-restraints excluded: chain G residue 197 ASP Chi-restraints excluded: chain O residue 4 LEU Chi-restraints excluded: chain O residue 107 THR Chi-restraints excluded: chain 2 residue 41 SER Chi-restraints excluded: chain 7 residue 72 LEU Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 73 SER Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain I residue 29 THR Chi-restraints excluded: chain I residue 39 SER Chi-restraints excluded: chain N residue 39 ASN Chi-restraints excluded: chain N residue 52 LEU Chi-restraints excluded: chain N residue 115 MET Chi-restraints excluded: chain N residue 151 ILE Chi-restraints excluded: chain P residue 5 ILE Chi-restraints excluded: chain P residue 6 ILE Chi-restraints excluded: chain R residue 19 GLU Chi-restraints excluded: chain S residue 30 TRP Chi-restraints excluded: chain T residue 8 SER Chi-restraints excluded: chain T residue 28 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 160 optimal weight: 0.5980 chunk 429 optimal weight: 0.6980 chunk 94 optimal weight: 4.9990 chunk 279 optimal weight: 3.9990 chunk 117 optimal weight: 0.6980 chunk 476 optimal weight: 8.9990 chunk 395 optimal weight: 0.8980 chunk 220 optimal weight: 0.7980 chunk 39 optimal weight: 0.9980 chunk 157 optimal weight: 1.9990 chunk 250 optimal weight: 6.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 492 GLN ** B 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 492 GLN C 503 ASN E 445 GLN F 27 GLN F 458 GLN D 201 HIS ** D 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 364 ASN ** G 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 182 ASN H 15 GLN N 4 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.1376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 39565 Z= 0.166 Angle : 0.514 9.915 53506 Z= 0.265 Chirality : 0.041 0.151 6216 Planarity : 0.004 0.045 6813 Dihedral : 7.840 147.423 5695 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.92 % Favored : 98.06 % Rotamer: Outliers : 2.01 % Allowed : 16.17 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.12 % 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: 0.63 (0.12), residues: 5000 helix: 1.19 (0.10), residues: 2720 sheet: -0.14 (0.21), residues: 555 loop : -0.51 (0.15), residues: 1725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP R 28 HIS 0.002 0.001 HIS K 172 PHE 0.016 0.001 PHE 2 29 TYR 0.012 0.001 TYR P 36 ARG 0.011 0.000 ARG G 33 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10000 Ramachandran restraints generated. 5000 Oldfield, 0 Emsley, 5000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10000 Ramachandran restraints generated. 5000 Oldfield, 0 Emsley, 5000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 626 residues out of total 4096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 545 time to evaluate : 5.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 78 LEU cc_start: 0.7975 (tp) cc_final: 0.7741 (tp) REVERT: A 101 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.7499 (mt-10) REVERT: A 381 ARG cc_start: 0.7327 (OUTLIER) cc_final: 0.6550 (mtp85) REVERT: B 54 GLU cc_start: 0.7323 (OUTLIER) cc_final: 0.6810 (tm-30) REVERT: B 195 GLU cc_start: 0.6834 (tp30) cc_final: 0.6502 (tp30) REVERT: E 112 LYS cc_start: 0.8166 (OUTLIER) cc_final: 0.7882 (mtpt) REVERT: E 249 GLN cc_start: 0.8025 (OUTLIER) cc_final: 0.7391 (mp10) REVERT: F 15 ARG cc_start: 0.7679 (OUTLIER) cc_final: 0.6892 (ptm-80) REVERT: F 252 GLN cc_start: 0.7821 (mm-40) cc_final: 0.7599 (mm-40) REVERT: F 422 GLN cc_start: 0.7266 (OUTLIER) cc_final: 0.6865 (mt0) REVERT: D 132 GLU cc_start: 0.7586 (OUTLIER) cc_final: 0.7060 (mp0) REVERT: D 318 ASP cc_start: 0.8270 (OUTLIER) cc_final: 0.7859 (m-30) REVERT: D 470 VAL cc_start: 0.8017 (m) cc_final: 0.7782 (t) REVERT: G 166 ARG cc_start: 0.7480 (OUTLIER) cc_final: 0.6996 (mtp85) REVERT: O 146 GLN cc_start: 0.7609 (mm-40) cc_final: 0.7129 (mm-40) REVERT: 4 62 LEU cc_start: 0.7185 (OUTLIER) cc_final: 0.6950 (mp) REVERT: 6 7 LYS cc_start: 0.7744 (mttp) cc_final: 0.7532 (mptt) REVERT: R 32 ARG cc_start: 0.7519 (mmp-170) cc_final: 0.6663 (mtp-110) outliers start: 81 outliers final: 36 residues processed: 589 average time/residue: 1.6196 time to fit residues: 1147.1735 Evaluate side-chains 571 residues out of total 4096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 524 time to evaluate : 4.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 71 LEU Chi-restraints excluded: chain L residue 74 GLU Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain M residue 107 SER Chi-restraints excluded: chain M residue 112 VAL Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 349 GLN Chi-restraints excluded: chain A residue 381 ARG Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain C residue 54 GLU Chi-restraints excluded: chain C residue 132 LYS Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 497 LEU Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 112 LYS Chi-restraints excluded: chain E residue 249 GLN Chi-restraints excluded: chain E residue 266 GLN Chi-restraints excluded: chain E residue 340 ARG Chi-restraints excluded: chain E residue 440 THR Chi-restraints excluded: chain F residue 15 ARG Chi-restraints excluded: chain F residue 134 GLU Chi-restraints excluded: chain F residue 422 GLN Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 127 MET Chi-restraints excluded: chain D residue 132 GLU Chi-restraints excluded: chain D residue 292 MET Chi-restraints excluded: chain D residue 318 ASP Chi-restraints excluded: chain D residue 344 GLU Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain G residue 35 GLU Chi-restraints excluded: chain G residue 166 ARG Chi-restraints excluded: chain G residue 169 ILE Chi-restraints excluded: chain O residue 107 THR Chi-restraints excluded: chain 2 residue 41 SER Chi-restraints excluded: chain 4 residue 62 LEU Chi-restraints excluded: chain 6 residue 66 MET Chi-restraints excluded: chain 7 residue 72 LEU Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain I residue 29 THR Chi-restraints excluded: chain N residue 39 ASN Chi-restraints excluded: chain N residue 151 ILE Chi-restraints excluded: chain P residue 5 ILE Chi-restraints excluded: chain P residue 28 MET Chi-restraints excluded: chain S residue 30 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 459 optimal weight: 0.9990 chunk 53 optimal weight: 4.9990 chunk 271 optimal weight: 10.0000 chunk 348 optimal weight: 0.9990 chunk 269 optimal weight: 8.9990 chunk 401 optimal weight: 5.9990 chunk 266 optimal weight: 0.5980 chunk 475 optimal weight: 7.9990 chunk 297 optimal weight: 2.9990 chunk 289 optimal weight: 0.8980 chunk 219 optimal weight: 4.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 416 GLN A 492 GLN C 503 ASN E 445 GLN F 27 GLN F 458 GLN D 201 HIS ** D 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 260 ASN D 364 ASN ** G 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 182 ASN N 4 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.1422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 39565 Z= 0.215 Angle : 0.525 10.414 53506 Z= 0.270 Chirality : 0.042 0.157 6216 Planarity : 0.004 0.046 6813 Dihedral : 7.732 148.022 5695 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.16 % Favored : 97.82 % Rotamer: Outliers : 2.20 % Allowed : 16.90 % Favored : 80.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.12 % 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: 0.76 (0.12), residues: 5000 helix: 1.32 (0.10), residues: 2689 sheet: -0.10 (0.21), residues: 567 loop : -0.46 (0.15), residues: 1744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 28 HIS 0.004 0.001 HIS B 476 PHE 0.020 0.001 PHE H 45 TYR 0.018 0.001 TYR B 446 ARG 0.011 0.000 ARG G 33 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10000 Ramachandran restraints generated. 5000 Oldfield, 0 Emsley, 5000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10000 Ramachandran restraints generated. 5000 Oldfield, 0 Emsley, 5000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 626 residues out of total 4096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 537 time to evaluate : 4.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.7516 (mt-10) REVERT: A 381 ARG cc_start: 0.7326 (OUTLIER) cc_final: 0.6574 (mtp85) REVERT: B 54 GLU cc_start: 0.7330 (OUTLIER) cc_final: 0.6811 (tm-30) REVERT: E 112 LYS cc_start: 0.8164 (OUTLIER) cc_final: 0.7873 (mtpt) REVERT: E 249 GLN cc_start: 0.8050 (OUTLIER) cc_final: 0.7396 (mp10) REVERT: E 415 ARG cc_start: 0.7806 (OUTLIER) cc_final: 0.6789 (mpt180) REVERT: F 15 ARG cc_start: 0.7690 (OUTLIER) cc_final: 0.6928 (ptm-80) REVERT: F 252 GLN cc_start: 0.7829 (mm-40) cc_final: 0.7613 (mm-40) REVERT: D 132 GLU cc_start: 0.7573 (OUTLIER) cc_final: 0.7040 (mp0) REVERT: D 318 ASP cc_start: 0.8294 (OUTLIER) cc_final: 0.7881 (m-30) REVERT: D 470 VAL cc_start: 0.8019 (m) cc_final: 0.7783 (t) REVERT: G 166 ARG cc_start: 0.7487 (OUTLIER) cc_final: 0.7001 (mtp85) REVERT: G 195 ASP cc_start: 0.7492 (OUTLIER) cc_final: 0.7236 (m-30) REVERT: O 146 GLN cc_start: 0.7532 (mm-40) cc_final: 0.7040 (mm-40) REVERT: 4 62 LEU cc_start: 0.7179 (OUTLIER) cc_final: 0.6954 (mp) REVERT: R 32 ARG cc_start: 0.7527 (mmp-170) cc_final: 0.6699 (mtp-110) outliers start: 89 outliers final: 49 residues processed: 584 average time/residue: 1.6020 time to fit residues: 1125.6145 Evaluate side-chains 591 residues out of total 4096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 530 time to evaluate : 4.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 71 LEU Chi-restraints excluded: chain L residue 74 GLU Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain L residue 103 ILE Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain M residue 107 SER Chi-restraints excluded: chain M residue 112 VAL Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 196 LYS Chi-restraints excluded: chain A residue 349 GLN Chi-restraints excluded: chain A residue 381 ARG Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain C residue 54 GLU Chi-restraints excluded: chain C residue 132 LYS Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 497 LEU Chi-restraints excluded: chain E residue 112 LYS Chi-restraints excluded: chain E residue 249 GLN Chi-restraints excluded: chain E residue 266 GLN Chi-restraints excluded: chain E residue 294 THR Chi-restraints excluded: chain E residue 340 ARG Chi-restraints excluded: chain E residue 415 ARG Chi-restraints excluded: chain E residue 440 THR Chi-restraints excluded: chain F residue 15 ARG Chi-restraints excluded: chain F residue 134 GLU Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 115 GLN Chi-restraints excluded: chain D residue 127 MET Chi-restraints excluded: chain D residue 132 GLU Chi-restraints excluded: chain D residue 292 MET Chi-restraints excluded: chain D residue 318 ASP Chi-restraints excluded: chain D residue 344 GLU Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain G residue 35 GLU Chi-restraints excluded: chain G residue 166 ARG Chi-restraints excluded: chain G residue 169 ILE Chi-restraints excluded: chain G residue 195 ASP Chi-restraints excluded: chain G residue 197 ASP Chi-restraints excluded: chain O residue 107 THR Chi-restraints excluded: chain 2 residue 41 SER Chi-restraints excluded: chain 4 residue 62 LEU Chi-restraints excluded: chain 6 residue 66 MET Chi-restraints excluded: chain 7 residue 72 LEU Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain I residue 29 THR Chi-restraints excluded: chain I residue 39 SER Chi-restraints excluded: chain N residue 39 ASN Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain N residue 115 MET Chi-restraints excluded: chain N residue 151 ILE Chi-restraints excluded: chain N residue 199 LEU Chi-restraints excluded: chain P residue 5 ILE Chi-restraints excluded: chain P residue 28 MET Chi-restraints excluded: chain P residue 30 LEU Chi-restraints excluded: chain S residue 30 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 293 optimal weight: 5.9990 chunk 189 optimal weight: 7.9990 chunk 283 optimal weight: 0.9980 chunk 143 optimal weight: 1.9990 chunk 93 optimal weight: 0.6980 chunk 92 optimal weight: 0.7980 chunk 302 optimal weight: 6.9990 chunk 323 optimal weight: 5.9990 chunk 234 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 chunk 373 optimal weight: 2.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 416 GLN A 492 GLN C 503 ASN E 445 GLN F 27 GLN F 458 GLN ** D 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 364 ASN ** G 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 182 ASN H 15 GLN N 4 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.1461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 39565 Z= 0.234 Angle : 0.541 11.047 53506 Z= 0.277 Chirality : 0.042 0.162 6216 Planarity : 0.004 0.048 6813 Dihedral : 7.706 148.752 5695 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.14 % Favored : 97.84 % Rotamer: Outliers : 2.03 % Allowed : 17.37 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.12 % 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: 0.79 (0.12), residues: 5000 helix: 1.34 (0.10), residues: 2685 sheet: -0.08 (0.21), residues: 567 loop : -0.43 (0.15), residues: 1748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP R 28 HIS 0.004 0.001 HIS B 476 PHE 0.021 0.001 PHE H 45 TYR 0.021 0.001 TYR S 31 ARG 0.013 0.000 ARG G 33 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10000 Ramachandran restraints generated. 5000 Oldfield, 0 Emsley, 5000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10000 Ramachandran restraints generated. 5000 Oldfield, 0 Emsley, 5000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 616 residues out of total 4096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 534 time to evaluate : 4.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7517 (mt-10) REVERT: A 381 ARG cc_start: 0.7338 (OUTLIER) cc_final: 0.6580 (mtp85) REVERT: B 54 GLU cc_start: 0.7317 (OUTLIER) cc_final: 0.6793 (tm-30) REVERT: E 112 LYS cc_start: 0.8163 (OUTLIER) cc_final: 0.7861 (mtpt) REVERT: E 249 GLN cc_start: 0.8055 (OUTLIER) cc_final: 0.7399 (mp10) REVERT: F 15 ARG cc_start: 0.7691 (OUTLIER) cc_final: 0.6928 (ptm-80) REVERT: F 252 GLN cc_start: 0.7809 (mm-40) cc_final: 0.7599 (mm-40) REVERT: D 132 GLU cc_start: 0.7599 (OUTLIER) cc_final: 0.7072 (mp0) REVERT: D 318 ASP cc_start: 0.8295 (OUTLIER) cc_final: 0.7882 (m-30) REVERT: D 470 VAL cc_start: 0.8019 (m) cc_final: 0.7783 (t) REVERT: G 166 ARG cc_start: 0.7483 (OUTLIER) cc_final: 0.6988 (mtp85) REVERT: G 195 ASP cc_start: 0.7509 (OUTLIER) cc_final: 0.7249 (m-30) REVERT: O 146 GLN cc_start: 0.7589 (mm-40) cc_final: 0.7079 (mm-40) REVERT: R 32 ARG cc_start: 0.7527 (mmp-170) cc_final: 0.6714 (mtp-110) outliers start: 82 outliers final: 51 residues processed: 580 average time/residue: 1.6569 time to fit residues: 1159.3789 Evaluate side-chains 588 residues out of total 4096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 527 time to evaluate : 4.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 71 LEU Chi-restraints excluded: chain L residue 74 GLU Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain M residue 107 SER Chi-restraints excluded: chain M residue 112 VAL Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 196 LYS Chi-restraints excluded: chain A residue 349 GLN Chi-restraints excluded: chain A residue 381 ARG Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain B residue 143 ARG Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain C residue 54 GLU Chi-restraints excluded: chain C residue 132 LYS Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 464 PHE Chi-restraints excluded: chain E residue 112 LYS Chi-restraints excluded: chain E residue 249 GLN Chi-restraints excluded: chain E residue 266 GLN Chi-restraints excluded: chain E residue 294 THR Chi-restraints excluded: chain E residue 340 ARG Chi-restraints excluded: chain E residue 440 THR Chi-restraints excluded: chain F residue 15 ARG Chi-restraints excluded: chain F residue 134 GLU Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 127 MET Chi-restraints excluded: chain D residue 132 GLU Chi-restraints excluded: chain D residue 292 MET Chi-restraints excluded: chain D residue 318 ASP Chi-restraints excluded: chain D residue 344 GLU Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain G residue 35 GLU Chi-restraints excluded: chain G residue 166 ARG Chi-restraints excluded: chain G residue 169 ILE Chi-restraints excluded: chain G residue 195 ASP Chi-restraints excluded: chain G residue 197 ASP Chi-restraints excluded: chain O residue 9 VAL Chi-restraints excluded: chain O residue 107 THR Chi-restraints excluded: chain O residue 166 ILE Chi-restraints excluded: chain 2 residue 41 SER Chi-restraints excluded: chain 7 residue 72 LEU Chi-restraints excluded: chain 7 residue 75 MET Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain I residue 29 THR Chi-restraints excluded: chain I residue 39 SER Chi-restraints excluded: chain N residue 39 ASN Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain N residue 151 ILE Chi-restraints excluded: chain N residue 199 LEU Chi-restraints excluded: chain N residue 213 VAL Chi-restraints excluded: chain P residue 6 ILE Chi-restraints excluded: chain P residue 28 MET Chi-restraints excluded: chain P residue 30 LEU Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain S residue 30 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 432 optimal weight: 0.8980 chunk 455 optimal weight: 0.2980 chunk 415 optimal weight: 3.9990 chunk 442 optimal weight: 4.9990 chunk 266 optimal weight: 0.6980 chunk 192 optimal weight: 5.9990 chunk 347 optimal weight: 3.9990 chunk 135 optimal weight: 0.0030 chunk 400 optimal weight: 5.9990 chunk 418 optimal weight: 0.8980 chunk 441 optimal weight: 3.9990 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 115 GLN A 492 GLN C 503 ASN ** E 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 445 GLN F 27 GLN F 458 GLN D 115 GLN D 201 HIS ** D 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 364 ASN ** G 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 182 ASN N 4 ASN R 44 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 39565 Z= 0.148 Angle : 0.513 11.618 53506 Z= 0.261 Chirality : 0.041 0.164 6216 Planarity : 0.004 0.054 6813 Dihedral : 7.332 147.702 5695 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.92 % Favored : 98.06 % Rotamer: Outliers : 1.67 % Allowed : 17.91 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.12 % 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: 1.03 (0.12), residues: 5000 helix: 1.47 (0.10), residues: 2724 sheet: 0.05 (0.22), residues: 543 loop : -0.27 (0.15), residues: 1733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP R 28 HIS 0.003 0.001 HIS B 476 PHE 0.015 0.001 PHE H 45 TYR 0.022 0.001 TYR B 446 ARG 0.014 0.000 ARG G 33 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10000 Ramachandran restraints generated. 5000 Oldfield, 0 Emsley, 5000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10000 Ramachandran restraints generated. 5000 Oldfield, 0 Emsley, 5000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 615 residues out of total 4096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 548 time to evaluate : 4.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 40 ARG cc_start: 0.7089 (OUTLIER) cc_final: 0.6790 (ttm170) REVERT: A 381 ARG cc_start: 0.7276 (OUTLIER) cc_final: 0.6498 (mtp85) REVERT: A 393 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.7505 (mt-10) REVERT: B 54 GLU cc_start: 0.7298 (OUTLIER) cc_final: 0.6777 (tm-30) REVERT: C 423 ARG cc_start: 0.7546 (mpt180) cc_final: 0.7334 (mtt90) REVERT: E 112 LYS cc_start: 0.8139 (OUTLIER) cc_final: 0.7888 (mtpt) REVERT: E 249 GLN cc_start: 0.7997 (OUTLIER) cc_final: 0.7410 (mp10) REVERT: D 132 GLU cc_start: 0.7552 (OUTLIER) cc_final: 0.7002 (mp0) REVERT: D 318 ASP cc_start: 0.8237 (OUTLIER) cc_final: 0.7819 (m-30) REVERT: D 470 VAL cc_start: 0.8020 (m) cc_final: 0.7775 (t) REVERT: G 33 ARG cc_start: 0.7079 (mtp-110) cc_final: 0.6863 (ttm110) REVERT: G 166 ARG cc_start: 0.7483 (OUTLIER) cc_final: 0.7004 (mtp85) REVERT: O 146 GLN cc_start: 0.7518 (mm-40) cc_final: 0.7313 (mm-40) REVERT: R 32 ARG cc_start: 0.7493 (mmp-170) cc_final: 0.6696 (mtp-110) outliers start: 67 outliers final: 30 residues processed: 587 average time/residue: 1.5996 time to fit residues: 1123.6169 Evaluate side-chains 561 residues out of total 4096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 522 time to evaluate : 4.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 74 GLU Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain M residue 40 ARG Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain M residue 107 SER Chi-restraints excluded: chain A residue 381 ARG Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 474 SER Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain C residue 54 GLU Chi-restraints excluded: chain C residue 132 LYS Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 464 PHE Chi-restraints excluded: chain E residue 112 LYS Chi-restraints excluded: chain E residue 249 GLN Chi-restraints excluded: chain E residue 294 THR Chi-restraints excluded: chain E residue 340 ARG Chi-restraints excluded: chain F residue 134 GLU Chi-restraints excluded: chain F residue 434 LEU Chi-restraints excluded: chain D residue 115 GLN Chi-restraints excluded: chain D residue 127 MET Chi-restraints excluded: chain D residue 132 GLU Chi-restraints excluded: chain D residue 318 ASP Chi-restraints excluded: chain D residue 344 GLU Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain G residue 35 GLU Chi-restraints excluded: chain G residue 166 ARG Chi-restraints excluded: chain G residue 169 ILE Chi-restraints excluded: chain O residue 107 THR Chi-restraints excluded: chain 2 residue 41 SER Chi-restraints excluded: chain 7 residue 72 LEU Chi-restraints excluded: chain 7 residue 75 MET Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain N residue 39 ASN Chi-restraints excluded: chain N residue 199 LEU Chi-restraints excluded: chain N residue 213 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 290 optimal weight: 0.1980 chunk 468 optimal weight: 2.9990 chunk 285 optimal weight: 4.9990 chunk 222 optimal weight: 3.9990 chunk 325 optimal weight: 0.9990 chunk 491 optimal weight: 9.9990 chunk 452 optimal weight: 2.9990 chunk 391 optimal weight: 0.6980 chunk 40 optimal weight: 9.9990 chunk 302 optimal weight: 6.9990 chunk 239 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 115 GLN A 475 GLN A 492 GLN B 475 GLN B 492 GLN C 503 ASN E 445 GLN F 27 GLN F 458 GLN ** D 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 260 ASN D 364 ASN ** G 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 182 ASN H 15 GLN N 4 ASN N 56 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 39565 Z= 0.223 Angle : 0.541 12.134 53506 Z= 0.275 Chirality : 0.042 0.179 6216 Planarity : 0.004 0.050 6813 Dihedral : 7.426 147.812 5695 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.98 % Favored : 98.00 % Rotamer: Outliers : 1.15 % Allowed : 18.72 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.12 % 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: 1.01 (0.12), residues: 5000 helix: 1.48 (0.10), residues: 2690 sheet: 0.02 (0.22), residues: 537 loop : -0.28 (0.15), residues: 1773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP R 28 HIS 0.004 0.001 HIS B 476 PHE 0.030 0.001 PHE B 464 TYR 0.024 0.001 TYR S 31 ARG 0.012 0.000 ARG G 33 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10000 Ramachandran restraints generated. 5000 Oldfield, 0 Emsley, 5000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10000 Ramachandran restraints generated. 5000 Oldfield, 0 Emsley, 5000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 585 residues out of total 4096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 539 time to evaluate : 4.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 40 ARG cc_start: 0.7136 (OUTLIER) cc_final: 0.6831 (ttm170) REVERT: A 381 ARG cc_start: 0.7331 (OUTLIER) cc_final: 0.6564 (mtp85) REVERT: A 393 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7487 (mt-10) REVERT: B 54 GLU cc_start: 0.7336 (OUTLIER) cc_final: 0.6820 (tm-30) REVERT: B 195 GLU cc_start: 0.6818 (tp30) cc_final: 0.6520 (tp30) REVERT: C 423 ARG cc_start: 0.7572 (mpt180) cc_final: 0.7365 (mtt90) REVERT: E 112 LYS cc_start: 0.8144 (OUTLIER) cc_final: 0.7859 (mtpt) REVERT: E 249 GLN cc_start: 0.8048 (OUTLIER) cc_final: 0.7417 (mp10) REVERT: D 132 GLU cc_start: 0.7561 (OUTLIER) cc_final: 0.7008 (mp0) REVERT: D 318 ASP cc_start: 0.8286 (OUTLIER) cc_final: 0.7872 (m-30) REVERT: D 470 VAL cc_start: 0.8021 (m) cc_final: 0.7779 (t) REVERT: G 166 ARG cc_start: 0.7505 (OUTLIER) cc_final: 0.7009 (mtp85) REVERT: O 146 GLN cc_start: 0.7570 (mm-40) cc_final: 0.7359 (mm-40) REVERT: R 32 ARG cc_start: 0.7514 (mmp-170) cc_final: 0.6718 (mtp-110) outliers start: 46 outliers final: 25 residues processed: 566 average time/residue: 1.6169 time to fit residues: 1100.6229 Evaluate side-chains 560 residues out of total 4096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 526 time to evaluate : 3.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 74 GLU Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain M residue 40 ARG Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain M residue 107 SER Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 381 ARG Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain C residue 54 GLU Chi-restraints excluded: chain C residue 132 LYS Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain E residue 112 LYS Chi-restraints excluded: chain E residue 249 GLN Chi-restraints excluded: chain E residue 294 THR Chi-restraints excluded: chain E residue 340 ARG Chi-restraints excluded: chain F residue 134 GLU Chi-restraints excluded: chain D residue 127 MET Chi-restraints excluded: chain D residue 132 GLU Chi-restraints excluded: chain D residue 318 ASP Chi-restraints excluded: chain D residue 344 GLU Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain G residue 35 GLU Chi-restraints excluded: chain G residue 166 ARG Chi-restraints excluded: chain G residue 169 ILE Chi-restraints excluded: chain O residue 107 THR Chi-restraints excluded: chain 2 residue 41 SER Chi-restraints excluded: chain 7 residue 72 LEU Chi-restraints excluded: chain 7 residue 75 MET Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain N residue 39 ASN Chi-restraints excluded: chain N residue 199 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 310 optimal weight: 4.9990 chunk 416 optimal weight: 2.9990 chunk 119 optimal weight: 4.9990 chunk 360 optimal weight: 9.9990 chunk 57 optimal weight: 0.8980 chunk 108 optimal weight: 4.9990 chunk 391 optimal weight: 0.7980 chunk 163 optimal weight: 0.0020 chunk 402 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 72 optimal weight: 5.9990 overall best weight: 1.3392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 475 GLN A 492 GLN B 475 GLN B 492 GLN C 503 ASN E 445 GLN F 27 GLN F 458 GLN ** D 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 364 ASN ** G 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 182 ASN N 4 ASN N 56 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.139185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.102622 restraints weight = 67995.399| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 2.24 r_work: 0.3135 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3027 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3027 r_free = 0.3027 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3027 r_free = 0.3027 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3027 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 39565 Z= 0.218 Angle : 0.542 13.000 53506 Z= 0.276 Chirality : 0.042 0.165 6216 Planarity : 0.004 0.053 6813 Dihedral : 7.435 147.490 5695 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.08 % Favored : 97.90 % Rotamer: Outliers : 1.37 % Allowed : 18.74 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.12 % 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: 1.01 (0.12), residues: 5000 helix: 1.43 (0.10), residues: 2722 sheet: 0.03 (0.22), residues: 554 loop : -0.20 (0.15), residues: 1724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP R 28 HIS 0.004 0.001 HIS B 476 PHE 0.019 0.001 PHE H 45 TYR 0.023 0.001 TYR S 31 ARG 0.013 0.000 ARG G 33 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19177.16 seconds wall clock time: 338 minutes 8.46 seconds (20288.46 seconds total)