Starting phenix.real_space_refine (version: dev) on Thu Feb 23 11:33:49 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yy0_11001/02_2023/6yy0_11001_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yy0_11001/02_2023/6yy0_11001.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yy0_11001/02_2023/6yy0_11001.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yy0_11001/02_2023/6yy0_11001.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yy0_11001/02_2023/6yy0_11001_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yy0_11001/02_2023/6yy0_11001_trim_updated.pdb" } resolution = 3.23 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "A GLU 13": "OE1" <-> "OE2" Residue "A ASP 20": "OD1" <-> "OD2" Residue "A GLU 26": "OE1" <-> "OE2" Residue "A ARG 45": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 50": "OE1" <-> "OE2" Residue "A GLU 67": "OE1" <-> "OE2" Residue "A PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 84": "OE1" <-> "OE2" Residue "A ASP 96": "OD1" <-> "OD2" Residue "A GLU 101": "OE1" <-> "OE2" Residue "A ASP 116": "OD1" <-> "OD2" Residue "A ASP 181": "OD1" <-> "OD2" Residue "A TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 222": "OD1" <-> "OD2" Residue "A TYR 228": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 255": "OE1" <-> "OE2" Residue "A TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 268": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 297": "OD1" <-> "OD2" Residue "A GLU 307": "OE1" <-> "OE2" Residue "A ASP 347": "OD1" <-> "OD2" Residue "A TYR 358": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 381": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 393": "OE1" <-> "OE2" Residue "A PHE 406": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 433": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 452": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 492": "OE1" <-> "OE2" Residue "A PHE 504": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 508": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 24": "OD1" <-> "OD2" Residue "B ASP 36": "OD1" <-> "OD2" Residue "B GLU 50": "OE1" <-> "OE2" Residue "B PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 79": "OD1" <-> "OD2" Residue "B GLU 102": "OE1" <-> "OE2" Residue "B ARG 143": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 195": "OE1" <-> "OE2" Residue "B ASP 224": "OD1" <-> "OD2" Residue "B TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 268": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 269": "OD1" <-> "OD2" Residue "B ASP 270": "OD1" <-> "OD2" Residue "B PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 307": "OE1" <-> "OE2" Residue "B TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 351": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 398": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 399": "OE1" <-> "OE2" Residue "B TYR 433": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 446": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 452": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 494": "OD1" <-> "OD2" Residue "B PHE 504": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 20": "OD1" <-> "OD2" Residue "C ASP 24": "OD1" <-> "OD2" Residue "C ASP 36": "OD1" <-> "OD2" Residue "C GLU 50": "OE1" <-> "OE2" Residue "C GLU 67": "OE1" <-> "OE2" Residue "C ASP 69": "OD1" <-> "OD2" Residue "C PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 86": "OD1" <-> "OD2" Residue "C GLU 101": "OE1" <-> "OE2" Residue "C GLU 165": "OE1" <-> "OE2" Residue "C ASP 170": "OD1" <-> "OD2" Residue "C PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 195": "OE1" <-> "OE2" Residue "C ARG 219": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ASP 222": "OD1" <-> "OD2" Residue "C ASP 224": "OD1" <-> "OD2" Residue "C ASP 238": "OD1" <-> "OD2" Residue "C TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 255": "OE1" <-> "OE2" Residue "C TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 259": "OD1" <-> "OD2" Residue "C ARG 291": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 314": "OD1" <-> "OD2" Residue "C PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 328": "OE1" <-> "OE2" Residue "C PHE 351": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 353": "OE1" <-> "OE2" Residue "C GLU 355": "OE1" <-> "OE2" Residue "C TYR 358": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 373": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 440": "OE1" <-> "OE2" Residue "C TYR 452": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 457": "OE1" <-> "OE2" Residue "C GLU 465": "OE1" <-> "OE2" Residue "C PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 484": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ASP 494": "OD1" <-> "OD2" Residue "D PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 30": "OD1" <-> "OD2" Residue "D GLU 31": "OE1" <-> "OE2" Residue "D GLU 52": "OE1" <-> "OE2" Residue "D GLU 93": "OE1" <-> "OE2" Residue "D GLU 123": "OE1" <-> "OE2" Residue "D TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 196": "OE1" <-> "OE2" Residue "D ASP 199": "OD1" <-> "OD2" Residue "D TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 203": "OE1" <-> "OE2" Residue "D TYR 223": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 245": "OE1" <-> "OE2" Residue "D TYR 246": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 247": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 265": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 298": "OE1" <-> "OE2" Residue "D ASP 320": "OD1" <-> "OD2" Residue "D GLU 345": "OE1" <-> "OE2" Residue "D ASP 353": "OD1" <-> "OD2" Residue "D ASP 356": "OD1" <-> "OD2" Residue "D GLU 370": "OE1" <-> "OE2" Residue "D TYR 385": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 390": "OD1" <-> "OD2" Residue "D GLU 402": "OE1" <-> "OE2" Residue "D ASP 404": "OD1" <-> "OD2" Residue "D PHE 428": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 445": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 454": "OD1" <-> "OD2" Residue "D PHE 461": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 468": "OE1" <-> "OE2" Residue "D ASP 475": "OD1" <-> "OD2" Residue "D GLU 479": "OE1" <-> "OE2" Residue "E PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 46": "OE1" <-> "OE2" Residue "E ASP 107": "OD1" <-> "OD2" Residue "E PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 129": "OE1" <-> "OE2" Residue "E ASP 145": "OD1" <-> "OD2" Residue "E PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 199": "OD1" <-> "OD2" Residue "E GLU 206": "OE1" <-> "OE2" Residue "E ASP 214": "OD1" <-> "OD2" Residue "E TYR 246": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 247": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 320": "OD1" <-> "OD2" Residue "E ASP 334": "OD1" <-> "OD2" Residue "E GLU 345": "OE1" <-> "OE2" Residue "E ASP 353": "OD1" <-> "OD2" Residue "E ASP 363": "OD1" <-> "OD2" Residue "E GLU 370": "OE1" <-> "OE2" Residue "E ASP 373": "OD1" <-> "OD2" Residue "E GLU 403": "OE1" <-> "OE2" Residue "E PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 426": "OE1" <-> "OE2" Residue "E GLU 440": "OE1" <-> "OE2" Residue "E PHE 445": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 461": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 475": "OD1" <-> "OD2" Residue "F GLU 59": "OE1" <-> "OE2" Residue "F ASP 68": "OD1" <-> "OD2" Residue "F GLU 108": "OE1" <-> "OE2" Residue "F PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 123": "OE1" <-> "OE2" Residue "F PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 129": "OE1" <-> "OE2" Residue "F GLU 133": "OE1" <-> "OE2" Residue "F TYR 150": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 192": "OE1" <-> "OE2" Residue "F ASP 199": "OD1" <-> "OD2" Residue "F GLU 203": "OE1" <-> "OE2" Residue "F GLU 206": "OE1" <-> "OE2" Residue "F GLU 228": "OE1" <-> "OE2" Residue "F PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 265": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 271": "OE1" <-> "OE2" Residue "F TYR 315": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 330": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 349": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 353": "OD1" <-> "OD2" Residue "F ASP 356": "OD1" <-> "OD2" Residue "F TYR 372": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 385": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 390": "OD1" <-> "OD2" Residue "F GLU 402": "OE1" <-> "OE2" Residue "F GLU 403": "OE1" <-> "OE2" Residue "F ASP 404": "OD1" <-> "OD2" Residue "F PHE 445": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 452": "OE1" <-> "OE2" Residue "F TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 461": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 475": "OD1" <-> "OD2" Residue "G GLU 37": "OE1" <-> "OE2" Residue "G TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ASP 56": "OD1" <-> "OD2" Residue "G ASP 74": "OD1" <-> "OD2" Residue "G ARG 75": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G GLU 92": "OE1" <-> "OE2" Residue "G ARG 118": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 147": "OE1" <-> "OE2" Residue "G PHE 155": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 157": "OE1" <-> "OE2" Residue "G TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 174": "OE1" <-> "OE2" Residue "G GLU 175": "OE1" <-> "OE2" Residue "G ASP 182": "OD1" <-> "OD2" Residue "G GLU 188": "OE1" <-> "OE2" Residue "G GLU 206": "OE1" <-> "OE2" Residue "G ASP 244": "OD1" <-> "OD2" Residue "G PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ASP 37": "OD1" <-> "OD2" Residue "H GLU 68": "OE1" <-> "OE2" Residue "H TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 95": "OE1" <-> "OE2" Residue "H GLU 113": "OE1" <-> "OE2" Residue "I TYR 3": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I ARG 5": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I TYR 11": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I ARG 13": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I TYR 14": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I GLU 29": "OE1" <-> "OE2" Residue "J ARG 25": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J GLU 29": "OE1" <-> "OE2" Residue "J TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S PHE 1": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S GLU 38": "OE1" <-> "OE2" Residue "S GLU 91": "OE1" <-> "OE2" Residue "S ARG 94": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "S PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S ARG 165": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "S GLU 188": "OE1" <-> "OE2" Residue "b TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b ASP 106": "OD1" <-> "OD2" Residue "b ASP 109": "OD1" <-> "OD2" Residue "b ARG 121": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b ARG 129": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b GLU 169": "OE1" <-> "OE2" Residue "b ASP 200": "OD1" <-> "OD2" Residue "d PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "d GLU 17": "OE1" <-> "OE2" Residue "d GLU 35": "OE1" <-> "OE2" Residue "d ASP 52": "OD1" <-> "OD2" Residue "d TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "d PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "d GLU 82": "OE1" <-> "OE2" Residue "d GLU 92": "OE1" <-> "OE2" Residue "d GLU 102": "OE1" <-> "OE2" Residue "d GLU 113": "OE1" <-> "OE2" Residue "d PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "d ASP 134": "OD1" <-> "OD2" Residue "d TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "d ARG 155": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "h GLU 17": "OE1" <-> "OE2" Residue "h TYR 18": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "h TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "h PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "h PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "h PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "h ASP 65": "OD1" <-> "OD2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 61162 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 7839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 508, 7839 Classifications: {'peptide': 508} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 489} Chain: "B" Number of atoms: 7393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 477, 7393 Classifications: {'peptide': 477} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 458} Chain breaks: 1 Chain: "C" Number of atoms: 7699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 498, 7699 Classifications: {'peptide': 498} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 479} Chain breaks: 1 Chain: "D" Number of atoms: 7163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 7163 Classifications: {'peptide': 469} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 444} Chain: "E" Number of atoms: 7132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 7132 Classifications: {'peptide': 467} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 442} Chain: "F" Number of atoms: 7131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 7131 Classifications: {'peptide': 467} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 442} Chain: "G" Number of atoms: 4300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 4300 Classifications: {'peptide': 272} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 266} Chain: "H" Number of atoms: 1957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1957 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 4, 'TRANS': 127} Chain: "I" Number of atoms: 764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 764 Classifications: {'peptide': 47} Modifications used: {'NH3': 1} Link IDs: {'TRANS': 46} Chain: "J" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 731 Classifications: {'peptide': 47} Link IDs: {'TRANS': 46} Chain: "S" Number of atoms: 3004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 3004 Classifications: {'peptide': 188} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 8, 'TRANS': 179} Chain: "b" Number of atoms: 2274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 2274 Classifications: {'peptide': 136} Link IDs: {'TRANS': 135} Chain: "d" Number of atoms: 2570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 2570 Classifications: {'peptide': 156} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 144} Chain: "h" Number of atoms: 1009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 1009 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 5, 'TRANS': 56} 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: "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: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 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: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Time building chain proxies: 21.19, per 1000 atoms: 0.35 Number of scatterers: 61162 At special positions: 0 Unit cell: (149.864, 135.192, 188.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 101 16.00 P 15 15.00 Mg 5 11.99 O 5858 8.00 N 5260 7.00 C 19097 6.00 H 30826 1.00 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: 42.20 Conformation dependent library (CDL) restraints added in 4.5 seconds 7788 Ramachandran restraints generated. 3894 Oldfield, 0 Emsley, 3894 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7212 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 145 helices and 24 sheets defined 44.0% alpha, 11.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.73 Creating SS restraints... Processing helix chain 'A' and resid 9 through 16 Processing helix chain 'A' and resid 101 through 103 No H-bonds generated for 'chain 'A' and resid 101 through 103' Processing helix chain 'A' and resid 151 through 156 Processing helix chain 'A' and resid 175 through 190 removed outlier: 3.879A pdb=" N GLN A 186 " --> pdb=" O THR A 182 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N LYS A 187 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N ARG A 188 " --> pdb=" O ILE A 184 " (cutoff:3.500A) removed outlier: 4.778A 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 240 through 259 Proline residue: A 247 - end of helix removed outlier: 3.997A pdb=" N PHE A 257 " --> pdb=" O MET A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 284 removed outlier: 3.552A pdb=" N VAL A 276 " --> pdb=" O SER A 272 " (cutoff:3.500A) 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 299 through 308 removed outlier: 3.738A pdb=" N LEU A 305 " --> pdb=" O LEU A 301 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N ARG A 308 " --> pdb=" O ARG A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 345 Processing helix chain 'A' and resid 355 through 358 No H-bonds generated for 'chain 'A' and resid 355 through 358' Processing helix chain 'A' and resid 375 through 378 Processing helix chain 'A' and resid 381 through 398 removed outlier: 4.087A pdb=" N THR A 389 " --> pdb=" O GLN A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 404 No H-bonds generated for 'chain 'A' and resid 402 through 404' Processing helix chain 'A' and resid 412 through 428 Processing helix chain 'A' and resid 438 through 449 Processing helix chain 'A' and resid 458 through 475 removed outlier: 4.163A pdb=" N THR A 462 " --> pdb=" O PRO A 458 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N LYS A 463 " --> pdb=" O SER A 459 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASN A 466 " --> pdb=" O THR A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 486 Processing helix chain 'A' and resid 491 through 505 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: 4.363A pdb=" N LYS B 187 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N ARG B 188 " --> pdb=" O ILE B 184 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N PHE B 189 " --> pdb=" O ASN B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 222 Processing helix chain 'B' and resid 240 through 259 Proline residue: B 247 - end of helix removed outlier: 4.178A pdb=" N PHE B 257 " --> pdb=" O MET B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 284 removed outlier: 3.531A pdb=" N ALA B 275 " --> pdb=" O LEU B 271 " (cutoff:3.500A) 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: 3.831A pdb=" N LEU B 305 " --> pdb=" O LEU B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 345 Processing helix chain 'B' and resid 354 through 359 Processing helix chain 'B' and resid 375 through 377 No H-bonds generated for 'chain 'B' and resid 375 through 377' Processing helix chain 'B' and resid 381 through 399 removed outlier: 3.903A pdb=" N VAL B 386 " --> pdb=" O ALA B 382 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N THR B 389 " --> pdb=" O GLN B 385 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU B 399 " --> pdb=" O ALA B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 428 Processing helix chain 'B' and resid 438 through 449 Processing helix chain 'B' and resid 461 through 474 removed outlier: 3.826A pdb=" N SER B 470 " --> pdb=" O ASN B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 486 Processing helix chain 'B' and resid 491 through 507 Processing helix chain 'C' and resid 7 through 17 removed outlier: 3.573A pdb=" N ARG C 15 " --> pdb=" O ILE C 11 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ILE C 16 " --> pdb=" O LEU C 12 " (cutoff:3.500A) 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 155 Processing helix chain 'C' and resid 175 through 191 removed outlier: 3.619A pdb=" N GLN C 186 " --> pdb=" O THR C 182 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N LYS C 187 " --> pdb=" O ILE C 183 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N ARG C 188 " --> pdb=" O ILE C 184 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N PHE C 189 " --> pdb=" O ASN C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 222 Processing helix chain 'C' and resid 240 through 260 removed outlier: 3.627A pdb=" N LEU C 245 " --> pdb=" O PRO C 241 " (cutoff:3.500A) Proline residue: C 247 - end of helix removed outlier: 3.814A pdb=" N PHE C 257 " --> pdb=" O MET C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 284 removed outlier: 3.701A pdb=" N VAL C 276 " --> pdb=" O SER C 272 " (cutoff:3.500A) 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 296 through 308 removed outlier: 4.252A pdb=" N PHE C 299 " --> pdb=" O GLY C 296 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N TYR C 300 " --> pdb=" O ASP C 297 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU C 301 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ARG C 304 " --> pdb=" O LEU C 301 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU C 306 " --> pdb=" O SER C 303 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N GLU C 307 " --> pdb=" O ARG C 304 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG C 308 " --> pdb=" O LEU C 305 " (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 381 through 399 removed outlier: 3.527A pdb=" N GLY C 388 " --> pdb=" O LYS C 384 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N THR C 389 " --> pdb=" O GLN C 385 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLU C 399 " --> pdb=" O ALA C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 412 through 427 Processing helix chain 'C' and resid 438 through 449 Processing helix chain 'C' and resid 453 through 455 No H-bonds generated for 'chain 'C' and resid 453 through 455' Processing helix chain 'C' and resid 461 through 475 removed outlier: 4.073A pdb=" N SER C 474 " --> pdb=" O SER C 470 " (cutoff:3.500A) Processing helix chain 'C' and resid 477 through 486 Processing helix chain 'C' and resid 491 through 506 removed outlier: 3.559A pdb=" N ALA C 506 " --> pdb=" O THR C 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 129 No H-bonds generated for 'chain 'D' and resid 127 through 129' Processing helix chain 'D' and resid 142 through 147 Processing helix chain 'D' and resid 166 through 176 Processing helix chain 'D' and resid 194 through 207 Processing helix chain 'D' and resid 230 through 249 removed outlier: 3.671A pdb=" N ARG D 235 " --> pdb=" O GLY D 231 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ALA D 237 " --> pdb=" O ARG D 233 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N LEU D 238 " --> pdb=" O ALA D 234 " (cutoff:3.500A) Processing helix chain 'D' and resid 263 through 270 Processing helix chain 'D' and resid 274 through 276 No H-bonds generated for 'chain 'D' and resid 274 through 276' Processing helix chain 'D' and resid 289 through 297 removed outlier: 3.704A pdb=" N MET D 296 " --> pdb=" O ASP D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 319 No H-bonds generated for 'chain 'D' and resid 317 through 319' Processing helix chain 'D' and resid 324 through 332 removed outlier: 4.372A pdb=" N ALA D 331 " --> pdb=" O ALA D 327 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N HIS D 332 " --> pdb=" O THR D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 341 through 344 No H-bonds generated for 'chain 'D' and resid 341 through 344' Processing helix chain 'D' and resid 369 through 392 removed outlier: 3.868A pdb=" N ASP D 390 " --> pdb=" O LYS D 386 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ILE D 391 " --> pdb=" O SER D 387 " (cutoff:3.500A) Processing helix chain 'D' and resid 397 through 399 No H-bonds generated for 'chain 'D' and resid 397 through 399' Processing helix chain 'D' and resid 404 through 417 Processing helix chain 'D' and resid 426 through 429 No H-bonds generated for 'chain 'D' and resid 426 through 429' Processing helix chain 'D' and resid 438 through 450 Processing helix chain 'D' and resid 458 through 461 Processing helix chain 'D' and resid 467 through 479 Processing helix chain 'E' and resid 92 through 94 No H-bonds generated for 'chain 'E' and resid 92 through 94' Processing helix chain 'E' and resid 142 through 147 Processing helix chain 'E' and resid 166 through 179 Processing helix chain 'E' and resid 194 through 207 Processing helix chain 'E' and resid 230 through 233 No H-bonds generated for 'chain 'E' and resid 230 through 233' Processing helix chain 'E' and resid 236 through 249 removed outlier: 3.768A pdb=" N PHE E 247 " --> pdb=" O VAL E 243 " (cutoff:3.500A) Processing helix chain 'E' and resid 262 through 276 Processing helix chain 'E' and resid 289 through 297 removed outlier: 3.967A pdb=" N MET E 296 " --> pdb=" O ASP E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 317 through 319 No H-bonds generated for 'chain 'E' and resid 317 through 319' Processing helix chain 'E' and resid 324 through 329 Processing helix chain 'E' and resid 341 through 344 No H-bonds generated for 'chain 'E' and resid 341 through 344' Processing helix chain 'E' and resid 364 through 367 No H-bonds generated for 'chain 'E' and resid 364 through 367' Processing helix chain 'E' and resid 369 through 395 removed outlier: 3.918A pdb=" N ASP E 390 " --> pdb=" O LYS E 386 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ILE E 391 " --> pdb=" O SER E 387 " (cutoff:3.500A) Processing helix chain 'E' and resid 397 through 399 No H-bonds generated for 'chain 'E' and resid 397 through 399' Processing helix chain 'E' and resid 402 through 418 removed outlier: 3.605A pdb=" N LEU E 406 " --> pdb=" O GLU E 402 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N THR E 407 " --> pdb=" O GLU E 403 " (cutoff:3.500A) Processing helix chain 'E' and resid 426 through 429 No H-bonds generated for 'chain 'E' and resid 426 through 429' Processing helix chain 'E' and resid 438 through 450 Processing helix chain 'E' and resid 458 through 461 Processing helix chain 'E' and resid 467 through 478 Processing helix chain 'F' and resid 92 through 94 No H-bonds generated for 'chain 'F' and resid 92 through 94' Processing helix chain 'F' and resid 142 through 146 Processing helix chain 'F' and resid 166 through 179 Processing helix chain 'F' and resid 194 through 207 Processing helix chain 'F' and resid 230 through 234 Processing helix chain 'F' and resid 237 through 249 removed outlier: 3.627A pdb=" N PHE F 247 " --> pdb=" O VAL F 243 " (cutoff:3.500A) Processing helix chain 'F' and resid 262 through 276 removed outlier: 3.981A pdb=" N GLN F 267 " --> pdb=" O ARG F 264 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA F 268 " --> pdb=" O PHE F 265 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N SER F 273 " --> pdb=" O SER F 270 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ALA F 274 " --> pdb=" O GLU F 271 " (cutoff:3.500A) Processing helix chain 'F' and resid 289 through 297 Processing helix chain 'F' and resid 317 through 319 No H-bonds generated for 'chain 'F' and resid 317 through 319' Processing helix chain 'F' and resid 324 through 332 removed outlier: 4.448A pdb=" N ALA F 331 " --> pdb=" O ALA F 327 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N HIS F 332 " --> pdb=" O THR F 328 " (cutoff:3.500A) Processing helix chain 'F' and resid 341 through 346 Processing helix chain 'F' and resid 370 through 394 removed outlier: 4.419A pdb=" N ASP F 390 " --> pdb=" O LYS F 386 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N ILE F 391 " --> pdb=" O SER F 387 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE F 394 " --> pdb=" O ASP F 390 " (cutoff:3.500A) Processing helix chain 'F' and resid 402 through 417 Processing helix chain 'F' and resid 426 through 429 No H-bonds generated for 'chain 'F' and resid 426 through 429' Processing helix chain 'F' and resid 438 through 450 Processing helix chain 'F' and resid 458 through 460 No H-bonds generated for 'chain 'F' and resid 458 through 460' Processing helix chain 'F' and resid 467 through 477 Processing helix chain 'G' and resid 3 through 54 Proline residue: G 40 - end of helix removed outlier: 4.516A pdb=" N LEU G 51 " --> pdb=" O GLY G 47 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N TYR G 52 " --> pdb=" O SER G 48 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLU G 53 " --> pdb=" O LEU G 49 " (cutoff:3.500A) Processing helix chain 'G' and resid 82 through 99 Processing helix chain 'G' and resid 110 through 115 Processing helix chain 'G' and resid 138 through 150 Processing helix chain 'G' and resid 181 through 185 Processing helix chain 'G' and resid 188 through 191 Processing helix chain 'G' and resid 200 through 270 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 106 through 119 Processing helix chain 'H' and resid 125 through 145 Processing helix chain 'I' and resid 3 through 6 No H-bonds generated for 'chain 'I' and resid 3 through 6' Processing helix chain 'I' and resid 11 through 23 Processing helix chain 'I' and resid 28 through 35 Processing helix chain 'J' and resid 15 through 18 No H-bonds generated for 'chain 'J' and resid 15 through 18' Processing helix chain 'J' and resid 21 through 52 removed outlier: 3.667A pdb=" N TYR J 33 " --> pdb=" O GLU J 29 " (cutoff:3.500A) Processing helix chain 'S' and resid 14 through 27 Processing helix chain 'S' and resid 32 through 45 removed outlier: 3.542A pdb=" N GLN S 44 " --> pdb=" O LEU S 40 " (cutoff:3.500A) Processing helix chain 'S' and resid 49 through 55 Processing helix chain 'S' and resid 62 through 76 Processing helix chain 'S' and resid 80 through 91 Processing helix chain 'S' and resid 98 through 112 removed outlier: 3.667A pdb=" N VAL S 111 " --> pdb=" O THR S 107 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N HIS S 112 " --> pdb=" O MET S 108 " (cutoff:3.500A) Processing helix chain 'S' and resid 128 through 141 Processing helix chain 'S' and resid 175 through 187 Processing helix chain 'b' and resid 79 through 186 removed outlier: 3.966A pdb=" N GLN b 88 " --> pdb=" O LYS b 84 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LYS b 89 " --> pdb=" O LEU b 85 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU b 93 " --> pdb=" O LYS b 89 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LYS b 102 " --> pdb=" O GLN b 98 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N LYS b 120 " --> pdb=" O ALA b 116 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ARG b 121 " --> pdb=" O LEU b 117 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N HIS b 122 " --> pdb=" O VAL b 118 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N TYR b 123 " --> pdb=" O GLN b 119 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N LEU b 124 " --> pdb=" O LYS b 120 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N PHE b 125 " --> pdb=" O ARG b 121 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLN b 183 " --> pdb=" O LYS b 179 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N SER b 186 " --> pdb=" O VAL b 182 " (cutoff:3.500A) Processing helix chain 'b' and resid 190 through 206 Processing helix chain 'd' and resid 15 through 17 No H-bonds generated for 'chain 'd' and resid 15 through 17' Processing helix chain 'd' and resid 24 through 43 removed outlier: 4.084A pdb=" N SER d 29 " --> pdb=" O ALA d 25 " (cutoff:3.500A) Processing helix chain 'd' and resid 53 through 59 Processing helix chain 'd' and resid 63 through 75 Processing helix chain 'd' and resid 87 through 98 Processing helix chain 'd' and resid 103 through 122 Processing helix chain 'd' and resid 132 through 138 Processing helix chain 'd' and resid 140 through 142 No H-bonds generated for 'chain 'd' and resid 140 through 142' Processing helix chain 'h' and resid 9 through 23 Processing helix chain 'h' and resid 32 through 50 removed outlier: 3.942A pdb=" N GLN h 36 " --> pdb=" O GLY h 32 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 28 through 30 removed outlier: 6.345A pdb=" N GLY A 72 " --> pdb=" O LEU A 64 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N HIS A 42 " --> pdb=" O VAL A 31 " (cutoff:3.500A) removed outlier: 5.471A 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: 3.898A pdb=" N ALA A 125 " --> pdb=" O VAL A 99 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 164 through 169 removed outlier: 8.254A pdb=" N GLU A 165 " --> pdb=" O LEU A 321 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ALA A 323 " --> pdb=" O GLU A 165 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N ILE A 167 " --> pdb=" O ALA A 323 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N GLY A 169 " --> pdb=" O PRO A 325 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N ILE A 327 " --> pdb=" O GLY A 169 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N TYR A 268 " --> pdb=" O LEU A 324 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N TYR A 200 " --> pdb=" O LEU A 265 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N ILE A 267 " --> pdb=" O TYR A 200 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N ILE A 202 " --> pdb=" O ILE A 267 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N ASP A 269 " --> pdb=" O ILE A 202 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N VAL A 204 " --> pdb=" O ASP A 269 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 28 through 30 removed outlier: 6.076A pdb=" N GLY B 72 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N HIS B 42 " --> pdb=" O VAL B 31 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N VAL B 31 " --> pdb=" O HIS B 42 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 96 through 99 removed outlier: 4.007A pdb=" N ALA B 125 " --> pdb=" O VAL B 99 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 167 through 169 Processing sheet with id= G, first strand: chain 'B' and resid 229 through 234 removed outlier: 8.815A pdb=" N ILE B 230 " --> pdb=" O LEU B 199 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N CYS B 201 " --> pdb=" O ILE B 230 " (cutoff:3.500A) removed outlier: 8.176A pdb=" N VAL B 232 " --> pdb=" O CYS B 201 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N TYR B 203 " --> pdb=" O VAL B 232 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N ALA B 234 " --> pdb=" O TYR B 203 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N ALA B 205 " --> pdb=" O ALA B 234 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N HIS B 263 " --> pdb=" O TYR B 200 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N ILE B 202 " --> pdb=" O HIS B 263 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N LEU B 265 " --> pdb=" O ILE B 202 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N VAL B 204 " --> pdb=" O LEU B 265 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N ILE B 267 " --> pdb=" O VAL B 204 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N ILE B 206 " --> pdb=" O ILE B 267 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ASP B 269 " --> pdb=" O ILE B 206 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N SER B 320 " --> pdb=" O ALA B 264 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N ILE B 266 " --> pdb=" O SER B 320 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N THR B 322 " --> pdb=" O ILE B 266 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N TYR B 268 " --> pdb=" O THR B 322 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'C' and resid 29 through 35 removed outlier: 6.641A pdb=" N ARG C 40 " --> pdb=" O LEU C 32 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ILE C 34 " --> pdb=" O ILE C 38 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ILE C 38 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N VAL C 74 " --> pdb=" O SER C 63 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N SER C 63 " --> pdb=" O VAL C 74 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 96 through 99 removed outlier: 4.263A pdb=" N ALA C 125 " --> pdb=" O VAL C 99 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 164 through 169 removed outlier: 8.284A pdb=" N GLU C 165 " --> pdb=" O LEU C 321 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N ALA C 323 " --> pdb=" O GLU C 165 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N ILE C 167 " --> pdb=" O ALA C 323 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N GLY C 169 " --> pdb=" O PRO C 325 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ILE C 327 " --> pdb=" O GLY C 169 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N TYR C 268 " --> pdb=" O LEU C 324 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N TYR C 200 " --> pdb=" O LEU C 265 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N ILE C 267 " --> pdb=" O TYR C 200 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N ILE C 202 " --> pdb=" O ILE C 267 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N ASP C 269 " --> pdb=" O ILE C 202 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N VAL C 204 " --> pdb=" O ASP C 269 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 14 through 16 removed outlier: 6.633A pdb=" N ARG D 63 " --> pdb=" O ALA D 54 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N HIS D 56 " --> pdb=" O THR D 61 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N THR D 61 " --> pdb=" O HIS D 56 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N GLN D 28 " --> pdb=" O ILE D 17 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N ILE D 17 " --> pdb=" O GLN D 28 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 87 through 90 removed outlier: 4.252A pdb=" N GLN D 116 " --> pdb=" O VAL D 90 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 155 through 160 removed outlier: 7.537A pdb=" N ILE D 156 " --> pdb=" O ILE D 308 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N SER D 310 " --> pdb=" O ILE D 156 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N LEU D 158 " --> pdb=" O SER D 310 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N GLN D 312 " --> pdb=" O LEU D 158 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N GLY D 160 " --> pdb=" O GLN D 312 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N ILE D 314 " --> pdb=" O GLY D 160 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N TYR D 184 " --> pdb=" O LEU D 256 " (cutoff:3.500A) removed outlier: 8.649A pdb=" N PHE D 258 " --> pdb=" O TYR D 184 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N VAL D 186 " --> pdb=" O PHE D 258 " (cutoff:3.500A) removed outlier: 8.259A pdb=" N ASP D 260 " --> pdb=" O VAL D 186 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ALA D 188 " --> pdb=" O ASP D 260 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ALA D 220 " --> pdb=" O PHE D 187 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N GLY D 189 " --> pdb=" O ALA D 220 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VAL D 222 " --> pdb=" O GLY D 189 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 14 through 16 removed outlier: 6.563A pdb=" N ARG E 63 " --> pdb=" O ALA E 54 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N HIS E 56 " --> pdb=" O THR E 61 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N THR E 61 " --> pdb=" O HIS E 56 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N GLN E 28 " --> pdb=" O ILE E 17 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N ILE E 17 " --> pdb=" O GLN E 28 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 87 through 89 Processing sheet with id= P, first strand: chain 'E' and resid 336 through 338 removed outlier: 6.368A pdb=" N GLY E 157 " --> pdb=" O THR E 337 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ALA E 220 " --> pdb=" O PHE E 187 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N GLY E 189 " --> pdb=" O ALA E 220 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL E 222 " --> pdb=" O GLY E 189 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N GLY E 191 " --> pdb=" O VAL E 222 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N GLY E 224 " --> pdb=" O GLY E 191 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'F' and resid 14 through 16 removed outlier: 4.482A pdb=" N LYS F 78 " --> pdb=" O GLN F 43 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ARG F 63 " --> pdb=" O ALA F 54 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N HIS F 56 " --> pdb=" O THR F 61 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N THR F 61 " --> pdb=" O HIS F 56 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA F 19 " --> pdb=" O ASP F 26 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N GLN F 28 " --> pdb=" O ILE F 17 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N ILE F 17 " --> pdb=" O GLN F 28 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'F' and resid 87 through 89 Processing sheet with id= S, first strand: chain 'F' and resid 156 through 160 removed outlier: 3.594A pdb=" N LEU F 257 " --> pdb=" O THR F 309 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'G' and resid 170 through 178 removed outlier: 6.475A pdb=" N LYS G 172 " --> pdb=" O PHE G 165 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N PHE G 165 " --> pdb=" O LYS G 172 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N GLU G 174 " --> pdb=" O ASN G 163 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N ASN G 163 " --> pdb=" O GLU G 174 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N LYS G 176 " --> pdb=" O ILE G 161 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N ILE G 161 " --> pdb=" O LYS G 176 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N ILE G 178 " --> pdb=" O SER G 159 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N SER G 159 " --> pdb=" O ILE G 178 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N ASN G 163 " --> pdb=" O VAL G 71 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N GLU G 102 " --> pdb=" O HIS G 66 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N ILE G 68 " --> pdb=" O GLU G 102 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N LYS G 104 " --> pdb=" O ILE G 68 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N GLY G 70 " --> pdb=" O LYS G 104 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ILE G 106 " --> pdb=" O GLY G 70 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N GLY G 107 " --> pdb=" O LEU G 125 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N THR G 127 " --> pdb=" O GLY G 107 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'H' and resid 45 through 47 removed outlier: 3.712A pdb=" N GLN H 35 " --> pdb=" O HIS H 66 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'H' and resid 54 through 57 Processing sheet with id= W, first strand: chain 'S' and resid 115 through 117 removed outlier: 7.445A pdb=" N VAL S 147 " --> pdb=" O VAL S 116 " (cutoff:3.500A) No H-bonds generated for sheet with id= W Processing sheet with id= X, first strand: chain 'S' and resid 152 through 154 removed outlier: 7.289A pdb=" N LYS S 153 " --> pdb=" O CYS S 118 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N VAL S 120 " --> pdb=" O LYS S 153 " (cutoff:3.500A) 1291 hydrogen bonds defined for protein. 3738 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: 21.30 Time building geometry restraints manager: 44.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 30815 1.03 - 1.22: 34 1.22 - 1.42: 12167 1.42 - 1.61: 18384 1.61 - 1.81: 191 Bond restraints: 61591 Sorted by residual: bond pdb=" C4 ATP A 600 " pdb=" C5 ATP A 600 " ideal model delta sigma weight residual 1.388 1.462 -0.074 1.00e-02 1.00e+04 5.53e+01 bond pdb=" C4 ATP C 600 " pdb=" C5 ATP C 600 " ideal model delta sigma weight residual 1.388 1.462 -0.074 1.00e-02 1.00e+04 5.47e+01 bond pdb=" C4 ATP B 600 " pdb=" C5 ATP B 600 " ideal model delta sigma weight residual 1.388 1.461 -0.073 1.00e-02 1.00e+04 5.37e+01 bond pdb=" C5 ATP A 600 " pdb=" C6 ATP A 600 " ideal model delta sigma weight residual 1.409 1.473 -0.064 1.00e-02 1.00e+04 4.12e+01 bond pdb=" C5 ATP C 600 " pdb=" C6 ATP C 600 " ideal model delta sigma weight residual 1.409 1.472 -0.063 1.00e-02 1.00e+04 3.96e+01 ... (remaining 61586 not shown) Histogram of bond angle deviations from ideal: 99.43 - 106.80: 944 106.80 - 114.18: 77261 114.18 - 121.56: 22746 121.56 - 128.93: 10742 128.93 - 136.31: 110 Bond angle restraints: 111803 Sorted by residual: angle pdb=" PB ATP A 600 " pdb=" O3B ATP A 600 " pdb=" PG ATP A 600 " ideal model delta sigma weight residual 139.87 115.95 23.92 1.00e+00 1.00e+00 5.72e+02 angle pdb=" PB ATP C 600 " pdb=" O3B ATP C 600 " pdb=" PG ATP C 600 " ideal model delta sigma weight residual 139.87 118.01 21.86 1.00e+00 1.00e+00 4.78e+02 angle pdb=" PA ATP B 600 " pdb=" O3A ATP B 600 " pdb=" PB ATP B 600 " ideal model delta sigma weight residual 136.83 117.99 18.84 1.00e+00 1.00e+00 3.55e+02 angle pdb=" PB ATP B 600 " pdb=" O3B ATP B 600 " pdb=" PG ATP B 600 " ideal model delta sigma weight residual 139.87 121.56 18.31 1.00e+00 1.00e+00 3.35e+02 angle pdb=" PA ATP C 600 " pdb=" O3A ATP C 600 " pdb=" PB ATP C 600 " ideal model delta sigma weight residual 136.83 121.45 15.38 1.00e+00 1.00e+00 2.37e+02 ... (remaining 111798 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.49: 23467 30.49 - 60.97: 724 60.97 - 91.46: 59 91.46 - 121.94: 0 121.94 - 152.43: 1 Dihedral angle restraints: 24251 sinusoidal: 11751 harmonic: 12500 Sorted by residual: dihedral pdb=" C5' ADP E 600 " pdb=" O5' ADP E 600 " pdb=" PA ADP E 600 " pdb=" O2A ADP E 600 " ideal model delta sinusoidal sigma weight residual 300.00 147.57 152.43 1 2.00e+01 2.50e-03 4.53e+01 dihedral pdb=" CA GLN H 132 " pdb=" C GLN H 132 " pdb=" N ILE H 133 " pdb=" CA ILE H 133 " ideal model delta harmonic sigma weight residual 180.00 152.80 27.20 0 5.00e+00 4.00e-02 2.96e+01 dihedral pdb=" CA GLN E 312 " pdb=" C GLN E 312 " pdb=" N ALA E 313 " pdb=" CA ALA E 313 " ideal model delta harmonic sigma weight residual 180.00 159.22 20.78 0 5.00e+00 4.00e-02 1.73e+01 ... (remaining 24248 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 3241 0.038 - 0.076: 1165 0.076 - 0.115: 313 0.115 - 0.153: 102 0.153 - 0.191: 3 Chirality restraints: 4824 Sorted by residual: chirality pdb=" CA GLN H 132 " pdb=" N GLN H 132 " pdb=" C GLN H 132 " pdb=" CB GLN H 132 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.12e-01 chirality pdb=" C2' ATP A 600 " pdb=" C1' ATP A 600 " pdb=" C3' ATP A 600 " pdb=" O2' ATP A 600 " both_signs ideal model delta sigma weight residual False -2.68 -2.51 -0.17 2.00e-01 2.50e+01 7.17e-01 chirality pdb=" CA GLU h 42 " pdb=" N GLU h 42 " pdb=" C GLU h 42 " pdb=" CB GLU h 42 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.31e-01 ... (remaining 4821 not shown) Planarity restraints: 9121 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU C 457 " 0.046 5.00e-02 4.00e+02 6.82e-02 7.44e+00 pdb=" N PRO C 458 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO C 458 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO C 458 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP h 5 " -0.044 5.00e-02 4.00e+02 6.71e-02 7.21e+00 pdb=" N PRO h 6 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO h 6 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO h 6 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN H 132 " 0.013 2.00e-02 2.50e+03 2.55e-02 6.49e+00 pdb=" C GLN H 132 " -0.044 2.00e-02 2.50e+03 pdb=" O GLN H 132 " 0.016 2.00e-02 2.50e+03 pdb=" N ILE H 133 " 0.015 2.00e-02 2.50e+03 ... (remaining 9118 not shown) Histogram of nonbonded interaction distances: 1.52 - 2.14: 2055 2.14 - 2.75: 120034 2.75 - 3.37: 176596 3.37 - 3.98: 232554 3.98 - 4.60: 368768 Nonbonded interactions: 900007 Sorted by model distance: nonbonded pdb="HE21 GLN A 163 " pdb=" OE1 GLU A 165 " model vdw 1.524 1.850 nonbonded pdb=" OE1 GLU E 370 " pdb=" H GLU E 370 " model vdw 1.536 1.850 nonbonded pdb=" OG SER G 72 " pdb=" H SER G 73 " model vdw 1.557 1.850 nonbonded pdb="HH12 ARG D 45 " pdb=" O GLU D 71 " model vdw 1.558 1.850 nonbonded pdb=" O GLN B 186 " pdb="HD22 ASN B 190 " model vdw 1.558 1.850 ... (remaining 900002 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 'A' and ((resid 23 and (name N or name CA or name C or name O or name CB \ or name CG1 or name CG2 or name HA or name HB or name HG11 or name HG12 or name \ HG13 or name HG21 or name HG22 or name HG23)) or resid 24 through 401 or (resid \ 411 and (name N or name CA or name C or name O or name CB or name CG or name OD1 \ or name OD2 or name HA or name HB2 or name HB3)) or resid 412 through 508 or re \ sid 600 through 601)) selection = chain 'B' selection = (chain 'C' and ((resid 23 and (name N or name CA or name C or name O or name CB \ or name CG1 or name CG2 or name HA or name HB or name HG11 or name HG12 or name \ HG13 or name HG21 or name HG22 or name HG23)) or resid 24 through 401 or (resid \ 411 and (name N or name CA or name C or name O or name CB or name CG or name OD1 \ or name OD2 or name HA or name HB2 or name HB3)) or resid 412 through 508 or re \ sid 600 through 601)) } ncs_group { reference = (chain 'D' and resid 13 through 479) selection = (chain 'E' and (resid 13 through 166 or (resid 167 and (name N or name CA or nam \ e C or name O or name CB or name OG1 or name CG2 or name H or name HA or name HB \ or name HG21 or name HG22 or name HG23)) or resid 168 through 479)) selection = (chain 'F' and resid 13 through 479) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 15 5.49 5 Mg 5 5.21 5 S 101 5.16 5 C 19097 2.51 5 N 5260 2.21 5 O 5858 1.98 5 H 30826 0.53 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.75 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: 6.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.700 Extract box with map and model: 28.050 Check model and map are aligned: 0.670 Process input model: 152.620 Find NCS groups from input model: 2.130 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Set scattering table: 0.430 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:2.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 193.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 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 0.074 30765 Z= 0.389 Angle : 0.678 23.922 41597 Z= 0.429 Chirality : 0.044 0.191 4824 Planarity : 0.004 0.068 5364 Dihedral : 15.269 152.429 11594 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.45 % Favored : 91.55 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.16 % 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: -0.84 (0.14), residues: 3894 helix: 0.50 (0.13), residues: 1732 sheet: -1.58 (0.21), residues: 605 loop : -1.23 (0.16), residues: 1557 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7788 Ramachandran restraints generated. 3894 Oldfield, 0 Emsley, 3894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7788 Ramachandran restraints generated. 3894 Oldfield, 0 Emsley, 3894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 176 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Evaluate side-chains 441 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 441 time to evaluate : 3.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 441 average time/residue: 0.9572 time to fit residues: 643.9199 Evaluate side-chains 398 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 398 time to evaluate : 3.786 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.7778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 324 optimal weight: 4.9990 chunk 291 optimal weight: 5.9990 chunk 161 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 chunk 196 optimal weight: 2.9990 chunk 155 optimal weight: 1.9990 chunk 300 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 183 optimal weight: 1.9990 chunk 224 optimal weight: 2.9990 chunk 348 optimal weight: 1.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 349 GLN F 227 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.0573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.051 30765 Z= 0.332 Angle : 0.566 8.538 41597 Z= 0.291 Chirality : 0.043 0.167 4824 Planarity : 0.004 0.060 5364 Dihedral : 5.561 133.831 4287 Min Nonbonded Distance : 1.640 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer Outliers : 0.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.14), residues: 3894 helix: 0.74 (0.13), residues: 1740 sheet: -1.46 (0.21), residues: 583 loop : -1.23 (0.16), residues: 1571 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7788 Ramachandran restraints generated. 3894 Oldfield, 0 Emsley, 3894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7788 Ramachandran restraints generated. 3894 Oldfield, 0 Emsley, 3894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 176 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Evaluate side-chains 416 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 406 time to evaluate : 3.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 10 residues processed: 409 average time/residue: 0.9615 time to fit residues: 596.8624 Evaluate side-chains 404 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 394 time to evaluate : 3.785 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 10 outliers final: 1 residues processed: 10 average time/residue: 0.5366 time to fit residues: 14.7891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 193 optimal weight: 0.7980 chunk 108 optimal weight: 3.9990 chunk 290 optimal weight: 4.9990 chunk 237 optimal weight: 1.9990 chunk 96 optimal weight: 6.9990 chunk 349 optimal weight: 3.9990 chunk 377 optimal weight: 5.9990 chunk 311 optimal weight: 3.9990 chunk 346 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 280 optimal weight: 0.9980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.0703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.046 30765 Z= 0.324 Angle : 0.547 8.681 41597 Z= 0.279 Chirality : 0.042 0.144 4824 Planarity : 0.003 0.049 5364 Dihedral : 5.323 109.434 4287 Min Nonbonded Distance : 1.665 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer Outliers : 0.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.16 % 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: -0.50 (0.14), residues: 3894 helix: 0.86 (0.13), residues: 1741 sheet: -1.41 (0.21), residues: 590 loop : -1.18 (0.16), residues: 1563 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7788 Ramachandran restraints generated. 3894 Oldfield, 0 Emsley, 3894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7788 Ramachandran restraints generated. 3894 Oldfield, 0 Emsley, 3894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 176 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Evaluate side-chains 414 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 408 time to evaluate : 4.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 409 average time/residue: 0.9629 time to fit residues: 601.4291 Evaluate side-chains 398 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 394 time to evaluate : 3.811 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 4 average time/residue: 0.5777 time to fit residues: 9.0071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 345 optimal weight: 3.9990 chunk 262 optimal weight: 0.8980 chunk 181 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 166 optimal weight: 2.9990 chunk 234 optimal weight: 0.8980 chunk 350 optimal weight: 8.9990 chunk 371 optimal weight: 9.9990 chunk 183 optimal weight: 2.9990 chunk 332 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.0826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.041 30765 Z= 0.321 Angle : 0.543 8.663 41597 Z= 0.277 Chirality : 0.042 0.141 4824 Planarity : 0.003 0.047 5364 Dihedral : 5.118 65.069 4287 Min Nonbonded Distance : 1.689 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer Outliers : 0.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.16 % 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: -0.42 (0.14), residues: 3894 helix: 0.96 (0.13), residues: 1743 sheet: -1.39 (0.21), residues: 585 loop : -1.17 (0.16), residues: 1566 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7788 Ramachandran restraints generated. 3894 Oldfield, 0 Emsley, 3894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7788 Ramachandran restraints generated. 3894 Oldfield, 0 Emsley, 3894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 176 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Evaluate side-chains 414 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 397 time to evaluate : 3.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 15 residues processed: 407 average time/residue: 0.9644 time to fit residues: 594.5267 Evaluate side-chains 405 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 390 time to evaluate : 3.814 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 2 residues processed: 15 average time/residue: 0.5827 time to fit residues: 20.9075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 309 optimal weight: 0.9990 chunk 210 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 276 optimal weight: 2.9990 chunk 153 optimal weight: 1.9990 chunk 316 optimal weight: 0.6980 chunk 256 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 189 optimal weight: 1.9990 chunk 333 optimal weight: 0.7980 chunk 93 optimal weight: 3.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 78 ASN F 116 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.0947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 30765 Z= 0.249 Angle : 0.519 8.321 41597 Z= 0.262 Chirality : 0.041 0.141 4824 Planarity : 0.003 0.047 5364 Dihedral : 4.912 47.473 4287 Min Nonbonded Distance : 1.731 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer Outliers : 0.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.16 % 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: -0.23 (0.14), residues: 3894 helix: 1.13 (0.13), residues: 1740 sheet: -1.35 (0.21), residues: 586 loop : -1.08 (0.16), residues: 1568 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7788 Ramachandran restraints generated. 3894 Oldfield, 0 Emsley, 3894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7788 Ramachandran restraints generated. 3894 Oldfield, 0 Emsley, 3894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 176 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Evaluate side-chains 415 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 404 time to evaluate : 3.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 9 residues processed: 410 average time/residue: 0.9411 time to fit residues: 589.5682 Evaluate side-chains 399 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 390 time to evaluate : 3.782 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 2 residues processed: 9 average time/residue: 0.5373 time to fit residues: 13.7727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 124 optimal weight: 0.9980 chunk 334 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 217 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 371 optimal weight: 1.9990 chunk 308 optimal weight: 1.9990 chunk 172 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 195 optimal weight: 0.8980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 477 GLN ** S 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.1032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 30765 Z= 0.262 Angle : 0.518 8.513 41597 Z= 0.262 Chirality : 0.041 0.140 4824 Planarity : 0.003 0.053 5364 Dihedral : 4.842 46.488 4287 Min Nonbonded Distance : 1.725 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer Outliers : 0.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.16 % 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: -0.15 (0.14), residues: 3894 helix: 1.22 (0.13), residues: 1742 sheet: -1.35 (0.21), residues: 589 loop : -1.04 (0.16), residues: 1563 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7788 Ramachandran restraints generated. 3894 Oldfield, 0 Emsley, 3894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7788 Ramachandran restraints generated. 3894 Oldfield, 0 Emsley, 3894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 176 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Evaluate side-chains 410 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 397 time to evaluate : 3.886 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 11 residues processed: 404 average time/residue: 0.9450 time to fit residues: 583.7411 Evaluate side-chains 400 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 389 time to evaluate : 3.784 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 2 residues processed: 11 average time/residue: 0.5313 time to fit residues: 15.8244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 358 optimal weight: 7.9990 chunk 41 optimal weight: 3.9990 chunk 211 optimal weight: 1.9990 chunk 271 optimal weight: 0.6980 chunk 210 optimal weight: 0.8980 chunk 312 optimal weight: 2.9990 chunk 207 optimal weight: 1.9990 chunk 370 optimal weight: 0.0470 chunk 231 optimal weight: 2.9990 chunk 225 optimal weight: 0.9980 chunk 170 optimal weight: 1.9990 overall best weight: 0.9280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 132 GLN S 34 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.1144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 30765 Z= 0.193 Angle : 0.501 9.145 41597 Z= 0.252 Chirality : 0.040 0.139 4824 Planarity : 0.003 0.058 5364 Dihedral : 4.672 46.905 4287 Min Nonbonded Distance : 1.758 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer Outliers : 0.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.16 % 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: 0.06 (0.14), residues: 3894 helix: 1.39 (0.13), residues: 1743 sheet: -1.27 (0.21), residues: 587 loop : -0.92 (0.16), residues: 1564 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7788 Ramachandran restraints generated. 3894 Oldfield, 0 Emsley, 3894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7788 Ramachandran restraints generated. 3894 Oldfield, 0 Emsley, 3894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 176 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Evaluate side-chains 416 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 410 time to evaluate : 3.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 5 residues processed: 413 average time/residue: 0.9697 time to fit residues: 613.5047 Evaluate side-chains 396 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 391 time to evaluate : 3.819 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 5 average time/residue: 0.5728 time to fit residues: 10.1132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 228 optimal weight: 1.9990 chunk 147 optimal weight: 2.9990 chunk 221 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 235 optimal weight: 0.5980 chunk 252 optimal weight: 2.9990 chunk 182 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 290 optimal weight: 4.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.1154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 30765 Z= 0.283 Angle : 0.523 9.229 41597 Z= 0.264 Chirality : 0.041 0.141 4824 Planarity : 0.003 0.063 5364 Dihedral : 4.754 46.878 4287 Min Nonbonded Distance : 1.715 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer Outliers : 0.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.16 % 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: -0.00 (0.14), residues: 3894 helix: 1.32 (0.13), residues: 1750 sheet: -1.30 (0.21), residues: 589 loop : -0.94 (0.16), residues: 1555 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7788 Ramachandran restraints generated. 3894 Oldfield, 0 Emsley, 3894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7788 Ramachandran restraints generated. 3894 Oldfield, 0 Emsley, 3894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 176 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Evaluate side-chains 404 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 397 time to evaluate : 3.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 403 average time/residue: 0.9405 time to fit residues: 576.5704 Evaluate side-chains 398 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 393 time to evaluate : 3.769 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 5 average time/residue: 0.5718 time to fit residues: 9.9131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 336 optimal weight: 0.9980 chunk 354 optimal weight: 7.9990 chunk 323 optimal weight: 5.9990 chunk 344 optimal weight: 7.9990 chunk 207 optimal weight: 1.9990 chunk 150 optimal weight: 2.9990 chunk 270 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 311 optimal weight: 2.9990 chunk 326 optimal weight: 0.9980 chunk 343 optimal weight: 0.8980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.1186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.032 30765 Z= 0.256 Angle : 0.517 9.265 41597 Z= 0.261 Chirality : 0.041 0.139 4824 Planarity : 0.003 0.067 5364 Dihedral : 4.728 47.169 4287 Min Nonbonded Distance : 1.732 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer Outliers : 0.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.16 % 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: 0.08 (0.14), residues: 3894 helix: 1.40 (0.13), residues: 1734 sheet: -1.26 (0.21), residues: 587 loop : -0.88 (0.16), residues: 1573 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7788 Ramachandran restraints generated. 3894 Oldfield, 0 Emsley, 3894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7788 Ramachandran restraints generated. 3894 Oldfield, 0 Emsley, 3894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 176 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Evaluate side-chains 402 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 395 time to evaluate : 4.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 6 residues processed: 399 average time/residue: 0.9772 time to fit residues: 599.4503 Evaluate side-chains 396 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 390 time to evaluate : 4.621 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 6 average time/residue: 0.7198 time to fit residues: 14.3478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 226 optimal weight: 0.6980 chunk 364 optimal weight: 3.9990 chunk 222 optimal weight: 0.9980 chunk 173 optimal weight: 0.5980 chunk 253 optimal weight: 1.9990 chunk 382 optimal weight: 8.9990 chunk 352 optimal weight: 0.7980 chunk 304 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 235 optimal weight: 1.9990 chunk 186 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.1263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 30765 Z= 0.206 Angle : 0.504 8.896 41597 Z= 0.253 Chirality : 0.040 0.139 4824 Planarity : 0.003 0.069 5364 Dihedral : 4.619 47.565 4287 Min Nonbonded Distance : 1.757 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer Outliers : 0.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.16 % 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: 0.22 (0.14), residues: 3894 helix: 1.52 (0.13), residues: 1733 sheet: -1.21 (0.21), residues: 587 loop : -0.81 (0.16), residues: 1574 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7788 Ramachandran restraints generated. 3894 Oldfield, 0 Emsley, 3894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7788 Ramachandran restraints generated. 3894 Oldfield, 0 Emsley, 3894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 176 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Evaluate side-chains 402 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 397 time to evaluate : 3.841 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 400 average time/residue: 0.9455 time to fit residues: 579.3170 Evaluate side-chains 390 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 386 time to evaluate : 3.817 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 4 average time/residue: 0.5769 time to fit residues: 9.1015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 241 optimal weight: 1.9990 chunk 324 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 280 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 305 optimal weight: 1.9990 chunk 127 optimal weight: 0.6980 chunk 313 optimal weight: 0.9990 chunk 38 optimal weight: 0.5980 chunk 56 optimal weight: 0.1980 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.129088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.096984 restraints weight = 117233.534| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 1.42 r_work: 0.2873 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.2759 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3486 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3486 r_free = 0.3486 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3486 r_free = 0.3486 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3486 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.025 30765 Z= 0.164 Angle : 0.490 8.599 41597 Z= 0.245 Chirality : 0.040 0.139 4824 Planarity : 0.003 0.069 5364 Dihedral : 4.456 47.748 4287 Min Nonbonded Distance : 1.781 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer Outliers : 0.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.14), residues: 3894 helix: 1.69 (0.13), residues: 1722 sheet: -1.13 (0.21), residues: 586 loop : -0.74 (0.16), residues: 1586 =============================================================================== Job complete usr+sys time: 11466.71 seconds wall clock time: 199 minutes 31.30 seconds (11971.30 seconds total)