Starting phenix.real_space_refine (version: dev) on Fri Apr 8 04:37:29 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5y5y_6811/04_2022/5y5y_6811_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5y5y_6811/04_2022/5y5y_6811.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5y5y_6811/04_2022/5y5y_6811.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5y5y_6811/04_2022/5y5y_6811.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5y5y_6811/04_2022/5y5y_6811_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5y5y_6811/04_2022/5y5y_6811_updated.pdb" } resolution = 4.7 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= 0.030 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A GLU 32": "OE1" <-> "OE2" Residue "A GLU 38": "OE1" <-> "OE2" Residue "A PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 53": "OE1" <-> "OE2" Residue "A GLU 74": "OE1" <-> "OE2" Residue "A ASP 85": "OD1" <-> "OD2" Residue "A GLU 96": "OE1" <-> "OE2" Residue "A TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 128": "OE1" <-> "OE2" Residue "A GLU 140": "OE1" <-> "OE2" Residue "A PHE 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 152": "OD1" <-> "OD2" Residue "A GLU 169": "OE1" <-> "OE2" Residue "A GLU 170": "OE1" <-> "OE2" Residue "A ASP 177": "OD1" <-> "OD2" Residue "A ASP 200": "OD1" <-> "OD2" Residue "A PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 213": "OD1" <-> "OD2" Residue "A PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 248": "OD1" <-> "OD2" Residue "A TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 257": "OE1" <-> "OE2" Residue "A GLU 261": "OE1" <-> "OE2" Residue "A ASP 264": "OD1" <-> "OD2" Residue "A GLU 268": "OE1" <-> "OE2" Residue "A GLU 271": "OE1" <-> "OE2" Residue "A ARG 284": "NH1" <-> "NH2" Residue "A GLU 311": "OE1" <-> "OE2" Residue "A ASP 315": "OD1" <-> "OD2" Residue "A PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 325": "OD1" <-> "OD2" Residue "A GLU 332": "OE1" <-> "OE2" Residue "A GLU 342": "OE1" <-> "OE2" Residue "A GLU 343": "OE1" <-> "OE2" Residue "A GLU 347": "OE1" <-> "OE2" Residue "A GLU 348": "OE1" <-> "OE2" Residue "A TYR 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 374": "OE1" <-> "OE2" Residue "A GLU 375": "OE1" <-> "OE2" Residue "A ASP 390": "OD1" <-> "OD2" Residue "A ASP 410": "OD1" <-> "OD2" Residue "A PHE 419": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 431": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 441": "OE1" <-> "OE2" Residue "A GLU 445": "OE1" <-> "OE2" Residue "A ASP 446": "OD1" <-> "OD2" Residue "A GLU 449": "OE1" <-> "OE2" Residue "A ASP 452": "OD1" <-> "OD2" Residue "A GLU 456": "OE1" <-> "OE2" Residue "A GLU 461": "OE1" <-> "OE2" Residue "A ASP 478": "OD1" <-> "OD2" Residue "A GLU 480": "OE1" <-> "OE2" Residue "A TYR 500": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 502": "OE1" <-> "OE2" Residue "A PHE 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 525": "OE1" <-> "OE2" Residue "A GLU 546": "OE1" <-> "OE2" Residue "A GLU 556": "OE1" <-> "OE2" Residue "A TYR 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 564": "OE1" <-> "OE2" Residue "B TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 32": "OE1" <-> "OE2" Residue "B GLU 33": "OE1" <-> "OE2" Residue "B ARG 41": "NH1" <-> "NH2" Residue "B PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 53": "OE1" <-> "OE2" Residue "B GLU 62": "OE1" <-> "OE2" Residue "B GLU 96": "OE1" <-> "OE2" Residue "B TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 114": "OE1" <-> "OE2" Residue "B GLU 128": "OE1" <-> "OE2" Residue "B PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 159": "OE1" <-> "OE2" Residue "B GLU 165": "OE1" <-> "OE2" Residue "B GLU 170": "OE1" <-> "OE2" Residue "B GLU 176": "OE1" <-> "OE2" Residue "B PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 213": "OD1" <-> "OD2" Residue "B PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 271": "OE1" <-> "OE2" Residue "B GLU 300": "OE1" <-> "OE2" Residue "B PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 332": "OE1" <-> "OE2" Residue "B GLU 347": "OE1" <-> "OE2" Residue "B TYR 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 363": "OE1" <-> "OE2" Residue "B GLU 374": "OE1" <-> "OE2" Residue "B GLU 375": "OE1" <-> "OE2" Residue "B ASP 390": "OD1" <-> "OD2" Residue "B GLU 393": "OE1" <-> "OE2" Residue "B TYR 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 431": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 436": "OD1" <-> "OD2" Residue "B TYR 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 445": "OE1" <-> "OE2" Residue "B GLU 449": "OE1" <-> "OE2" Residue "B ASP 452": "OD1" <-> "OD2" Residue "B GLU 466": "OE1" <-> "OE2" Residue "B ASP 474": "OD1" <-> "OD2" Residue "B GLU 492": "OE1" <-> "OE2" Residue "B ASP 493": "OD1" <-> "OD2" Residue "B TYR 500": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 525": "OE1" <-> "OE2" Residue "B GLU 527": "OE1" <-> "OE2" Residue "B GLU 538": "OE1" <-> "OE2" Residue "B GLU 546": "OE1" <-> "OE2" Residue "B GLU 556": "OE1" <-> "OE2" Residue "B GLU 557": "OE1" <-> "OE2" Residue "B PHE 559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 564": "OE1" <-> "OE2" Residue "B GLU 565": "OE1" <-> "OE2" Residue "B GLU 569": "OE1" <-> "OE2" Residue "B PHE 574": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 26": "OD1" <-> "OD2" Residue "C ASP 43": "OD1" <-> "OD2" Residue "C ASP 45": "OD1" <-> "OD2" Residue "C TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 53": "OE1" <-> "OE2" Residue "C GLU 74": "OE1" <-> "OE2" Residue "C ASP 85": "OD1" <-> "OD2" Residue "C GLU 92": "OE1" <-> "OE2" Residue "C TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 112": "OD1" <-> "OD2" Residue "C GLU 114": "OE1" <-> "OE2" Residue "C ASP 127": "OD1" <-> "OD2" Residue "C PHE 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 152": "OD1" <-> "OD2" Residue "C ASP 177": "OD1" <-> "OD2" Residue "C PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 213": "OD1" <-> "OD2" Residue "C ASP 248": "OD1" <-> "OD2" Residue "C GLU 257": "OE1" <-> "OE2" Residue "C GLU 261": "OE1" <-> "OE2" Residue "C GLU 268": "OE1" <-> "OE2" Residue "C GLU 271": "OE1" <-> "OE2" Residue "C GLU 300": "OE1" <-> "OE2" Residue "C PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 336": "OE1" <-> "OE2" Residue "C GLU 347": "OE1" <-> "OE2" Residue "C TYR 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 363": "OE1" <-> "OE2" Residue "C GLU 375": "OE1" <-> "OE2" Residue "C ASP 390": "OD1" <-> "OD2" Residue "C GLU 393": "OE1" <-> "OE2" Residue "C ASP 410": "OD1" <-> "OD2" Residue "C PHE 431": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 445": "OE1" <-> "OE2" Residue "C ASP 452": "OD1" <-> "OD2" Residue "C GLU 456": "OE1" <-> "OE2" Residue "C ASP 474": "OD1" <-> "OD2" Residue "C ASP 478": "OD1" <-> "OD2" Residue "C GLU 480": "OE1" <-> "OE2" Residue "C TYR 500": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 502": "OE1" <-> "OE2" Residue "C PHE 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 525": "OE1" <-> "OE2" Residue "C GLU 527": "OE1" <-> "OE2" Residue "C ASP 537": "OD1" <-> "OD2" Residue "C GLU 538": "OE1" <-> "OE2" Residue "C TYR 553": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 558": "OE1" <-> "OE2" Residue "C PHE 563": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 574": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 7": "OE1" <-> "OE2" Residue "D TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 26": "OD1" <-> "OD2" Residue "D ASP 37": "OD1" <-> "OD2" Residue "D GLU 52": "OE1" <-> "OE2" Residue "D TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 62": "OE1" <-> "OE2" Residue "D PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 128": "OE1" <-> "OE2" Residue "D ASP 176": "OD1" <-> "OD2" Residue "D GLU 182": "OE1" <-> "OE2" Residue "D GLU 184": "OE1" <-> "OE2" Residue "D PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 200": "OE1" <-> "OE2" Residue "D PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 207": "OE1" <-> "OE2" Residue "D PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 209": "OE1" <-> "OE2" Residue "D ASP 226": "OD1" <-> "OD2" Residue "D GLU 230": "OE1" <-> "OE2" Residue "D GLU 243": "OE1" <-> "OE2" Residue "D PHE 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 248": "OE1" <-> "OE2" Residue "D TYR 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 259": "OD1" <-> "OD2" Residue "D GLU 265": "OE1" <-> "OE2" Residue "D GLU 269": "OE1" <-> "OE2" Residue "D GLU 276": "OE1" <-> "OE2" Residue "D GLU 296": "OE1" <-> "OE2" Residue "D GLU 302": "OE1" <-> "OE2" Residue "D ASP 318": "OD1" <-> "OD2" Residue "D ASP 319": "OD1" <-> "OD2" Residue "D ASP 320": "OD1" <-> "OD2" Residue "D GLU 334": "OE1" <-> "OE2" Residue "D GLU 342": "OE1" <-> "OE2" Residue "D TYR 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 353": "OD1" <-> "OD2" Residue "D GLU 373": "OE1" <-> "OE2" Residue "D ASP 380": "OD1" <-> "OD2" Residue "D ASP 391": "OD1" <-> "OD2" Residue "D ASP 402": "OD1" <-> "OD2" Residue "D ASP 408": "OD1" <-> "OD2" Residue "D TYR 411": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 414": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 433": "OE1" <-> "OE2" Residue "D GLU 434": "OE1" <-> "OE2" Residue "D TYR 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 22": "OE1" <-> "OE2" Residue "E ASP 26": "OD1" <-> "OD2" Residue "E ASP 34": "OD1" <-> "OD2" Residue "E ASP 37": "OD1" <-> "OD2" Residue "E GLU 52": "OE1" <-> "OE2" Residue "E TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 78": "OD1" <-> "OD2" Residue "E ASP 101": "OD1" <-> "OD2" Residue "E GLU 128": "OE1" <-> "OE2" Residue "E PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 180": "OE1" <-> "OE2" Residue "E GLU 182": "OE1" <-> "OE2" Residue "E GLU 184": "OE1" <-> "OE2" Residue "E GLU 200": "OE1" <-> "OE2" Residue "E GLU 207": "OE1" <-> "OE2" Residue "E GLU 209": "OE1" <-> "OE2" Residue "E ASP 225": "OD1" <-> "OD2" Residue "E PHE 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 259": "OD1" <-> "OD2" Residue "E GLU 275": "OE1" <-> "OE2" Residue "E GLU 296": "OE1" <-> "OE2" Residue "E ASP 319": "OD1" <-> "OD2" Residue "E ASP 320": "OD1" <-> "OD2" Residue "E ASP 327": "OD1" <-> "OD2" Residue "E GLU 334": "OE1" <-> "OE2" Residue "E GLU 342": "OE1" <-> "OE2" Residue "E ASP 353": "OD1" <-> "OD2" Residue "E ASP 374": "OD1" <-> "OD2" Residue "E TYR 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 402": "OD1" <-> "OD2" Residue "E GLU 406": "OE1" <-> "OE2" Residue "E ASP 408": "OD1" <-> "OD2" Residue "E PHE 414": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 419": "OE1" <-> "OE2" Residue "E PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 433": "OE1" <-> "OE2" Residue "E TYR 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 463": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 7": "OE1" <-> "OE2" Residue "F TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 34": "OD1" <-> "OD2" Residue "F ASP 37": "OD1" <-> "OD2" Residue "F GLU 49": "OE1" <-> "OE2" Residue "F GLU 52": "OE1" <-> "OE2" Residue "F GLU 53": "OE1" <-> "OE2" Residue "F TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 62": "OE1" <-> "OE2" Residue "F ASP 67": "OD1" <-> "OD2" Residue "F ASP 78": "OD1" <-> "OD2" Residue "F PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 109": "OE1" <-> "OE2" Residue "F ASP 139": "OD1" <-> "OD2" Residue "F GLU 162": "OE1" <-> "OE2" Residue "F GLU 180": "OE1" <-> "OE2" Residue "F GLU 182": "OE1" <-> "OE2" Residue "F GLU 184": "OE1" <-> "OE2" Residue "F GLU 185": "OE1" <-> "OE2" Residue "F PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 209": "OE1" <-> "OE2" Residue "F PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 225": "OD1" <-> "OD2" Residue "F ASP 226": "OD1" <-> "OD2" Residue "F PHE 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 259": "OD1" <-> "OD2" Residue "F TYR 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 265": "OE1" <-> "OE2" Residue "F GLU 275": "OE1" <-> "OE2" Residue "F GLU 276": "OE1" <-> "OE2" Residue "F TYR 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 296": "OE1" <-> "OE2" Residue "F GLU 302": "OE1" <-> "OE2" Residue "F ASP 318": "OD1" <-> "OD2" Residue "F ASP 320": "OD1" <-> "OD2" Residue "F TYR 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 391": "OD1" <-> "OD2" Residue "F GLU 401": "OE1" <-> "OE2" Residue "F GLU 406": "OE1" <-> "OE2" Residue "F PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 433": "OE1" <-> "OE2" Residue "F GLU 450": "OE1" <-> "OE2" Residue "F TYR 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 14": "NH1" <-> "NH2" Residue "G ARG 15": "NH1" <-> "NH2" Residue "G ASP 26": "OD1" <-> "OD2" Residue "G ARG 32": "NH1" <-> "NH2" Residue "G ASP 33": "OD1" <-> "OD2" Residue "G GLU 38": "OE1" <-> "OE2" Residue "G PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 48": "OE1" <-> "OE2" Residue "G ARG 50": "NH1" <-> "NH2" Residue "G ASP 54": "OD1" <-> "OD2" Residue "G GLU 74": "OE1" <-> "OE2" Residue "G GLU 92": "OE1" <-> "OE2" Residue "G ASP 110": "OD1" <-> "OD2" Residue "G ARG 132": "NH1" <-> "NH2" Residue "G TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 135": "OE1" <-> "OE2" Residue "G GLU 144": "OE1" <-> "OE2" Residue "G ARG 146": "NH1" <-> "NH2" Residue "G GLU 152": "OE1" <-> "OE2" Residue "G GLU 153": "OE1" <-> "OE2" Residue "G GLU 165": "OE1" <-> "OE2" Residue "G ARG 173": "NH1" <-> "NH2" Residue "G GLU 187": "OE1" <-> "OE2" Residue "G ARG 188": "NH1" <-> "NH2" Residue "G GLU 189": "OE1" <-> "OE2" Residue "G ASP 190": "OD1" <-> "OD2" Residue "G ARG 193": "NH1" <-> "NH2" Residue "G ARG 196": "NH1" <-> "NH2" Residue "G GLU 202": "OE1" <-> "OE2" Residue "G ARG 204": "NH1" <-> "NH2" Residue "H GLU 8": "OE1" <-> "OE2" Residue "H GLU 19": "OE1" <-> "OE2" Residue "H GLU 28": "OE1" <-> "OE2" Residue "H GLU 38": "OE1" <-> "OE2" Residue "H ASP 48": "OD1" <-> "OD2" Residue "H ASP 54": "OD1" <-> "OD2" Residue "H GLU 56": "OE1" <-> "OE2" Residue "H ARG 61": "NH1" <-> "NH2" Residue "H ASP 67": "OD1" <-> "OD2" Residue "H PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 85": "OD1" <-> "OD2" Residue "H TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 91": "NH1" <-> "NH2" Residue "H GLU 92": "OE1" <-> "OE2" Residue "H PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 60": "OE1" <-> "OE2" Residue "I GLU 70": "OE1" <-> "OE2" Residue "I GLU 82": "OE1" <-> "OE2" Residue "I GLU 93": "OE1" <-> "OE2" Residue "I GLU 95": "OE1" <-> "OE2" Residue "I GLU 109": "OE1" <-> "OE2" Residue "I GLU 117": "OE1" <-> "OE2" Residue "J GLU 35": "OE1" <-> "OE2" Residue "J ARG 47": "NH1" <-> "NH2" Residue "J GLU 50": "OE1" <-> "OE2" Residue "J GLU 65": "OE1" <-> "OE2" Residue "J ARG 72": "NH1" <-> "NH2" Residue "J GLU 78": "OE1" <-> "OE2" Residue "J GLU 81": "OE1" <-> "OE2" Residue "J GLU 158": "OE1" <-> "OE2" Residue "J ASP 172": "OD1" <-> "OD2" Residue "K GLU 60": "OE1" <-> "OE2" Residue "K GLU 101": "OE1" <-> "OE2" Residue "K GLU 117": "OE1" <-> "OE2" Residue "L GLU 35": "OE1" <-> "OE2" Residue "L ARG 47": "NH1" <-> "NH2" Residue "L GLU 50": "OE1" <-> "OE2" Residue "L ARG 72": "NH1" <-> "NH2" Residue "L GLU 78": "OE1" <-> "OE2" Residue "L GLU 81": "OE1" <-> "OE2" Residue "L GLU 92": "OE1" <-> "OE2" Residue "L GLU 145": "OE1" <-> "OE2" Residue "M TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 22": "OE1" <-> "OE2" Residue "M PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 27": "OE1" <-> "OE2" Residue "M GLU 42": "OE1" <-> "OE2" Residue "M GLU 48": "OE1" <-> "OE2" Residue "M ASP 56": "OD1" <-> "OD2" Residue "M GLU 79": "OE1" <-> "OE2" Residue "M ASP 92": "OD1" <-> "OD2" Residue "M GLU 111": "OE1" <-> "OE2" Residue "M GLU 122": "OE1" <-> "OE2" Residue "M GLU 165": "OE1" <-> "OE2" Residue "M GLU 174": "OE1" <-> "OE2" Residue "M ASP 175": "OD1" <-> "OD2" Residue "M ASP 190": "OD1" <-> "OD2" Residue "M GLU 195": "OE1" <-> "OE2" Residue "M PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 226": "OD1" <-> "OD2" Residue "M PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 237": "OD1" <-> "OD2" Residue "M GLU 262": "OE1" <-> "OE2" Residue "M ASP 279": "OD1" <-> "OD2" Residue "M GLU 296": "OE1" <-> "OE2" Residue "M GLU 318": "OE1" <-> "OE2" Residue "M GLU 319": "OE1" <-> "OE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 32159 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 4472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 577, 4472 Classifications: {'peptide': 577} Link IDs: {'PTRANS': 34, 'TRANS': 541, 'PCIS': 1} Chain: "B" Number of atoms: 4472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 577, 4472 Classifications: {'peptide': 577} Link IDs: {'PTRANS': 34, 'TRANS': 541, 'PCIS': 1} Chain: "C" Number of atoms: 4472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 577, 4472 Classifications: {'peptide': 577} Link IDs: {'PTRANS': 34, 'TRANS': 541, 'PCIS': 1} Chain: "D" Number of atoms: 3596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3596 Classifications: {'peptide': 459} Link IDs: {'PTRANS': 25, 'TRANS': 432, 'PCIS': 1} Chain: "E" Number of atoms: 3596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3596 Classifications: {'peptide': 459} Link IDs: {'PTRANS': 25, 'TRANS': 432, 'PCIS': 1} Chain: "F" Number of atoms: 3596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3596 Classifications: {'peptide': 459} Link IDs: {'PTRANS': 25, 'TRANS': 432, 'PCIS': 1} Chain: "G" Number of atoms: 1642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1642 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 9, 'TRANS': 200} Chain: "H" Number of atoms: 758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 758 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 5, 'TRANS': 94} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "I" Number of atoms: 451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 451 Classifications: {'peptide': 61} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 1, 'TRANS': 59} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "J" Number of atoms: 1043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1043 Classifications: {'peptide': 152} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 7, 'TRANS': 144} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 138 Unresolved non-hydrogen angles: 166 Unresolved non-hydrogen dihedrals: 109 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 9, 'ARG:plan': 5, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 74 Chain: "K" Number of atoms: 451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 451 Classifications: {'peptide': 61} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 1, 'TRANS': 59} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "L" Number of atoms: 1043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1043 Classifications: {'peptide': 152} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 7, 'TRANS': 144} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 138 Unresolved non-hydrogen angles: 166 Unresolved non-hydrogen dihedrals: 109 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 9, 'ARG:plan': 5, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 74 Chain: "M" Number of atoms: 2513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2513 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 12, 'TRANS': 307} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 17.47, per 1000 atoms: 0.54 Number of scatterers: 32159 At special positions: 0 Unit cell: (147, 148.4, 205.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 105 16.00 P 4 15.00 O 6043 8.00 N 5636 7.00 C 20371 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS M 267 " - pdb=" SG CYS M 322 " distance=2.04 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: 13.91 Conformation dependent library (CDL) restraints added in 5.1 seconds 8268 Ramachandran restraints generated. 4134 Oldfield, 0 Emsley, 4134 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7624 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 142 helices and 32 sheets defined 41.1% alpha, 7.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.04 Creating SS restraints... Processing helix chain 'A' and resid 91 through 97 Processing helix chain 'A' and resid 210 through 212 No H-bonds generated for 'chain 'A' and resid 210 through 212' Processing helix chain 'A' and resid 236 through 238 No H-bonds generated for 'chain 'A' and resid 236 through 238' Processing helix chain 'A' and resid 241 through 243 No H-bonds generated for 'chain 'A' and resid 241 through 243' Processing helix chain 'A' and resid 259 through 263 Processing helix chain 'A' and resid 269 through 271 No H-bonds generated for 'chain 'A' and resid 269 through 271' Processing helix chain 'A' and resid 281 through 283 No H-bonds generated for 'chain 'A' and resid 281 through 283' Processing helix chain 'A' and resid 298 through 316 removed outlier: 4.733A pdb=" N ILE A 303 " --> pdb=" O ARG A 299 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N TYR A 304 " --> pdb=" O GLU A 300 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N VAL A 305 " --> pdb=" O ALA A 301 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLY A 306 " --> pdb=" O SER A 302 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR A 308 " --> pdb=" O TYR A 304 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG A 314 " --> pdb=" O ALA A 310 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLN A 316 " --> pdb=" O TYR A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 341 removed outlier: 3.586A pdb=" N ARG A 335 " --> pdb=" O GLU A 332 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N SER A 339 " --> pdb=" O GLU A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 349 No H-bonds generated for 'chain 'A' and resid 347 through 349' Processing helix chain 'A' and resid 356 through 362 removed outlier: 4.046A pdb=" N ALA A 360 " --> pdb=" O ALA A 356 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N PHE A 361 " --> pdb=" O ARG A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 399 removed outlier: 4.159A pdb=" N THR A 399 " --> pdb=" O VAL A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 416 removed outlier: 4.236A pdb=" N ARG A 416 " --> pdb=" O SER A 412 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 412 through 416' Processing helix chain 'A' and resid 436 through 442 Processing helix chain 'A' and resid 447 through 471 removed outlier: 3.946A pdb=" N ILE A 454 " --> pdb=" O LEU A 450 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ARG A 460 " --> pdb=" O GLU A 456 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N ALA A 462 " --> pdb=" O LEU A 458 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N GLY A 463 " --> pdb=" O GLN A 459 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LEU A 464 " --> pdb=" O ARG A 460 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ILE A 467 " --> pdb=" O GLY A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 493 removed outlier: 3.612A pdb=" N VAL A 483 " --> pdb=" O ALA A 479 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE A 484 " --> pdb=" O GLU A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 532 removed outlier: 3.575A pdb=" N LYS A 517 " --> pdb=" O TYR A 513 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N MET A 518 " --> pdb=" O GLY A 514 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE A 519 " --> pdb=" O ILE A 515 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N LEU A 520 " --> pdb=" O MET A 516 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LYS A 531 " --> pdb=" O GLU A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 540 Processing helix chain 'A' and resid 543 through 553 removed outlier: 3.756A pdb=" N ARG A 547 " --> pdb=" O PRO A 543 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N ARG A 552 " --> pdb=" O ILE A 548 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N TYR A 553 " --> pdb=" O GLY A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 575 Proline residue: A 560 - end of helix removed outlier: 3.532A pdb=" N LYS A 568 " --> pdb=" O GLU A 564 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N GLN A 571 " --> pdb=" O MET A 567 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLY A 572 " --> pdb=" O LYS A 568 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N PHE A 574 " --> pdb=" O ILE A 570 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LYS A 575 " --> pdb=" O GLN A 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 97 removed outlier: 3.964A pdb=" N LYS B 97 " --> pdb=" O ARG B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 216 removed outlier: 3.733A pdb=" N LEU B 215 " --> pdb=" O ILE B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 244 removed outlier: 3.971A pdb=" N GLN B 238 " --> pdb=" O LYS B 234 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA B 242 " --> pdb=" O GLN B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 271 removed outlier: 4.297A pdb=" N VAL B 265 " --> pdb=" O MET B 262 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N PHE B 269 " --> pdb=" O LEU B 266 " (cutoff:3.500A) Proline residue: B 270 - end of helix Processing helix chain 'B' and resid 281 through 284 Processing helix chain 'B' and resid 296 through 316 removed outlier: 4.679A pdb=" N ILE B 303 " --> pdb=" O ARG B 299 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N TYR B 304 " --> pdb=" O GLU B 300 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLY B 306 " --> pdb=" O SER B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 340 removed outlier: 4.393A pdb=" N GLU B 332 " --> pdb=" O SER B 328 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ALA B 333 " --> pdb=" O ARG B 329 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU B 334 " --> pdb=" O TRP B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 360 No H-bonds generated for 'chain 'B' and resid 357 through 360' Processing helix chain 'B' and resid 394 through 402 removed outlier: 3.881A pdb=" N ARG B 401 " --> pdb=" O GLN B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 415 No H-bonds generated for 'chain 'B' and resid 412 through 415' Processing helix chain 'B' and resid 424 through 426 No H-bonds generated for 'chain 'B' and resid 424 through 426' Processing helix chain 'B' and resid 430 through 442 removed outlier: 4.237A pdb=" N SER B 433 " --> pdb=" O LEU B 430 " (cutoff:3.500A) Proline residue: B 437 - end of helix Processing helix chain 'B' and resid 447 through 465 removed outlier: 3.650A pdb=" N ARG B 451 " --> pdb=" O TYR B 447 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU B 456 " --> pdb=" O ASP B 452 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N LEU B 457 " --> pdb=" O ALA B 453 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N LEU B 458 " --> pdb=" O ILE B 454 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLN B 459 " --> pdb=" O SER B 455 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLY B 463 " --> pdb=" O GLN B 459 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N LEU B 464 " --> pdb=" O ARG B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 492 removed outlier: 3.763A pdb=" N ILE B 484 " --> pdb=" O GLU B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 521 removed outlier: 4.080A pdb=" N GLY B 514 " --> pdb=" O LYS B 510 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 530 removed outlier: 3.573A pdb=" N ALA B 528 " --> pdb=" O LYS B 524 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE B 530 " --> pdb=" O ALA B 526 " (cutoff:3.500A) Processing helix chain 'B' and resid 539 through 541 No H-bonds generated for 'chain 'B' and resid 539 through 541' Processing helix chain 'B' and resid 544 through 549 removed outlier: 3.581A pdb=" N ILE B 548 " --> pdb=" O VAL B 544 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 573 removed outlier: 3.559A pdb=" N ALA B 566 " --> pdb=" O TYR B 562 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N LYS B 568 " --> pdb=" O GLU B 564 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLU B 569 " --> pdb=" O GLU B 565 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ILE B 570 " --> pdb=" O ALA B 566 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLN B 571 " --> pdb=" O MET B 567 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLY B 572 " --> pdb=" O LYS B 568 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 97 Processing helix chain 'C' and resid 210 through 214 Processing helix chain 'C' and resid 233 through 243 removed outlier: 3.605A pdb=" N THR C 237 " --> pdb=" O LYS C 234 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N GLN C 238 " --> pdb=" O THR C 235 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS C 243 " --> pdb=" O SER C 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 271 removed outlier: 5.350A pdb=" N VAL C 265 " --> pdb=" O GLU C 261 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N PHE C 269 " --> pdb=" O VAL C 265 " (cutoff:3.500A) Proline residue: C 270 - end of helix Processing helix chain 'C' and resid 281 through 284 Processing helix chain 'C' and resid 296 through 316 removed outlier: 3.820A pdb=" N ARG C 299 " --> pdb=" O VAL C 296 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE C 303 " --> pdb=" O GLU C 300 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N VAL C 307 " --> pdb=" O TYR C 304 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLU C 311 " --> pdb=" O THR C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 341 removed outlier: 4.192A pdb=" N SER C 339 " --> pdb=" O ARG C 335 " (cutoff:3.500A) Processing helix chain 'C' and resid 354 through 363 removed outlier: 4.336A pdb=" N ALA C 360 " --> pdb=" O ALA C 356 " (cutoff:3.500A) Processing helix chain 'C' and resid 394 through 397 No H-bonds generated for 'chain 'C' and resid 394 through 397' Processing helix chain 'C' and resid 411 through 416 removed outlier: 3.822A pdb=" N PHE C 415 " --> pdb=" O ALA C 411 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ARG C 416 " --> pdb=" O SER C 412 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 411 through 416' Processing helix chain 'C' and resid 436 through 442 removed outlier: 3.751A pdb=" N GLU C 441 " --> pdb=" O PRO C 437 " (cutoff:3.500A) Processing helix chain 'C' and resid 452 through 470 removed outlier: 3.934A pdb=" N LEU C 457 " --> pdb=" O ALA C 453 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA C 462 " --> pdb=" O LEU C 458 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLY C 463 " --> pdb=" O GLN C 459 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU C 464 " --> pdb=" O ARG C 460 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLU C 466 " --> pdb=" O ALA C 462 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N ILE C 467 " --> pdb=" O GLY C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 478 through 492 removed outlier: 4.079A pdb=" N LEU C 482 " --> pdb=" O ASP C 478 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N VAL C 483 " --> pdb=" O ALA C 479 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE C 484 " --> pdb=" O GLU C 480 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLU C 485 " --> pdb=" O ARG C 481 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE C 489 " --> pdb=" O GLU C 485 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ARG C 491 " --> pdb=" O GLY C 487 " (cutoff:3.500A) Processing helix chain 'C' and resid 509 through 532 removed outlier: 3.562A pdb=" N MET C 518 " --> pdb=" O GLY C 514 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE C 519 " --> pdb=" O ILE C 515 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU C 520 " --> pdb=" O MET C 516 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LYS C 524 " --> pdb=" O LEU C 520 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LYS C 531 " --> pdb=" O GLU C 527 " (cutoff:3.500A) Processing helix chain 'C' and resid 536 through 539 removed outlier: 3.518A pdb=" N ILE C 539 " --> pdb=" O ILE C 536 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 536 through 539' Processing helix chain 'C' and resid 544 through 550 removed outlier: 3.956A pdb=" N ARG C 550 " --> pdb=" O GLU C 546 " (cutoff:3.500A) Processing helix chain 'C' and resid 556 through 575 Proline residue: C 560 - end of helix removed outlier: 3.658A pdb=" N PHE C 563 " --> pdb=" O PRO C 560 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N GLU C 564 " --> pdb=" O ALA C 561 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLU C 565 " --> pdb=" O TYR C 562 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA C 566 " --> pdb=" O PHE C 563 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLY C 572 " --> pdb=" O GLU C 569 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ALA C 573 " --> pdb=" O ILE C 570 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N PHE C 574 " --> pdb=" O GLN C 571 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 140 No H-bonds generated for 'chain 'D' and resid 137 through 140' Processing helix chain 'D' and resid 160 through 170 removed outlier: 3.811A pdb=" N ILE D 167 " --> pdb=" O ILE D 163 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 184 No H-bonds generated for 'chain 'D' and resid 182 through 184' Processing helix chain 'D' and resid 200 through 211 removed outlier: 3.860A pdb=" N ILE D 205 " --> pdb=" O LEU D 201 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N THR D 211 " --> pdb=" O GLU D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 214 through 216 No H-bonds generated for 'chain 'D' and resid 214 through 216' Processing helix chain 'D' and resid 228 through 249 removed outlier: 3.882A pdb=" N ILE D 232 " --> pdb=" O THR D 228 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU D 233 " --> pdb=" O ILE D 229 " (cutoff:3.500A) Proline residue: D 235 - end of helix removed outlier: 3.657A pdb=" N ALA D 238 " --> pdb=" O THR D 234 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N TYR D 244 " --> pdb=" O THR D 240 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU D 245 " --> pdb=" O VAL D 241 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA D 246 " --> pdb=" O ALA D 242 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLU D 248 " --> pdb=" O TYR D 244 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 274 removed outlier: 3.810A pdb=" N GLU D 269 " --> pdb=" O GLU D 265 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE D 270 " --> pdb=" O ALA D 266 " (cutoff:3.500A) Processing helix chain 'D' and resid 285 through 294 removed outlier: 4.259A pdb=" N TYR D 288 " --> pdb=" O GLY D 285 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N THR D 289 " --> pdb=" O TYR D 286 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N THR D 293 " --> pdb=" O ASP D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 332 removed outlier: 4.217A pdb=" N THR D 329 " --> pdb=" O ILE D 325 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N TYR D 331 " --> pdb=" O ASP D 327 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ILE D 332 " --> pdb=" O LEU D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 341 through 346 Processing helix chain 'D' and resid 374 through 399 removed outlier: 4.461A pdb=" N LEU D 382 " --> pdb=" O SER D 379 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N TYR D 383 " --> pdb=" O ASP D 380 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ALA D 385 " --> pdb=" O LEU D 382 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ALA D 387 " --> pdb=" O SER D 384 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASP D 391 " --> pdb=" O ASN D 388 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ARG D 393 " --> pdb=" O VAL D 390 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N VAL D 396 " --> pdb=" O ARG D 393 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE D 399 " --> pdb=" O VAL D 396 " (cutoff:3.500A) Processing helix chain 'D' and resid 406 through 420 removed outlier: 3.592A pdb=" N TYR D 411 " --> pdb=" O ASN D 407 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU D 412 " --> pdb=" O ASP D 408 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLN D 413 " --> pdb=" O ARG D 409 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ALA D 415 " --> pdb=" O TYR D 411 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASP D 416 " --> pdb=" O LEU D 412 " (cutoff:3.500A) Processing helix chain 'D' and resid 432 through 445 removed outlier: 3.602A pdb=" N LEU D 436 " --> pdb=" O ILE D 432 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE D 438 " --> pdb=" O GLU D 434 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA D 439 " --> pdb=" O SER D 435 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N MET D 445 " --> pdb=" O ALA D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 456 through 461 Processing helix chain 'E' and resid 136 through 141 Processing helix chain 'E' and resid 161 through 169 removed outlier: 3.697A pdb=" N ARG E 169 " --> pdb=" O ALA E 165 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 184 No H-bonds generated for 'chain 'E' and resid 182 through 184' Processing helix chain 'E' and resid 198 through 209 removed outlier: 3.930A pdb=" N PHE E 204 " --> pdb=" O GLU E 200 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ILE E 205 " --> pdb=" O LEU E 201 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N GLN E 206 " --> pdb=" O SER E 202 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLU E 207 " --> pdb=" O TYR E 203 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N PHE E 208 " --> pdb=" O PHE E 204 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLU E 209 " --> pdb=" O ILE E 205 " (cutoff:3.500A) Processing helix chain 'E' and resid 228 through 247 removed outlier: 3.875A pdb=" N THR E 234 " --> pdb=" O ARG E 231 " (cutoff:3.500A) Proline residue: E 235 - end of helix removed outlier: 4.047A pdb=" N LEU E 239 " --> pdb=" O ARG E 236 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE E 247 " --> pdb=" O TYR E 244 " (cutoff:3.500A) Processing helix chain 'E' and resid 261 through 273 removed outlier: 4.080A pdb=" N GLU E 269 " --> pdb=" O GLU E 265 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ILE E 270 " --> pdb=" O ALA E 266 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLY E 271 " --> pdb=" O LEU E 267 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ALA E 273 " --> pdb=" O GLU E 269 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 295 removed outlier: 3.502A pdb=" N THR E 293 " --> pdb=" O THR E 289 " (cutoff:3.500A) Processing helix chain 'E' and resid 324 through 332 removed outlier: 4.633A pdb=" N THR E 329 " --> pdb=" O ILE E 325 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY E 330 " --> pdb=" O PRO E 326 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TYR E 331 " --> pdb=" O ASP E 327 " (cutoff:3.500A) Processing helix chain 'E' and resid 375 through 399 removed outlier: 5.042A pdb=" N ASP E 380 " --> pdb=" O LYS E 376 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLN E 381 " --> pdb=" O GLN E 377 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N TYR E 383 " --> pdb=" O SER E 379 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ASN E 388 " --> pdb=" O SER E 384 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLY E 389 " --> pdb=" O ALA E 385 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ILE E 392 " --> pdb=" O ASN E 388 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ALA E 397 " --> pdb=" O ARG E 393 " (cutoff:3.500A) Processing helix chain 'E' and resid 409 through 422 removed outlier: 3.504A pdb=" N PHE E 422 " --> pdb=" O PHE E 418 " (cutoff:3.500A) Processing helix chain 'E' and resid 432 through 445 removed outlier: 3.564A pdb=" N ALA E 441 " --> pdb=" O GLN E 437 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N MET E 445 " --> pdb=" O ALA E 441 " (cutoff:3.500A) Processing helix chain 'E' and resid 456 through 461 removed outlier: 3.633A pdb=" N GLY E 460 " --> pdb=" O ASP E 457 " (cutoff:3.500A) Processing helix chain 'F' and resid 138 through 141 No H-bonds generated for 'chain 'F' and resid 138 through 141' Processing helix chain 'F' and resid 160 through 170 removed outlier: 4.192A pdb=" N ALA F 164 " --> pdb=" O ALA F 160 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLN F 166 " --> pdb=" O GLU F 162 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ILE F 167 " --> pdb=" O ILE F 163 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA F 168 " --> pdb=" O ALA F 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 199 through 209 removed outlier: 3.863A pdb=" N GLU F 207 " --> pdb=" O TYR F 203 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE F 208 " --> pdb=" O PHE F 204 " (cutoff:3.500A) Processing helix chain 'F' and resid 228 through 231 removed outlier: 3.777A pdb=" N ARG F 231 " --> pdb=" O THR F 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 228 through 231' Processing helix chain 'F' and resid 234 through 247 removed outlier: 3.678A pdb=" N TYR F 244 " --> pdb=" O THR F 240 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU F 245 " --> pdb=" O VAL F 241 " (cutoff:3.500A) Processing helix chain 'F' and resid 261 through 274 removed outlier: 3.760A pdb=" N GLU F 265 " --> pdb=" O THR F 261 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ILE F 270 " --> pdb=" O ALA F 266 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLY F 271 " --> pdb=" O LEU F 267 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA F 272 " --> pdb=" O ARG F 268 " (cutoff:3.500A) Processing helix chain 'F' and resid 285 through 290 removed outlier: 4.120A pdb=" N TYR F 288 " --> pdb=" O GLY F 285 " (cutoff:3.500A) Processing helix chain 'F' and resid 293 through 296 No H-bonds generated for 'chain 'F' and resid 293 through 296' Processing helix chain 'F' and resid 324 through 332 removed outlier: 3.910A pdb=" N TYR F 331 " --> pdb=" O ASP F 327 " (cutoff:3.500A) Processing helix chain 'F' and resid 341 through 346 removed outlier: 5.429A pdb=" N LYS F 346 " --> pdb=" O GLU F 342 " (cutoff:3.500A) Processing helix chain 'F' and resid 376 through 399 removed outlier: 3.916A pdb=" N ASP F 380 " --> pdb=" O LYS F 376 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE F 392 " --> pdb=" O ASN F 388 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ARG F 393 " --> pdb=" O GLY F 389 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS F 394 " --> pdb=" O VAL F 390 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU F 395 " --> pdb=" O ASP F 391 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ALA F 397 " --> pdb=" O ARG F 393 " (cutoff:3.500A) Processing helix chain 'F' and resid 408 through 420 removed outlier: 4.098A pdb=" N ASP F 416 " --> pdb=" O LEU F 412 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ALA F 417 " --> pdb=" O GLN F 413 " (cutoff:3.500A) Processing helix chain 'F' and resid 432 through 445 removed outlier: 3.656A pdb=" N LEU F 436 " --> pdb=" O ILE F 432 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE F 438 " --> pdb=" O GLU F 434 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N MET F 445 " --> pdb=" O ALA F 441 " (cutoff:3.500A) Processing helix chain 'F' and resid 456 through 461 removed outlier: 3.518A pdb=" N GLY F 460 " --> pdb=" O LYS F 456 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 45 removed outlier: 3.576A pdb=" N LEU G 18 " --> pdb=" O ARG G 14 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N LYS G 29 " --> pdb=" O VAL G 25 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N LYS G 30 " --> pdb=" O ASP G 26 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N ALA G 34 " --> pdb=" O LYS G 30 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N LEU G 35 " --> pdb=" O LYS G 31 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N PHE G 40 " --> pdb=" O VAL G 36 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLY G 41 " --> pdb=" O ALA G 37 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU G 42 " --> pdb=" O GLU G 38 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N GLU G 45 " --> pdb=" O GLY G 41 " (cutoff:3.500A) Processing helix chain 'G' and resid 48 through 63 removed outlier: 3.613A pdb=" N ALA G 52 " --> pdb=" O GLU G 48 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLN G 55 " --> pdb=" O LYS G 51 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ALA G 56 " --> pdb=" O ALA G 52 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA G 60 " --> pdb=" O ALA G 56 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 78 Processing helix chain 'G' and resid 121 through 132 removed outlier: 3.666A pdb=" N PHE G 130 " --> pdb=" O ALA G 126 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ARG G 131 " --> pdb=" O SER G 127 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ARG G 132 " --> pdb=" O ARG G 128 " (cutoff:3.500A) Processing helix chain 'G' and resid 134 through 166 removed outlier: 3.675A pdb=" N ARG G 139 " --> pdb=" O GLU G 135 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL G 140 " --> pdb=" O ALA G 136 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N THR G 145 " --> pdb=" O ALA G 141 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ARG G 146 " --> pdb=" O ASN G 142 " (cutoff:3.500A) Processing helix chain 'G' and resid 168 through 207 removed outlier: 3.598A pdb=" N ARG G 177 " --> pdb=" O ARG G 173 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N PHE G 178 " --> pdb=" O ALA G 174 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N GLU G 187 " --> pdb=" O LEU G 183 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG G 188 " --> pdb=" O GLU G 184 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLU G 189 " --> pdb=" O GLN G 185 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASP G 190 " --> pdb=" O ARG G 186 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG G 196 " --> pdb=" O PHE G 192 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE G 197 " --> pdb=" O ARG G 193 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS G 198 " --> pdb=" O LEU G 194 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLU G 207 " --> pdb=" O ALA G 203 " (cutoff:3.500A) Processing helix chain 'H' and resid 7 through 15 removed outlier: 6.120A pdb=" N GLY H 12 " --> pdb=" O GLU H 8 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N PHE H 13 " --> pdb=" O THR H 9 " (cutoff:3.500A) Processing helix chain 'H' and resid 30 through 39 removed outlier: 3.671A pdb=" N THR H 35 " --> pdb=" O SER H 31 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ARG H 39 " --> pdb=" O THR H 35 " (cutoff:3.500A) Processing helix chain 'H' and resid 56 through 63 removed outlier: 4.338A pdb=" N MET H 63 " --> pdb=" O GLU H 60 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 93 removed outlier: 3.800A pdb=" N GLU H 87 " --> pdb=" O GLY H 83 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N MET H 90 " --> pdb=" O VAL H 86 " (cutoff:3.500A) Processing helix chain 'I' and resid 61 through 105 removed outlier: 3.638A pdb=" N LYS I 65 " --> pdb=" O GLU I 61 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA I 86 " --> pdb=" O GLU I 82 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ALA I 94 " --> pdb=" O GLU I 90 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ALA I 105 " --> pdb=" O GLU I 101 " (cutoff:3.500A) Processing helix chain 'I' and resid 109 through 119 removed outlier: 3.801A pdb=" N VAL I 118 " --> pdb=" O VAL I 114 " (cutoff:3.500A) Processing helix chain 'J' and resid 36 through 91 removed outlier: 4.110A pdb=" N ALA J 40 " --> pdb=" O GLU J 36 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU J 41 " --> pdb=" O LYS J 37 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN J 43 " --> pdb=" O LYS J 39 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ALA J 44 " --> pdb=" O ALA J 40 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLU J 46 " --> pdb=" O LEU J 42 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU J 49 " --> pdb=" O ARG J 45 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N ALA J 56 " --> pdb=" O GLN J 52 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA J 60 " --> pdb=" O ALA J 56 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY J 77 " --> pdb=" O THR J 73 " (cutoff:3.500A) Processing helix chain 'J' and resid 100 through 114 removed outlier: 3.932A pdb=" N ARG J 105 " --> pdb=" O PRO J 101 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N LYS J 106 " --> pdb=" O GLU J 102 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LEU J 107 " --> pdb=" O VAL J 103 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA J 114 " --> pdb=" O GLU J 110 " (cutoff:3.500A) Processing helix chain 'J' and resid 127 through 130 No H-bonds generated for 'chain 'J' and resid 127 through 130' Processing helix chain 'J' and resid 133 through 136 No H-bonds generated for 'chain 'J' and resid 133 through 136' Processing helix chain 'J' and resid 167 through 178 removed outlier: 3.593A pdb=" N ARG J 173 " --> pdb=" O ALA J 169 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ASP J 176 " --> pdb=" O ASP J 172 " (cutoff:3.500A) Processing helix chain 'J' and resid 181 through 186 Processing helix chain 'K' and resid 62 through 103 removed outlier: 3.935A pdb=" N GLU K 77 " --> pdb=" O TYR K 73 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LYS K 97 " --> pdb=" O GLU K 93 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG K 100 " --> pdb=" O ALA K 96 " (cutoff:3.500A) Processing helix chain 'K' and resid 108 through 119 Processing helix chain 'L' and resid 36 through 92 removed outlier: 4.368A pdb=" N ALA L 44 " --> pdb=" O ALA L 40 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLU L 46 " --> pdb=" O LEU L 42 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU L 49 " --> pdb=" O ARG L 45 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA L 55 " --> pdb=" O ALA L 51 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N ALA L 56 " --> pdb=" O GLN L 52 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ALA L 63 " --> pdb=" O ARG L 59 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU L 82 " --> pdb=" O GLU L 78 " (cutoff:3.500A) Processing helix chain 'L' and resid 100 through 114 removed outlier: 4.209A pdb=" N ARG L 105 " --> pdb=" O PRO L 101 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N LYS L 106 " --> pdb=" O GLU L 102 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU L 107 " --> pdb=" O VAL L 103 " (cutoff:3.500A) Processing helix chain 'L' and resid 128 through 130 No H-bonds generated for 'chain 'L' and resid 128 through 130' Processing helix chain 'L' and resid 133 through 136 No H-bonds generated for 'chain 'L' and resid 133 through 136' Processing helix chain 'L' and resid 167 through 178 removed outlier: 3.670A pdb=" N MET L 171 " --> pdb=" O LEU L 167 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG L 173 " --> pdb=" O ALA L 169 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N ASP L 176 " --> pdb=" O ASP L 172 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ALA L 177 " --> pdb=" O ARG L 173 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N MET L 178 " --> pdb=" O ALA L 174 " (cutoff:3.500A) Processing helix chain 'L' and resid 181 through 186 Processing helix chain 'M' and resid 6 through 18 removed outlier: 3.626A pdb=" N ALA M 10 " --> pdb=" O ALA M 6 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLY M 17 " --> pdb=" O ARG M 13 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N THR M 18 " --> pdb=" O VAL M 14 " (cutoff:3.500A) Processing helix chain 'M' and resid 22 through 28 Processing helix chain 'M' and resid 33 through 41 Processing helix chain 'M' and resid 44 through 48 removed outlier: 3.708A pdb=" N GLY M 47 " --> pdb=" O VAL M 44 " (cutoff:3.500A) Processing helix chain 'M' and resid 54 through 68 removed outlier: 3.548A pdb=" N LYS M 67 " --> pdb=" O ARG M 63 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU M 68 " --> pdb=" O THR M 64 " (cutoff:3.500A) Processing helix chain 'M' and resid 72 through 74 No H-bonds generated for 'chain 'M' and resid 72 through 74' Processing helix chain 'M' and resid 79 through 105 removed outlier: 3.500A pdb=" N LEU M 87 " --> pdb=" O ALA M 83 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASN M 91 " --> pdb=" O LEU M 87 " (cutoff:3.500A) Processing helix chain 'M' and resid 109 through 111 No H-bonds generated for 'chain 'M' and resid 109 through 111' Processing helix chain 'M' and resid 121 through 128 Processing helix chain 'M' and resid 133 through 141 Processing helix chain 'M' and resid 146 through 155 Processing helix chain 'M' and resid 161 through 183 removed outlier: 3.754A pdb=" N LYS M 178 " --> pdb=" O GLU M 174 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLY M 182 " --> pdb=" O LYS M 178 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N LEU M 183 " --> pdb=" O ALA M 179 " (cutoff:3.500A) Processing helix chain 'M' and resid 186 through 206 Processing helix chain 'M' and resid 214 through 216 No H-bonds generated for 'chain 'M' and resid 214 through 216' Processing helix chain 'M' and resid 227 through 234 Processing helix chain 'M' and resid 238 through 242 Processing helix chain 'M' and resid 250 through 252 No H-bonds generated for 'chain 'M' and resid 250 through 252' Processing helix chain 'M' and resid 258 through 275 removed outlier: 3.695A pdb=" N LYS M 275 " --> pdb=" O LYS M 271 " (cutoff:3.500A) Processing helix chain 'M' and resid 284 through 309 Processing helix chain 'M' and resid 313 through 320 removed outlier: 4.125A pdb=" N GLU M 317 " --> pdb=" O ALA M 314 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N GLU M 318 " --> pdb=" O GLN M 315 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL M 320 " --> pdb=" O GLU M 317 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 28 through 30 removed outlier: 3.556A pdb=" N LYS A 29 " --> pdb=" O VAL A 65 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ILE A 2 " --> pdb=" O SER A 66 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ILE A 15 " --> pdb=" O GLN A 7 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N ILE A 9 " --> pdb=" O ALA A 13 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N ALA A 13 " --> pdb=" O ILE A 9 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 73 through 75 removed outlier: 3.805A pdb=" N VAL A 73 " --> pdb=" O TRP A 187 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N TRP A 187 " --> pdb=" O VAL A 73 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU A 75 " --> pdb=" O HIS A 185 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 116 through 119 removed outlier: 4.169A pdb=" N GLY A 164 " --> pdb=" O TRP A 119 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 137 through 140 Processing sheet with id= E, first strand: chain 'A' and resid 249 through 254 removed outlier: 3.859A pdb=" N VAL A 249 " --> pdb=" O SER A 319 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N ALA A 377 " --> pdb=" O VAL A 320 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N LEU A 322 " --> pdb=" O ALA A 377 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N THR A 379 " --> pdb=" O LEU A 322 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N ALA A 324 " --> pdb=" O THR A 379 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 157 through 160 removed outlier: 6.512A pdb=" N VAL A 174 " --> pdb=" O LYS A 158 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N VAL A 160 " --> pdb=" O VAL A 172 " (cutoff:3.500A) removed outlier: 8.688A pdb=" N VAL A 172 " --> pdb=" O VAL A 160 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N LEU A 181 " --> pdb=" O VAL A 172 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 63 through 66 removed outlier: 4.631A pdb=" N ILE B 2 " --> pdb=" O SER B 66 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ILE B 15 " --> pdb=" O GLN B 7 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N ILE B 9 " --> pdb=" O ALA B 13 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N ALA B 13 " --> pdb=" O ILE B 9 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 72 through 75 Processing sheet with id= I, first strand: chain 'B' and resid 223 through 226 removed outlier: 8.292A pdb=" N ALA B 224 " --> pdb=" O VAL B 378 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ILE B 380 " --> pdb=" O ALA B 224 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N ILE B 226 " --> pdb=" O ILE B 380 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N GLY B 382 " --> pdb=" O ILE B 226 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N VAL B 320 " --> pdb=" O THR B 379 " (cutoff:3.500A) removed outlier: 9.128A pdb=" N VAL B 381 " --> pdb=" O VAL B 320 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N LEU B 322 " --> pdb=" O VAL B 381 " (cutoff:3.500A) removed outlier: 8.214A pdb=" N ALA B 383 " --> pdb=" O LEU B 322 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ALA B 324 " --> pdb=" O ALA B 383 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE B 288 " --> pdb=" O TYR B 252 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 367 through 369 removed outlier: 4.201A pdb=" N VAL B 368 " --> pdb=" O GLY B 376 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLY B 376 " --> pdb=" O VAL B 368 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'B' and resid 157 through 160 removed outlier: 3.845A pdb=" N VAL B 174 " --> pdb=" O LYS B 158 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 28 through 30 Processing sheet with id= M, first strand: chain 'C' and resid 72 through 75 removed outlier: 4.390A pdb=" N VAL C 73 " --> pdb=" O TRP C 187 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N TRP C 187 " --> pdb=" O VAL C 73 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 164 through 166 removed outlier: 3.918A pdb=" N GLY C 164 " --> pdb=" O TRP C 119 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N ALA C 118 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ILE C 147 " --> pdb=" O LEU C 135 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N THR C 137 " --> pdb=" O HIS C 145 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N HIS C 145 " --> pdb=" O THR C 137 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N PHE C 143 " --> pdb=" O PRO C 139 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 285 through 288 removed outlier: 6.962A pdb=" N VAL C 250 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N ILE C 288 " --> pdb=" O VAL C 250 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N TYR C 252 " --> pdb=" O ILE C 288 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL C 249 " --> pdb=" O SER C 319 " (cutoff:3.500A) removed outlier: 8.574A pdb=" N VAL C 320 " --> pdb=" O GLU C 375 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ALA C 377 " --> pdb=" O VAL C 320 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N LEU C 322 " --> pdb=" O ALA C 377 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N THR C 379 " --> pdb=" O LEU C 322 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLY C 376 " --> pdb=" O VAL C 368 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 156 through 160 removed outlier: 4.159A pdb=" N ARG C 156 " --> pdb=" O GLU C 176 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N VAL C 174 " --> pdb=" O LYS C 158 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N VAL C 160 " --> pdb=" O VAL C 172 " (cutoff:3.500A) removed outlier: 8.650A pdb=" N VAL C 172 " --> pdb=" O VAL C 160 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N VAL C 172 " --> pdb=" O LEU C 181 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N LEU C 181 " --> pdb=" O VAL C 172 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N VAL C 174 " --> pdb=" O THR C 179 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N THR C 179 " --> pdb=" O VAL C 174 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 19 through 21 removed outlier: 3.725A pdb=" N GLN D 46 " --> pdb=" O GLN D 58 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ALA D 31 " --> pdb=" O VAL D 47 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'D' and resid 81 through 84 removed outlier: 3.925A pdb=" N LEU D 82 " --> pdb=" O LEU D 112 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LYS D 110 " --> pdb=" O VAL D 84 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 149 through 154 removed outlier: 8.437A pdb=" N LEU D 150 " --> pdb=" O VAL D 308 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N GLN D 310 " --> pdb=" O LEU D 150 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N ILE D 152 " --> pdb=" O GLN D 310 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N SER D 154 " --> pdb=" O PRO D 312 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N LEU D 314 " --> pdb=" O SER D 154 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE D 313 " --> pdb=" O LEU D 257 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 193 through 196 removed outlier: 3.864A pdb=" N ASN D 222 " --> pdb=" O ALA D 193 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY D 195 " --> pdb=" O ASN D 222 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain 'E' and resid 55 through 57 removed outlier: 4.202A pdb=" N TYR E 13 " --> pdb=" O PHE E 20 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'E' and resid 42 through 45 removed outlier: 6.228A pdb=" N ASP E 34 " --> pdb=" O LEU E 75 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N LEU E 75 " --> pdb=" O ASP E 34 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N LYS E 36 " --> pdb=" O VAL E 73 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N VAL E 73 " --> pdb=" O LYS E 36 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'E' and resid 81 through 84 removed outlier: 4.337A pdb=" N LYS E 110 " --> pdb=" O VAL E 84 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'E' and resid 151 through 154 removed outlier: 7.905A pdb=" N SER E 154 " --> pdb=" O PRO E 312 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N LEU E 314 " --> pdb=" O SER E 154 " (cutoff:3.500A) No H-bonds generated for sheet with id= X Processing sheet with id= Y, first strand: chain 'E' and resid 187 through 189 removed outlier: 5.199A pdb=" N HIS E 252 " --> pdb=" O ALA E 188 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N SER E 307 " --> pdb=" O VAL E 253 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N VAL E 255 " --> pdb=" O SER E 307 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N THR E 309 " --> pdb=" O VAL E 255 " (cutoff:3.500A) No H-bonds generated for sheet with id= Y Processing sheet with id= Z, first strand: chain 'F' and resid 54 through 58 removed outlier: 3.795A pdb=" N VAL F 21 " --> pdb=" O ALA F 55 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N TYR F 13 " --> pdb=" O PHE F 20 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N GLU F 22 " --> pdb=" O ILE F 11 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ILE F 11 " --> pdb=" O GLU F 22 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'F' and resid 32 through 34 Processing sheet with id= AB, first strand: chain 'F' and resid 81 through 84 removed outlier: 3.513A pdb=" N VAL F 84 " --> pdb=" O LYS F 110 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LYS F 110 " --> pdb=" O VAL F 84 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'F' and resid 336 through 338 removed outlier: 3.573A pdb=" N VAL F 218 " --> pdb=" O VAL F 189 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'G' and resid 89 through 92 Processing sheet with id= AE, first strand: chain 'J' and resid 120 through 122 Processing sheet with id= AF, first strand: chain 'L' and resid 151 through 154 1009 hydrogen bonds defined for protein. 2694 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: 9.94 Time building geometry restraints manager: 14.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 6487 1.33 - 1.46: 12047 1.46 - 1.59: 14009 1.59 - 1.72: 3 1.72 - 1.86: 196 Bond restraints: 32742 Sorted by residual: bond pdb=" CA LEU A 358 " pdb=" C LEU A 358 " ideal model delta sigma weight residual 1.525 1.392 0.133 1.02e-02 9.61e+03 1.69e+02 bond pdb=" CA GLN B 477 " pdb=" C GLN B 477 " ideal model delta sigma weight residual 1.533 1.466 0.067 5.60e-03 3.19e+04 1.42e+02 bond pdb=" CA GLU C 449 " pdb=" C GLU C 449 " ideal model delta sigma weight residual 1.523 1.438 0.085 8.40e-03 1.42e+04 1.02e+02 bond pdb=" CA ASP F 353 " pdb=" C ASP F 353 " ideal model delta sigma weight residual 1.519 1.423 0.096 9.50e-03 1.11e+04 1.02e+02 bond pdb=" CA ILE D 277 " pdb=" C ILE D 277 " ideal model delta sigma weight residual 1.522 1.452 0.071 7.10e-03 1.98e+04 9.86e+01 ... (remaining 32737 not shown) Histogram of bond angle deviations from ideal: 86.29 - 97.23: 93 97.23 - 108.16: 5642 108.16 - 119.10: 21991 119.10 - 130.04: 16487 130.04 - 140.98: 165 Bond angle restraints: 44378 Sorted by residual: angle pdb=" N ALA G 46 " pdb=" CA ALA G 46 " pdb=" C ALA G 46 " ideal model delta sigma weight residual 111.02 134.13 -23.11 1.22e+00 6.72e-01 3.59e+02 angle pdb=" CA PHE C 415 " pdb=" CB PHE C 415 " pdb=" CG PHE C 415 " ideal model delta sigma weight residual 113.80 100.21 13.59 1.00e+00 1.00e+00 1.85e+02 angle pdb=" CA PHE G 130 " pdb=" CB PHE G 130 " pdb=" CG PHE G 130 " ideal model delta sigma weight residual 113.80 100.52 13.28 1.00e+00 1.00e+00 1.76e+02 angle pdb=" CA PHE F 421 " pdb=" CB PHE F 421 " pdb=" CG PHE F 421 " ideal model delta sigma weight residual 113.80 101.13 12.67 1.00e+00 1.00e+00 1.61e+02 angle pdb=" CA PHE F 247 " pdb=" CB PHE F 247 " pdb=" CG PHE F 247 " ideal model delta sigma weight residual 113.80 101.16 12.64 1.00e+00 1.00e+00 1.60e+02 ... (remaining 44373 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.46: 19010 33.46 - 66.92: 781 66.92 - 100.37: 151 100.37 - 133.83: 1 133.83 - 167.29: 3 Dihedral angle restraints: 19946 sinusoidal: 8036 harmonic: 11910 Sorted by residual: dihedral pdb=" CA LYS E 6 " pdb=" C LYS E 6 " pdb=" N GLU E 7 " pdb=" CA GLU E 7 " ideal model delta harmonic sigma weight residual -180.00 -68.89 -111.11 0 5.00e+00 4.00e-02 4.94e+02 dihedral pdb=" CA LYS F 6 " pdb=" C LYS F 6 " pdb=" N GLU F 7 " pdb=" CA GLU F 7 " ideal model delta harmonic sigma weight residual -180.00 -109.99 -70.01 0 5.00e+00 4.00e-02 1.96e+02 dihedral pdb=" CA LYS D 6 " pdb=" C LYS D 6 " pdb=" N GLU D 7 " pdb=" CA GLU D 7 " ideal model delta harmonic sigma weight residual -180.00 -112.69 -67.31 0 5.00e+00 4.00e-02 1.81e+02 ... (remaining 19943 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.159: 3577 0.159 - 0.318: 1041 0.318 - 0.477: 287 0.477 - 0.637: 65 0.637 - 0.796: 17 Chirality restraints: 4987 Sorted by residual: chirality pdb=" CA THR C 98 " pdb=" N THR C 98 " pdb=" C THR C 98 " pdb=" CB THR C 98 " both_signs ideal model delta sigma weight residual False 2.53 1.73 0.80 2.00e-01 2.50e+01 1.58e+01 chirality pdb=" CA LEU A 458 " pdb=" N LEU A 458 " pdb=" C LEU A 458 " pdb=" CB LEU A 458 " both_signs ideal model delta sigma weight residual False 2.51 1.74 0.77 2.00e-01 2.50e+01 1.47e+01 chirality pdb=" CA THR D 234 " pdb=" N THR D 234 " pdb=" C THR D 234 " pdb=" CB THR D 234 " both_signs ideal model delta sigma weight residual False 2.53 1.77 0.76 2.00e-01 2.50e+01 1.44e+01 ... (remaining 4984 not shown) Planarity restraints: 5831 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 252 " -0.432 2.00e-02 2.50e+03 2.36e-01 1.12e+03 pdb=" CG TYR C 252 " 0.097 2.00e-02 2.50e+03 pdb=" CD1 TYR C 252 " 0.206 2.00e-02 2.50e+03 pdb=" CD2 TYR C 252 " 0.191 2.00e-02 2.50e+03 pdb=" CE1 TYR C 252 " 0.145 2.00e-02 2.50e+03 pdb=" CE2 TYR C 252 " 0.144 2.00e-02 2.50e+03 pdb=" CZ TYR C 252 " 0.008 2.00e-02 2.50e+03 pdb=" OH TYR C 252 " -0.360 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' ADP C 600 " -0.354 2.00e-02 2.50e+03 1.92e-01 1.01e+03 pdb=" C2 ADP C 600 " 0.110 2.00e-02 2.50e+03 pdb=" C4 ADP C 600 " 0.063 2.00e-02 2.50e+03 pdb=" C5 ADP C 600 " 0.164 2.00e-02 2.50e+03 pdb=" C6 ADP C 600 " -0.006 2.00e-02 2.50e+03 pdb=" C8 ADP C 600 " 0.132 2.00e-02 2.50e+03 pdb=" N1 ADP C 600 " 0.027 2.00e-02 2.50e+03 pdb=" N3 ADP C 600 " 0.038 2.00e-02 2.50e+03 pdb=" N6 ADP C 600 " -0.399 2.00e-02 2.50e+03 pdb=" N7 ADP C 600 " 0.238 2.00e-02 2.50e+03 pdb=" N9 ADP C 600 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 304 " 0.384 2.00e-02 2.50e+03 1.98e-01 7.80e+02 pdb=" CG TYR A 304 " -0.130 2.00e-02 2.50e+03 pdb=" CD1 TYR A 304 " -0.179 2.00e-02 2.50e+03 pdb=" CD2 TYR A 304 " -0.181 2.00e-02 2.50e+03 pdb=" CE1 TYR A 304 " -0.087 2.00e-02 2.50e+03 pdb=" CE2 TYR A 304 " -0.086 2.00e-02 2.50e+03 pdb=" CZ TYR A 304 " 0.018 2.00e-02 2.50e+03 pdb=" OH TYR A 304 " 0.261 2.00e-02 2.50e+03 ... (remaining 5828 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 6979 2.78 - 3.31: 35781 3.31 - 3.84: 51175 3.84 - 4.37: 62688 4.37 - 4.90: 94854 Nonbonded interactions: 251477 Sorted by model distance: nonbonded pdb=" N PRO C 420 " pdb=" O PRO C 420 " model vdw 2.246 2.496 nonbonded pdb=" N ILE E 352 " pdb=" O ILE E 352 " model vdw 2.249 2.496 nonbonded pdb=" N PRO F 312 " pdb=" O PRO F 312 " model vdw 2.254 2.496 nonbonded pdb=" N PRO B 227 " pdb=" O PRO B 227 " model vdw 2.259 2.496 nonbonded pdb=" N ASP E 353 " pdb=" O ASP E 353 " model vdw 2.278 2.496 ... (remaining 251472 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 1 through 577) selection = chain 'B' selection = (chain 'C' and resid 1 through 577) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'J' selection = chain 'L' } 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: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 105 5.16 5 C 20371 2.51 5 N 5636 2.21 5 O 6043 1.98 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.610 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: 0.030 Extract box with map and model: 5.970 Check model and map are aligned: 0.440 Convert atoms to be neutral: 0.240 Process input model: 78.510 Find NCS groups from input model: 1.910 Set up NCS constraints: 0.210 Set refine NCS operators: 0.000 Set scattering table: 0.020 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 90.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 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 : 0.027 0.133 32742 Z= 1.743 Angle : 2.875 23.111 44378 Z= 1.865 Chirality : 0.169 0.796 4987 Planarity : 0.032 0.240 5831 Dihedral : 18.506 167.287 12319 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 8.61 % Allowed : 16.33 % Favored : 75.06 % Rotamer Outliers : 9.44 % Cbeta Deviations : 3.36 % Peptide Plane: Cis-proline : 2.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -5.44 (0.10), residues: 4134 helix: -3.50 (0.09), residues: 1587 sheet: -3.44 (0.21), residues: 409 loop : -3.80 (0.11), residues: 2138 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8268 Ramachandran restraints generated. 4134 Oldfield, 0 Emsley, 4134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8268 Ramachandran restraints generated. 4134 Oldfield, 0 Emsley, 4134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1549 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 310 poor density : 1239 time to evaluate : 3.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 TARDY: cannot create tardy model for: "MET I 104 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET J 134 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET J 171 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET J 178 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET K 104 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET L 134 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET L 171 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET L 178 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "CYS M 322 " (corrupted residue). Skipping it. outliers start: 310 outliers final: 114 residues processed: 1429 average time/residue: 0.4474 time to fit residues: 994.2750 Evaluate side-chains 894 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 780 time to evaluate : 3.769 Switching outliers to nearest non-outliers outliers start: 114 outliers final: 0 residues processed: 114 average time/residue: 0.2989 time to fit residues: 67.0583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 411 random chunks: chunk 347 optimal weight: 6.9990 chunk 311 optimal weight: 2.9990 chunk 172 optimal weight: 0.9990 chunk 106 optimal weight: 2.9990 chunk 210 optimal weight: 0.9990 chunk 166 optimal weight: 3.9990 chunk 322 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 195 optimal weight: 2.9990 chunk 239 optimal weight: 1.9990 chunk 373 optimal weight: 5.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 HIS ** A 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 498 ASN B 196 GLN B 283 HIS B 293 ASN ** B 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 496 GLN C 238 GLN ** C 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 132 GLN D 142 ASN ** D 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 170 GLN D 336 GLN D 363 ASN D 424 ASN D 427 GLN D 429 ASN ** E 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 364 ASN E 448 GLN F 129 GLN F 166 GLN F 338 GLN ** F 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 124 ASN L 184 GLN M 200 ASN M 208 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.4534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.068 32742 Z= 0.302 Angle : 0.969 13.661 44378 Z= 0.501 Chirality : 0.051 0.306 4987 Planarity : 0.008 0.133 5831 Dihedral : 8.299 158.780 4623 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.97 % Allowed : 10.64 % Favored : 88.39 % Rotamer Outliers : 0.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.67 % Cis-general : 0.00 % Twisted Proline : 0.44 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.66 (0.12), residues: 4134 helix: -1.95 (0.11), residues: 1620 sheet: -2.62 (0.22), residues: 447 loop : -2.79 (0.13), residues: 2067 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8268 Ramachandran restraints generated. 4134 Oldfield, 0 Emsley, 4134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8268 Ramachandran restraints generated. 4134 Oldfield, 0 Emsley, 4134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1120 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 1104 time to evaluate : 3.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET I 104 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET J 134 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET J 171 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET J 178 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET K 104 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET L 134 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET L 171 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET L 178 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "CYS M 322 " (corrupted residue). Skipping it. outliers start: 16 outliers final: 4 residues processed: 1113 average time/residue: 0.4357 time to fit residues: 771.8678 Evaluate side-chains 763 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 759 time to evaluate : 3.693 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2868 time to fit residues: 7.1603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 411 random chunks: chunk 207 optimal weight: 9.9990 chunk 115 optimal weight: 0.8980 chunk 310 optimal weight: 4.9990 chunk 254 optimal weight: 0.9980 chunk 102 optimal weight: 7.9990 chunk 373 optimal weight: 20.0000 chunk 403 optimal weight: 20.0000 chunk 332 optimal weight: 0.7980 chunk 370 optimal weight: 0.6980 chunk 127 optimal weight: 0.4980 chunk 299 optimal weight: 6.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 109 HIS B 397 GLN B 423 ASN ** B 501 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 148 GLN D 222 ASN ** D 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 364 ASN ** E 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 252 HIS E 407 ASN F 323 HIS ** F 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.5562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.057 32742 Z= 0.214 Angle : 0.801 10.917 44378 Z= 0.406 Chirality : 0.047 0.275 4987 Planarity : 0.006 0.081 5831 Dihedral : 7.023 136.185 4623 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.73 % Allowed : 9.34 % Favored : 89.94 % Rotamer Outliers : 0.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.69 (0.12), residues: 4134 helix: -0.99 (0.12), residues: 1628 sheet: -2.11 (0.23), residues: 464 loop : -2.38 (0.13), residues: 2042 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8268 Ramachandran restraints generated. 4134 Oldfield, 0 Emsley, 4134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8268 Ramachandran restraints generated. 4134 Oldfield, 0 Emsley, 4134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1006 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1003 time to evaluate : 3.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET I 104 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET J 134 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET J 171 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET J 178 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET K 104 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET L 134 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET L 171 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET L 178 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "CYS M 322 " (corrupted residue). Skipping it. outliers start: 3 outliers final: 0 residues processed: 1003 average time/residue: 0.4247 time to fit residues: 685.8529 Evaluate side-chains 738 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 738 time to evaluate : 3.668 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.0233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 411 random chunks: chunk 369 optimal weight: 9.9990 chunk 281 optimal weight: 4.9990 chunk 194 optimal weight: 0.9980 chunk 41 optimal weight: 5.9990 chunk 178 optimal weight: 9.9990 chunk 251 optimal weight: 0.0060 chunk 375 optimal weight: 0.7980 chunk 397 optimal weight: 9.9990 chunk 196 optimal weight: 6.9990 chunk 355 optimal weight: 20.0000 chunk 107 optimal weight: 1.9990 overall best weight: 1.7600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 496 GLN ** C 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 571 GLN ** D 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 222 ASN ** D 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 120 ASN ** E 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 161 ASN F 323 HIS ** F 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 124 ASN ** M 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.6020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.079 32742 Z= 0.231 Angle : 0.752 10.545 44378 Z= 0.378 Chirality : 0.046 0.290 4987 Planarity : 0.006 0.084 5831 Dihedral : 6.383 112.231 4623 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.60 % Allowed : 9.02 % Favored : 90.37 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.18 (0.13), residues: 4134 helix: -0.53 (0.13), residues: 1638 sheet: -1.55 (0.24), residues: 439 loop : -2.21 (0.13), residues: 2057 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8268 Ramachandran restraints generated. 4134 Oldfield, 0 Emsley, 4134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8268 Ramachandran restraints generated. 4134 Oldfield, 0 Emsley, 4134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 940 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 939 time to evaluate : 3.867 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 TARDY: cannot create tardy model for: "MET I 104 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET J 134 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET J 171 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET J 178 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET K 104 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET L 134 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET L 171 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET L 178 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "CYS M 322 " (corrupted residue). Skipping it. outliers start: 1 outliers final: 0 residues processed: 939 average time/residue: 0.4162 time to fit residues: 633.7268 Evaluate side-chains 702 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 702 time to evaluate : 3.731 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.1167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 411 random chunks: chunk 330 optimal weight: 10.0000 chunk 225 optimal weight: 6.9990 chunk 5 optimal weight: 0.8980 chunk 295 optimal weight: 0.5980 chunk 163 optimal weight: 1.9990 chunk 339 optimal weight: 7.9990 chunk 274 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 202 optimal weight: 3.9990 chunk 356 optimal weight: 9.9990 chunk 100 optimal weight: 6.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 238 GLN ** B 418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 58 GLN ** D 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 170 GLN ** D 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 120 ASN ** E 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 323 HIS ** E 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.6420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 32742 Z= 0.216 Angle : 0.732 9.365 44378 Z= 0.365 Chirality : 0.045 0.313 4987 Planarity : 0.006 0.085 5831 Dihedral : 6.112 112.147 4623 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.51 % Allowed : 8.39 % Favored : 91.10 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.13), residues: 4134 helix: -0.24 (0.13), residues: 1643 sheet: -1.22 (0.25), residues: 408 loop : -2.11 (0.13), residues: 2083 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8268 Ramachandran restraints generated. 4134 Oldfield, 0 Emsley, 4134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8268 Ramachandran restraints generated. 4134 Oldfield, 0 Emsley, 4134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 903 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 903 time to evaluate : 3.937 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 TARDY: cannot create tardy model for: "MET I 104 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET J 134 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET J 171 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET J 178 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET K 104 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET L 134 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET L 171 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET L 178 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "CYS M 322 " (corrupted residue). Skipping it. outliers start: 0 outliers final: 0 residues processed: 903 average time/residue: 0.4203 time to fit residues: 617.4468 Evaluate side-chains 685 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 685 time to evaluate : 3.779 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.1286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 411 random chunks: chunk 133 optimal weight: 2.9990 chunk 357 optimal weight: 0.0980 chunk 78 optimal weight: 6.9990 chunk 233 optimal weight: 0.9980 chunk 98 optimal weight: 10.0000 chunk 397 optimal weight: 10.0000 chunk 330 optimal weight: 9.9990 chunk 184 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 131 optimal weight: 7.9990 chunk 208 optimal weight: 4.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 290 ASN ** C 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 222 ASN E 120 ASN ** E 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 142 ASN G 166 GLN ** G 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.6649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.064 32742 Z= 0.264 Angle : 0.738 9.806 44378 Z= 0.369 Chirality : 0.045 0.351 4987 Planarity : 0.006 0.088 5831 Dihedral : 6.032 111.052 4623 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.48 % Allowed : 9.10 % Favored : 90.42 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.13), residues: 4134 helix: -0.09 (0.13), residues: 1629 sheet: -1.02 (0.26), residues: 388 loop : -1.99 (0.13), residues: 2117 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8268 Ramachandran restraints generated. 4134 Oldfield, 0 Emsley, 4134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8268 Ramachandran restraints generated. 4134 Oldfield, 0 Emsley, 4134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 868 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 867 time to evaluate : 3.935 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 TARDY: cannot create tardy model for: "MET I 104 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET J 134 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET J 171 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET J 178 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET K 104 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET L 134 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET L 171 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET L 178 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "CYS M 322 " (corrupted residue). Skipping it. outliers start: 1 outliers final: 0 residues processed: 868 average time/residue: 0.4058 time to fit residues: 576.1976 Evaluate side-chains 674 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 674 time to evaluate : 3.831 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.4157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 411 random chunks: chunk 383 optimal weight: 20.0000 chunk 44 optimal weight: 7.9990 chunk 226 optimal weight: 0.9990 chunk 290 optimal weight: 4.9990 chunk 224 optimal weight: 0.6980 chunk 334 optimal weight: 0.7980 chunk 222 optimal weight: 3.9990 chunk 396 optimal weight: 9.9990 chunk 247 optimal weight: 4.9990 chunk 241 optimal weight: 5.9990 chunk 182 optimal weight: 0.1980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 HIS ** C 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 222 ASN E 46 GLN E 120 ASN ** E 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.6928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.067 32742 Z= 0.197 Angle : 0.711 12.034 44378 Z= 0.351 Chirality : 0.045 0.298 4987 Planarity : 0.006 0.086 5831 Dihedral : 5.775 102.687 4623 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.53 % Allowed : 8.08 % Favored : 91.39 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.13), residues: 4134 helix: 0.11 (0.13), residues: 1648 sheet: -1.08 (0.25), residues: 427 loop : -1.89 (0.14), residues: 2059 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8268 Ramachandran restraints generated. 4134 Oldfield, 0 Emsley, 4134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8268 Ramachandran restraints generated. 4134 Oldfield, 0 Emsley, 4134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 892 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 891 time to evaluate : 3.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET I 104 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET J 134 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET J 171 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET J 178 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET K 104 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET L 134 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET L 171 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET L 178 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "CYS M 322 " (corrupted residue). Skipping it. outliers start: 1 outliers final: 0 residues processed: 892 average time/residue: 0.4154 time to fit residues: 602.5974 Evaluate side-chains 687 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 687 time to evaluate : 3.706 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.0396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 411 random chunks: chunk 245 optimal weight: 7.9990 chunk 158 optimal weight: 0.8980 chunk 236 optimal weight: 8.9990 chunk 119 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 251 optimal weight: 0.1980 chunk 269 optimal weight: 5.9990 chunk 195 optimal weight: 2.9990 chunk 36 optimal weight: 7.9990 chunk 311 optimal weight: 9.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 ASN ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 23 ASN E 120 ASN ** E 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 97 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.7072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 32742 Z= 0.257 Angle : 0.743 9.702 44378 Z= 0.369 Chirality : 0.046 0.286 4987 Planarity : 0.006 0.083 5831 Dihedral : 5.777 93.472 4623 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.46 % Allowed : 9.43 % Favored : 90.11 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.13), residues: 4134 helix: 0.13 (0.13), residues: 1627 sheet: -0.87 (0.26), residues: 416 loop : -1.91 (0.13), residues: 2091 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8268 Ramachandran restraints generated. 4134 Oldfield, 0 Emsley, 4134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8268 Ramachandran restraints generated. 4134 Oldfield, 0 Emsley, 4134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 839 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 837 time to evaluate : 3.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET I 104 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET J 134 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET J 171 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET J 178 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET K 104 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET L 134 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET L 171 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET L 178 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "CYS M 322 " (corrupted residue). Skipping it. outliers start: 2 outliers final: 1 residues processed: 839 average time/residue: 0.4353 time to fit residues: 590.5327 Evaluate side-chains 657 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 656 time to evaluate : 3.637 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2980 time to fit residues: 5.4515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 411 random chunks: chunk 360 optimal weight: 20.0000 chunk 379 optimal weight: 3.9990 chunk 346 optimal weight: 20.0000 chunk 369 optimal weight: 10.0000 chunk 222 optimal weight: 9.9990 chunk 160 optimal weight: 7.9990 chunk 289 optimal weight: 0.9980 chunk 113 optimal weight: 8.9990 chunk 333 optimal weight: 10.0000 chunk 349 optimal weight: 10.0000 chunk 367 optimal weight: 0.9980 overall best weight: 4.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 469 GLN ** A 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 498 ASN C 7 GLN ** C 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 95 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.7167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.069 32742 Z= 0.426 Angle : 0.872 12.496 44378 Z= 0.439 Chirality : 0.049 0.283 4987 Planarity : 0.007 0.086 5831 Dihedral : 6.224 92.694 4623 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 17.92 Ramachandran Plot: Outliers : 0.48 % Allowed : 10.81 % Favored : 88.70 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.13), residues: 4134 helix: -0.08 (0.13), residues: 1613 sheet: -1.14 (0.25), residues: 462 loop : -2.04 (0.14), residues: 2059 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8268 Ramachandran restraints generated. 4134 Oldfield, 0 Emsley, 4134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8268 Ramachandran restraints generated. 4134 Oldfield, 0 Emsley, 4134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 795 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 795 time to evaluate : 4.015 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 TARDY: cannot create tardy model for: "MET I 104 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET J 134 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET J 171 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET J 178 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET K 104 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET L 134 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET L 171 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET L 178 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "CYS M 322 " (corrupted residue). Skipping it. outliers start: 0 outliers final: 0 residues processed: 795 average time/residue: 0.4688 time to fit residues: 606.7527 Evaluate side-chains 626 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 626 time to evaluate : 4.222 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.4127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 411 random chunks: chunk 242 optimal weight: 4.9990 chunk 390 optimal weight: 6.9990 chunk 238 optimal weight: 1.9990 chunk 185 optimal weight: 0.9980 chunk 271 optimal weight: 7.9990 chunk 409 optimal weight: 0.0970 chunk 376 optimal weight: 9.9990 chunk 326 optimal weight: 7.9990 chunk 33 optimal weight: 0.7980 chunk 251 optimal weight: 0.7980 chunk 199 optimal weight: 0.0870 overall best weight: 0.5556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 129 GLN D 142 ASN ** E 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 407 ASN ** E 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 427 GLN ** F 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 363 ASN G 181 GLN G 185 GLN L 130 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.7537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 32742 Z= 0.184 Angle : 0.738 9.658 44378 Z= 0.363 Chirality : 0.046 0.326 4987 Planarity : 0.006 0.097 5831 Dihedral : 5.811 97.276 4623 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.46 % Allowed : 7.62 % Favored : 91.92 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.13), residues: 4134 helix: 0.37 (0.13), residues: 1608 sheet: -1.18 (0.24), residues: 476 loop : -1.83 (0.14), residues: 2050 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8268 Ramachandran restraints generated. 4134 Oldfield, 0 Emsley, 4134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8268 Ramachandran restraints generated. 4134 Oldfield, 0 Emsley, 4134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 862 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 861 time to evaluate : 3.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET I 104 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET J 134 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET J 171 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET J 178 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET K 104 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET L 134 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET L 171 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET L 178 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "CYS M 322 " (corrupted residue). Skipping it. outliers start: 1 outliers final: 0 residues processed: 861 average time/residue: 0.4260 time to fit residues: 594.8253 Evaluate side-chains 680 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 680 time to evaluate : 3.777 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.2464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 411 random chunks: chunk 258 optimal weight: 10.0000 chunk 347 optimal weight: 9.9990 chunk 99 optimal weight: 4.9990 chunk 300 optimal weight: 0.9990 chunk 48 optimal weight: 6.9990 chunk 90 optimal weight: 6.9990 chunk 326 optimal weight: 9.9990 chunk 136 optimal weight: 3.9990 chunk 335 optimal weight: 10.0000 chunk 41 optimal weight: 5.9990 chunk 60 optimal weight: 9.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 290 ASN ** B 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 498 ASN C 7 GLN ** C 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 23 ASN ** E 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.130129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.102977 restraints weight = 68194.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.105268 restraints weight = 45736.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.106239 restraints weight = 32854.520| |-----------------------------------------------------------------------------| r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.7511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.076 32742 Z= 0.428 Angle : 0.872 12.638 44378 Z= 0.438 Chirality : 0.050 0.324 4987 Planarity : 0.007 0.094 5831 Dihedral : 6.268 97.314 4623 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 19.21 Ramachandran Plot: Outliers : 0.48 % Allowed : 10.74 % Favored : 88.78 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.13), residues: 4134 helix: 0.00 (0.13), residues: 1604 sheet: -1.25 (0.24), residues: 478 loop : -2.02 (0.14), residues: 2052 =============================================================================== Job complete usr+sys time: 9545.65 seconds wall clock time: 171 minutes 6.54 seconds (10266.54 seconds total)