Starting phenix.real_space_refine on Fri Mar 22 03:48:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5y5y_6811/03_2024/5y5y_6811_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5y5y_6811/03_2024/5y5y_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_6811/03_2024/5y5y_6811.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5y5y_6811/03_2024/5y5y_6811.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5y5y_6811/03_2024/5y5y_6811_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5y5y_6811/03_2024/5y5y_6811_updated.pdb" } resolution = 4.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.030 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 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. 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: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 541} Chain: "B" Number of atoms: 4472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 577, 4472 Classifications: {'peptide': 577} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 541} Chain: "C" Number of atoms: 4472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 577, 4472 Classifications: {'peptide': 577} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 541} Chain: "D" Number of atoms: 3596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3596 Classifications: {'peptide': 459} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 432} Chain: "E" Number of atoms: 3596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3596 Classifications: {'peptide': 459} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 432} Chain: "F" Number of atoms: 3596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3596 Classifications: {'peptide': 459} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 432} 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: 17.05, per 1000 atoms: 0.53 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: 12.58 Conformation dependent library (CDL) restraints added in 6.1 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: 5.79 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: 9.72 Time building geometry restraints manager: 13.63 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 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: 0.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 4.950 Check model and map are aligned: 0.520 Set scattering table: 0.310 Process input model: 81.570 Find NCS groups from input model: 1.950 Set up NCS constraints: 0.230 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 93.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 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 : 4.73 Ramachandran Plot: Outliers : 8.61 % Allowed : 16.33 % Favored : 75.06 % Rotamer: Outliers : 9.44 % Allowed : 11.78 % Favored : 78.78 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.297 0.040 TRP A 424 HIS 0.013 0.003 HIS L 130 PHE 0.203 0.035 PHE F 421 TYR 0.432 0.050 TYR C 252 ARG 0.019 0.002 ARG E 146 *********************** 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 : 3.518 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. 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. REVERT: A 91 LEU cc_start: 0.8834 (mp) cc_final: 0.8071 (mp) REVERT: A 133 MET cc_start: 0.7860 (mtt) cc_final: 0.7539 (mtp) REVERT: A 134 VAL cc_start: 0.9237 (OUTLIER) cc_final: 0.8883 (m) REVERT: A 140 GLU cc_start: 0.6537 (tt0) cc_final: 0.6305 (tt0) REVERT: A 159 GLU cc_start: 0.7246 (OUTLIER) cc_final: 0.6445 (mp0) REVERT: A 189 VAL cc_start: 0.8415 (OUTLIER) cc_final: 0.8205 (t) REVERT: A 207 THR cc_start: 0.9306 (OUTLIER) cc_final: 0.9010 (m) REVERT: A 234 LYS cc_start: 0.8860 (OUTLIER) cc_final: 0.8442 (ttpt) REVERT: A 262 MET cc_start: 0.8282 (tpp) cc_final: 0.7126 (mmp) REVERT: A 273 THR cc_start: 0.7650 (m) cc_final: 0.7050 (t) REVERT: A 379 THR cc_start: 0.9074 (m) cc_final: 0.8363 (m) REVERT: A 425 ASN cc_start: 0.8774 (m110) cc_final: 0.8311 (t0) REVERT: A 465 GLN cc_start: 0.7766 (mm-40) cc_final: 0.7248 (mm-40) REVERT: A 500 TYR cc_start: 0.7025 (m-80) cc_final: 0.6344 (m-80) REVERT: A 519 ILE cc_start: 0.8934 (pt) cc_final: 0.8684 (mm) REVERT: B 52 TYR cc_start: 0.7845 (m-80) cc_final: 0.6496 (m-10) REVERT: B 62 GLU cc_start: 0.8577 (mt-10) cc_final: 0.7765 (mt-10) REVERT: B 87 ILE cc_start: 0.9285 (pt) cc_final: 0.8637 (mm) REVERT: B 109 HIS cc_start: 0.8199 (OUTLIER) cc_final: 0.7836 (m-70) REVERT: B 144 THR cc_start: 0.9185 (OUTLIER) cc_final: 0.8897 (m) REVERT: B 156 ARG cc_start: 0.6376 (mmp-170) cc_final: 0.5642 (mmm160) REVERT: B 186 THR cc_start: 0.8609 (p) cc_final: 0.8298 (t) REVERT: B 198 LYS cc_start: 0.6029 (ttpt) cc_final: 0.5600 (tttt) REVERT: B 199 LEU cc_start: 0.8508 (mt) cc_final: 0.8064 (tp) REVERT: B 257 GLU cc_start: 0.7440 (tt0) cc_final: 0.7206 (tt0) REVERT: B 322 LEU cc_start: 0.9160 (tt) cc_final: 0.8636 (tt) REVERT: B 367 LYS cc_start: 0.8513 (OUTLIER) cc_final: 0.7939 (tptm) REVERT: B 368 VAL cc_start: 0.8883 (m) cc_final: 0.8673 (p) REVERT: B 439 TYR cc_start: 0.8825 (OUTLIER) cc_final: 0.8421 (m-80) REVERT: B 450 LEU cc_start: 0.8445 (mt) cc_final: 0.7823 (mm) REVERT: B 452 ASP cc_start: 0.9084 (p0) cc_final: 0.8621 (p0) REVERT: B 458 LEU cc_start: 0.8346 (pp) cc_final: 0.7924 (pp) REVERT: B 490 ILE cc_start: 0.8982 (mm) cc_final: 0.8414 (mm) REVERT: B 516 MET cc_start: 0.8045 (ptm) cc_final: 0.7667 (ttp) REVERT: B 545 LEU cc_start: 0.8837 (mp) cc_final: 0.8544 (mt) REVERT: C 50 GLN cc_start: 0.8119 (OUTLIER) cc_final: 0.7322 (tp40) REVERT: C 64 VAL cc_start: 0.8381 (t) cc_final: 0.8093 (t) REVERT: C 119 TRP cc_start: 0.9259 (OUTLIER) cc_final: 0.8543 (t-100) REVERT: C 160 VAL cc_start: 0.9001 (t) cc_final: 0.8788 (p) REVERT: C 184 TYR cc_start: 0.8265 (p90) cc_final: 0.7795 (p90) REVERT: C 205 PHE cc_start: 0.8770 (OUTLIER) cc_final: 0.8518 (t80) REVERT: C 240 SER cc_start: 0.9219 (m) cc_final: 0.8587 (t) REVERT: C 244 TRP cc_start: 0.8531 (m100) cc_final: 0.7566 (m100) REVERT: C 264 ASP cc_start: 0.8713 (m-30) cc_final: 0.8170 (m-30) REVERT: C 300 GLU cc_start: 0.8527 (tt0) cc_final: 0.8285 (tm-30) REVERT: C 344 MET cc_start: 0.8615 (mmt) cc_final: 0.8232 (mmt) REVERT: C 413 LEU cc_start: 0.9378 (tp) cc_final: 0.8972 (mm) REVERT: C 490 ILE cc_start: 0.8568 (mm) cc_final: 0.8089 (mm) REVERT: C 506 TYR cc_start: 0.8201 (t80) cc_final: 0.7780 (t80) REVERT: C 552 ARG cc_start: 0.8694 (ptt90) cc_final: 0.8180 (ptt90) REVERT: D 18 LEU cc_start: 0.8965 (mt) cc_final: 0.8694 (tp) REVERT: D 61 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7458 (pm20) REVERT: D 81 ARG cc_start: 0.7432 (OUTLIER) cc_final: 0.6717 (ppt90) REVERT: D 85 SER cc_start: 0.8036 (OUTLIER) cc_final: 0.7287 (m) REVERT: D 100 ILE cc_start: 0.8495 (mm) cc_final: 0.8194 (tp) REVERT: D 173 VAL cc_start: 0.9072 (OUTLIER) cc_final: 0.8845 (m) REVERT: D 178 SER cc_start: 0.8650 (m) cc_final: 0.8250 (t) REVERT: D 207 GLU cc_start: 0.7185 (OUTLIER) cc_final: 0.6910 (tp30) REVERT: D 244 TYR cc_start: 0.7876 (t80) cc_final: 0.7333 (t80) REVERT: D 251 TYR cc_start: 0.8124 (OUTLIER) cc_final: 0.7540 (m-80) REVERT: D 269 GLU cc_start: 0.7489 (mm-30) cc_final: 0.7275 (mm-30) REVERT: D 388 ASN cc_start: 0.9163 (m-40) cc_final: 0.8850 (t0) REVERT: D 423 ILE cc_start: 0.8786 (OUTLIER) cc_final: 0.8557 (tp) REVERT: D 436 LEU cc_start: 0.9190 (mt) cc_final: 0.8950 (mt) REVERT: E 59 VAL cc_start: 0.8969 (t) cc_final: 0.8751 (p) REVERT: E 82 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8569 (tp) REVERT: E 93 PHE cc_start: 0.7303 (OUTLIER) cc_final: 0.6967 (t80) REVERT: E 112 LEU cc_start: 0.8419 (pt) cc_final: 0.8164 (pp) REVERT: E 126 LYS cc_start: 0.8580 (ttpt) cc_final: 0.8104 (tttp) REVERT: E 136 SER cc_start: 0.9467 (p) cc_final: 0.9222 (t) REVERT: E 269 GLU cc_start: 0.7956 (mt-10) cc_final: 0.7752 (mt-10) REVERT: E 278 PRO cc_start: 0.8910 (Cg_exo) cc_final: 0.8637 (Cg_endo) REVERT: E 296 GLU cc_start: 0.7525 (tp30) cc_final: 0.7163 (tp30) REVERT: E 307 SER cc_start: 0.8368 (p) cc_final: 0.8067 (m) REVERT: F 19 LEU cc_start: 0.8784 (tt) cc_final: 0.8484 (tt) REVERT: F 53 GLU cc_start: 0.8969 (OUTLIER) cc_final: 0.6557 (tm-30) REVERT: F 54 TYR cc_start: 0.8539 (p90) cc_final: 0.7820 (p90) REVERT: F 57 ILE cc_start: 0.9106 (OUTLIER) cc_final: 0.8846 (mt) REVERT: F 58 GLN cc_start: 0.8749 (tt0) cc_final: 0.8476 (tt0) REVERT: F 73 VAL cc_start: 0.8792 (t) cc_final: 0.8552 (t) REVERT: F 89 LEU cc_start: 0.8953 (mt) cc_final: 0.8414 (mt) REVERT: F 139 ASP cc_start: 0.8597 (m-30) cc_final: 0.8296 (m-30) REVERT: F 148 GLN cc_start: 0.8965 (tt0) cc_final: 0.8296 (tt0) REVERT: F 194 MET cc_start: 0.7626 (OUTLIER) cc_final: 0.6401 (mpm) REVERT: F 201 LEU cc_start: 0.9218 (OUTLIER) cc_final: 0.8925 (tp) REVERT: F 219 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8218 (pp) REVERT: F 239 LEU cc_start: 0.8551 (mt) cc_final: 0.8295 (mm) REVERT: F 316 MET cc_start: 0.9004 (pp-130) cc_final: 0.8553 (ppp) REVERT: F 334 GLU cc_start: 0.6889 (mt-10) cc_final: 0.6511 (mt-10) REVERT: F 357 SER cc_start: 0.7907 (m) cc_final: 0.7635 (p) REVERT: F 377 GLN cc_start: 0.9083 (mt0) cc_final: 0.8804 (mt0) REVERT: F 393 ARG cc_start: 0.8649 (ttm170) cc_final: 0.8137 (ttm-80) REVERT: F 412 LEU cc_start: 0.8758 (tp) cc_final: 0.8401 (tt) REVERT: F 419 GLU cc_start: 0.8795 (OUTLIER) cc_final: 0.7752 (pt0) REVERT: F 425 GLN cc_start: 0.8449 (tt0) cc_final: 0.8147 (tt0) REVERT: F 450 GLU cc_start: 0.7042 (mm-30) cc_final: 0.6638 (mm-30) REVERT: G 147 LEU cc_start: 0.7946 (tp) cc_final: 0.7397 (tt) REVERT: G 165 GLU cc_start: 0.7294 (mt-10) cc_final: 0.6428 (tp30) REVERT: G 177 ARG cc_start: 0.8103 (OUTLIER) cc_final: 0.7887 (mtm180) REVERT: G 193 ARG cc_start: 0.7947 (ttm110) cc_final: 0.7687 (ttm110) REVERT: H 28 GLU cc_start: 0.5331 (OUTLIER) cc_final: 0.4441 (pm20) REVERT: I 118 VAL cc_start: 0.6215 (m) cc_final: 0.5978 (p) REVERT: J 79 VAL cc_start: 0.6038 (t) cc_final: 0.5791 (t) REVERT: J 88 ARG cc_start: 0.8117 (mtp180) cc_final: 0.7696 (tpt170) REVERT: J 128 LEU cc_start: 0.6119 (tp) cc_final: 0.5893 (tp) REVERT: J 182 VAL cc_start: 0.8217 (m) cc_final: 0.7442 (t) REVERT: J 186 LEU cc_start: 0.8744 (mt) cc_final: 0.8050 (mt) REVERT: K 108 ASP cc_start: 0.6868 (OUTLIER) cc_final: 0.5190 (t70) REVERT: L 53 TYR cc_start: 0.6900 (t80) cc_final: 0.6625 (t80) REVERT: L 88 ARG cc_start: 0.6913 (ttm110) cc_final: 0.6582 (ttm-80) REVERT: L 152 VAL cc_start: 0.7761 (t) cc_final: 0.7259 (p) REVERT: M 97 GLN cc_start: 0.6560 (mt0) cc_final: 0.6243 (tt0) REVERT: M 157 GLU cc_start: 0.4546 (OUTLIER) cc_final: 0.1693 (tm-30) REVERT: M 269 LEU cc_start: 0.8373 (mt) cc_final: 0.8082 (tt) REVERT: M 289 TYR cc_start: 0.6155 (t80) cc_final: 0.5793 (t80) outliers start: 310 outliers final: 112 residues processed: 1429 average time/residue: 0.4499 time to fit residues: 995.2305 Evaluate side-chains 960 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 817 time to evaluate : 3.375 ------------------------------------------------------------------------------- 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: 5.9990 chunk 311 optimal weight: 3.9990 chunk 172 optimal weight: 0.9980 chunk 106 optimal weight: 0.7980 chunk 210 optimal weight: 2.9990 chunk 166 optimal weight: 2.9990 chunk 322 optimal weight: 2.9990 chunk 124 optimal weight: 5.9990 chunk 195 optimal weight: 3.9990 chunk 239 optimal weight: 5.9990 chunk 373 optimal weight: 6.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- 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 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 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 170 GLN ** D 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 336 GLN D 363 ASN D 424 ASN D 427 GLN D 429 ASN E 142 ASN ** E 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 129 GLN F 166 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: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.4396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 32742 Z= 0.318 Angle : 0.976 10.927 44378 Z= 0.508 Chirality : 0.051 0.303 4987 Planarity : 0.008 0.134 5831 Dihedral : 8.304 158.793 4623 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.97 % Allowed : 11.32 % Favored : 87.71 % Rotamer: Outliers : 0.21 % Allowed : 6.43 % Favored : 93.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.67 % Cis-general : 0.00 % Twisted Proline : 0.44 % 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: -3.71 (0.12), residues: 4134 helix: -1.99 (0.11), residues: 1626 sheet: -2.69 (0.22), residues: 468 loop : -2.80 (0.13), residues: 2040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP B 330 HIS 0.011 0.002 HIS A 418 PHE 0.033 0.003 PHE M 36 TYR 0.046 0.003 TYR F 383 ARG 0.009 0.001 ARG B 364 *********************** 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 1125 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 1118 time to evaluate : 3.335 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 TARDY: cannot create tardy model for: "CYS M 322 " (corrupted residue). Skipping it. REVERT: A 79 MET cc_start: 0.7018 (mtp) cc_final: 0.6004 (ttm) REVERT: A 133 MET cc_start: 0.7463 (mtt) cc_final: 0.6110 (mtp) REVERT: A 182 LYS cc_start: 0.8126 (mptt) cc_final: 0.7917 (mppt) REVERT: A 207 THR cc_start: 0.9238 (t) cc_final: 0.8855 (p) REVERT: A 282 MET cc_start: 0.6909 (mmm) cc_final: 0.6413 (mmm) REVERT: A 290 ASN cc_start: 0.8750 (t0) cc_final: 0.8422 (t0) REVERT: A 291 THR cc_start: 0.8698 (m) cc_final: 0.8414 (m) REVERT: A 293 ASN cc_start: 0.8780 (p0) cc_final: 0.8423 (p0) REVERT: A 294 MET cc_start: 0.7231 (mtp) cc_final: 0.6598 (mtp) REVERT: A 343 GLU cc_start: 0.6948 (tt0) cc_final: 0.6680 (tt0) REVERT: A 344 MET cc_start: 0.8829 (ttm) cc_final: 0.8598 (ttp) REVERT: A 379 THR cc_start: 0.8759 (m) cc_final: 0.8411 (m) REVERT: A 424 TRP cc_start: 0.6701 (p90) cc_final: 0.6273 (p90) REVERT: A 425 ASN cc_start: 0.8654 (m110) cc_final: 0.7395 (t0) REVERT: A 436 ASP cc_start: 0.8453 (m-30) cc_final: 0.8164 (m-30) REVERT: A 495 LEU cc_start: 0.9551 (mt) cc_final: 0.9233 (mt) REVERT: A 519 ILE cc_start: 0.9268 (pt) cc_final: 0.8880 (mm) REVERT: B 52 TYR cc_start: 0.7526 (m-80) cc_final: 0.7125 (m-80) REVERT: B 79 MET cc_start: 0.7894 (tpt) cc_final: 0.7269 (tpt) REVERT: B 87 ILE cc_start: 0.9114 (pt) cc_final: 0.8510 (mm) REVERT: B 133 MET cc_start: 0.7697 (ttm) cc_final: 0.7118 (ttp) REVERT: B 156 ARG cc_start: 0.5913 (mmp-170) cc_final: 0.5563 (mmm160) REVERT: B 209 MET cc_start: 0.8412 (mmm) cc_final: 0.8203 (mmm) REVERT: B 244 TRP cc_start: 0.7957 (m100) cc_final: 0.7601 (m100) REVERT: B 257 GLU cc_start: 0.7732 (tt0) cc_final: 0.7291 (tt0) REVERT: B 263 THR cc_start: 0.8813 (p) cc_final: 0.8601 (p) REVERT: B 311 GLU cc_start: 0.5929 (mt-10) cc_final: 0.5667 (mt-10) REVERT: B 443 VAL cc_start: 0.8364 (t) cc_final: 0.7265 (t) REVERT: B 459 GLN cc_start: 0.7968 (mt0) cc_final: 0.7707 (tp40) REVERT: B 504 ASP cc_start: 0.7223 (p0) cc_final: 0.7004 (p0) REVERT: B 507 CYS cc_start: 0.7703 (t) cc_final: 0.7447 (t) REVERT: B 516 MET cc_start: 0.7715 (ptm) cc_final: 0.7384 (ttm) REVERT: C 94 ILE cc_start: 0.8886 (mp) cc_final: 0.8605 (tp) REVERT: C 249 VAL cc_start: 0.8848 (m) cc_final: 0.8580 (p) REVERT: C 300 GLU cc_start: 0.8399 (tt0) cc_final: 0.8140 (tm-30) REVERT: C 413 LEU cc_start: 0.9096 (tp) cc_final: 0.8750 (mm) REVERT: C 468 VAL cc_start: 0.8874 (t) cc_final: 0.8564 (t) REVERT: C 493 ASP cc_start: 0.7612 (m-30) cc_final: 0.6899 (m-30) REVERT: D 124 ARG cc_start: 0.8570 (mtm110) cc_final: 0.8257 (ttp-110) REVERT: D 137 THR cc_start: 0.7551 (t) cc_final: 0.7242 (t) REVERT: D 148 GLN cc_start: 0.8255 (tp40) cc_final: 0.8003 (tt0) REVERT: D 170 GLN cc_start: 0.7238 (tp40) cc_final: 0.6833 (tp40) REVERT: D 214 LEU cc_start: 0.7448 (tt) cc_final: 0.7214 (tt) REVERT: D 319 ASP cc_start: 0.7844 (m-30) cc_final: 0.7559 (t70) REVERT: D 342 GLU cc_start: 0.6959 (pt0) cc_final: 0.6335 (pt0) REVERT: D 383 TYR cc_start: 0.9018 (t80) cc_final: 0.8613 (t80) REVERT: D 429 ASN cc_start: 0.8486 (t0) cc_final: 0.7933 (t0) REVERT: D 443 LEU cc_start: 0.9229 (mm) cc_final: 0.8945 (tp) REVERT: D 462 TYR cc_start: 0.6394 (m-80) cc_final: 0.5773 (m-80) REVERT: E 126 LYS cc_start: 0.8484 (ttpt) cc_final: 0.8264 (tttm) REVERT: E 187 PHE cc_start: 0.8426 (t80) cc_final: 0.8155 (t80) REVERT: E 206 GLN cc_start: 0.8236 (pp30) cc_final: 0.7978 (pp30) REVERT: E 243 GLU cc_start: 0.8061 (tp30) cc_final: 0.7611 (tp30) REVERT: E 307 SER cc_start: 0.8687 (p) cc_final: 0.8154 (m) REVERT: E 316 MET cc_start: 0.7945 (ptm) cc_final: 0.7678 (ptm) REVERT: E 358 LEU cc_start: 0.9084 (tp) cc_final: 0.8732 (tp) REVERT: E 432 ILE cc_start: 0.7746 (tp) cc_final: 0.6898 (tp) REVERT: E 445 MET cc_start: 0.8323 (mmp) cc_final: 0.7992 (mmm) REVERT: F 89 LEU cc_start: 0.9065 (mt) cc_final: 0.8754 (mt) REVERT: F 137 THR cc_start: 0.9136 (p) cc_final: 0.8804 (p) REVERT: F 176 ASP cc_start: 0.7872 (p0) cc_final: 0.7154 (p0) REVERT: F 203 TYR cc_start: 0.9284 (t80) cc_final: 0.9002 (t80) REVERT: F 219 LEU cc_start: 0.8053 (pt) cc_final: 0.7750 (pp) REVERT: F 221 LEU cc_start: 0.8183 (mt) cc_final: 0.7489 (tt) REVERT: F 239 LEU cc_start: 0.8736 (mt) cc_final: 0.8463 (mm) REVERT: F 255 VAL cc_start: 0.9171 (t) cc_final: 0.8908 (m) REVERT: F 260 MET cc_start: 0.7617 (tpp) cc_final: 0.7326 (tpp) REVERT: F 276 GLU cc_start: 0.7477 (mt-10) cc_final: 0.7189 (mt-10) REVERT: F 280 ARG cc_start: 0.8616 (tpp80) cc_final: 0.8259 (ttt90) REVERT: F 461 LYS cc_start: 0.8420 (mtpt) cc_final: 0.7947 (ttmt) REVERT: G 11 LEU cc_start: 0.8343 (tp) cc_final: 0.8067 (tt) REVERT: G 32 ARG cc_start: 0.8127 (mmp80) cc_final: 0.7750 (mmp80) REVERT: G 147 LEU cc_start: 0.7869 (tp) cc_final: 0.7381 (tt) REVERT: G 152 GLU cc_start: 0.7841 (pt0) cc_final: 0.7450 (pp20) REVERT: G 159 ARG cc_start: 0.8699 (ttm110) cc_final: 0.8039 (ttm110) REVERT: G 177 ARG cc_start: 0.7364 (mpp80) cc_final: 0.6995 (mtm180) REVERT: G 193 ARG cc_start: 0.8196 (ttm110) cc_final: 0.7842 (ttm110) REVERT: G 194 LEU cc_start: 0.9190 (tp) cc_final: 0.8870 (tt) REVERT: H 66 ARG cc_start: 0.7628 (tpt-90) cc_final: 0.6954 (ptt90) REVERT: I 118 VAL cc_start: 0.6147 (m) cc_final: 0.5905 (p) REVERT: J 128 LEU cc_start: 0.6025 (tp) cc_final: 0.5764 (tp) REVERT: J 182 VAL cc_start: 0.7337 (m) cc_final: 0.6720 (t) REVERT: M 317 GLU cc_start: 0.6532 (pt0) cc_final: 0.5583 (pt0) outliers start: 7 outliers final: 2 residues processed: 1121 average time/residue: 0.4394 time to fit residues: 773.2878 Evaluate side-chains 798 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 796 time to evaluate : 3.603 ------------------------------------------------------------------------------- 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: 3.9990 chunk 310 optimal weight: 7.9990 chunk 254 optimal weight: 1.9990 chunk 102 optimal weight: 4.9990 chunk 373 optimal weight: 0.9980 chunk 403 optimal weight: 0.7980 chunk 332 optimal weight: 9.9990 chunk 370 optimal weight: 0.0770 chunk 127 optimal weight: 10.0000 chunk 299 optimal weight: 4.9990 overall best weight: 1.5742 ------------------------------------------------------------------------------- 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 423 ASN ** B 501 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 50 GLN C 246 ASN ** C 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 222 ASN ** D 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 46 GLN E 252 HIS ** F 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 429 ASN ** M 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.5358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 32742 Z= 0.244 Angle : 0.815 10.627 44378 Z= 0.415 Chirality : 0.047 0.299 4987 Planarity : 0.006 0.081 5831 Dihedral : 7.141 138.372 4623 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.75 % Allowed : 9.97 % Favored : 89.28 % Rotamer: Outliers : 0.06 % Allowed : 4.60 % Favored : 95.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.70 (0.12), residues: 4134 helix: -1.02 (0.12), residues: 1632 sheet: -2.03 (0.23), residues: 462 loop : -2.39 (0.13), residues: 2040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP C 244 HIS 0.007 0.001 HIS D 252 PHE 0.038 0.002 PHE C 269 TYR 0.055 0.002 TYR F 383 ARG 0.013 0.001 ARG F 410 *********************** 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 996 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 994 time to evaluate : 3.939 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. 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 TARDY: cannot create tardy model for: "CYS M 322 " (corrupted residue). Skipping it. REVERT: A 79 MET cc_start: 0.7087 (mtp) cc_final: 0.6356 (ttm) REVERT: A 207 THR cc_start: 0.9306 (t) cc_final: 0.8927 (p) REVERT: A 282 MET cc_start: 0.7041 (mmm) cc_final: 0.6628 (mmm) REVERT: A 290 ASN cc_start: 0.8656 (t0) cc_final: 0.8222 (t0) REVERT: A 293 ASN cc_start: 0.8819 (p0) cc_final: 0.8420 (p0) REVERT: A 294 MET cc_start: 0.7225 (mtp) cc_final: 0.6668 (mtp) REVERT: A 319 SER cc_start: 0.9038 (m) cc_final: 0.8664 (p) REVERT: A 397 GLN cc_start: 0.7963 (mt0) cc_final: 0.7391 (mt0) REVERT: A 425 ASN cc_start: 0.8227 (m110) cc_final: 0.7531 (t0) REVERT: A 429 SER cc_start: 0.9035 (t) cc_final: 0.8558 (m) REVERT: A 519 ILE cc_start: 0.9226 (pt) cc_final: 0.8720 (mm) REVERT: B 79 MET cc_start: 0.8208 (tpt) cc_final: 0.7288 (tpt) REVERT: B 87 ILE cc_start: 0.9111 (pt) cc_final: 0.8452 (mm) REVERT: B 91 LEU cc_start: 0.8741 (mt) cc_final: 0.8330 (mm) REVERT: B 156 ARG cc_start: 0.5611 (mmp-170) cc_final: 0.5080 (mmm160) REVERT: B 214 VAL cc_start: 0.8984 (t) cc_final: 0.8761 (t) REVERT: B 257 GLU cc_start: 0.7625 (tt0) cc_final: 0.7317 (tt0) REVERT: B 459 GLN cc_start: 0.8284 (mt0) cc_final: 0.7745 (tp40) REVERT: B 507 CYS cc_start: 0.7591 (t) cc_final: 0.7298 (t) REVERT: B 516 MET cc_start: 0.7784 (ptm) cc_final: 0.7465 (ttp) REVERT: C 2 ILE cc_start: 0.7996 (mm) cc_final: 0.7713 (mm) REVERT: C 39 ILE cc_start: 0.8366 (mp) cc_final: 0.8090 (mm) REVERT: C 240 SER cc_start: 0.8700 (m) cc_final: 0.8419 (t) REVERT: C 323 MET cc_start: 0.7040 (ppp) cc_final: 0.6794 (ppp) REVERT: C 458 LEU cc_start: 0.8941 (mt) cc_final: 0.8724 (mt) REVERT: C 468 VAL cc_start: 0.8901 (t) cc_final: 0.8700 (t) REVERT: D 62 GLU cc_start: 0.6686 (mm-30) cc_final: 0.6436 (mm-30) REVERT: D 75 LEU cc_start: 0.9268 (tt) cc_final: 0.9013 (tt) REVERT: D 137 THR cc_start: 0.7414 (t) cc_final: 0.7173 (t) REVERT: D 269 GLU cc_start: 0.6714 (mm-30) cc_final: 0.6343 (mm-30) REVERT: D 296 GLU cc_start: 0.8155 (mm-30) cc_final: 0.7506 (mm-30) REVERT: D 300 VAL cc_start: 0.9145 (t) cc_final: 0.8515 (t) REVERT: D 443 LEU cc_start: 0.9221 (mm) cc_final: 0.8997 (tp) REVERT: E 141 MET cc_start: 0.7174 (ttt) cc_final: 0.6966 (ttt) REVERT: E 142 ASN cc_start: 0.8766 (m-40) cc_final: 0.7911 (m110) REVERT: E 206 GLN cc_start: 0.8256 (pp30) cc_final: 0.8021 (pp30) REVERT: E 243 GLU cc_start: 0.8100 (tp30) cc_final: 0.7577 (tp30) REVERT: E 281 ARG cc_start: 0.6388 (mtt180) cc_final: 0.6095 (mtt180) REVERT: E 293 THR cc_start: 0.8395 (t) cc_final: 0.8188 (m) REVERT: E 300 VAL cc_start: 0.8717 (m) cc_final: 0.8062 (m) REVERT: E 307 SER cc_start: 0.7966 (p) cc_final: 0.7742 (m) REVERT: E 383 TYR cc_start: 0.7596 (t80) cc_final: 0.7342 (t80) REVERT: E 388 ASN cc_start: 0.7183 (m-40) cc_final: 0.6940 (t0) REVERT: E 429 ASN cc_start: 0.8227 (t0) cc_final: 0.7787 (m-40) REVERT: E 445 MET cc_start: 0.8343 (mmp) cc_final: 0.8131 (mpp) REVERT: F 34 ASP cc_start: 0.7577 (p0) cc_final: 0.7329 (p0) REVERT: F 89 LEU cc_start: 0.9039 (mt) cc_final: 0.8438 (mt) REVERT: F 137 THR cc_start: 0.9042 (p) cc_final: 0.8705 (p) REVERT: F 139 ASP cc_start: 0.8479 (m-30) cc_final: 0.8260 (p0) REVERT: F 140 VAL cc_start: 0.9516 (t) cc_final: 0.9244 (t) REVERT: F 176 ASP cc_start: 0.8079 (p0) cc_final: 0.7302 (p0) REVERT: F 219 LEU cc_start: 0.8418 (pt) cc_final: 0.7815 (pp) REVERT: F 221 LEU cc_start: 0.8071 (mt) cc_final: 0.7510 (tt) REVERT: F 239 LEU cc_start: 0.8685 (mt) cc_final: 0.8432 (mm) REVERT: F 260 MET cc_start: 0.7603 (tpp) cc_final: 0.7396 (tpp) REVERT: F 265 GLU cc_start: 0.8900 (mm-30) cc_final: 0.8468 (mm-30) REVERT: F 280 ARG cc_start: 0.8612 (tpp80) cc_final: 0.8039 (ttt90) REVERT: F 408 ASP cc_start: 0.7606 (m-30) cc_final: 0.7202 (m-30) REVERT: F 461 LYS cc_start: 0.8332 (mtpt) cc_final: 0.7987 (ttmt) REVERT: G 47 MET cc_start: 0.4095 (tpp) cc_final: 0.3083 (tpp) REVERT: G 145 THR cc_start: 0.7926 (t) cc_final: 0.7417 (t) REVERT: G 147 LEU cc_start: 0.7537 (tp) cc_final: 0.7274 (tt) REVERT: G 193 ARG cc_start: 0.8297 (ttm110) cc_final: 0.8078 (ttm110) REVERT: G 194 LEU cc_start: 0.9076 (tp) cc_final: 0.8678 (tt) REVERT: H 61 ARG cc_start: 0.7350 (mtt180) cc_final: 0.7076 (mtp180) REVERT: H 81 PHE cc_start: 0.6842 (t80) cc_final: 0.5949 (t80) REVERT: I 99 VAL cc_start: 0.7003 (m) cc_final: 0.6639 (m) REVERT: J 128 LEU cc_start: 0.6212 (tp) cc_final: 0.5926 (tp) REVERT: J 182 VAL cc_start: 0.7108 (m) cc_final: 0.6767 (p) REVERT: M 191 TYR cc_start: 0.5051 (t80) cc_final: 0.4628 (t80) REVERT: M 234 MET cc_start: 0.8133 (ptm) cc_final: 0.7850 (ttp) REVERT: M 317 GLU cc_start: 0.6927 (pt0) cc_final: 0.5760 (pt0) outliers start: 2 outliers final: 0 residues processed: 994 average time/residue: 0.4515 time to fit residues: 721.8439 Evaluate side-chains 741 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 741 time to evaluate : 3.457 ------------------------------------------------------------------------------- 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: 20.0000 chunk 281 optimal weight: 4.9990 chunk 194 optimal weight: 0.9990 chunk 41 optimal weight: 5.9990 chunk 178 optimal weight: 0.0270 chunk 251 optimal weight: 0.0170 chunk 375 optimal weight: 6.9990 chunk 397 optimal weight: 9.9990 chunk 196 optimal weight: 1.9990 chunk 355 optimal weight: 20.0000 chunk 107 optimal weight: 9.9990 overall best weight: 1.6082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 HIS ** A 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 120 ASN F 323 HIS ** F 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 142 ASN ** M 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.5913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 32742 Z= 0.221 Angle : 0.751 10.279 44378 Z= 0.377 Chirality : 0.046 0.304 4987 Planarity : 0.006 0.078 5831 Dihedral : 6.429 112.975 4623 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.58 % Allowed : 8.76 % Favored : 90.66 % Rotamer: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % 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: -0.49 (0.13), residues: 1630 sheet: -1.53 (0.24), residues: 429 loop : -2.24 (0.13), residues: 2075 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP L 175 HIS 0.005 0.001 HIS A 418 PHE 0.029 0.002 PHE C 269 TYR 0.044 0.002 TYR F 383 ARG 0.010 0.001 ARG J 45 *********************** 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 966 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 966 time to evaluate : 3.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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 TARDY: cannot create tardy model for: "CYS M 322 " (corrupted residue). Skipping it. REVERT: A 207 THR cc_start: 0.9365 (t) cc_final: 0.8988 (p) REVERT: A 269 PHE cc_start: 0.7959 (m-80) cc_final: 0.7740 (m-80) REVERT: A 282 MET cc_start: 0.7010 (mmm) cc_final: 0.6559 (mmm) REVERT: A 293 ASN cc_start: 0.8917 (p0) cc_final: 0.8503 (p0) REVERT: A 344 MET cc_start: 0.8761 (ttp) cc_final: 0.7756 (ptm) REVERT: A 425 ASN cc_start: 0.8353 (m110) cc_final: 0.7502 (t0) REVERT: A 429 SER cc_start: 0.8972 (t) cc_final: 0.8527 (m) REVERT: A 446 ASP cc_start: 0.8142 (p0) cc_final: 0.7620 (p0) REVERT: A 507 CYS cc_start: 0.8505 (m) cc_final: 0.8007 (t) REVERT: B 52 TYR cc_start: 0.7691 (m-80) cc_final: 0.7331 (m-80) REVERT: B 75 LEU cc_start: 0.8360 (mt) cc_final: 0.8134 (mt) REVERT: B 79 MET cc_start: 0.8148 (tpt) cc_final: 0.7284 (tpt) REVERT: B 87 ILE cc_start: 0.8857 (pt) cc_final: 0.8477 (mm) REVERT: B 91 LEU cc_start: 0.8670 (mt) cc_final: 0.8234 (mm) REVERT: B 143 PHE cc_start: 0.7622 (m-10) cc_final: 0.7374 (m-10) REVERT: B 255 CYS cc_start: 0.8086 (p) cc_final: 0.7834 (p) REVERT: B 257 GLU cc_start: 0.7822 (tt0) cc_final: 0.7333 (tt0) REVERT: B 282 MET cc_start: 0.6859 (mtt) cc_final: 0.6547 (ttm) REVERT: B 311 GLU cc_start: 0.5286 (tt0) cc_final: 0.4698 (tt0) REVERT: B 393 GLU cc_start: 0.7192 (pm20) cc_final: 0.6978 (pm20) REVERT: B 459 GLN cc_start: 0.8497 (mt0) cc_final: 0.7889 (tp40) REVERT: B 482 LEU cc_start: 0.8606 (mm) cc_final: 0.8290 (mm) REVERT: B 507 CYS cc_start: 0.7837 (t) cc_final: 0.7387 (t) REVERT: B 508 SER cc_start: 0.8706 (p) cc_final: 0.8491 (t) REVERT: C 39 ILE cc_start: 0.8197 (mp) cc_final: 0.7832 (mm) REVERT: C 240 SER cc_start: 0.8760 (m) cc_final: 0.8513 (t) REVERT: C 248 ASP cc_start: 0.6736 (m-30) cc_final: 0.6416 (m-30) REVERT: C 261 GLU cc_start: 0.7346 (mt-10) cc_final: 0.6923 (mt-10) REVERT: C 294 MET cc_start: 0.9147 (mtt) cc_final: 0.8817 (mtt) REVERT: C 340 ARG cc_start: 0.8026 (mmp80) cc_final: 0.7788 (mmp80) REVERT: C 367 LYS cc_start: 0.9108 (ttmt) cc_final: 0.8060 (ttpp) REVERT: D 37 ASP cc_start: 0.8841 (p0) cc_final: 0.8531 (p0) REVERT: D 56 VAL cc_start: 0.8849 (t) cc_final: 0.8463 (t) REVERT: D 62 GLU cc_start: 0.6496 (mm-30) cc_final: 0.6202 (mm-30) REVERT: D 191 PHE cc_start: 0.8503 (t80) cc_final: 0.8067 (t80) REVERT: D 260 MET cc_start: 0.8001 (mmp) cc_final: 0.7746 (mmp) REVERT: D 269 GLU cc_start: 0.6981 (mm-30) cc_final: 0.6439 (mm-30) REVERT: D 275 GLU cc_start: 0.8806 (tp30) cc_final: 0.8023 (tp30) REVERT: D 296 GLU cc_start: 0.7782 (mm-30) cc_final: 0.7483 (mm-30) REVERT: D 300 VAL cc_start: 0.8999 (t) cc_final: 0.8761 (t) REVERT: E 232 ILE cc_start: 0.8779 (mt) cc_final: 0.8536 (mp) REVERT: E 243 GLU cc_start: 0.7964 (tp30) cc_final: 0.7517 (tp30) REVERT: E 289 THR cc_start: 0.8801 (m) cc_final: 0.8556 (t) REVERT: E 300 VAL cc_start: 0.8417 (m) cc_final: 0.8004 (m) REVERT: E 307 SER cc_start: 0.8066 (p) cc_final: 0.7865 (m) REVERT: E 425 GLN cc_start: 0.8803 (pt0) cc_final: 0.8566 (pt0) REVERT: F 89 LEU cc_start: 0.8798 (mt) cc_final: 0.8407 (mt) REVERT: F 140 VAL cc_start: 0.9546 (t) cc_final: 0.9340 (t) REVERT: F 176 ASP cc_start: 0.8302 (p0) cc_final: 0.7436 (p0) REVERT: F 219 LEU cc_start: 0.8415 (pt) cc_final: 0.7709 (pp) REVERT: F 221 LEU cc_start: 0.8099 (mt) cc_final: 0.7507 (tt) REVERT: F 239 LEU cc_start: 0.8671 (mt) cc_final: 0.8416 (mm) REVERT: F 254 LEU cc_start: 0.8528 (mt) cc_final: 0.8263 (mt) REVERT: F 265 GLU cc_start: 0.8980 (mm-30) cc_final: 0.8489 (mm-30) REVERT: F 280 ARG cc_start: 0.8569 (tpp80) cc_final: 0.8059 (ttt90) REVERT: G 32 ARG cc_start: 0.8162 (mmp80) cc_final: 0.7800 (mmp80) REVERT: G 145 THR cc_start: 0.7727 (t) cc_final: 0.7340 (t) REVERT: G 156 LYS cc_start: 0.8146 (ttmm) cc_final: 0.7898 (ttmm) REVERT: G 159 ARG cc_start: 0.8185 (ttm110) cc_final: 0.7643 (ttm110) REVERT: G 191 THR cc_start: 0.9427 (p) cc_final: 0.8901 (t) REVERT: G 194 LEU cc_start: 0.8864 (tp) cc_final: 0.8434 (tt) REVERT: H 66 ARG cc_start: 0.7327 (tpt-90) cc_final: 0.6800 (ptt90) REVERT: I 89 ARG cc_start: 0.6750 (ttm110) cc_final: 0.5088 (tpt-90) REVERT: J 182 VAL cc_start: 0.7074 (m) cc_final: 0.6737 (p) REVERT: K 80 GLU cc_start: 0.4440 (mt-10) cc_final: 0.2166 (tm-30) REVERT: L 78 GLU cc_start: 0.8109 (pp20) cc_final: 0.7803 (pp20) REVERT: M 112 VAL cc_start: 0.6191 (t) cc_final: 0.5987 (t) outliers start: 0 outliers final: 0 residues processed: 966 average time/residue: 0.4141 time to fit residues: 644.8486 Evaluate side-chains 732 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 732 time to evaluate : 3.614 ------------------------------------------------------------------------------- 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: 9.9990 chunk 225 optimal weight: 0.9980 chunk 5 optimal weight: 10.0000 chunk 295 optimal weight: 0.8980 chunk 163 optimal weight: 6.9990 chunk 339 optimal weight: 8.9990 chunk 274 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 202 optimal weight: 4.9990 chunk 356 optimal weight: 6.9990 chunk 100 optimal weight: 0.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 418 HIS ** C 238 GLN ** 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 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 222 ASN E 120 ASN E 170 GLN E 364 ASN E 407 ASN ** F 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 181 GLN J 124 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.6268 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= 0.255 Angle : 0.755 9.722 44378 Z= 0.377 Chirality : 0.046 0.322 4987 Planarity : 0.006 0.080 5831 Dihedral : 6.252 121.502 4623 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 14.47 Ramachandran Plot: Outliers : 0.53 % Allowed : 9.31 % Favored : 90.15 % Rotamer: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % 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: -1.89 (0.13), residues: 4134 helix: -0.26 (0.13), residues: 1627 sheet: -1.30 (0.25), residues: 431 loop : -2.08 (0.13), residues: 2076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.002 TRP C 244 HIS 0.010 0.001 HIS F 323 PHE 0.025 0.002 PHE M 109 TYR 0.057 0.002 TYR F 383 ARG 0.019 0.001 ARG K 74 *********************** 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 913 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 913 time to evaluate : 3.571 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 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. REVERT: A 207 THR cc_start: 0.9433 (t) cc_final: 0.9097 (p) REVERT: A 269 PHE cc_start: 0.8097 (m-80) cc_final: 0.7738 (m-80) REVERT: A 282 MET cc_start: 0.6919 (mmm) cc_final: 0.6369 (mmm) REVERT: A 293 ASN cc_start: 0.9011 (p0) cc_final: 0.8452 (p0) REVERT: A 425 ASN cc_start: 0.8616 (m110) cc_final: 0.7631 (t0) REVERT: A 450 LEU cc_start: 0.7630 (tt) cc_final: 0.7351 (tt) REVERT: A 468 VAL cc_start: 0.8482 (t) cc_final: 0.8256 (t) REVERT: A 492 GLU cc_start: 0.8342 (tt0) cc_final: 0.7820 (tt0) REVERT: A 507 CYS cc_start: 0.8427 (m) cc_final: 0.8132 (m) REVERT: B 28 CYS cc_start: 0.6299 (t) cc_final: 0.5854 (t) REVERT: B 52 TYR cc_start: 0.7705 (m-80) cc_final: 0.7449 (m-80) REVERT: B 79 MET cc_start: 0.8254 (tpt) cc_final: 0.7771 (tpt) REVERT: B 87 ILE cc_start: 0.8862 (pt) cc_final: 0.8509 (mm) REVERT: B 91 LEU cc_start: 0.8709 (mt) cc_final: 0.8228 (mm) REVERT: B 193 ARG cc_start: 0.7823 (mtt180) cc_final: 0.6580 (mtt90) REVERT: B 255 CYS cc_start: 0.8204 (p) cc_final: 0.7948 (p) REVERT: B 257 GLU cc_start: 0.7979 (tt0) cc_final: 0.7717 (tt0) REVERT: B 340 ARG cc_start: 0.7908 (tpp80) cc_final: 0.7561 (tpp80) REVERT: B 399 THR cc_start: 0.9368 (p) cc_final: 0.9155 (p) REVERT: B 408 ARG cc_start: 0.8288 (ttt180) cc_final: 0.7956 (ttm170) REVERT: B 459 GLN cc_start: 0.8433 (mt0) cc_final: 0.7931 (tp40) REVERT: B 516 MET cc_start: 0.7521 (ttp) cc_final: 0.7312 (ttp) REVERT: C 39 ILE cc_start: 0.8392 (mp) cc_final: 0.7905 (mm) REVERT: C 200 ASP cc_start: 0.8785 (t0) cc_final: 0.8561 (t0) REVERT: C 248 ASP cc_start: 0.6770 (m-30) cc_final: 0.6459 (m-30) REVERT: C 290 ASN cc_start: 0.8789 (t0) cc_final: 0.8038 (t0) REVERT: C 294 MET cc_start: 0.9103 (mtt) cc_final: 0.8718 (mtt) REVERT: C 367 LYS cc_start: 0.9165 (ttmt) cc_final: 0.8153 (ttpp) REVERT: C 370 THR cc_start: 0.8270 (p) cc_final: 0.7934 (p) REVERT: C 468 VAL cc_start: 0.8961 (t) cc_final: 0.8703 (t) REVERT: D 37 ASP cc_start: 0.8822 (p0) cc_final: 0.8539 (p0) REVERT: D 56 VAL cc_start: 0.9009 (t) cc_final: 0.8345 (t) REVERT: D 62 GLU cc_start: 0.6424 (mm-30) cc_final: 0.6201 (mm-30) REVERT: D 163 ILE cc_start: 0.9117 (mt) cc_final: 0.8914 (mt) REVERT: D 260 MET cc_start: 0.8049 (mmp) cc_final: 0.7758 (mmp) REVERT: D 269 GLU cc_start: 0.6915 (mm-30) cc_final: 0.6417 (mm-30) REVERT: D 296 GLU cc_start: 0.7961 (mm-30) cc_final: 0.7466 (mm-30) REVERT: D 371 THR cc_start: 0.8778 (t) cc_final: 0.8429 (m) REVERT: D 408 ASP cc_start: 0.8478 (p0) cc_final: 0.8253 (p0) REVERT: E 135 ILE cc_start: 0.8861 (mm) cc_final: 0.8642 (mm) REVERT: E 243 GLU cc_start: 0.7969 (tp30) cc_final: 0.7499 (tp30) REVERT: E 425 GLN cc_start: 0.8868 (pt0) cc_final: 0.8540 (pt0) REVERT: F 89 LEU cc_start: 0.8709 (mt) cc_final: 0.8307 (mt) REVERT: F 139 ASP cc_start: 0.8451 (m-30) cc_final: 0.8161 (m-30) REVERT: F 156 SER cc_start: 0.8659 (m) cc_final: 0.8416 (p) REVERT: F 176 ASP cc_start: 0.8274 (p0) cc_final: 0.7466 (p0) REVERT: F 221 LEU cc_start: 0.8292 (mt) cc_final: 0.7516 (tt) REVERT: F 239 LEU cc_start: 0.8714 (mt) cc_final: 0.8499 (mm) REVERT: F 254 LEU cc_start: 0.8611 (mt) cc_final: 0.8361 (mt) REVERT: F 280 ARG cc_start: 0.8547 (tpp80) cc_final: 0.8107 (ttt90) REVERT: G 47 MET cc_start: 0.3541 (tpp) cc_final: 0.3192 (tpp) REVERT: G 159 ARG cc_start: 0.7912 (ttm110) cc_final: 0.7570 (ttm110) REVERT: H 66 ARG cc_start: 0.7354 (tpt-90) cc_final: 0.6769 (ptt-90) REVERT: I 78 ARG cc_start: 0.6458 (ttp-110) cc_final: 0.5240 (ptm-80) REVERT: I 89 ARG cc_start: 0.6608 (ttm110) cc_final: 0.5132 (tpt-90) REVERT: J 182 VAL cc_start: 0.7143 (m) cc_final: 0.6755 (p) REVERT: L 94 LEU cc_start: 0.5712 (tp) cc_final: 0.5029 (mp) REVERT: L 162 GLN cc_start: 0.6546 (mp10) cc_final: 0.6274 (mp10) outliers start: 0 outliers final: 0 residues processed: 913 average time/residue: 0.4169 time to fit residues: 612.8339 Evaluate side-chains 704 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 704 time to evaluate : 3.769 ------------------------------------------------------------------------------- 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: 0.0970 chunk 357 optimal weight: 6.9990 chunk 78 optimal weight: 6.9990 chunk 233 optimal weight: 0.6980 chunk 98 optimal weight: 9.9990 chunk 397 optimal weight: 8.9990 chunk 330 optimal weight: 9.9990 chunk 184 optimal weight: 2.9990 chunk 33 optimal weight: 6.9990 chunk 131 optimal weight: 0.3980 chunk 208 optimal weight: 2.9990 overall best weight: 1.4382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 397 GLN B 290 ASN B 501 HIS ** C 238 GLN ** 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 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 161 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.6533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 32742 Z= 0.204 Angle : 0.718 11.155 44378 Z= 0.355 Chirality : 0.045 0.269 4987 Planarity : 0.005 0.081 5831 Dihedral : 5.967 111.770 4623 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.56 % Allowed : 8.20 % Favored : 91.24 % Rotamer: Outliers : 0.03 % Allowed : 2.71 % Favored : 97.26 % 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: -0.05 (0.13), residues: 1620 sheet: -1.21 (0.24), residues: 444 loop : -1.99 (0.13), residues: 2070 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP C 244 HIS 0.008 0.001 HIS F 323 PHE 0.028 0.002 PHE G 70 TYR 0.030 0.001 TYR F 383 ARG 0.009 0.000 ARG D 297 *********************** 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 918 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 917 time to evaluate : 3.962 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 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 revert: symmetry clash TARDY: cannot create tardy model for: "CYS M 322 " (corrupted residue). Skipping it. REVERT: A 262 MET cc_start: 0.8234 (mmp) cc_final: 0.7912 (mmp) REVERT: A 269 PHE cc_start: 0.8160 (m-80) cc_final: 0.7775 (m-80) REVERT: A 282 MET cc_start: 0.6922 (mmm) cc_final: 0.6449 (mmm) REVERT: A 293 ASN cc_start: 0.8949 (p0) cc_final: 0.8468 (p0) REVERT: A 379 THR cc_start: 0.9031 (m) cc_final: 0.8781 (t) REVERT: A 425 ASN cc_start: 0.8553 (m110) cc_final: 0.7622 (t0) REVERT: A 446 ASP cc_start: 0.8237 (p0) cc_final: 0.7734 (p0) REVERT: A 464 LEU cc_start: 0.9045 (mt) cc_final: 0.8794 (mt) REVERT: A 507 CYS cc_start: 0.8582 (m) cc_final: 0.8302 (t) REVERT: A 530 ILE cc_start: 0.8811 (mm) cc_final: 0.8494 (mm) REVERT: B 75 LEU cc_start: 0.8434 (mt) cc_final: 0.8198 (mt) REVERT: B 79 MET cc_start: 0.7924 (tpt) cc_final: 0.7237 (tpt) REVERT: B 87 ILE cc_start: 0.8837 (pt) cc_final: 0.8489 (mm) REVERT: B 91 LEU cc_start: 0.8708 (mt) cc_final: 0.8380 (mm) REVERT: B 130 ARG cc_start: 0.7951 (ttp80) cc_final: 0.7402 (ttp80) REVERT: B 133 MET cc_start: 0.7491 (ttm) cc_final: 0.6893 (ttp) REVERT: B 238 GLN cc_start: 0.7863 (tp40) cc_final: 0.7627 (tp40) REVERT: B 340 ARG cc_start: 0.7738 (tpp80) cc_final: 0.7470 (tpp80) REVERT: B 396 THR cc_start: 0.7781 (m) cc_final: 0.5699 (m) REVERT: B 399 THR cc_start: 0.9339 (p) cc_final: 0.9114 (p) REVERT: B 449 GLU cc_start: 0.8487 (mp0) cc_final: 0.8265 (mm-30) REVERT: B 501 HIS cc_start: 0.6733 (OUTLIER) cc_final: 0.6367 (m170) REVERT: C 2 ILE cc_start: 0.7864 (mm) cc_final: 0.7509 (mm) REVERT: C 39 ILE cc_start: 0.8325 (mp) cc_final: 0.7860 (mm) REVERT: C 94 ILE cc_start: 0.8748 (mp) cc_final: 0.8387 (tp) REVERT: C 135 LEU cc_start: 0.9116 (mt) cc_final: 0.8902 (mt) REVERT: C 183 MET cc_start: 0.7094 (ppp) cc_final: 0.6421 (ptm) REVERT: C 248 ASP cc_start: 0.6712 (m-30) cc_final: 0.6423 (m-30) REVERT: C 290 ASN cc_start: 0.8662 (t0) cc_final: 0.8390 (t0) REVERT: C 323 MET cc_start: 0.6725 (ppp) cc_final: 0.6504 (ppp) REVERT: C 367 LYS cc_start: 0.9166 (ttmt) cc_final: 0.8218 (ttpp) REVERT: C 370 THR cc_start: 0.8352 (p) cc_final: 0.7993 (p) REVERT: D 37 ASP cc_start: 0.8736 (p0) cc_final: 0.8468 (p0) REVERT: D 56 VAL cc_start: 0.9074 (t) cc_final: 0.8862 (t) REVERT: D 88 MET cc_start: 0.8101 (mtp) cc_final: 0.7507 (ttt) REVERT: D 163 ILE cc_start: 0.9133 (mt) cc_final: 0.8918 (mt) REVERT: D 260 MET cc_start: 0.8144 (mmp) cc_final: 0.7751 (mmp) REVERT: D 269 GLU cc_start: 0.6962 (mm-30) cc_final: 0.6311 (mm-30) REVERT: D 296 GLU cc_start: 0.7782 (mm-30) cc_final: 0.7452 (mm-30) REVERT: D 371 THR cc_start: 0.8746 (t) cc_final: 0.8403 (m) REVERT: D 408 ASP cc_start: 0.8591 (p0) cc_final: 0.8362 (p0) REVERT: D 443 LEU cc_start: 0.9121 (mm) cc_final: 0.8844 (pp) REVERT: E 47 VAL cc_start: 0.8685 (t) cc_final: 0.8439 (m) REVERT: E 52 GLU cc_start: 0.7257 (pt0) cc_final: 0.6844 (pm20) REVERT: E 162 GLU cc_start: 0.6784 (mm-30) cc_final: 0.6487 (mm-30) REVERT: E 191 PHE cc_start: 0.7391 (t80) cc_final: 0.7189 (t80) REVERT: E 206 GLN cc_start: 0.7862 (pp30) cc_final: 0.7195 (pp30) REVERT: E 425 GLN cc_start: 0.8678 (pt0) cc_final: 0.8424 (pt0) REVERT: E 429 ASN cc_start: 0.8264 (t0) cc_final: 0.6910 (m-40) REVERT: F 73 VAL cc_start: 0.8471 (t) cc_final: 0.8254 (t) REVERT: F 89 LEU cc_start: 0.8780 (mt) cc_final: 0.8328 (mt) REVERT: F 139 ASP cc_start: 0.8425 (m-30) cc_final: 0.8166 (m-30) REVERT: F 156 SER cc_start: 0.8576 (m) cc_final: 0.8356 (p) REVERT: F 176 ASP cc_start: 0.8309 (p0) cc_final: 0.7505 (p0) REVERT: F 221 LEU cc_start: 0.8285 (mt) cc_final: 0.7631 (tt) REVERT: F 239 LEU cc_start: 0.8690 (mt) cc_final: 0.8472 (mm) REVERT: F 254 LEU cc_start: 0.8552 (mt) cc_final: 0.8213 (mt) REVERT: G 23 LYS cc_start: 0.7352 (tppt) cc_final: 0.6823 (tppt) REVERT: G 29 LYS cc_start: 0.3799 (tptt) cc_final: 0.3519 (tptp) REVERT: G 32 ARG cc_start: 0.8205 (mmp-170) cc_final: 0.7986 (mmp-170) REVERT: G 47 MET cc_start: 0.3103 (tpp) cc_final: 0.2780 (tpp) REVERT: G 159 ARG cc_start: 0.7887 (ttm110) cc_final: 0.7225 (ttt90) REVERT: G 173 ARG cc_start: 0.8767 (mmm-85) cc_final: 0.8328 (ttp-170) REVERT: H 66 ARG cc_start: 0.7500 (tpt-90) cc_final: 0.6915 (ptt-90) REVERT: I 89 ARG cc_start: 0.6785 (ttm110) cc_final: 0.5121 (tpt-90) REVERT: J 49 LEU cc_start: 0.4363 (mm) cc_final: 0.3820 (mm) REVERT: L 94 LEU cc_start: 0.5638 (tp) cc_final: 0.5013 (mp) outliers start: 1 outliers final: 0 residues processed: 918 average time/residue: 0.4133 time to fit residues: 613.3022 Evaluate side-chains 730 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 729 time to evaluate : 3.425 ------------------------------------------------------------------------------- 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: 3.9990 chunk 44 optimal weight: 5.9990 chunk 226 optimal weight: 4.9990 chunk 290 optimal weight: 10.0000 chunk 224 optimal weight: 3.9990 chunk 334 optimal weight: 10.0000 chunk 222 optimal weight: 4.9990 chunk 396 optimal weight: 9.9990 chunk 247 optimal weight: 0.1980 chunk 241 optimal weight: 6.9990 chunk 182 optimal weight: 2.9990 overall best weight: 3.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 290 ASN ** B 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 50 GLN ** C 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 323 HIS E 448 GLN F 170 GLN F 338 GLN ** F 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.6723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.106 32742 Z= 0.325 Angle : 0.811 10.679 44378 Z= 0.405 Chirality : 0.048 0.245 4987 Planarity : 0.006 0.071 5831 Dihedral : 6.071 98.845 4623 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 16.04 Ramachandran Plot: Outliers : 0.53 % Allowed : 10.28 % Favored : 89.19 % Rotamer: Outliers : 0.03 % Allowed : 2.22 % Favored : 97.75 % 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: -1.75 (0.13), residues: 4134 helix: -0.14 (0.13), residues: 1638 sheet: -1.17 (0.24), residues: 446 loop : -2.04 (0.13), residues: 2050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 244 HIS 0.011 0.002 HIS A 418 PHE 0.024 0.003 PHE B 269 TYR 0.054 0.002 TYR F 383 ARG 0.009 0.001 ARG E 360 *********************** 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 857 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 856 time to evaluate : 3.563 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 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 revert: symmetry clash TARDY: cannot create tardy model for: "CYS M 322 " (corrupted residue). Skipping it. REVERT: A 79 MET cc_start: 0.7365 (mtp) cc_final: 0.6386 (ttm) REVERT: A 88 GLN cc_start: 0.7263 (tp40) cc_final: 0.7019 (tp40) REVERT: A 255 CYS cc_start: 0.8491 (p) cc_final: 0.8233 (p) REVERT: A 262 MET cc_start: 0.8294 (mmp) cc_final: 0.7868 (mmp) REVERT: A 263 THR cc_start: 0.9193 (p) cc_final: 0.8985 (p) REVERT: A 285 THR cc_start: 0.8259 (m) cc_final: 0.7876 (m) REVERT: A 291 THR cc_start: 0.8572 (m) cc_final: 0.8195 (m) REVERT: A 293 ASN cc_start: 0.8812 (p0) cc_final: 0.8261 (p0) REVERT: A 344 MET cc_start: 0.8484 (ttp) cc_final: 0.7837 (ptm) REVERT: A 425 ASN cc_start: 0.8926 (m110) cc_final: 0.8011 (t0) REVERT: A 468 VAL cc_start: 0.8161 (t) cc_final: 0.7788 (t) REVERT: A 478 ASP cc_start: 0.8323 (t0) cc_final: 0.7924 (t0) REVERT: A 495 LEU cc_start: 0.9233 (mm) cc_final: 0.8785 (tp) REVERT: A 507 CYS cc_start: 0.8722 (m) cc_final: 0.8401 (t) REVERT: B 79 MET cc_start: 0.7631 (tpt) cc_final: 0.7081 (tpt) REVERT: B 87 ILE cc_start: 0.8942 (pt) cc_final: 0.8564 (mm) REVERT: B 91 LEU cc_start: 0.8683 (mt) cc_final: 0.8297 (mm) REVERT: B 130 ARG cc_start: 0.7835 (ttp80) cc_final: 0.7294 (tmm-80) REVERT: B 133 MET cc_start: 0.7973 (ttm) cc_final: 0.7244 (ttp) REVERT: B 244 TRP cc_start: 0.8053 (m100) cc_final: 0.7790 (m100) REVERT: B 255 CYS cc_start: 0.8337 (p) cc_final: 0.8037 (p) REVERT: B 311 GLU cc_start: 0.6079 (tm-30) cc_final: 0.5515 (tm-30) REVERT: B 322 LEU cc_start: 0.8765 (tt) cc_final: 0.8469 (tt) REVERT: B 482 LEU cc_start: 0.8629 (mm) cc_final: 0.8257 (mm) REVERT: B 516 MET cc_start: 0.8258 (mtp) cc_final: 0.7499 (ttp) REVERT: C 39 ILE cc_start: 0.8337 (mp) cc_final: 0.8024 (mm) REVERT: C 94 ILE cc_start: 0.8858 (mp) cc_final: 0.8356 (tp) REVERT: C 206 LEU cc_start: 0.9064 (mm) cc_final: 0.8778 (mm) REVERT: C 248 ASP cc_start: 0.7139 (m-30) cc_final: 0.6746 (m-30) REVERT: C 367 LYS cc_start: 0.9272 (ttmt) cc_final: 0.8297 (ttpp) REVERT: D 37 ASP cc_start: 0.8760 (p0) cc_final: 0.8415 (p0) REVERT: D 88 MET cc_start: 0.8253 (mtp) cc_final: 0.7613 (ttm) REVERT: D 214 LEU cc_start: 0.7573 (tt) cc_final: 0.7339 (tt) REVERT: D 225 ASP cc_start: 0.8054 (p0) cc_final: 0.7848 (p0) REVERT: D 269 GLU cc_start: 0.6794 (mm-30) cc_final: 0.6393 (mm-30) REVERT: D 296 GLU cc_start: 0.7467 (mm-30) cc_final: 0.7094 (mm-30) REVERT: D 371 THR cc_start: 0.8874 (t) cc_final: 0.8606 (m) REVERT: D 383 TYR cc_start: 0.9122 (t80) cc_final: 0.8847 (t80) REVERT: D 408 ASP cc_start: 0.8618 (p0) cc_final: 0.8340 (p0) REVERT: E 114 ILE cc_start: 0.8791 (pt) cc_final: 0.8583 (pt) REVERT: E 120 ASN cc_start: 0.8689 (t0) cc_final: 0.8405 (t0) REVERT: E 206 GLN cc_start: 0.7962 (pp30) cc_final: 0.7606 (pp30) REVERT: E 307 SER cc_start: 0.8234 (p) cc_final: 0.7953 (m) REVERT: E 316 MET cc_start: 0.8566 (ptm) cc_final: 0.8209 (ptp) REVERT: E 349 TYR cc_start: 0.7626 (t80) cc_final: 0.7130 (t80) REVERT: E 425 GLN cc_start: 0.8775 (pt0) cc_final: 0.8549 (pt0) REVERT: F 53 GLU cc_start: 0.8706 (pm20) cc_final: 0.7166 (tm-30) REVERT: F 60 PHE cc_start: 0.8661 (m-10) cc_final: 0.8140 (m-80) REVERT: F 89 LEU cc_start: 0.8781 (mt) cc_final: 0.8326 (mt) REVERT: F 138 ILE cc_start: 0.8633 (mm) cc_final: 0.8143 (mm) REVERT: F 139 ASP cc_start: 0.8385 (m-30) cc_final: 0.8147 (m-30) REVERT: F 170 GLN cc_start: 0.8706 (OUTLIER) cc_final: 0.8439 (mp10) REVERT: F 176 ASP cc_start: 0.8481 (p0) cc_final: 0.7681 (p0) REVERT: F 221 LEU cc_start: 0.8444 (mt) cc_final: 0.7542 (tt) REVERT: F 239 LEU cc_start: 0.8665 (mt) cc_final: 0.7945 (mm) REVERT: F 316 MET cc_start: 0.9015 (ppp) cc_final: 0.8534 (ppp) REVERT: F 325 ILE cc_start: 0.8886 (mt) cc_final: 0.8590 (mt) REVERT: G 47 MET cc_start: 0.4094 (tpp) cc_final: 0.3703 (tpp) REVERT: G 159 ARG cc_start: 0.7745 (ttm110) cc_final: 0.6848 (ttt90) REVERT: G 173 ARG cc_start: 0.8710 (mmm-85) cc_final: 0.8233 (ttp-170) REVERT: G 191 THR cc_start: 0.9472 (p) cc_final: 0.8861 (t) REVERT: G 192 PHE cc_start: 0.7610 (m-10) cc_final: 0.7392 (m-10) REVERT: H 1 MET cc_start: 0.7807 (mmm) cc_final: 0.6859 (mmt) REVERT: H 18 LEU cc_start: 0.6611 (tp) cc_final: 0.6118 (mm) REVERT: H 66 ARG cc_start: 0.7483 (tpt-90) cc_final: 0.6957 (ptt-90) REVERT: I 78 ARG cc_start: 0.6175 (ttp-110) cc_final: 0.4986 (ptm-80) REVERT: I 85 LEU cc_start: 0.7703 (pp) cc_final: 0.7448 (pp) REVERT: I 89 ARG cc_start: 0.6709 (ttm110) cc_final: 0.5159 (tpt-90) REVERT: L 94 LEU cc_start: 0.5903 (tp) cc_final: 0.5188 (mp) outliers start: 1 outliers final: 0 residues processed: 857 average time/residue: 0.4066 time to fit residues: 564.6272 Evaluate side-chains 687 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 686 time to evaluate : 3.525 ------------------------------------------------------------------------------- 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: 2.9990 chunk 158 optimal weight: 3.9990 chunk 236 optimal weight: 6.9990 chunk 119 optimal weight: 7.9990 chunk 77 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 251 optimal weight: 0.8980 chunk 269 optimal weight: 9.9990 chunk 195 optimal weight: 0.9980 chunk 36 optimal weight: 6.9990 chunk 311 optimal weight: 1.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 ASN B 290 ASN B 397 GLN ** B 423 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 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 222 ASN ** F 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.6992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 32742 Z= 0.234 Angle : 0.739 9.114 44378 Z= 0.366 Chirality : 0.046 0.228 4987 Planarity : 0.005 0.069 5831 Dihedral : 5.866 91.118 4623 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.48 % Allowed : 8.59 % Favored : 90.93 % Rotamer: Outliers : 0.03 % Allowed : 1.22 % Favored : 98.75 % 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: -1.56 (0.13), residues: 4134 helix: 0.07 (0.13), residues: 1627 sheet: -1.12 (0.24), residues: 450 loop : -1.96 (0.13), residues: 2057 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP L 175 HIS 0.006 0.001 HIS F 323 PHE 0.019 0.002 PHE G 70 TYR 0.036 0.002 TYR F 383 ARG 0.007 0.001 ARG A 329 *********************** 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 868 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 867 time to evaluate : 3.619 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 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. REVERT: A 79 MET cc_start: 0.7408 (mtp) cc_final: 0.6579 (ttm) REVERT: A 88 GLN cc_start: 0.7260 (tp40) cc_final: 0.6826 (tp40) REVERT: A 262 MET cc_start: 0.8213 (mmp) cc_final: 0.7077 (mmp) REVERT: A 290 ASN cc_start: 0.7788 (OUTLIER) cc_final: 0.7448 (t0) REVERT: A 293 ASN cc_start: 0.8616 (p0) cc_final: 0.7911 (p0) REVERT: A 344 MET cc_start: 0.8508 (ttp) cc_final: 0.7886 (ptp) REVERT: A 363 GLU cc_start: 0.8328 (tm-30) cc_final: 0.8110 (tm-30) REVERT: A 425 ASN cc_start: 0.8999 (m110) cc_final: 0.7736 (t0) REVERT: A 449 GLU cc_start: 0.6833 (mm-30) cc_final: 0.6537 (mm-30) REVERT: A 478 ASP cc_start: 0.8188 (t0) cc_final: 0.7836 (t0) REVERT: A 495 LEU cc_start: 0.9145 (mm) cc_final: 0.8724 (mt) REVERT: A 507 CYS cc_start: 0.8707 (m) cc_final: 0.8382 (t) REVERT: B 1 MET cc_start: 0.7581 (pmm) cc_final: 0.6871 (pmm) REVERT: B 75 LEU cc_start: 0.8435 (mt) cc_final: 0.8214 (mt) REVERT: B 79 MET cc_start: 0.8057 (tpt) cc_final: 0.7359 (tpt) REVERT: B 87 ILE cc_start: 0.8908 (pt) cc_final: 0.8582 (mm) REVERT: B 91 LEU cc_start: 0.8706 (mt) cc_final: 0.8336 (mm) REVERT: B 130 ARG cc_start: 0.7765 (ttp80) cc_final: 0.7226 (tmm-80) REVERT: B 133 MET cc_start: 0.8030 (ttm) cc_final: 0.7392 (ttp) REVERT: B 238 GLN cc_start: 0.7746 (tp40) cc_final: 0.7433 (tp40) REVERT: B 311 GLU cc_start: 0.5880 (tm-30) cc_final: 0.5568 (tm-30) REVERT: B 340 ARG cc_start: 0.8024 (tpp80) cc_final: 0.7509 (tpp80) REVERT: B 396 THR cc_start: 0.7740 (m) cc_final: 0.5952 (m) REVERT: B 446 ASP cc_start: 0.7534 (p0) cc_final: 0.7196 (p0) REVERT: B 482 LEU cc_start: 0.8400 (mm) cc_final: 0.7973 (tp) REVERT: B 516 MET cc_start: 0.8157 (mtp) cc_final: 0.7378 (ttp) REVERT: C 94 ILE cc_start: 0.8807 (mp) cc_final: 0.8325 (tp) REVERT: C 183 MET cc_start: 0.7365 (ppp) cc_final: 0.6280 (ptp) REVERT: C 200 ASP cc_start: 0.8714 (t0) cc_final: 0.8413 (p0) REVERT: C 248 ASP cc_start: 0.6928 (m-30) cc_final: 0.6613 (m-30) REVERT: C 294 MET cc_start: 0.9049 (mtt) cc_final: 0.8707 (mtt) REVERT: C 367 LYS cc_start: 0.9281 (ttmt) cc_final: 0.8423 (ttpp) REVERT: C 370 THR cc_start: 0.8728 (p) cc_final: 0.8491 (p) REVERT: C 458 LEU cc_start: 0.9042 (mt) cc_final: 0.8798 (mt) REVERT: D 37 ASP cc_start: 0.8673 (p0) cc_final: 0.8374 (p0) REVERT: D 225 ASP cc_start: 0.8083 (p0) cc_final: 0.7789 (p0) REVERT: D 269 GLU cc_start: 0.7110 (mm-30) cc_final: 0.6601 (mm-30) REVERT: D 371 THR cc_start: 0.8854 (t) cc_final: 0.8610 (m) REVERT: D 383 TYR cc_start: 0.9092 (t80) cc_final: 0.8833 (t80) REVERT: E 120 ASN cc_start: 0.8816 (t0) cc_final: 0.8571 (t0) REVERT: E 206 GLN cc_start: 0.8034 (pp30) cc_final: 0.7533 (pp30) REVERT: E 215 SER cc_start: 0.7668 (p) cc_final: 0.7305 (p) REVERT: E 425 GLN cc_start: 0.8784 (pt0) cc_final: 0.8545 (pt0) REVERT: F 53 GLU cc_start: 0.8661 (pm20) cc_final: 0.7111 (tm-30) REVERT: F 89 LEU cc_start: 0.8776 (mt) cc_final: 0.8205 (mt) REVERT: F 139 ASP cc_start: 0.8425 (m-30) cc_final: 0.8092 (m-30) REVERT: F 156 SER cc_start: 0.9018 (m) cc_final: 0.8773 (m) REVERT: F 176 ASP cc_start: 0.8310 (p0) cc_final: 0.7455 (p0) REVERT: F 221 LEU cc_start: 0.8323 (mt) cc_final: 0.7543 (tt) REVERT: F 254 LEU cc_start: 0.8638 (mt) cc_final: 0.8434 (mt) REVERT: F 310 GLN cc_start: 0.8694 (mm-40) cc_final: 0.7893 (mm-40) REVERT: F 316 MET cc_start: 0.8939 (ppp) cc_final: 0.8517 (ppp) REVERT: F 381 GLN cc_start: 0.8068 (mm-40) cc_final: 0.7858 (mm-40) REVERT: F 425 GLN cc_start: 0.8076 (tp40) cc_final: 0.7851 (mm110) REVERT: G 29 LYS cc_start: 0.3974 (tptt) cc_final: 0.3721 (tptp) REVERT: G 47 MET cc_start: 0.4299 (tpp) cc_final: 0.3916 (tpp) REVERT: G 123 THR cc_start: 0.8539 (m) cc_final: 0.8296 (m) REVERT: G 173 ARG cc_start: 0.8665 (mmm-85) cc_final: 0.8126 (ttp-170) REVERT: H 1 MET cc_start: 0.7568 (mmm) cc_final: 0.6616 (mmt) REVERT: H 18 LEU cc_start: 0.6826 (tp) cc_final: 0.6207 (mm) REVERT: H 66 ARG cc_start: 0.7580 (tpt-90) cc_final: 0.7005 (ptt-90) REVERT: I 78 ARG cc_start: 0.5926 (ttp-110) cc_final: 0.4766 (ptm-80) REVERT: I 89 ARG cc_start: 0.6682 (ttm110) cc_final: 0.5176 (tpt-90) REVERT: J 49 LEU cc_start: 0.4626 (mm) cc_final: 0.3862 (mm) REVERT: L 94 LEU cc_start: 0.5951 (tp) cc_final: 0.5317 (mp) outliers start: 1 outliers final: 0 residues processed: 867 average time/residue: 0.4127 time to fit residues: 582.0602 Evaluate side-chains 703 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 702 time to evaluate : 3.568 ------------------------------------------------------------------------------- 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: 30.0000 chunk 379 optimal weight: 5.9990 chunk 346 optimal weight: 6.9990 chunk 369 optimal weight: 6.9990 chunk 222 optimal weight: 8.9990 chunk 160 optimal weight: 7.9990 chunk 289 optimal weight: 0.7980 chunk 113 optimal weight: 9.9990 chunk 333 optimal weight: 8.9990 chunk 349 optimal weight: 20.0000 chunk 367 optimal weight: 2.9990 overall best weight: 4.7588 ------------------------------------------------------------------------------- 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** B 290 ASN ** B 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 498 ASN ** C 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.7094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 32742 Z= 0.427 Angle : 0.875 10.346 44378 Z= 0.440 Chirality : 0.049 0.357 4987 Planarity : 0.006 0.075 5831 Dihedral : 6.298 84.709 4623 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 19.01 Ramachandran Plot: Outliers : 0.46 % Allowed : 10.74 % Favored : 88.80 % Rotamer: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % 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: -1.85 (0.13), residues: 4134 helix: -0.19 (0.13), residues: 1609 sheet: -1.15 (0.24), residues: 444 loop : -2.13 (0.13), residues: 2081 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 424 HIS 0.009 0.002 HIS E 375 PHE 0.023 0.003 PHE C 313 TYR 0.058 0.003 TYR F 383 ARG 0.024 0.001 ARG F 410 *********************** 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 808 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 808 time to evaluate : 3.485 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 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. REVERT: A 79 MET cc_start: 0.7552 (mtp) cc_final: 0.6785 (ttm) REVERT: A 88 GLN cc_start: 0.7384 (tp40) cc_final: 0.7146 (tp40) REVERT: A 122 MET cc_start: 0.6361 (mpp) cc_final: 0.6032 (mmm) REVERT: A 252 TYR cc_start: 0.8781 (t80) cc_final: 0.8576 (t80) REVERT: A 336 GLU cc_start: 0.6357 (tt0) cc_final: 0.6121 (tt0) REVERT: A 344 MET cc_start: 0.8569 (ttp) cc_final: 0.8156 (ptm) REVERT: A 425 ASN cc_start: 0.9103 (m110) cc_final: 0.8066 (t0) REVERT: A 468 VAL cc_start: 0.8134 (t) cc_final: 0.7928 (t) REVERT: A 495 LEU cc_start: 0.9246 (mm) cc_final: 0.8660 (tp) REVERT: A 507 CYS cc_start: 0.8774 (m) cc_final: 0.8429 (t) REVERT: B 75 LEU cc_start: 0.8676 (mt) cc_final: 0.8288 (mt) REVERT: B 79 MET cc_start: 0.7973 (tpt) cc_final: 0.7594 (tpt) REVERT: B 87 ILE cc_start: 0.9000 (pt) cc_final: 0.8598 (mm) REVERT: B 91 LEU cc_start: 0.8783 (mt) cc_final: 0.8425 (mm) REVERT: B 193 ARG cc_start: 0.7032 (mtt90) cc_final: 0.6800 (mtt90) REVERT: B 255 CYS cc_start: 0.8395 (p) cc_final: 0.8157 (p) REVERT: B 328 SER cc_start: 0.8308 (m) cc_final: 0.8026 (t) REVERT: B 396 THR cc_start: 0.7865 (m) cc_final: 0.6103 (m) REVERT: B 446 ASP cc_start: 0.7727 (p0) cc_final: 0.6992 (p0) REVERT: B 516 MET cc_start: 0.8140 (mtp) cc_final: 0.7768 (mtp) REVERT: C 94 ILE cc_start: 0.8846 (mp) cc_final: 0.8359 (tp) REVERT: C 183 MET cc_start: 0.7519 (ppp) cc_final: 0.6543 (ptp) REVERT: C 184 TYR cc_start: 0.8066 (p90) cc_final: 0.7790 (p90) REVERT: C 248 ASP cc_start: 0.6815 (m-30) cc_final: 0.6501 (m-30) REVERT: C 294 MET cc_start: 0.9097 (mtt) cc_final: 0.8839 (mtt) REVERT: C 367 LYS cc_start: 0.9354 (ttmt) cc_final: 0.8458 (ttpp) REVERT: D 37 ASP cc_start: 0.8718 (p0) cc_final: 0.8487 (p0) REVERT: D 142 ASN cc_start: 0.8690 (p0) cc_final: 0.8485 (p0) REVERT: D 191 PHE cc_start: 0.8772 (t80) cc_final: 0.8258 (t80) REVERT: D 225 ASP cc_start: 0.8202 (p0) cc_final: 0.7964 (p0) REVERT: D 269 GLU cc_start: 0.6838 (mm-30) cc_final: 0.6309 (mm-30) REVERT: D 371 THR cc_start: 0.9062 (t) cc_final: 0.8813 (m) REVERT: E 120 ASN cc_start: 0.9121 (t0) cc_final: 0.8860 (t0) REVERT: E 206 GLN cc_start: 0.8124 (pp30) cc_final: 0.7541 (pp30) REVERT: E 215 SER cc_start: 0.7732 (p) cc_final: 0.7090 (p) REVERT: E 425 GLN cc_start: 0.8701 (pt0) cc_final: 0.8465 (pt0) REVERT: F 53 GLU cc_start: 0.8812 (pm20) cc_final: 0.7227 (tm-30) REVERT: F 60 PHE cc_start: 0.8681 (m-10) cc_final: 0.8228 (m-80) REVERT: F 89 LEU cc_start: 0.8972 (mt) cc_final: 0.8532 (mt) REVERT: F 176 ASP cc_start: 0.8595 (p0) cc_final: 0.7521 (p0) REVERT: F 221 LEU cc_start: 0.8514 (mt) cc_final: 0.7695 (tt) REVERT: F 316 MET cc_start: 0.8973 (ppp) cc_final: 0.8471 (ppp) REVERT: F 325 ILE cc_start: 0.8757 (mt) cc_final: 0.8528 (mt) REVERT: G 47 MET cc_start: 0.4893 (tpp) cc_final: 0.4548 (tpp) REVERT: G 147 LEU cc_start: 0.8123 (tp) cc_final: 0.7750 (tt) REVERT: G 173 ARG cc_start: 0.8787 (mmm-85) cc_final: 0.8224 (ttp-170) REVERT: H 1 MET cc_start: 0.7670 (mmm) cc_final: 0.6724 (mmt) REVERT: H 18 LEU cc_start: 0.6874 (tp) cc_final: 0.6374 (mm) REVERT: H 66 ARG cc_start: 0.7556 (tpt-90) cc_final: 0.7108 (ptt-90) REVERT: I 85 LEU cc_start: 0.7755 (pp) cc_final: 0.7451 (pp) REVERT: I 89 ARG cc_start: 0.6709 (ttm110) cc_final: 0.5196 (tpt-90) REVERT: L 94 LEU cc_start: 0.6106 (tp) cc_final: 0.5567 (mp) outliers start: 0 outliers final: 0 residues processed: 808 average time/residue: 0.4317 time to fit residues: 566.9881 Evaluate side-chains 641 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 641 time to evaluate : 3.412 ------------------------------------------------------------------------------- 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: 6.9990 chunk 390 optimal weight: 20.0000 chunk 238 optimal weight: 5.9990 chunk 185 optimal weight: 1.9990 chunk 271 optimal weight: 0.9980 chunk 409 optimal weight: 20.0000 chunk 376 optimal weight: 0.0040 chunk 326 optimal weight: 9.9990 chunk 33 optimal weight: 0.9990 chunk 251 optimal weight: 2.9990 chunk 199 optimal weight: 2.9990 overall best weight: 1.3998 ------------------------------------------------------------------------------- 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** ** B 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 397 GLN ** D 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 363 ASN ** L 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.7380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 32742 Z= 0.207 Angle : 0.752 15.215 44378 Z= 0.373 Chirality : 0.046 0.217 4987 Planarity : 0.005 0.124 5831 Dihedral : 5.949 84.580 4623 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 14.55 Ramachandran Plot: Outliers : 0.46 % Allowed : 8.08 % Favored : 91.46 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % 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: -1.51 (0.13), residues: 4134 helix: 0.17 (0.13), residues: 1616 sheet: -1.20 (0.24), residues: 449 loop : -1.94 (0.13), residues: 2069 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP L 175 HIS 0.006 0.001 HIS M 145 PHE 0.024 0.002 PHE B 563 TYR 0.057 0.002 TYR F 383 ARG 0.009 0.001 ARG F 360 ********************** 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 853 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 853 time to evaluate : 3.925 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 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. REVERT: A 79 MET cc_start: 0.7148 (mtp) cc_final: 0.6591 (ttm) REVERT: A 122 MET cc_start: 0.6472 (mpp) cc_final: 0.6236 (mmm) REVERT: A 293 ASN cc_start: 0.8583 (p0) cc_final: 0.7758 (p0) REVERT: A 337 ILE cc_start: 0.8935 (mt) cc_final: 0.8181 (mt) REVERT: A 344 MET cc_start: 0.8531 (ttp) cc_final: 0.8189 (ptm) REVERT: A 425 ASN cc_start: 0.8945 (m110) cc_final: 0.7745 (t0) REVERT: A 468 VAL cc_start: 0.7863 (t) cc_final: 0.7631 (t) REVERT: A 495 LEU cc_start: 0.9192 (mm) cc_final: 0.8774 (tp) REVERT: A 507 CYS cc_start: 0.8637 (m) cc_final: 0.8365 (t) REVERT: A 530 ILE cc_start: 0.8582 (mm) cc_final: 0.8353 (mm) REVERT: B 1 MET cc_start: 0.7635 (pmm) cc_final: 0.6953 (pmm) REVERT: B 75 LEU cc_start: 0.8608 (mt) cc_final: 0.8003 (mt) REVERT: B 79 MET cc_start: 0.7874 (tpt) cc_final: 0.7365 (tpt) REVERT: B 87 ILE cc_start: 0.8880 (pt) cc_final: 0.8519 (mm) REVERT: B 91 LEU cc_start: 0.8847 (mt) cc_final: 0.8469 (mm) REVERT: B 148 LEU cc_start: 0.7255 (tp) cc_final: 0.6857 (tp) REVERT: B 238 GLN cc_start: 0.7700 (tp40) cc_final: 0.7447 (tp40) REVERT: B 255 CYS cc_start: 0.8248 (p) cc_final: 0.7990 (p) REVERT: B 311 GLU cc_start: 0.5930 (tm-30) cc_final: 0.5636 (tm-30) REVERT: B 340 ARG cc_start: 0.8066 (tpp80) cc_final: 0.7553 (tpp80) REVERT: B 396 THR cc_start: 0.7723 (m) cc_final: 0.5789 (m) REVERT: B 482 LEU cc_start: 0.8508 (mm) cc_final: 0.7890 (tp) REVERT: B 516 MET cc_start: 0.8091 (mtp) cc_final: 0.7648 (mtp) REVERT: B 536 ILE cc_start: 0.7031 (pt) cc_final: 0.6776 (pt) REVERT: B 550 ARG cc_start: 0.6837 (ttp-170) cc_final: 0.6435 (ttp-170) REVERT: C 20 LEU cc_start: 0.7919 (mm) cc_final: 0.7627 (mp) REVERT: C 183 MET cc_start: 0.7212 (ppp) cc_final: 0.5893 (ptp) REVERT: C 200 ASP cc_start: 0.8672 (t0) cc_final: 0.8333 (p0) REVERT: C 294 MET cc_start: 0.9045 (mtt) cc_final: 0.8678 (mtt) REVERT: C 367 LYS cc_start: 0.9288 (ttmt) cc_final: 0.8610 (ttpp) REVERT: C 370 THR cc_start: 0.8780 (p) cc_final: 0.8541 (p) REVERT: D 37 ASP cc_start: 0.8741 (p0) cc_final: 0.8417 (p0) REVERT: D 76 VAL cc_start: 0.9070 (t) cc_final: 0.7340 (t) REVERT: D 191 PHE cc_start: 0.8707 (t80) cc_final: 0.8225 (t80) REVERT: D 233 LEU cc_start: 0.8825 (mm) cc_final: 0.8452 (mt) REVERT: D 237 MET cc_start: 0.7099 (ttm) cc_final: 0.6879 (ttp) REVERT: D 269 GLU cc_start: 0.7157 (mm-30) cc_final: 0.6730 (mm-30) REVERT: D 296 GLU cc_start: 0.7842 (mm-30) cc_final: 0.7413 (mm-30) REVERT: D 371 THR cc_start: 0.8901 (t) cc_final: 0.8670 (m) REVERT: E 120 ASN cc_start: 0.9037 (t0) cc_final: 0.8786 (t0) REVERT: E 162 GLU cc_start: 0.7066 (mm-30) cc_final: 0.6646 (mm-30) REVERT: E 206 GLN cc_start: 0.8068 (pp30) cc_final: 0.7469 (pp30) REVERT: E 215 SER cc_start: 0.7179 (p) cc_final: 0.6856 (p) REVERT: E 425 GLN cc_start: 0.8738 (pt0) cc_final: 0.8504 (pt0) REVERT: F 35 ILE cc_start: 0.8951 (mp) cc_final: 0.8708 (mt) REVERT: F 36 LYS cc_start: 0.8898 (tptp) cc_final: 0.8667 (tppp) REVERT: F 53 GLU cc_start: 0.8661 (pm20) cc_final: 0.7073 (tm-30) REVERT: F 89 LEU cc_start: 0.8850 (mt) cc_final: 0.8410 (mt) REVERT: F 139 ASP cc_start: 0.8316 (m-30) cc_final: 0.8031 (m-30) REVERT: F 176 ASP cc_start: 0.8460 (p0) cc_final: 0.7512 (p0) REVERT: F 221 LEU cc_start: 0.8363 (mt) cc_final: 0.7635 (tt) REVERT: F 316 MET cc_start: 0.8841 (ppp) cc_final: 0.8404 (ppp) REVERT: F 425 GLN cc_start: 0.8092 (tp40) cc_final: 0.7867 (mm110) REVERT: G 147 LEU cc_start: 0.8206 (tp) cc_final: 0.7887 (tt) REVERT: G 173 ARG cc_start: 0.8569 (mmm-85) cc_final: 0.7884 (ttp-170) REVERT: G 187 GLU cc_start: 0.6697 (mt-10) cc_final: 0.6415 (mt-10) REVERT: G 196 ARG cc_start: 0.6605 (mmt90) cc_final: 0.6297 (mmt-90) REVERT: H 1 MET cc_start: 0.7525 (mmm) cc_final: 0.6702 (mmt) REVERT: H 18 LEU cc_start: 0.6906 (tp) cc_final: 0.6157 (mm) REVERT: H 66 ARG cc_start: 0.7584 (tpt-90) cc_final: 0.7078 (ptt-90) REVERT: I 85 LEU cc_start: 0.7976 (pp) cc_final: 0.7529 (pp) REVERT: I 89 ARG cc_start: 0.6589 (ttm110) cc_final: 0.5159 (tpt-90) REVERT: J 49 LEU cc_start: 0.4735 (mm) cc_final: 0.4075 (mm) REVERT: J 128 LEU cc_start: 0.6178 (tp) cc_final: 0.5848 (tp) REVERT: K 97 LYS cc_start: 0.7761 (tppt) cc_final: 0.7195 (tptm) REVERT: L 66 LEU cc_start: 0.8691 (tp) cc_final: 0.8467 (tp) REVERT: L 94 LEU cc_start: 0.5798 (tp) cc_final: 0.5376 (mp) REVERT: M 241 LEU cc_start: 0.7555 (mt) cc_final: 0.7010 (mt) outliers start: 0 outliers final: 0 residues processed: 853 average time/residue: 0.4147 time to fit residues: 577.4358 Evaluate side-chains 685 residues out of total 3376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 685 time to evaluate : 3.770 ------------------------------------------------------------------------------- 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: 8.9990 chunk 347 optimal weight: 6.9990 chunk 99 optimal weight: 0.9990 chunk 300 optimal weight: 6.9990 chunk 48 optimal weight: 6.9990 chunk 90 optimal weight: 5.9990 chunk 326 optimal weight: 6.9990 chunk 136 optimal weight: 3.9990 chunk 335 optimal weight: 7.9990 chunk 41 optimal weight: 0.9990 chunk 60 optimal weight: 10.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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** ** B 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 498 ASN ** C 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.130131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.103178 restraints weight = 67113.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.105231 restraints weight = 44811.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.106765 restraints weight = 30262.233| |-----------------------------------------------------------------------------| r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.7406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 32742 Z= 0.365 Angle : 0.838 13.176 44378 Z= 0.419 Chirality : 0.048 0.316 4987 Planarity : 0.006 0.098 5831 Dihedral : 6.167 89.246 4623 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 18.28 Ramachandran Plot: Outliers : 0.48 % Allowed : 10.50 % Favored : 89.02 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % 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: -1.76 (0.13), residues: 4134 helix: -0.09 (0.13), residues: 1602 sheet: -1.14 (0.24), residues: 452 loop : -2.09 (0.13), residues: 2080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP J 175 HIS 0.006 0.002 HIS F 323 PHE 0.024 0.003 PHE C 141 TYR 0.040 0.002 TYR F 383 ARG 0.009 0.001 ARG G 186 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9705.57 seconds wall clock time: 172 minutes 33.72 seconds (10353.72 seconds total)