Starting phenix.real_space_refine on Wed Mar 13 03:13:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z1r_11039/03_2024/6z1r_11039_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z1r_11039/03_2024/6z1r_11039.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z1r_11039/03_2024/6z1r_11039.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z1r_11039/03_2024/6z1r_11039.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z1r_11039/03_2024/6z1r_11039_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z1r_11039/03_2024/6z1r_11039_trim_updated.pdb" } resolution = 3.29 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 15 5.49 5 Mg 5 5.21 5 S 120 5.16 5 C 20661 2.51 5 N 5593 2.21 5 O 6223 1.98 5 H 33137 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 27": "OE1" <-> "OE2" Residue "A ASP 36": "OD1" <-> "OD2" Residue "A GLU 51": "OE1" <-> "OE2" Residue "A PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 79": "OD1" <-> "OD2" Residue "A ASP 96": "OD1" <-> "OD2" Residue "A GLU 102": "OE1" <-> "OE2" Residue "A ARG 143": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 170": "OD1" <-> "OD2" Residue "A ASP 181": "OD1" <-> "OD2" Residue "A PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 224": "OD1" <-> "OD2" Residue "A TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 268": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 269": "OD1" <-> "OD2" Residue "A ARG 286": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 287": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 291": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 314": "OD1" <-> "OD2" Residue "A GLU 328": "OE1" <-> "OE2" Residue "A ASP 333": "OD1" <-> "OD2" Residue "A TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 347": "OD1" <-> "OD2" Residue "A GLU 355": "OE1" <-> "OE2" Residue "A PHE 357": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 403": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 406": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 433": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 440": "OE1" <-> "OE2" Residue "A ASP 454": "OD1" <-> "OD2" Residue "A PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 465": "OE1" <-> "OE2" Residue "A GLU 499": "OE1" <-> "OE2" Residue "B GLU 50": "OE1" <-> "OE2" Residue "B GLU 51": "OE1" <-> "OE2" Residue "B ASP 96": "OD1" <-> "OD2" Residue "B GLU 101": "OE1" <-> "OE2" Residue "B ASP 109": "OD1" <-> "OD2" Residue "B ASP 116": "OD1" <-> "OD2" Residue "B PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 194": "OD1" <-> "OD2" Residue "B GLU 195": "OE1" <-> "OE2" Residue "B TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 219": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ASP 224": "OD1" <-> "OD2" Residue "B TYR 228": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 255": "OE1" <-> "OE2" Residue "B PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 259": "OD1" <-> "OD2" Residue "B ARG 291": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 333": "OD1" <-> "OD2" Residue "B PHE 351": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 353": "OE1" <-> "OE2" Residue "B ARG 362": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 373": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 403": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 426": "OE1" <-> "OE2" Residue "B TYR 433": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 440": "OE1" <-> "OE2" Residue "B TYR 452": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 465": "OE1" <-> "OE2" Residue "B ARG 484": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ASP 486": "OD1" <-> "OD2" Residue "B PHE 504": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 508": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 14": "OE1" <-> "OE2" Residue "C ASP 24": "OD1" <-> "OD2" Residue "C ASP 36": "OD1" <-> "OD2" Residue "C ARG 45": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 54": "OE1" <-> "OE2" Residue "C PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 69": "OD1" <-> "OD2" Residue "C PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 86": "OD1" <-> "OD2" Residue "C ASP 96": "OD1" <-> "OD2" Residue "C ASP 154": "OD1" <-> "OD2" Residue "C ASP 170": "OD1" <-> "OD2" Residue "C PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 194": "OD1" <-> "OD2" Residue "C GLU 195": "OE1" <-> "OE2" Residue "C TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 255": "OE1" <-> "OE2" Residue "C TYR 268": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 291": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 307": "OE1" <-> "OE2" Residue "C ASP 314": "OD1" <-> "OD2" Residue "C ASP 333": "OD1" <-> "OD2" Residue "C PHE 351": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 357": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 358": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 381": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 403": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 411": "OD1" <-> "OD2" Residue "C TYR 433": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 446": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 454": "OD1" <-> "OD2" Residue "C GLU 457": "OE1" <-> "OE2" Residue "C ASP 494": "OD1" <-> "OD2" Residue "C GLU 499": "OE1" <-> "OE2" Residue "C PHE 504": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 508": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 509": "OE1" <-> "OE2" Residue "D ARG 16": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D GLU 41": "OE1" <-> "OE2" Residue "D ASP 81": "OD1" <-> "OD2" Residue "D PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 123": "OE1" <-> "OE2" Residue "D GLU 126": "OE1" <-> "OE2" Residue "D PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 129": "OE1" <-> "OE2" Residue "D GLU 133": "OE1" <-> "OE2" Residue "D TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 199": "OD1" <-> "OD2" Residue "D GLU 203": "OE1" <-> "OE2" Residue "D TYR 223": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 246": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 247": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 249": "OD1" <-> "OD2" Residue "D GLU 271": "OE1" <-> "OE2" Residue "D TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 298": "OE1" <-> "OE2" Residue "D GLU 345": "OE1" <-> "OE2" Residue "D ASP 363": "OD1" <-> "OD2" Residue "D TYR 372": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 373": "OD1" <-> "OD2" Residue "D GLU 402": "OE1" <-> "OE2" Residue "D GLU 403": "OE1" <-> "OE2" Residue "D PHE 417": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 445": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 454": "OD1" <-> "OD2" Residue "D PHE 461": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 468": "OE1" <-> "OE2" Residue "D GLU 469": "OE1" <-> "OE2" Residue "D ASP 475": "OD1" <-> "OD2" Residue "D GLU 479": "OE1" <-> "OE2" Residue "E ASP 26": "OD1" <-> "OD2" Residue "E GLU 31": "OE1" <-> "OE2" Residue "E GLU 59": "OE1" <-> "OE2" Residue "E PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 126": "OE1" <-> "OE2" Residue "E PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 133": "OE1" <-> "OE2" Residue "E TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 223": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 245": "OE1" <-> "OE2" Residue "E TYR 246": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 247": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 251": "OE1" <-> "OE2" Residue "E ASP 254": "OD1" <-> "OD2" Residue "E PHE 263": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 330": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 353": "OD1" <-> "OD2" Residue "E ASP 398": "OD1" <-> "OD2" Residue "E PHE 417": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 445": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 452": "OE1" <-> "OE2" Residue "E TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 461": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 468": "OE1" <-> "OE2" Residue "E GLU 469": "OE1" <-> "OE2" Residue "E ASP 475": "OD1" <-> "OD2" Residue "F GLU 41": "OE1" <-> "OE2" Residue "F GLU 59": "OE1" <-> "OE2" Residue "F GLU 93": "OE1" <-> "OE2" Residue "F GLU 126": "OE1" <-> "OE2" Residue "F GLU 133": "OE1" <-> "OE2" Residue "F GLU 135": "OE1" <-> "OE2" Residue "F TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 203": "OE1" <-> "OE2" Residue "F GLU 228": "OE1" <-> "OE2" Residue "F GLU 245": "OE1" <-> "OE2" Residue "F PHE 247": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 271": "OE1" <-> "OE2" Residue "F TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 292": "OD1" <-> "OD2" Residue "F GLU 298": "OE1" <-> "OE2" Residue "F ASP 320": "OD1" <-> "OD2" Residue "F GLU 345": "OE1" <-> "OE2" Residue "F TYR 349": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 353": "OD1" <-> "OD2" Residue "F ASP 363": "OD1" <-> "OD2" Residue "F GLU 370": "OE1" <-> "OE2" Residue "F ASP 384": "OD1" <-> "OD2" Residue "F PHE 417": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 428": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 445": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 452": "OE1" <-> "OE2" Residue "F PHE 461": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 468": "OE1" <-> "OE2" Residue "F GLU 469": "OE1" <-> "OE2" Residue "F ASP 475": "OD1" <-> "OD2" Residue "G GLU 35": "OE1" <-> "OE2" Residue "G TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ARG 75": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G GLU 102": "OE1" <-> "OE2" Residue "G ARG 118": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 147": "OE1" <-> "OE2" Residue "G TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 154": "OE1" <-> "OE2" Residue "G PHE 155": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 157": "OE1" <-> "OE2" Residue "G PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ARG 166": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G GLU 174": "OE1" <-> "OE2" Residue "G GLU 175": "OE1" <-> "OE2" Residue "G ASP 194": "OD1" <-> "OD2" Residue "G ASP 195": "OD1" <-> "OD2" Residue "G ASP 199": "OD1" <-> "OD2" Residue "G TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 219": "OE1" <-> "OE2" Residue "G GLU 241": "OE1" <-> "OE2" Residue "G ASP 244": "OD1" <-> "OD2" Residue "G PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 264": "OE1" <-> "OE2" Residue "H PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 68": "OE1" <-> "OE2" Residue "H PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ASP 87": "OD1" <-> "OD2" Residue "H ASP 101": "OD1" <-> "OD2" Residue "H GLU 113": "OE1" <-> "OE2" Residue "H GLU 130": "OE1" <-> "OE2" Residue "I ARG 5": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 13": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 25": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J GLU 26": "OE1" <-> "OE2" Residue "J GLU 30": "OE1" <-> "OE2" Residue "J TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J GLU 40": "OE1" <-> "OE2" Residue "J GLU 52": "OE1" <-> "OE2" Residue "K ARG 38": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L ASP 1": "OD1" <-> "OD2" Residue "L PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L ARG 38": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L GLU 58": "OE1" <-> "OE2" Residue "L PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M ASP 3": "OD1" <-> "OD2" Residue "M TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M GLU 58": "OE1" <-> "OE2" Residue "M PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N ARG 38": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N GLU 58": "OE1" <-> "OE2" Residue "O ASP 1": "OD1" <-> "OD2" Residue "O PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O GLU 58": "OE1" <-> "OE2" Residue "O PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P ARG 38": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "P PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q ARG 38": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Q PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S PHE 1": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S GLU 15": "OE1" <-> "OE2" Residue "S TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S GLU 36": "OE1" <-> "OE2" Residue "S ARG 94": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "S PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S GLU 115": "OE1" <-> "OE2" Residue "S GLU 128": "OE1" <-> "OE2" Residue "S GLU 133": "OE1" <-> "OE2" Residue "S ARG 165": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b GLU 142": "OE1" <-> "OE2" Residue "b TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b ASP 156": "OD1" <-> "OD2" Residue "b GLU 171": "OE1" <-> "OE2" Residue "h ASP 13": "OD1" <-> "OD2" Residue "h TYR 18": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "h GLU 34": "OE1" <-> "OE2" Residue "h PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "h TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 65754 Number of models: 1 Model: "" Number of chains: 32 Chain: "A" Number of atoms: 7521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 7521 Classifications: {'peptide': 486} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 467} Chain: "B" Number of atoms: 7658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 495, 7658 Classifications: {'peptide': 495} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 476} Chain breaks: 1 Chain: "C" Number of atoms: 7742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 501, 7742 Classifications: {'peptide': 501} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 482} Chain breaks: 1 Chain: "D" Number of atoms: 7163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 7163 Classifications: {'peptide': 469} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 444} Chain: "E" Number of atoms: 7132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 7132 Classifications: {'peptide': 467} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 442} Chain: "F" Number of atoms: 7131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 7131 Classifications: {'peptide': 467} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 442} Chain: "G" Number of atoms: 4300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 4300 Classifications: {'peptide': 272} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 266} Chain: "H" Number of atoms: 1957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1957 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 4, 'TRANS': 127} Chain: "I" Number of atoms: 764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 764 Classifications: {'peptide': 47} Modifications used: {'NH3': 1} Link IDs: {'TRANS': 46} Chain: "J" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 731 Classifications: {'peptide': 47} Link IDs: {'TRANS': 46} Chain: "K" Number of atoms: 1060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1060 Classifications: {'peptide': 74} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 72} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 1077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1077 Classifications: {'peptide': 75} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "M" Number of atoms: 1060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1060 Classifications: {'peptide': 74} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 72} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "N" Number of atoms: 1060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1060 Classifications: {'peptide': 74} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 72} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "O" Number of atoms: 1060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1060 Classifications: {'peptide': 74} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 72} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "P" Number of atoms: 1060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1060 Classifications: {'peptide': 74} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 72} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "Q" Number of atoms: 1060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1060 Classifications: {'peptide': 74} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 72} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 1060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1060 Classifications: {'peptide': 74} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 72} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "S" Number of atoms: 3004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 3004 Classifications: {'peptide': 188} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 8, 'TRANS': 179} Chain: "b" Number of atoms: 1247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 1247 Classifications: {'peptide': 72} Link IDs: {'TRANS': 71} Chain: "h" Number of atoms: 711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 711 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 2, 'TRANS': 39} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Time building chain proxies: 23.31, per 1000 atoms: 0.35 Number of scatterers: 65754 At special positions: 0 Unit cell: (143.576, 129.952, 237.896, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 120 16.00 P 15 15.00 Mg 5 11.99 O 6223 8.00 N 5593 7.00 C 20661 6.00 H 33137 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 42.49 Conformation dependent library (CDL) restraints added in 6.1 seconds 8416 Ramachandran restraints generated. 4208 Oldfield, 0 Emsley, 4208 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7750 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 154 helices and 23 sheets defined 49.3% alpha, 10.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.03 Creating SS restraints... Processing helix chain 'A' and resid 79 through 81 No H-bonds generated for 'chain 'A' and resid 79 through 81' Processing helix chain 'A' and resid 151 through 156 Processing helix chain 'A' and resid 175 through 190 removed outlier: 3.562A pdb=" N GLN A 186 " --> pdb=" O THR A 182 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N LYS A 187 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N ARG A 188 " --> pdb=" O ILE A 184 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N PHE A 189 " --> pdb=" O ASN A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 222 Processing helix chain 'A' and resid 240 through 260 Proline residue: A 247 - end of helix removed outlier: 4.012A pdb=" N PHE A 257 " --> pdb=" O MET A 253 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASN A 260 " --> pdb=" O TYR A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 285 Processing helix chain 'A' and resid 291 through 293 No H-bonds generated for 'chain 'A' and resid 291 through 293' Processing helix chain 'A' and resid 300 through 308 removed outlier: 3.704A pdb=" N LEU A 305 " --> pdb=" O LEU A 301 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N ARG A 308 " --> pdb=" O ARG A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 316 No H-bonds generated for 'chain 'A' and resid 314 through 316' Processing helix chain 'A' and resid 330 through 332 No H-bonds generated for 'chain 'A' and resid 330 through 332' Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 354 through 358 Processing helix chain 'A' and resid 375 through 378 removed outlier: 3.522A pdb=" N ALA A 378 " --> pdb=" O GLY A 375 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 375 through 378' Processing helix chain 'A' and resid 381 through 399 removed outlier: 4.571A pdb=" N THR A 389 " --> pdb=" O GLN A 385 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU A 392 " --> pdb=" O GLY A 388 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU A 399 " --> pdb=" O ALA A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 405 removed outlier: 3.712A pdb=" N GLN A 405 " --> pdb=" O ALA A 402 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 402 through 405' Processing helix chain 'A' and resid 412 through 427 removed outlier: 3.778A pdb=" N VAL A 422 " --> pdb=" O LEU A 418 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ARG A 423 " --> pdb=" O SER A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 450 Processing helix chain 'A' and resid 458 through 475 removed outlier: 4.416A pdb=" N THR A 462 " --> pdb=" O SER A 459 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N LEU A 469 " --> pdb=" O ASN A 466 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLN A 475 " --> pdb=" O VAL A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 486 Processing helix chain 'A' and resid 491 through 506 Processing helix chain 'B' and resid 10 through 16 Processing helix chain 'B' and resid 79 through 81 No H-bonds generated for 'chain 'B' and resid 79 through 81' Processing helix chain 'B' and resid 151 through 155 Processing helix chain 'B' and resid 175 through 187 removed outlier: 3.683A pdb=" N GLN B 186 " --> pdb=" O THR B 182 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N LYS B 187 " --> pdb=" O ILE B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 222 Processing helix chain 'B' and resid 240 through 260 removed outlier: 3.698A pdb=" N LEU B 245 " --> pdb=" O PRO B 241 " (cutoff:3.500A) Proline residue: B 247 - end of helix removed outlier: 4.172A pdb=" N PHE B 257 " --> pdb=" O MET B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 285 Processing helix chain 'B' and resid 291 through 293 No H-bonds generated for 'chain 'B' and resid 291 through 293' Processing helix chain 'B' and resid 296 through 298 No H-bonds generated for 'chain 'B' and resid 296 through 298' Processing helix chain 'B' and resid 300 through 308 removed outlier: 3.710A pdb=" N LEU B 305 " --> pdb=" O LEU B 301 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ARG B 308 " --> pdb=" O ARG B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 316 No H-bonds generated for 'chain 'B' and resid 314 through 316' Processing helix chain 'B' and resid 330 through 332 No H-bonds generated for 'chain 'B' and resid 330 through 332' Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 354 through 358 removed outlier: 3.501A pdb=" N TYR B 358 " --> pdb=" O THR B 354 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 354 through 358' Processing helix chain 'B' and resid 381 through 400 removed outlier: 4.213A pdb=" N THR B 389 " --> pdb=" O GLN B 385 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N MET B 390 " --> pdb=" O VAL B 386 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL B 400 " --> pdb=" O GLN B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 428 Processing helix chain 'B' and resid 438 through 449 Processing helix chain 'B' and resid 458 through 475 removed outlier: 4.351A pdb=" N THR B 462 " --> pdb=" O SER B 459 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N PHE B 464 " --> pdb=" O ILE B 461 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ILE B 473 " --> pdb=" O SER B 470 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLN B 475 " --> pdb=" O VAL B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 485 Processing helix chain 'B' and resid 491 through 506 Processing helix chain 'C' and resid 9 through 16 removed outlier: 3.981A pdb=" N GLU C 14 " --> pdb=" O SER C 10 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 22 No H-bonds generated for 'chain 'C' and resid 20 through 22' Processing helix chain 'C' and resid 151 through 156 Processing helix chain 'C' and resid 175 through 190 removed outlier: 3.652A pdb=" N GLN C 186 " --> pdb=" O THR C 182 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N LYS C 187 " --> pdb=" O ILE C 183 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N ARG C 188 " --> pdb=" O ILE C 184 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N PHE C 189 " --> pdb=" O ASN C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 222 Processing helix chain 'C' and resid 240 through 260 Proline residue: C 247 - end of helix removed outlier: 3.873A pdb=" N PHE C 257 " --> pdb=" O MET C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 284 removed outlier: 3.621A pdb=" N VAL C 276 " --> pdb=" O SER C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 293 No H-bonds generated for 'chain 'C' and resid 291 through 293' Processing helix chain 'C' and resid 300 through 308 removed outlier: 3.847A pdb=" N LEU C 305 " --> pdb=" O LEU C 301 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ARG C 308 " --> pdb=" O ARG C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 316 No H-bonds generated for 'chain 'C' and resid 314 through 316' Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 375 through 378 Processing helix chain 'C' and resid 381 through 397 removed outlier: 3.913A pdb=" N THR C 389 " --> pdb=" O GLN C 385 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU C 392 " --> pdb=" O GLY C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 427 Processing helix chain 'C' and resid 438 through 450 Processing helix chain 'C' and resid 458 through 475 removed outlier: 4.287A pdb=" N THR C 462 " --> pdb=" O PRO C 458 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N LYS C 463 " --> pdb=" O SER C 459 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ASN C 466 " --> pdb=" O THR C 462 " (cutoff:3.500A) Processing helix chain 'C' and resid 477 through 486 Processing helix chain 'C' and resid 491 through 506 Processing helix chain 'D' and resid 127 through 129 No H-bonds generated for 'chain 'D' and resid 127 through 129' Processing helix chain 'D' and resid 142 through 147 Processing helix chain 'D' and resid 166 through 180 removed outlier: 3.704A pdb=" N LYS D 179 " --> pdb=" O ASN D 175 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA D 180 " --> pdb=" O ASN D 176 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 207 Processing helix chain 'D' and resid 230 through 233 No H-bonds generated for 'chain 'D' and resid 230 through 233' Processing helix chain 'D' and resid 236 through 249 Processing helix chain 'D' and resid 264 through 276 removed outlier: 3.843A pdb=" N GLY D 269 " --> pdb=" O PHE D 265 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ALA D 274 " --> pdb=" O SER D 270 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N LEU D 275 " --> pdb=" O GLU D 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 289 through 297 removed outlier: 4.188A pdb=" N MET D 296 " --> pdb=" O ASP D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 319 No H-bonds generated for 'chain 'D' and resid 317 through 319' Processing helix chain 'D' and resid 324 through 332 removed outlier: 4.525A pdb=" N ALA D 331 " --> pdb=" O ALA D 327 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N HIS D 332 " --> pdb=" O THR D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 341 through 345 Processing helix chain 'D' and resid 369 through 395 removed outlier: 3.993A pdb=" N ASP D 390 " --> pdb=" O LYS D 386 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ILE D 391 " --> pdb=" O SER D 387 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ILE D 394 " --> pdb=" O ASP D 390 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 418 Processing helix chain 'D' and resid 426 through 429 No H-bonds generated for 'chain 'D' and resid 426 through 429' Processing helix chain 'D' and resid 438 through 450 Processing helix chain 'D' and resid 458 through 461 Processing helix chain 'D' and resid 467 through 480 Processing helix chain 'E' and resid 142 through 146 Processing helix chain 'E' and resid 166 through 180 Processing helix chain 'E' and resid 194 through 207 Processing helix chain 'E' and resid 230 through 233 No H-bonds generated for 'chain 'E' and resid 230 through 233' Processing helix chain 'E' and resid 236 through 249 Processing helix chain 'E' and resid 263 through 276 Processing helix chain 'E' and resid 289 through 297 removed outlier: 3.769A pdb=" N MET E 296 " --> pdb=" O ASP E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 317 through 319 No H-bonds generated for 'chain 'E' and resid 317 through 319' Processing helix chain 'E' and resid 324 through 330 Processing helix chain 'E' and resid 341 through 344 No H-bonds generated for 'chain 'E' and resid 341 through 344' Processing helix chain 'E' and resid 364 through 367 No H-bonds generated for 'chain 'E' and resid 364 through 367' Processing helix chain 'E' and resid 369 through 394 removed outlier: 3.955A pdb=" N ASP E 390 " --> pdb=" O LYS E 386 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ILE E 391 " --> pdb=" O SER E 387 " (cutoff:3.500A) Processing helix chain 'E' and resid 397 through 399 No H-bonds generated for 'chain 'E' and resid 397 through 399' Processing helix chain 'E' and resid 402 through 418 Processing helix chain 'E' and resid 426 through 429 No H-bonds generated for 'chain 'E' and resid 426 through 429' Processing helix chain 'E' and resid 438 through 450 Processing helix chain 'E' and resid 458 through 460 No H-bonds generated for 'chain 'E' and resid 458 through 460' Processing helix chain 'E' and resid 467 through 478 removed outlier: 3.688A pdb=" N ALA E 478 " --> pdb=" O ALA E 474 " (cutoff:3.500A) Processing helix chain 'F' and resid 92 through 94 No H-bonds generated for 'chain 'F' and resid 92 through 94' Processing helix chain 'F' and resid 142 through 147 Processing helix chain 'F' and resid 166 through 180 removed outlier: 3.609A pdb=" N ALA F 180 " --> pdb=" O ASN F 176 " (cutoff:3.500A) Processing helix chain 'F' and resid 194 through 205 Processing helix chain 'F' and resid 230 through 233 No H-bonds generated for 'chain 'F' and resid 230 through 233' Processing helix chain 'F' and resid 236 through 249 removed outlier: 3.732A pdb=" N PHE F 247 " --> pdb=" O VAL F 243 " (cutoff:3.500A) Processing helix chain 'F' and resid 263 through 271 Processing helix chain 'F' and resid 289 through 297 removed outlier: 3.593A pdb=" N MET F 296 " --> pdb=" O ASP F 292 " (cutoff:3.500A) Processing helix chain 'F' and resid 317 through 319 No H-bonds generated for 'chain 'F' and resid 317 through 319' Processing helix chain 'F' and resid 324 through 331 removed outlier: 4.771A pdb=" N ALA F 331 " --> pdb=" O ALA F 327 " (cutoff:3.500A) Processing helix chain 'F' and resid 341 through 346 removed outlier: 3.640A pdb=" N LEU F 346 " --> pdb=" O ALA F 342 " (cutoff:3.500A) Processing helix chain 'F' and resid 369 through 395 removed outlier: 4.231A pdb=" N ASP F 390 " --> pdb=" O LYS F 386 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N ILE F 391 " --> pdb=" O SER F 387 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ILE F 394 " --> pdb=" O ASP F 390 " (cutoff:3.500A) Processing helix chain 'F' and resid 397 through 399 No H-bonds generated for 'chain 'F' and resid 397 through 399' Processing helix chain 'F' and resid 402 through 418 Processing helix chain 'F' and resid 426 through 429 No H-bonds generated for 'chain 'F' and resid 426 through 429' Processing helix chain 'F' and resid 438 through 450 Processing helix chain 'F' and resid 458 through 461 Processing helix chain 'F' and resid 467 through 478 Processing helix chain 'G' and resid 3 through 54 removed outlier: 4.069A pdb=" N LYS G 39 " --> pdb=" O GLU G 35 " (cutoff:3.500A) Proline residue: G 40 - end of helix removed outlier: 3.535A pdb=" N VAL G 43 " --> pdb=" O LYS G 39 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N LEU G 51 " --> pdb=" O GLY G 47 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N TYR G 52 " --> pdb=" O SER G 48 " (cutoff:3.500A) Processing helix chain 'G' and resid 81 through 99 removed outlier: 4.114A pdb=" N ALA G 99 " --> pdb=" O ASN G 95 " (cutoff:3.500A) Processing helix chain 'G' and resid 110 through 116 Processing helix chain 'G' and resid 138 through 150 Processing helix chain 'G' and resid 181 through 186 removed outlier: 3.504A pdb=" N SER G 186 " --> pdb=" O ASP G 182 " (cutoff:3.500A) Processing helix chain 'G' and resid 188 through 192 removed outlier: 4.075A pdb=" N ILE G 192 " --> pdb=" O SER G 189 " (cutoff:3.500A) Processing helix chain 'G' and resid 200 through 270 removed outlier: 3.947A pdb=" N LYS G 245 " --> pdb=" O GLU G 241 " (cutoff:3.500A) Processing helix chain 'H' and resid 100 through 102 No H-bonds generated for 'chain 'H' and resid 100 through 102' Processing helix chain 'H' and resid 105 through 120 removed outlier: 4.011A pdb=" N LEU H 120 " --> pdb=" O GLN H 116 " (cutoff:3.500A) Processing helix chain 'H' and resid 125 through 145 Processing helix chain 'I' and resid 11 through 24 Processing helix chain 'I' and resid 28 through 34 removed outlier: 4.224A pdb=" N ALA I 32 " --> pdb=" O THR I 28 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ASN I 33 " --> pdb=" O GLU I 29 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 18 Processing helix chain 'J' and resid 21 through 51 Processing helix chain 'K' and resid 2 through 38 removed outlier: 4.373A pdb=" N PHE K 8 " --> pdb=" O THR K 4 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N VAL K 16 " --> pdb=" O GLY K 12 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N GLY K 17 " --> pdb=" O ALA K 13 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N VAL K 18 " --> pdb=" O ALA K 14 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N ALA K 19 " --> pdb=" O THR K 15 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N GLY K 20 " --> pdb=" O VAL K 16 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER K 21 " --> pdb=" O GLY K 17 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ILE K 33 " --> pdb=" O PHE K 29 " (cutoff:3.500A) Processing helix chain 'K' and resid 44 through 73 removed outlier: 5.277A pdb=" N ILE K 51 " --> pdb=" O SER K 48 " (cutoff:3.500A) Processing helix chain 'L' and resid 6 through 38 removed outlier: 4.352A pdb=" N GLY L 17 " --> pdb=" O ALA L 13 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N VAL L 18 " --> pdb=" O ALA L 14 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N ALA L 19 " --> pdb=" O THR L 15 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N GLY L 20 " --> pdb=" O VAL L 16 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N SER L 21 " --> pdb=" O GLY L 17 " (cutoff:3.500A) Processing helix chain 'L' and resid 45 through 73 removed outlier: 3.963A pdb=" N CYS L 64 " --> pdb=" O MET L 60 " (cutoff:3.500A) Processing helix chain 'M' and resid 2 through 38 removed outlier: 4.059A pdb=" N VAL M 16 " --> pdb=" O GLY M 12 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N GLY M 17 " --> pdb=" O ALA M 13 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N VAL M 18 " --> pdb=" O ALA M 14 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N ALA M 19 " --> pdb=" O THR M 15 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N GLY M 20 " --> pdb=" O VAL M 16 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N SER M 21 " --> pdb=" O GLY M 17 " (cutoff:3.500A) Processing helix chain 'M' and resid 45 through 73 Processing helix chain 'N' and resid 2 through 38 removed outlier: 3.711A pdb=" N VAL N 16 " --> pdb=" O GLY N 12 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLY N 17 " --> pdb=" O ALA N 13 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N VAL N 18 " --> pdb=" O ALA N 14 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N ALA N 19 " --> pdb=" O THR N 15 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N GLY N 20 " --> pdb=" O VAL N 16 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N SER N 21 " --> pdb=" O GLY N 17 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ILE N 33 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 45 through 73 removed outlier: 3.761A pdb=" N TYR N 49 " --> pdb=" O GLN N 45 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N MET N 60 " --> pdb=" O LEU N 56 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLY N 61 " --> pdb=" O SER N 57 " (cutoff:3.500A) Processing helix chain 'O' and resid 2 through 38 removed outlier: 4.191A pdb=" N VAL O 16 " --> pdb=" O GLY O 12 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N GLY O 17 " --> pdb=" O ALA O 13 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N VAL O 18 " --> pdb=" O ALA O 14 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N ALA O 19 " --> pdb=" O THR O 15 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N GLY O 20 " --> pdb=" O VAL O 16 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N SER O 21 " --> pdb=" O GLY O 17 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ILE O 33 " --> pdb=" O PHE O 29 " (cutoff:3.500A) Processing helix chain 'O' and resid 45 through 72 removed outlier: 5.231A pdb=" N MET O 60 " --> pdb=" O LEU O 56 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLY O 61 " --> pdb=" O SER O 57 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 14 Processing helix chain 'P' and resid 16 through 38 removed outlier: 4.108A pdb=" N ILE P 25 " --> pdb=" O GLY P 22 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N LEU P 32 " --> pdb=" O PHE P 29 " (cutoff:3.500A) Processing helix chain 'P' and resid 44 through 73 removed outlier: 3.721A pdb=" N SER P 48 " --> pdb=" O GLN P 45 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N LEU P 56 " --> pdb=" O GLY P 53 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA P 59 " --> pdb=" O LEU P 56 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N MET P 60 " --> pdb=" O SER P 57 " (cutoff:3.500A) Processing helix chain 'Q' and resid 2 through 38 removed outlier: 3.620A pdb=" N THR Q 15 " --> pdb=" O ALA Q 11 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N VAL Q 16 " --> pdb=" O GLY Q 12 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N GLY Q 17 " --> pdb=" O ALA Q 13 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N VAL Q 18 " --> pdb=" O ALA Q 14 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N ALA Q 19 " --> pdb=" O THR Q 15 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N GLY Q 20 " --> pdb=" O VAL Q 16 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N SER Q 21 " --> pdb=" O GLY Q 17 " (cutoff:3.500A) Processing helix chain 'Q' and resid 46 through 73 removed outlier: 3.963A pdb=" N MET Q 60 " --> pdb=" O LEU Q 56 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLY Q 61 " --> pdb=" O SER Q 57 " (cutoff:3.500A) Processing helix chain 'R' and resid 2 through 38 removed outlier: 4.211A pdb=" N VAL R 16 " --> pdb=" O GLY R 12 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N GLY R 17 " --> pdb=" O ALA R 13 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N VAL R 18 " --> pdb=" O ALA R 14 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N ALA R 19 " --> pdb=" O THR R 15 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N GLY R 20 " --> pdb=" O VAL R 16 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N SER R 21 " --> pdb=" O GLY R 17 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE R 33 " --> pdb=" O PHE R 29 " (cutoff:3.500A) Processing helix chain 'R' and resid 45 through 73 removed outlier: 5.403A pdb=" N MET R 60 " --> pdb=" O LEU R 56 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLY R 61 " --> pdb=" O SER R 57 " (cutoff:3.500A) Processing helix chain 'S' and resid 14 through 27 Processing helix chain 'S' and resid 32 through 46 removed outlier: 3.775A pdb=" N GLN S 44 " --> pdb=" O LEU S 40 " (cutoff:3.500A) Processing helix chain 'S' and resid 49 through 56 removed outlier: 3.642A pdb=" N LEU S 56 " --> pdb=" O ALA S 52 " (cutoff:3.500A) Processing helix chain 'S' and resid 62 through 74 Processing helix chain 'S' and resid 80 through 92 Processing helix chain 'S' and resid 95 through 113 Proline residue: S 99 - end of helix removed outlier: 3.768A pdb=" N ILE S 102 " --> pdb=" O PRO S 99 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N SER S 103 " --> pdb=" O ALA S 100 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N VAL S 111 " --> pdb=" O MET S 108 " (cutoff:3.500A) Processing helix chain 'S' and resid 128 through 141 removed outlier: 3.810A pdb=" N SER S 140 " --> pdb=" O THR S 136 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N PHE S 141 " --> pdb=" O VAL S 137 " (cutoff:3.500A) Processing helix chain 'S' and resid 175 through 187 Processing helix chain 'b' and resid 139 through 184 removed outlier: 3.517A pdb=" N TYR b 148 " --> pdb=" O LEU b 144 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N HIS b 158 " --> pdb=" O ARG b 154 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLN b 183 " --> pdb=" O LYS b 179 " (cutoff:3.500A) Processing helix chain 'b' and resid 190 through 208 Processing helix chain 'h' and resid 10 through 24 removed outlier: 3.814A pdb=" N THR h 24 " --> pdb=" O THR h 20 " (cutoff:3.500A) Processing helix chain 'h' and resid 33 through 49 Processing sheet with id= A, first strand: chain 'A' and resid 28 through 30 removed outlier: 3.798A pdb=" N GLU A 51 " --> pdb=" O SER A 63 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N GLY A 72 " --> pdb=" O LEU A 64 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N HIS A 42 " --> pdb=" O VAL A 31 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N VAL A 31 " --> pdb=" O HIS A 42 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 96 through 98 Processing sheet with id= C, first strand: chain 'A' and resid 349 through 352 removed outlier: 7.251A pdb=" N LEU A 166 " --> pdb=" O ILE A 350 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N LEU A 352 " --> pdb=" O LEU A 166 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N ILE A 168 " --> pdb=" O LEU A 352 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 229 through 234 removed outlier: 7.057A pdb=" N CYS A 201 " --> pdb=" O ILE A 230 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N VAL A 232 " --> pdb=" O CYS A 201 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N TYR A 203 " --> pdb=" O VAL A 232 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N ALA A 234 " --> pdb=" O TYR A 203 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N ALA A 205 " --> pdb=" O ALA A 234 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N SER A 320 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N ILE A 266 " --> pdb=" O SER A 320 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N THR A 322 " --> pdb=" O ILE A 266 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N TYR A 268 " --> pdb=" O THR A 322 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 87 through 89 removed outlier: 6.712A pdb=" N ARG B 40 " --> pdb=" O LEU B 32 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N ILE B 34 " --> pdb=" O ILE B 38 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N ILE B 38 " --> pdb=" O ILE B 34 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N VAL B 74 " --> pdb=" O SER B 63 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N SER B 63 " --> pdb=" O VAL B 74 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 96 through 99 removed outlier: 4.002A pdb=" N ALA B 125 " --> pdb=" O VAL B 99 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 350 through 352 removed outlier: 8.069A pdb=" N GLU B 165 " --> pdb=" O LEU B 321 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N ALA B 323 " --> pdb=" O GLU B 165 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N ILE B 167 " --> pdb=" O ALA B 323 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N GLY B 169 " --> pdb=" O PRO B 325 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N ILE B 327 " --> pdb=" O GLY B 169 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N TYR B 268 " --> pdb=" O LEU B 324 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N TYR B 200 " --> pdb=" O LEU B 265 " (cutoff:3.500A) removed outlier: 8.161A pdb=" N ILE B 267 " --> pdb=" O TYR B 200 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N ILE B 202 " --> pdb=" O ILE B 267 " (cutoff:3.500A) removed outlier: 8.185A pdb=" N ASP B 269 " --> pdb=" O ILE B 202 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N VAL B 204 " --> pdb=" O ASP B 269 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ILE B 230 " --> pdb=" O TYR B 203 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N ALA B 205 " --> pdb=" O ILE B 230 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N VAL B 232 " --> pdb=" O ALA B 205 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 29 through 35 removed outlier: 6.734A pdb=" N ARG C 40 " --> pdb=" O LEU C 32 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N ILE C 34 " --> pdb=" O ILE C 38 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ILE C 38 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N VAL C 74 " --> pdb=" O SER C 63 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N SER C 63 " --> pdb=" O VAL C 74 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 96 through 99 removed outlier: 4.028A pdb=" N ALA C 125 " --> pdb=" O VAL C 99 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 350 through 352 removed outlier: 8.283A pdb=" N GLU C 165 " --> pdb=" O LEU C 321 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ALA C 323 " --> pdb=" O GLU C 165 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N ILE C 167 " --> pdb=" O ALA C 323 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N GLY C 169 " --> pdb=" O PRO C 325 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ILE C 327 " --> pdb=" O GLY C 169 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N TYR C 268 " --> pdb=" O LEU C 324 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 16 through 21 removed outlier: 6.554A pdb=" N ASP D 26 " --> pdb=" O VAL D 18 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N VAL D 20 " --> pdb=" O VAL D 24 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N VAL D 24 " --> pdb=" O VAL D 20 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N ILE D 65 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N VAL D 53 " --> pdb=" O ILE D 65 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 87 through 90 removed outlier: 4.133A pdb=" N GLN D 116 " --> pdb=" O VAL D 90 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 156 through 160 removed outlier: 3.933A pdb=" N LEU D 257 " --> pdb=" O THR D 309 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 14 through 16 removed outlier: 6.198A pdb=" N GLN E 28 " --> pdb=" O ILE E 17 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N ILE E 17 " --> pdb=" O GLN E 28 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 87 through 89 Processing sheet with id= P, first strand: chain 'E' and resid 335 through 338 removed outlier: 8.299A pdb=" N ILE E 156 " --> pdb=" O ILE E 308 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N SER E 310 " --> pdb=" O ILE E 156 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N LEU E 158 " --> pdb=" O SER E 310 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N GLN E 312 " --> pdb=" O LEU E 158 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'F' and resid 14 through 16 removed outlier: 4.337A pdb=" N LYS F 78 " --> pdb=" O GLN F 43 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ARG F 63 " --> pdb=" O ALA F 54 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N HIS F 56 " --> pdb=" O THR F 61 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N THR F 61 " --> pdb=" O HIS F 56 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N GLN F 28 " --> pdb=" O ILE F 17 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N ILE F 17 " --> pdb=" O GLN F 28 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'F' and resid 87 through 90 removed outlier: 4.565A pdb=" N GLN F 116 " --> pdb=" O VAL F 90 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'F' and resid 335 through 338 removed outlier: 6.811A pdb=" N TYR F 184 " --> pdb=" O LEU F 256 " (cutoff:3.500A) removed outlier: 8.485A pdb=" N PHE F 258 " --> pdb=" O TYR F 184 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N VAL F 186 " --> pdb=" O PHE F 258 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'G' and resid 172 through 178 removed outlier: 5.344A pdb=" N ASN G 163 " --> pdb=" O VAL G 71 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N GLY G 107 " --> pdb=" O LEU G 125 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N THR G 127 " --> pdb=" O GLY G 107 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'H' and resid 17 through 22 removed outlier: 3.600A pdb=" N ALA H 94 " --> pdb=" O ALA H 21 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'H' and resid 45 through 47 removed outlier: 7.025A pdb=" N HIS H 66 " --> pdb=" O ARG H 34 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N VAL H 36 " --> pdb=" O VAL H 64 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N VAL H 64 " --> pdb=" O VAL H 36 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N VAL H 38 " --> pdb=" O LEU H 62 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N LEU H 62 " --> pdb=" O VAL H 38 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'S' and resid 152 through 154 removed outlier: 8.035A pdb=" N LYS S 153 " --> pdb=" O CYS S 118 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N VAL S 120 " --> pdb=" O LYS S 153 " (cutoff:3.500A) 1590 hydrogen bonds defined for protein. 4398 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: 22.60 Time building geometry restraints manager: 44.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 33119 1.03 - 1.22: 76 1.22 - 1.42: 13112 1.42 - 1.61: 19685 1.61 - 1.81: 222 Bond restraints: 66214 Sorted by residual: bond pdb=" C4 ATP B 600 " pdb=" C5 ATP B 600 " ideal model delta sigma weight residual 1.388 1.463 -0.075 1.00e-02 1.00e+04 5.57e+01 bond pdb=" C4 ATP C 600 " pdb=" C5 ATP C 600 " ideal model delta sigma weight residual 1.388 1.460 -0.072 1.00e-02 1.00e+04 5.23e+01 bond pdb=" C4 ATP A 600 " pdb=" C5 ATP A 600 " ideal model delta sigma weight residual 1.388 1.459 -0.071 1.00e-02 1.00e+04 5.03e+01 bond pdb=" C5 ATP B 600 " pdb=" C6 ATP B 600 " ideal model delta sigma weight residual 1.409 1.471 -0.062 1.00e-02 1.00e+04 3.79e+01 bond pdb=" C5 ATP C 600 " pdb=" C6 ATP C 600 " ideal model delta sigma weight residual 1.409 1.470 -0.061 1.00e-02 1.00e+04 3.68e+01 ... (remaining 66209 not shown) Histogram of bond angle deviations from ideal: 96.84 - 104.74: 491 104.74 - 112.65: 79472 112.65 - 120.56: 24245 120.56 - 128.47: 15692 128.47 - 136.38: 145 Bond angle restraints: 120045 Sorted by residual: angle pdb=" PB ATP B 600 " pdb=" O3B ATP B 600 " pdb=" PG ATP B 600 " ideal model delta sigma weight residual 139.87 116.35 23.52 1.00e+00 1.00e+00 5.53e+02 angle pdb=" PB ATP C 600 " pdb=" O3B ATP C 600 " pdb=" PG ATP C 600 " ideal model delta sigma weight residual 139.87 116.49 23.38 1.00e+00 1.00e+00 5.47e+02 angle pdb=" PB ATP A 600 " pdb=" O3B ATP A 600 " pdb=" PG ATP A 600 " ideal model delta sigma weight residual 139.87 121.57 18.30 1.00e+00 1.00e+00 3.35e+02 angle pdb=" PA ATP B 600 " pdb=" O3A ATP B 600 " pdb=" PB ATP B 600 " ideal model delta sigma weight residual 136.83 119.64 17.19 1.00e+00 1.00e+00 2.96e+02 angle pdb=" PA ATP A 600 " pdb=" O3A ATP A 600 " pdb=" PB ATP A 600 " ideal model delta sigma weight residual 136.83 119.65 17.18 1.00e+00 1.00e+00 2.95e+02 ... (remaining 120040 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.52: 27996 20.52 - 41.03: 2115 41.03 - 61.55: 649 61.55 - 82.06: 58 82.06 - 102.58: 26 Dihedral angle restraints: 30844 sinusoidal: 17220 harmonic: 13624 Sorted by residual: dihedral pdb=" O2A ADP E 600 " pdb=" O3A ADP E 600 " pdb=" PA ADP E 600 " pdb=" PB ADP E 600 " ideal model delta sinusoidal sigma weight residual -60.00 -162.58 102.58 1 2.00e+01 2.50e-03 2.92e+01 dihedral pdb=" C5' ADP F 600 " pdb=" O5' ADP F 600 " pdb=" PA ADP F 600 " pdb=" O2A ADP F 600 " ideal model delta sinusoidal sigma weight residual -60.00 -153.71 93.71 1 2.00e+01 2.50e-03 2.56e+01 dihedral pdb=" O2A ADP D 600 " pdb=" O3A ADP D 600 " pdb=" PA ADP D 600 " pdb=" PB ADP D 600 " ideal model delta sinusoidal sigma weight residual -60.00 -148.31 88.31 1 2.00e+01 2.50e-03 2.33e+01 ... (remaining 30841 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 3873 0.048 - 0.095: 1079 0.095 - 0.143: 256 0.143 - 0.191: 10 0.191 - 0.239: 1 Chirality restraints: 5219 Sorted by residual: chirality pdb=" CG LEU R 56 " pdb=" CB LEU R 56 " pdb=" CD1 LEU R 56 " pdb=" CD2 LEU R 56 " both_signs ideal model delta sigma weight residual False -2.59 -2.83 0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" C2' ATP B 600 " pdb=" C1' ATP B 600 " pdb=" C3' ATP B 600 " pdb=" O2' ATP B 600 " both_signs ideal model delta sigma weight residual False -2.68 -2.50 -0.18 2.00e-01 2.50e+01 8.48e-01 chirality pdb=" C2' ATP A 600 " pdb=" C1' ATP A 600 " pdb=" C3' ATP A 600 " pdb=" O2' ATP A 600 " both_signs ideal model delta sigma weight residual False -2.68 -2.52 -0.16 2.00e-01 2.50e+01 6.20e-01 ... (remaining 5216 not shown) Planarity restraints: 9831 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR G 59 " 0.040 5.00e-02 4.00e+02 5.82e-02 5.43e+00 pdb=" N PRO G 60 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO G 60 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO G 60 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU S 48 " -0.032 5.00e-02 4.00e+02 4.80e-02 3.68e+00 pdb=" N PRO S 49 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO S 49 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO S 49 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE F 88 " 0.031 5.00e-02 4.00e+02 4.69e-02 3.51e+00 pdb=" N PRO F 89 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO F 89 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO F 89 " 0.026 5.00e-02 4.00e+02 ... (remaining 9828 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.13: 1980 2.13 - 2.74: 126508 2.74 - 3.36: 192691 3.36 - 3.98: 251587 3.98 - 4.60: 401732 Nonbonded interactions: 974498 Sorted by model distance: nonbonded pdb=" H ARG B 210 " pdb=" OE2 GLU E 298 " model vdw 1.507 1.850 nonbonded pdb="HH22 ARG B 139 " pdb=" O GLU B 307 " model vdw 1.538 1.850 nonbonded pdb=" OD1 ASP G 194 " pdb="HH21 ARG L 38 " model vdw 1.539 1.850 nonbonded pdb=" OD1 ASP F 363 " pdb=" H ASN F 365 " model vdw 1.552 1.850 nonbonded pdb=" OD1 ASP C 109 " pdb=" H ALA C 110 " model vdw 1.553 1.850 ... (remaining 974493 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 23 through 403 or (resid 411 and (name N or name CA or nam \ e C or name O or name CB or name CG or name OD1 or name OD2 or name HA or name H \ B2 or name HB3)) or resid 412 through 470 or (resid 471 and (name N or name CA o \ r name C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or \ name NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1)) \ or resid 472 through 508 or resid 600 through 601)) selection = (chain 'B' and ((resid 23 and (name N or name CA or name C or name O or name CB \ or name CG1 or name CG2 or name HA or name HB or name HG11 or name HG12 or name \ HG13 or name HG21 or name HG22 or name HG23)) or resid 24 through 403 or (resid \ 411 and (name N or name CA or name C or name O or name CB or name CG or name OD1 \ or name OD2 or name HA or name HB2 or name HB3)) or resid 412 through 470 or (r \ esid 471 and (name N or name CA or name C or name O or name CB or name CG or nam \ e ND1 or name CD2 or name CE1 or name NE2 or name H or name HA or name HB2 or na \ me HB3 or name HD2 or name HE1)) or resid 472 through 508 or resid 600 through 6 \ 01)) selection = (chain 'C' and ((resid 23 and (name N or name CA or name C or name O or name CB \ or name CG1 or name CG2 or name HA or name HB or name HG11 or name HG12 or name \ HG13 or name HG21 or name HG22 or name HG23)) or resid 24 through 470 or (resid \ 471 and (name N or name CA or name C or name O or name CB or name CG or name ND1 \ or name CD2 or name CE1 or name NE2 or name H or name HA or name HB2 or name HB \ 3 or name HD2 or name HE1)) or resid 472 through 508 or resid 600 through 601)) } ncs_group { reference = (chain 'D' and resid 13 through 479) selection = (chain 'E' and (resid 13 through 166 or (resid 167 and (name N or name CA or nam \ e C or name O or name CB or name OG1 or name CG2 or name H or name HA or name HB \ or name HG21 or name HG22 or name HG23)) or resid 168 through 479)) selection = (chain 'F' and resid 13 through 479) } ncs_group { reference = chain 'K' selection = (chain 'L' and resid 1 through 74) selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.75 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 5.940 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: 0.790 Extract box with map and model: 26.700 Check model and map are aligned: 0.760 Set scattering table: 0.460 Process input model: 167.840 Find NCS groups from input model: 2.400 Set up NCS constraints: 0.220 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:2.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 207.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 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 : 0.007 0.075 33077 Z= 0.465 Angle : 0.711 23.519 44726 Z= 0.440 Chirality : 0.045 0.239 5219 Planarity : 0.004 0.058 5731 Dihedral : 15.281 102.577 12318 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.15 % 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: -1.25 (0.13), residues: 4208 helix: 0.13 (0.11), residues: 2068 sheet: -1.72 (0.22), residues: 564 loop : -1.68 (0.15), residues: 1576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP b 176 HIS 0.011 0.001 HIS G 66 PHE 0.023 0.002 PHE M 8 TYR 0.017 0.002 TYR B 446 ARG 0.007 0.001 ARG A 171 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8416 Ramachandran restraints generated. 4208 Oldfield, 0 Emsley, 4208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8416 Ramachandran restraints generated. 4208 Oldfield, 0 Emsley, 4208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 176 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Evaluate side-chains 484 residues out of total 3402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 484 time to evaluate : 3.885 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: B 181 ASP cc_start: 0.7767 (m-30) cc_final: 0.7387 (m-30) REVERT: G 53 GLU cc_start: 0.7611 (tm-30) cc_final: 0.7407 (tm-30) REVERT: G 64 LYS cc_start: 0.7751 (mttm) cc_final: 0.7381 (ttpp) REVERT: G 147 GLU cc_start: 0.7989 (tp30) cc_final: 0.7685 (tp30) REVERT: H 131 ILE cc_start: 0.7581 (mt) cc_final: 0.7240 (mt) REVERT: J 47 LYS cc_start: 0.7513 (mtpt) cc_final: 0.7301 (mptt) REVERT: K 58 GLU cc_start: 0.7148 (tp30) cc_final: 0.6599 (tp30) REVERT: L 47 PHE cc_start: 0.7147 (t80) cc_final: 0.6871 (t80) REVERT: L 66 MET cc_start: 0.6532 (mmm) cc_final: 0.6147 (ppp) REVERT: M 66 MET cc_start: 0.6734 (mmp) cc_final: 0.6520 (mmp) REVERT: O 29 PHE cc_start: 0.7922 (m-80) cc_final: 0.7471 (m-10) REVERT: P 39 ASN cc_start: 0.8010 (t0) cc_final: 0.7702 (t0) REVERT: Q 47 PHE cc_start: 0.7517 (t80) cc_final: 0.7226 (t80) REVERT: R 27 THR cc_start: 0.8339 (m) cc_final: 0.8134 (m) REVERT: S 172 ASP cc_start: 0.8094 (t70) cc_final: 0.7828 (t0) REVERT: S 187 ARG cc_start: 0.8051 (tpp-160) cc_final: 0.7815 (mtt90) REVERT: b 140 TYR cc_start: 0.5750 (t80) cc_final: 0.5048 (p90) REVERT: b 141 ARG cc_start: 0.7722 (tpp80) cc_final: 0.7364 (mmt180) REVERT: b 169 GLU cc_start: 0.8229 (tp30) cc_final: 0.7881 (tp30) REVERT: b 207 LYS cc_start: 0.8358 (ttpt) cc_final: 0.8136 (tptp) outliers start: 0 outliers final: 0 residues processed: 484 average time/residue: 0.8900 time to fit residues: 684.6224 Evaluate side-chains 425 residues out of total 3402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 425 time to evaluate : 3.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 352 optimal weight: 6.9990 chunk 316 optimal weight: 3.9990 chunk 175 optimal weight: 2.9990 chunk 108 optimal weight: 0.0170 chunk 213 optimal weight: 1.9990 chunk 169 optimal weight: 0.6980 chunk 327 optimal weight: 10.0000 chunk 126 optimal weight: 1.9990 chunk 199 optimal weight: 1.9990 chunk 243 optimal weight: 1.9990 chunk 379 optimal weight: 5.9990 overall best weight: 1.3424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 GLN ** A 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 208 GLN C 349 GLN ** E 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 36 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.0693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 33077 Z= 0.264 Angle : 0.542 9.363 44726 Z= 0.282 Chirality : 0.041 0.153 5219 Planarity : 0.004 0.043 5731 Dihedral : 7.122 83.220 4766 Min Nonbonded Distance : 1.680 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 0.41 % Allowed : 5.09 % Favored : 94.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.13), residues: 4208 helix: 0.51 (0.12), residues: 2077 sheet: -1.52 (0.22), residues: 577 loop : -1.48 (0.16), residues: 1554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP b 176 HIS 0.005 0.001 HIS G 66 PHE 0.022 0.001 PHE M 47 TYR 0.018 0.001 TYR h 35 ARG 0.004 0.000 ARG G 202 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8416 Ramachandran restraints generated. 4208 Oldfield, 0 Emsley, 4208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8416 Ramachandran restraints generated. 4208 Oldfield, 0 Emsley, 4208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 176 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Evaluate side-chains 481 residues out of total 3402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 467 time to evaluate : 3.889 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: B 181 ASP cc_start: 0.7719 (m-30) cc_final: 0.7402 (m-30) REVERT: B 297 ASP cc_start: 0.7579 (t0) cc_final: 0.7374 (t0) REVERT: G 53 GLU cc_start: 0.7420 (tm-30) cc_final: 0.7204 (tm-30) REVERT: G 64 LYS cc_start: 0.7821 (mttm) cc_final: 0.7435 (ttpp) REVERT: G 102 GLU cc_start: 0.7008 (tt0) cc_final: 0.6598 (tt0) REVERT: G 147 GLU cc_start: 0.7975 (tp30) cc_final: 0.7593 (tp30) REVERT: K 58 GLU cc_start: 0.7060 (tp30) cc_final: 0.6649 (tp30) REVERT: K 73 PHE cc_start: 0.7083 (m-80) cc_final: 0.6529 (m-80) REVERT: L 47 PHE cc_start: 0.7045 (t80) cc_final: 0.6773 (t80) REVERT: L 60 MET cc_start: 0.7053 (tpt) cc_final: 0.6852 (tpt) REVERT: L 66 MET cc_start: 0.6507 (mmm) cc_final: 0.6156 (ppp) REVERT: M 66 MET cc_start: 0.6783 (mmp) cc_final: 0.6477 (mmp) REVERT: O 29 PHE cc_start: 0.7853 (m-80) cc_final: 0.7406 (m-10) REVERT: P 39 ASN cc_start: 0.8012 (t0) cc_final: 0.7719 (t0) REVERT: Q 47 PHE cc_start: 0.7539 (t80) cc_final: 0.7295 (t80) REVERT: R 27 THR cc_start: 0.8324 (m) cc_final: 0.8122 (m) REVERT: S 172 ASP cc_start: 0.7981 (t70) cc_final: 0.7765 (t0) REVERT: b 140 TYR cc_start: 0.5756 (t80) cc_final: 0.5060 (p90) REVERT: b 141 ARG cc_start: 0.7738 (tpp80) cc_final: 0.7394 (mmt180) outliers start: 14 outliers final: 12 residues processed: 472 average time/residue: 0.8885 time to fit residues: 671.9088 Evaluate side-chains 448 residues out of total 3402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 436 time to evaluate : 3.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 409 ASP Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 435 LEU Chi-restraints excluded: chain E residue 319 ASP Chi-restraints excluded: chain E residue 390 ASP Chi-restraints excluded: chain F residue 310 SER Chi-restraints excluded: chain K residue 28 VAL Chi-restraints excluded: chain L residue 70 LEU Chi-restraints excluded: chain O residue 41 SER Chi-restraints excluded: chain O residue 70 LEU Chi-restraints excluded: chain P residue 47 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 210 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 315 optimal weight: 4.9990 chunk 258 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 380 optimal weight: 7.9990 chunk 410 optimal weight: 5.9990 chunk 338 optimal weight: 4.9990 chunk 377 optimal weight: 6.9990 chunk 129 optimal weight: 0.7980 chunk 305 optimal weight: 3.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.0828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 33077 Z= 0.357 Angle : 0.554 7.704 44726 Z= 0.289 Chirality : 0.042 0.155 5219 Planarity : 0.004 0.042 5731 Dihedral : 6.836 73.564 4766 Min Nonbonded Distance : 1.647 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 0.68 % Allowed : 7.29 % Favored : 92.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.13), residues: 4208 helix: 0.61 (0.12), residues: 2073 sheet: -1.43 (0.22), residues: 574 loop : -1.41 (0.16), residues: 1561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP b 176 HIS 0.005 0.001 HIS b 172 PHE 0.018 0.001 PHE J 34 TYR 0.018 0.001 TYR h 35 ARG 0.003 0.000 ARG G 202 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8416 Ramachandran restraints generated. 4208 Oldfield, 0 Emsley, 4208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8416 Ramachandran restraints generated. 4208 Oldfield, 0 Emsley, 4208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 176 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Evaluate side-chains 466 residues out of total 3402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 443 time to evaluate : 3.969 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: B 181 ASP cc_start: 0.7746 (m-30) cc_final: 0.7422 (m-30) REVERT: B 297 ASP cc_start: 0.7676 (t0) cc_final: 0.7385 (t0) REVERT: C 140 ILE cc_start: 0.9110 (pt) cc_final: 0.8882 (tt) REVERT: G 53 GLU cc_start: 0.7364 (tm-30) cc_final: 0.7163 (tm-30) REVERT: G 64 LYS cc_start: 0.7618 (mttm) cc_final: 0.7391 (ttpp) REVERT: G 102 GLU cc_start: 0.7000 (tt0) cc_final: 0.6590 (tt0) REVERT: G 147 GLU cc_start: 0.8049 (tp30) cc_final: 0.7653 (tp30) REVERT: K 58 GLU cc_start: 0.6981 (tp30) cc_final: 0.6533 (tp30) REVERT: K 73 PHE cc_start: 0.6817 (m-80) cc_final: 0.6463 (m-80) REVERT: L 47 PHE cc_start: 0.7169 (t80) cc_final: 0.6893 (t80) REVERT: L 66 MET cc_start: 0.6525 (mmm) cc_final: 0.6094 (ppp) REVERT: O 29 PHE cc_start: 0.7799 (m-80) cc_final: 0.7032 (m-10) REVERT: P 39 ASN cc_start: 0.8045 (t0) cc_final: 0.7755 (t0) REVERT: Q 47 PHE cc_start: 0.7668 (t80) cc_final: 0.7407 (t80) REVERT: S 59 TYR cc_start: 0.7291 (m-80) cc_final: 0.7090 (m-80) REVERT: b 140 TYR cc_start: 0.5752 (t80) cc_final: 0.5054 (p90) REVERT: b 141 ARG cc_start: 0.7741 (tpp80) cc_final: 0.7400 (mmt180) outliers start: 23 outliers final: 16 residues processed: 453 average time/residue: 0.9263 time to fit residues: 679.4294 Evaluate side-chains 444 residues out of total 3402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 428 time to evaluate : 3.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 409 ASP Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 435 LEU Chi-restraints excluded: chain E residue 319 ASP Chi-restraints excluded: chain E residue 390 ASP Chi-restraints excluded: chain F residue 310 SER Chi-restraints excluded: chain F residue 435 LEU Chi-restraints excluded: chain H residue 96 GLU Chi-restraints excluded: chain I residue 29 GLU Chi-restraints excluded: chain L residue 54 PHE Chi-restraints excluded: chain L residue 70 LEU Chi-restraints excluded: chain O residue 70 LEU Chi-restraints excluded: chain P residue 47 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 375 optimal weight: 8.9990 chunk 285 optimal weight: 1.9990 chunk 197 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 181 optimal weight: 1.9990 chunk 255 optimal weight: 2.9990 chunk 381 optimal weight: 5.9990 chunk 404 optimal weight: 2.9990 chunk 199 optimal weight: 0.8980 chunk 361 optimal weight: 10.0000 chunk 108 optimal weight: 1.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.0961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 33077 Z= 0.355 Angle : 0.549 9.357 44726 Z= 0.285 Chirality : 0.042 0.157 5219 Planarity : 0.004 0.042 5731 Dihedral : 6.755 82.097 4766 Min Nonbonded Distance : 1.690 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 0.85 % Allowed : 8.44 % Favored : 90.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.13), residues: 4208 helix: 0.71 (0.12), residues: 2070 sheet: -1.38 (0.22), residues: 574 loop : -1.36 (0.16), residues: 1564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP b 176 HIS 0.006 0.001 HIS b 172 PHE 0.014 0.001 PHE J 34 TYR 0.023 0.001 TYR h 35 ARG 0.003 0.000 ARG G 202 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8416 Ramachandran restraints generated. 4208 Oldfield, 0 Emsley, 4208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8416 Ramachandran restraints generated. 4208 Oldfield, 0 Emsley, 4208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 176 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Evaluate side-chains 472 residues out of total 3402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 443 time to evaluate : 4.069 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: B 181 ASP cc_start: 0.7750 (m-30) cc_final: 0.7380 (m-30) REVERT: B 297 ASP cc_start: 0.7650 (t0) cc_final: 0.7327 (t0) REVERT: C 140 ILE cc_start: 0.9110 (pt) cc_final: 0.8870 (tt) REVERT: G 53 GLU cc_start: 0.7343 (tm-30) cc_final: 0.7132 (tm-30) REVERT: G 64 LYS cc_start: 0.7775 (mttm) cc_final: 0.7415 (ttpp) REVERT: G 102 GLU cc_start: 0.6989 (tt0) cc_final: 0.6580 (tt0) REVERT: G 147 GLU cc_start: 0.8061 (tp30) cc_final: 0.7661 (tp30) REVERT: K 58 GLU cc_start: 0.6984 (tp30) cc_final: 0.6582 (tp30) REVERT: K 73 PHE cc_start: 0.6819 (m-80) cc_final: 0.6520 (m-80) REVERT: L 47 PHE cc_start: 0.7150 (t80) cc_final: 0.6897 (t80) REVERT: L 60 MET cc_start: 0.6998 (tpt) cc_final: 0.6659 (tpt) REVERT: L 66 MET cc_start: 0.6519 (mmm) cc_final: 0.6104 (ppp) REVERT: M 44 GLN cc_start: 0.7456 (tp-100) cc_final: 0.6977 (tt0) REVERT: O 29 PHE cc_start: 0.7763 (m-80) cc_final: 0.7323 (m-10) REVERT: P 39 ASN cc_start: 0.8056 (t0) cc_final: 0.7765 (t0) REVERT: Q 47 PHE cc_start: 0.7654 (t80) cc_final: 0.7395 (t80) REVERT: b 140 TYR cc_start: 0.5740 (t80) cc_final: 0.5031 (p90) outliers start: 29 outliers final: 22 residues processed: 457 average time/residue: 0.8788 time to fit residues: 648.9918 Evaluate side-chains 450 residues out of total 3402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 428 time to evaluate : 3.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 409 ASP Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain B residue 502 THR Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 435 LEU Chi-restraints excluded: chain E residue 206 GLU Chi-restraints excluded: chain E residue 390 ASP Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain F residue 310 SER Chi-restraints excluded: chain F residue 435 LEU Chi-restraints excluded: chain H residue 96 GLU Chi-restraints excluded: chain I residue 29 GLU Chi-restraints excluded: chain K residue 25 ILE Chi-restraints excluded: chain L residue 54 PHE Chi-restraints excluded: chain L residue 70 LEU Chi-restraints excluded: chain O residue 41 SER Chi-restraints excluded: chain O residue 70 LEU Chi-restraints excluded: chain P residue 47 PHE Chi-restraints excluded: chain h residue 15 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 336 optimal weight: 5.9990 chunk 229 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 300 optimal weight: 7.9990 chunk 166 optimal weight: 2.9990 chunk 344 optimal weight: 6.9990 chunk 279 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 206 optimal weight: 1.9990 chunk 362 optimal weight: 7.9990 chunk 101 optimal weight: 0.7980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.1091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 33077 Z= 0.279 Angle : 0.525 8.810 44726 Z= 0.271 Chirality : 0.041 0.156 5219 Planarity : 0.003 0.041 5731 Dihedral : 6.478 83.733 4766 Min Nonbonded Distance : 1.730 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 0.85 % Allowed : 9.88 % Favored : 89.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.13), residues: 4208 helix: 0.86 (0.12), residues: 2072 sheet: -1.32 (0.22), residues: 577 loop : -1.25 (0.16), residues: 1559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP b 176 HIS 0.003 0.001 HIS F 371 PHE 0.015 0.001 PHE J 34 TYR 0.027 0.001 TYR h 35 ARG 0.003 0.000 ARG A 381 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8416 Ramachandran restraints generated. 4208 Oldfield, 0 Emsley, 4208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8416 Ramachandran restraints generated. 4208 Oldfield, 0 Emsley, 4208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 176 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Evaluate side-chains 473 residues out of total 3402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 444 time to evaluate : 3.981 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: B 181 ASP cc_start: 0.7751 (m-30) cc_final: 0.7434 (m-30) REVERT: B 297 ASP cc_start: 0.7640 (t0) cc_final: 0.7325 (t0) REVERT: C 140 ILE cc_start: 0.9125 (pt) cc_final: 0.8868 (tt) REVERT: G 64 LYS cc_start: 0.7851 (mttm) cc_final: 0.7484 (ttpp) REVERT: G 102 GLU cc_start: 0.7017 (tt0) cc_final: 0.6594 (tt0) REVERT: G 147 GLU cc_start: 0.8076 (tp30) cc_final: 0.7691 (tp30) REVERT: G 202 ARG cc_start: 0.7527 (OUTLIER) cc_final: 0.7042 (ptm160) REVERT: H 143 LYS cc_start: 0.8735 (tttp) cc_final: 0.8454 (ttmm) REVERT: K 58 GLU cc_start: 0.7024 (tp30) cc_final: 0.6631 (tp30) REVERT: L 47 PHE cc_start: 0.7155 (t80) cc_final: 0.6914 (t80) REVERT: L 60 MET cc_start: 0.6981 (tpt) cc_final: 0.6672 (tpt) REVERT: L 66 MET cc_start: 0.6433 (mmm) cc_final: 0.6053 (ppp) REVERT: M 44 GLN cc_start: 0.7460 (tp-100) cc_final: 0.6995 (tt0) REVERT: O 29 PHE cc_start: 0.7720 (m-80) cc_final: 0.6896 (m-10) REVERT: P 39 ASN cc_start: 0.8012 (t0) cc_final: 0.7772 (t0) REVERT: P 47 PHE cc_start: 0.7008 (OUTLIER) cc_final: 0.6497 (m-80) REVERT: Q 47 PHE cc_start: 0.7716 (t80) cc_final: 0.7462 (t80) REVERT: b 140 TYR cc_start: 0.5841 (t80) cc_final: 0.5062 (p90) outliers start: 29 outliers final: 20 residues processed: 457 average time/residue: 0.8887 time to fit residues: 655.8638 Evaluate side-chains 454 residues out of total 3402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 432 time to evaluate : 3.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 409 ASP Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 502 THR Chi-restraints excluded: chain C residue 389 THR Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 435 LEU Chi-restraints excluded: chain E residue 390 ASP Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain F residue 310 SER Chi-restraints excluded: chain F residue 435 LEU Chi-restraints excluded: chain G residue 202 ARG Chi-restraints excluded: chain I residue 29 GLU Chi-restraints excluded: chain K residue 25 ILE Chi-restraints excluded: chain L residue 54 PHE Chi-restraints excluded: chain L residue 70 LEU Chi-restraints excluded: chain O residue 41 SER Chi-restraints excluded: chain O residue 70 LEU Chi-restraints excluded: chain P residue 47 PHE Chi-restraints excluded: chain R residue 70 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 135 optimal weight: 2.9990 chunk 363 optimal weight: 6.9990 chunk 79 optimal weight: 1.9990 chunk 237 optimal weight: 3.9990 chunk 99 optimal weight: 4.9990 chunk 404 optimal weight: 5.9990 chunk 335 optimal weight: 6.9990 chunk 187 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 133 optimal weight: 0.9990 chunk 212 optimal weight: 1.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.1231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 33077 Z= 0.259 Angle : 0.514 8.855 44726 Z= 0.265 Chirality : 0.041 0.175 5219 Planarity : 0.003 0.040 5731 Dihedral : 6.213 81.278 4766 Min Nonbonded Distance : 1.735 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 1.06 % Allowed : 10.14 % Favored : 88.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.14), residues: 4208 helix: 0.98 (0.12), residues: 2074 sheet: -1.22 (0.23), residues: 565 loop : -1.16 (0.16), residues: 1569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP b 176 HIS 0.004 0.001 HIS b 172 PHE 0.022 0.001 PHE Q 54 TYR 0.023 0.001 TYR h 35 ARG 0.003 0.000 ARG A 381 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8416 Ramachandran restraints generated. 4208 Oldfield, 0 Emsley, 4208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8416 Ramachandran restraints generated. 4208 Oldfield, 0 Emsley, 4208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 176 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Evaluate side-chains 491 residues out of total 3402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 455 time to evaluate : 4.034 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: B 181 ASP cc_start: 0.7760 (m-30) cc_final: 0.7447 (m-30) REVERT: B 297 ASP cc_start: 0.7560 (t0) cc_final: 0.7251 (t0) REVERT: C 140 ILE cc_start: 0.9110 (pt) cc_final: 0.8868 (tt) REVERT: G 64 LYS cc_start: 0.7819 (mttm) cc_final: 0.7455 (ttpp) REVERT: G 147 GLU cc_start: 0.8115 (tp30) cc_final: 0.7744 (tp30) REVERT: G 202 ARG cc_start: 0.7525 (OUTLIER) cc_final: 0.7120 (ptm160) REVERT: H 143 LYS cc_start: 0.8730 (tttp) cc_final: 0.8439 (ttmm) REVERT: K 58 GLU cc_start: 0.7042 (tp30) cc_final: 0.6643 (tp30) REVERT: L 47 PHE cc_start: 0.7153 (t80) cc_final: 0.6905 (t80) REVERT: L 60 MET cc_start: 0.6990 (tpt) cc_final: 0.6675 (tpt) REVERT: L 66 MET cc_start: 0.6527 (mmm) cc_final: 0.6071 (ppp) REVERT: M 44 GLN cc_start: 0.7511 (tp-100) cc_final: 0.7060 (tt0) REVERT: O 29 PHE cc_start: 0.7656 (m-80) cc_final: 0.6828 (m-10) REVERT: P 47 PHE cc_start: 0.7000 (OUTLIER) cc_final: 0.6430 (m-80) REVERT: Q 47 PHE cc_start: 0.7697 (t80) cc_final: 0.7439 (t80) REVERT: Q 54 PHE cc_start: 0.6413 (t80) cc_final: 0.6114 (t80) REVERT: R 56 LEU cc_start: 0.8314 (OUTLIER) cc_final: 0.7811 (mm) REVERT: S 17 ARG cc_start: 0.8239 (mtm-85) cc_final: 0.8014 (mtt180) REVERT: b 140 TYR cc_start: 0.5839 (t80) cc_final: 0.5076 (p90) REVERT: h 47 LYS cc_start: 0.6257 (mttp) cc_final: 0.5872 (tttt) outliers start: 36 outliers final: 24 residues processed: 475 average time/residue: 0.8616 time to fit residues: 655.5921 Evaluate side-chains 464 residues out of total 3402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 437 time to evaluate : 3.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 409 ASP Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 502 THR Chi-restraints excluded: chain C residue 389 THR Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 435 LEU Chi-restraints excluded: chain E residue 206 GLU Chi-restraints excluded: chain E residue 390 ASP Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain F residue 310 SER Chi-restraints excluded: chain F residue 435 LEU Chi-restraints excluded: chain G residue 202 ARG Chi-restraints excluded: chain I residue 29 GLU Chi-restraints excluded: chain K residue 25 ILE Chi-restraints excluded: chain L residue 54 PHE Chi-restraints excluded: chain L residue 70 LEU Chi-restraints excluded: chain O residue 41 SER Chi-restraints excluded: chain O residue 47 PHE Chi-restraints excluded: chain O residue 70 LEU Chi-restraints excluded: chain P residue 47 PHE Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 70 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 389 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 230 optimal weight: 3.9990 chunk 295 optimal weight: 3.9990 chunk 228 optimal weight: 1.9990 chunk 340 optimal weight: 8.9990 chunk 225 optimal weight: 0.5980 chunk 402 optimal weight: 0.9980 chunk 252 optimal weight: 0.4980 chunk 245 optimal weight: 1.9990 chunk 186 optimal weight: 2.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.1323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 33077 Z= 0.236 Angle : 0.507 9.234 44726 Z= 0.260 Chirality : 0.041 0.168 5219 Planarity : 0.003 0.039 5731 Dihedral : 6.088 79.933 4766 Min Nonbonded Distance : 1.744 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 0.82 % Allowed : 10.79 % Favored : 88.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.14), residues: 4208 helix: 1.07 (0.12), residues: 2075 sheet: -1.16 (0.23), residues: 565 loop : -1.12 (0.16), residues: 1568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP b 176 HIS 0.003 0.001 HIS F 371 PHE 0.017 0.001 PHE Q 54 TYR 0.022 0.001 TYR h 35 ARG 0.003 0.000 ARG A 381 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8416 Ramachandran restraints generated. 4208 Oldfield, 0 Emsley, 4208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8416 Ramachandran restraints generated. 4208 Oldfield, 0 Emsley, 4208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 176 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Evaluate side-chains 478 residues out of total 3402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 450 time to evaluate : 3.893 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: B 181 ASP cc_start: 0.7757 (m-30) cc_final: 0.7443 (m-30) REVERT: B 297 ASP cc_start: 0.7540 (t0) cc_final: 0.7248 (t0) REVERT: C 140 ILE cc_start: 0.9103 (pt) cc_final: 0.8872 (tt) REVERT: G 64 LYS cc_start: 0.7843 (mttm) cc_final: 0.7482 (ttpp) REVERT: G 147 GLU cc_start: 0.8114 (tp30) cc_final: 0.7748 (tp30) REVERT: G 202 ARG cc_start: 0.7640 (OUTLIER) cc_final: 0.7243 (ptm160) REVERT: H 96 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.7497 (tt0) REVERT: K 58 GLU cc_start: 0.7051 (tp30) cc_final: 0.6650 (tp30) REVERT: L 60 MET cc_start: 0.6985 (tpt) cc_final: 0.6671 (tpt) REVERT: L 66 MET cc_start: 0.6510 (mmm) cc_final: 0.6143 (ppp) REVERT: M 44 GLN cc_start: 0.7494 (tp-100) cc_final: 0.7060 (tt0) REVERT: N 72 LEU cc_start: 0.6653 (tt) cc_final: 0.6423 (tp) REVERT: O 29 PHE cc_start: 0.7596 (m-80) cc_final: 0.7168 (m-10) REVERT: P 39 ASN cc_start: 0.8661 (t0) cc_final: 0.8241 (t0) REVERT: P 47 PHE cc_start: 0.7032 (OUTLIER) cc_final: 0.6409 (m-80) REVERT: Q 47 PHE cc_start: 0.7733 (t80) cc_final: 0.7494 (t80) REVERT: S 72 MET cc_start: 0.7015 (tpt) cc_final: 0.6809 (tmm) REVERT: b 140 TYR cc_start: 0.5821 (t80) cc_final: 0.5069 (p90) REVERT: h 47 LYS cc_start: 0.6248 (mttp) cc_final: 0.5865 (tttt) outliers start: 28 outliers final: 23 residues processed: 466 average time/residue: 0.8876 time to fit residues: 665.7294 Evaluate side-chains 462 residues out of total 3402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 436 time to evaluate : 3.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 409 ASP Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain B residue 502 THR Chi-restraints excluded: chain C residue 389 THR Chi-restraints excluded: chain D residue 435 LEU Chi-restraints excluded: chain E residue 30 ASP Chi-restraints excluded: chain E residue 206 GLU Chi-restraints excluded: chain E residue 390 ASP Chi-restraints excluded: chain F residue 26 ASP Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain F residue 310 SER Chi-restraints excluded: chain F residue 435 LEU Chi-restraints excluded: chain G residue 202 ARG Chi-restraints excluded: chain H residue 96 GLU Chi-restraints excluded: chain I residue 29 GLU Chi-restraints excluded: chain K residue 25 ILE Chi-restraints excluded: chain L residue 54 PHE Chi-restraints excluded: chain L residue 70 LEU Chi-restraints excluded: chain O residue 41 SER Chi-restraints excluded: chain O residue 47 PHE Chi-restraints excluded: chain O residue 70 LEU Chi-restraints excluded: chain P residue 47 PHE Chi-restraints excluded: chain R residue 70 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 249 optimal weight: 3.9990 chunk 160 optimal weight: 0.5980 chunk 240 optimal weight: 1.9990 chunk 121 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 256 optimal weight: 2.9990 chunk 274 optimal weight: 2.9990 chunk 199 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 316 optimal weight: 2.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 66 HIS ** H 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.1365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 33077 Z= 0.284 Angle : 0.520 11.604 44726 Z= 0.268 Chirality : 0.041 0.169 5219 Planarity : 0.003 0.039 5731 Dihedral : 6.096 79.946 4766 Min Nonbonded Distance : 1.715 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 0.94 % Allowed : 10.96 % Favored : 88.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.13), residues: 4208 helix: 1.08 (0.12), residues: 2068 sheet: -1.16 (0.23), residues: 565 loop : -1.09 (0.16), residues: 1575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP b 176 HIS 0.003 0.001 HIS H 66 PHE 0.023 0.001 PHE C 468 TYR 0.017 0.001 TYR h 35 ARG 0.003 0.000 ARG F 416 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8416 Ramachandran restraints generated. 4208 Oldfield, 0 Emsley, 4208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8416 Ramachandran restraints generated. 4208 Oldfield, 0 Emsley, 4208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 176 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Evaluate side-chains 473 residues out of total 3402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 441 time to evaluate : 4.814 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: B 181 ASP cc_start: 0.7770 (m-30) cc_final: 0.7448 (m-30) REVERT: B 297 ASP cc_start: 0.7630 (t0) cc_final: 0.7351 (t0) REVERT: C 140 ILE cc_start: 0.9111 (pt) cc_final: 0.8879 (tt) REVERT: G 64 LYS cc_start: 0.7830 (mttm) cc_final: 0.7515 (ttpp) REVERT: G 147 GLU cc_start: 0.8109 (tp30) cc_final: 0.7753 (tp30) REVERT: G 202 ARG cc_start: 0.7687 (OUTLIER) cc_final: 0.7278 (ptm160) REVERT: H 96 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.7553 (tt0) REVERT: K 58 GLU cc_start: 0.7057 (tp30) cc_final: 0.6663 (tp30) REVERT: L 60 MET cc_start: 0.6991 (tpt) cc_final: 0.6656 (tpt) REVERT: L 66 MET cc_start: 0.6483 (mmm) cc_final: 0.6011 (ppp) REVERT: M 44 GLN cc_start: 0.7466 (tp-100) cc_final: 0.7046 (tt0) REVERT: N 72 LEU cc_start: 0.6669 (tt) cc_final: 0.6412 (tp) REVERT: O 29 PHE cc_start: 0.7604 (m-80) cc_final: 0.7168 (m-10) REVERT: P 39 ASN cc_start: 0.8663 (t0) cc_final: 0.8237 (t0) REVERT: P 47 PHE cc_start: 0.7048 (OUTLIER) cc_final: 0.6362 (m-80) REVERT: Q 47 PHE cc_start: 0.7689 (t80) cc_final: 0.7434 (t80) REVERT: S 72 MET cc_start: 0.7027 (tpt) cc_final: 0.6824 (tmm) REVERT: b 140 TYR cc_start: 0.5819 (t80) cc_final: 0.5070 (p90) REVERT: h 47 LYS cc_start: 0.6227 (mttp) cc_final: 0.5928 (tttt) outliers start: 32 outliers final: 29 residues processed: 458 average time/residue: 0.8940 time to fit residues: 661.6228 Evaluate side-chains 467 residues out of total 3402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 435 time to evaluate : 3.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 409 ASP Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 502 THR Chi-restraints excluded: chain C residue 389 THR Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 435 LEU Chi-restraints excluded: chain E residue 30 ASP Chi-restraints excluded: chain E residue 206 GLU Chi-restraints excluded: chain E residue 390 ASP Chi-restraints excluded: chain F residue 26 ASP Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain F residue 270 SER Chi-restraints excluded: chain F residue 310 SER Chi-restraints excluded: chain F residue 435 LEU Chi-restraints excluded: chain G residue 202 ARG Chi-restraints excluded: chain H residue 96 GLU Chi-restraints excluded: chain I residue 29 GLU Chi-restraints excluded: chain K residue 25 ILE Chi-restraints excluded: chain L residue 54 PHE Chi-restraints excluded: chain L residue 70 LEU Chi-restraints excluded: chain L residue 71 ILE Chi-restraints excluded: chain N residue 25 ILE Chi-restraints excluded: chain O residue 41 SER Chi-restraints excluded: chain O residue 47 PHE Chi-restraints excluded: chain O residue 70 LEU Chi-restraints excluded: chain P residue 47 PHE Chi-restraints excluded: chain R residue 70 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 366 optimal weight: 7.9990 chunk 385 optimal weight: 3.9990 chunk 352 optimal weight: 6.9990 chunk 375 optimal weight: 0.7980 chunk 225 optimal weight: 1.9990 chunk 163 optimal weight: 2.9990 chunk 294 optimal weight: 8.9990 chunk 115 optimal weight: 0.9980 chunk 339 optimal weight: 5.9990 chunk 355 optimal weight: 6.9990 chunk 374 optimal weight: 5.9990 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 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.1312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 33077 Z= 0.386 Angle : 0.552 9.066 44726 Z= 0.287 Chirality : 0.043 0.175 5219 Planarity : 0.004 0.042 5731 Dihedral : 6.304 82.885 4766 Min Nonbonded Distance : 1.683 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 1.03 % Allowed : 11.43 % Favored : 87.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.13), residues: 4208 helix: 0.95 (0.12), residues: 2067 sheet: -1.33 (0.22), residues: 589 loop : -1.16 (0.16), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP b 176 HIS 0.003 0.001 HIS F 371 PHE 0.019 0.001 PHE J 34 TYR 0.018 0.001 TYR h 35 ARG 0.004 0.000 ARG F 416 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8416 Ramachandran restraints generated. 4208 Oldfield, 0 Emsley, 4208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8416 Ramachandran restraints generated. 4208 Oldfield, 0 Emsley, 4208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 176 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Evaluate side-chains 471 residues out of total 3402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 436 time to evaluate : 3.881 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: B 181 ASP cc_start: 0.7779 (m-30) cc_final: 0.7410 (m-30) REVERT: B 297 ASP cc_start: 0.7690 (t0) cc_final: 0.7389 (t0) REVERT: C 140 ILE cc_start: 0.9127 (pt) cc_final: 0.8882 (tt) REVERT: G 64 LYS cc_start: 0.7831 (mttm) cc_final: 0.7531 (ttpp) REVERT: G 147 GLU cc_start: 0.8117 (tp30) cc_final: 0.7764 (tp30) REVERT: G 202 ARG cc_start: 0.7774 (OUTLIER) cc_final: 0.7417 (ptm160) REVERT: H 96 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7498 (tt0) REVERT: K 58 GLU cc_start: 0.7048 (tp30) cc_final: 0.6642 (tp30) REVERT: K 73 PHE cc_start: 0.6643 (m-80) cc_final: 0.6386 (m-80) REVERT: L 60 MET cc_start: 0.7013 (tpt) cc_final: 0.6674 (tpt) REVERT: L 66 MET cc_start: 0.6542 (mmm) cc_final: 0.6068 (ppp) REVERT: M 44 GLN cc_start: 0.7484 (tp-100) cc_final: 0.7060 (tt0) REVERT: O 29 PHE cc_start: 0.7640 (m-80) cc_final: 0.7216 (m-10) REVERT: O 60 MET cc_start: 0.5932 (mmt) cc_final: 0.5561 (mmt) REVERT: P 47 PHE cc_start: 0.7222 (OUTLIER) cc_final: 0.6487 (m-80) REVERT: Q 47 PHE cc_start: 0.7696 (t80) cc_final: 0.7446 (t80) REVERT: S 72 MET cc_start: 0.7032 (tpt) cc_final: 0.6832 (tmm) REVERT: b 140 TYR cc_start: 0.5827 (t80) cc_final: 0.5074 (p90) REVERT: h 47 LYS cc_start: 0.6234 (mttp) cc_final: 0.5884 (tttt) outliers start: 35 outliers final: 29 residues processed: 454 average time/residue: 0.8708 time to fit residues: 633.9292 Evaluate side-chains 464 residues out of total 3402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 432 time to evaluate : 4.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 409 ASP Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 502 THR Chi-restraints excluded: chain C residue 389 THR Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 435 LEU Chi-restraints excluded: chain E residue 30 ASP Chi-restraints excluded: chain E residue 206 GLU Chi-restraints excluded: chain E residue 390 ASP Chi-restraints excluded: chain F residue 26 ASP Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain F residue 270 SER Chi-restraints excluded: chain F residue 310 SER Chi-restraints excluded: chain F residue 435 LEU Chi-restraints excluded: chain G residue 202 ARG Chi-restraints excluded: chain H residue 96 GLU Chi-restraints excluded: chain I residue 29 GLU Chi-restraints excluded: chain K residue 25 ILE Chi-restraints excluded: chain L residue 54 PHE Chi-restraints excluded: chain L residue 70 LEU Chi-restraints excluded: chain L residue 71 ILE Chi-restraints excluded: chain O residue 41 SER Chi-restraints excluded: chain O residue 47 PHE Chi-restraints excluded: chain O residue 70 LEU Chi-restraints excluded: chain P residue 47 PHE Chi-restraints excluded: chain R residue 70 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 246 optimal weight: 0.6980 chunk 397 optimal weight: 0.5980 chunk 242 optimal weight: 0.0970 chunk 188 optimal weight: 1.9990 chunk 275 optimal weight: 1.9990 chunk 416 optimal weight: 6.9990 chunk 383 optimal weight: 10.0000 chunk 331 optimal weight: 2.9990 chunk 34 optimal weight: 0.4980 chunk 256 optimal weight: 1.9990 chunk 203 optimal weight: 0.4980 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.1563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 33077 Z= 0.145 Angle : 0.490 9.843 44726 Z= 0.250 Chirality : 0.040 0.178 5219 Planarity : 0.003 0.039 5731 Dihedral : 5.924 87.076 4766 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.68 % Allowed : 11.93 % Favored : 87.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.14), residues: 4208 helix: 1.28 (0.12), residues: 2084 sheet: -1.03 (0.23), residues: 566 loop : -0.96 (0.16), residues: 1558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP b 176 HIS 0.003 0.001 HIS F 371 PHE 0.022 0.001 PHE L 47 TYR 0.017 0.001 TYR h 35 ARG 0.005 0.000 ARG F 416 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8416 Ramachandran restraints generated. 4208 Oldfield, 0 Emsley, 4208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8416 Ramachandran restraints generated. 4208 Oldfield, 0 Emsley, 4208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 176 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Evaluate side-chains 479 residues out of total 3402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 456 time to evaluate : 3.891 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: A 383 MET cc_start: 0.9111 (tpt) cc_final: 0.8803 (tpt) REVERT: B 181 ASP cc_start: 0.7727 (m-30) cc_final: 0.7422 (m-30) REVERT: G 64 LYS cc_start: 0.7829 (mttm) cc_final: 0.7540 (ttpp) REVERT: G 147 GLU cc_start: 0.8146 (tp30) cc_final: 0.7792 (tp30) REVERT: G 202 ARG cc_start: 0.7543 (OUTLIER) cc_final: 0.7143 (ptm160) REVERT: H 96 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7605 (tt0) REVERT: K 58 GLU cc_start: 0.7067 (tp30) cc_final: 0.6497 (tp30) REVERT: L 60 MET cc_start: 0.6983 (tpt) cc_final: 0.6545 (tpt) REVERT: L 66 MET cc_start: 0.6453 (mmm) cc_final: 0.6074 (ppp) REVERT: M 44 GLN cc_start: 0.7447 (tp-100) cc_final: 0.7033 (tt0) REVERT: P 39 ASN cc_start: 0.8577 (t0) cc_final: 0.8159 (t0) REVERT: P 47 PHE cc_start: 0.7262 (OUTLIER) cc_final: 0.6552 (m-80) REVERT: Q 47 PHE cc_start: 0.7646 (t80) cc_final: 0.7414 (t80) REVERT: S 72 MET cc_start: 0.7032 (tpt) cc_final: 0.6797 (tmm) REVERT: b 140 TYR cc_start: 0.5753 (t80) cc_final: 0.5034 (p90) REVERT: h 47 LYS cc_start: 0.6197 (mttp) cc_final: 0.5906 (tttt) outliers start: 23 outliers final: 18 residues processed: 467 average time/residue: 0.8653 time to fit residues: 651.1494 Evaluate side-chains 453 residues out of total 3402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 432 time to evaluate : 3.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 409 ASP Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain B residue 502 THR Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 435 LEU Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain F residue 270 SER Chi-restraints excluded: chain F residue 310 SER Chi-restraints excluded: chain F residue 435 LEU Chi-restraints excluded: chain G residue 202 ARG Chi-restraints excluded: chain H residue 96 GLU Chi-restraints excluded: chain K residue 25 ILE Chi-restraints excluded: chain L residue 70 LEU Chi-restraints excluded: chain L residue 71 ILE Chi-restraints excluded: chain O residue 47 PHE Chi-restraints excluded: chain O residue 70 LEU Chi-restraints excluded: chain P residue 47 PHE Chi-restraints excluded: chain R residue 70 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 263 optimal weight: 1.9990 chunk 353 optimal weight: 10.0000 chunk 101 optimal weight: 1.9990 chunk 305 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 chunk 332 optimal weight: 3.9990 chunk 139 optimal weight: 0.6980 chunk 341 optimal weight: 10.0000 chunk 42 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.122412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.086115 restraints weight = 138362.474| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 1.58 r_work: 0.2841 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.2723 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2682 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2682 r_free = 0.2682 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2682 r_free = 0.2682 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2682 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.1483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 33077 Z= 0.323 Angle : 0.535 9.707 44726 Z= 0.275 Chirality : 0.042 0.177 5219 Planarity : 0.003 0.039 5731 Dihedral : 6.088 87.952 4766 Min Nonbonded Distance : 1.683 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 0.79 % Allowed : 12.23 % Favored : 86.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.14), residues: 4208 helix: 1.18 (0.12), residues: 2083 sheet: -1.13 (0.23), residues: 579 loop : -1.01 (0.16), residues: 1546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP b 176 HIS 0.003 0.001 HIS b 172 PHE 0.016 0.001 PHE Q 54 TYR 0.016 0.001 TYR h 35 ARG 0.005 0.000 ARG J 37 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12973.38 seconds wall clock time: 225 minutes 35.44 seconds (13535.44 seconds total)