Starting phenix.real_space_refine (version: dev) on Thu Feb 23 17:36:35 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rfg_24441/02_2023/7rfg_24441_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rfg_24441/02_2023/7rfg_24441.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rfg_24441/02_2023/7rfg_24441.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rfg_24441/02_2023/7rfg_24441.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rfg_24441/02_2023/7rfg_24441_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rfg_24441/02_2023/7rfg_24441_trim_updated.pdb" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.295 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "A TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 43": "OD1" <-> "OD2" Residue "A ASP 47": "OD1" <-> "OD2" Residue "A ARG 57": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 75": "OE1" <-> "OE2" Residue "A PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 103": "OE1" <-> "OE2" Residue "A ARG 105": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 117": "OD1" <-> "OD2" Residue "A GLU 132": "OE1" <-> "OE2" Residue "A ARG 136": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 146": "OE1" <-> "OE2" Residue "A ASP 164": "OD1" <-> "OD2" Residue "A GLU 168": "OE1" <-> "OE2" Residue "A ASP 170": "OD1" <-> "OD2" Residue "A GLU 177": "OE1" <-> "OE2" Residue "A ARG 182": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 184": "OE1" <-> "OE2" Residue "A GLU 217": "OE1" <-> "OE2" Residue "A TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 239": "OD1" <-> "OD2" Residue "A ARG 253": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 255": "OD1" <-> "OD2" Residue "A ASP 256": "OD1" <-> "OD2" Residue "A ASP 261": "OD1" <-> "OD2" Residue "A ASP 269": "OD1" <-> "OD2" Residue "A TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 319": "OD1" <-> "OD2" Residue "A GLU 335": "OE1" <-> "OE2" Residue "A ARG 355": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 357": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 402": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 407": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 411": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 470": "OD1" <-> "OD2" Residue "A ARG 474": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 509": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 512": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 514": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 47": "OD1" <-> "OD2" Residue "B ARG 57": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 75": "OE1" <-> "OE2" Residue "B PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 103": "OE1" <-> "OE2" Residue "B ARG 105": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 117": "OD1" <-> "OD2" Residue "B GLU 132": "OE1" <-> "OE2" Residue "B ARG 136": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 164": "OD1" <-> "OD2" Residue "B GLU 168": "OE1" <-> "OE2" Residue "B ASP 170": "OD1" <-> "OD2" Residue "B ARG 182": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 184": "OE1" <-> "OE2" Residue "B ASP 214": "OD1" <-> "OD2" Residue "B GLU 217": "OE1" <-> "OE2" Residue "B TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 239": "OD1" <-> "OD2" Residue "B ARG 253": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 254": "OE1" <-> "OE2" Residue "B ASP 256": "OD1" <-> "OD2" Residue "B ASP 261": "OD1" <-> "OD2" Residue "B ASP 269": "OD1" <-> "OD2" Residue "B TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 319": "OD1" <-> "OD2" Residue "B ARG 355": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 357": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 402": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 404": "OD1" <-> "OD2" Residue "B ARG 407": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 411": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 470": "OD1" <-> "OD2" Residue "B ARG 474": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 512": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 514": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 43": "OD1" <-> "OD2" Residue "C GLU 48": "OE1" <-> "OE2" Residue "C ARG 57": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 75": "OE1" <-> "OE2" Residue "C PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 103": "OE1" <-> "OE2" Residue "C ARG 105": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 136": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 164": "OD1" <-> "OD2" Residue "C ASP 170": "OD1" <-> "OD2" Residue "C GLU 177": "OE1" <-> "OE2" Residue "C ARG 182": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 184": "OE1" <-> "OE2" Residue "C GLU 199": "OE1" <-> "OE2" Residue "C GLU 217": "OE1" <-> "OE2" Residue "C TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 239": "OD1" <-> "OD2" Residue "C ARG 253": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ASP 256": "OD1" <-> "OD2" Residue "C ASP 261": "OD1" <-> "OD2" Residue "C ASP 269": "OD1" <-> "OD2" Residue "C TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 319": "OD1" <-> "OD2" Residue "C GLU 335": "OE1" <-> "OE2" Residue "C ARG 355": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 357": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 402": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 407": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 411": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 421": "OE1" <-> "OE2" Residue "C ASP 470": "OD1" <-> "OD2" Residue "C ARG 474": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 509": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 510": "OE1" <-> "OE2" Residue "C ARG 512": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 514": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 47": "OD1" <-> "OD2" Residue "D GLU 48": "OE1" <-> "OE2" Residue "D ARG 57": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D GLU 75": "OE1" <-> "OE2" Residue "D PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 103": "OE1" <-> "OE2" Residue "D ARG 105": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 132": "OE1" <-> "OE2" Residue "D ARG 136": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 146": "OE1" <-> "OE2" Residue "D ASP 164": "OD1" <-> "OD2" Residue "D ASP 170": "OD1" <-> "OD2" Residue "D ARG 182": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D GLU 184": "OE1" <-> "OE2" Residue "D ASP 214": "OD1" <-> "OD2" Residue "D GLU 217": "OE1" <-> "OE2" Residue "D TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 239": "OD1" <-> "OD2" Residue "D ARG 253": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D GLU 254": "OE1" <-> "OE2" Residue "D ASP 256": "OD1" <-> "OD2" Residue "D ASP 261": "OD1" <-> "OD2" Residue "D ASP 269": "OD1" <-> "OD2" Residue "D TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 319": "OD1" <-> "OD2" Residue "D ARG 355": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D PHE 357": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 407": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D TYR 411": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 421": "OE1" <-> "OE2" Residue "D ASP 470": "OD1" <-> "OD2" Residue "D ARG 474": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 510": "OE1" <-> "OE2" Residue "D ARG 512": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D TYR 514": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 47": "OD1" <-> "OD2" Residue "E GLU 48": "OE1" <-> "OE2" Residue "E ARG 57": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E GLU 75": "OE1" <-> "OE2" Residue "E PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 103": "OE1" <-> "OE2" Residue "E ARG 105": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 129": "OD1" <-> "OD2" Residue "E ARG 136": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 146": "OE1" <-> "OE2" Residue "E ASP 164": "OD1" <-> "OD2" Residue "E GLU 168": "OE1" <-> "OE2" Residue "E GLU 177": "OE1" <-> "OE2" Residue "E ARG 182": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E GLU 184": "OE1" <-> "OE2" Residue "E GLU 199": "OE1" <-> "OE2" Residue "E ASP 214": "OD1" <-> "OD2" Residue "E GLU 217": "OE1" <-> "OE2" Residue "E TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 239": "OD1" <-> "OD2" Residue "E ARG 253": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ASP 256": "OD1" <-> "OD2" Residue "E ASP 261": "OD1" <-> "OD2" Residue "E ASP 269": "OD1" <-> "OD2" Residue "E TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 319": "OD1" <-> "OD2" Residue "E ARG 355": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E PHE 357": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 402": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 404": "OD1" <-> "OD2" Residue "E ARG 407": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E TYR 411": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 418": "OD1" <-> "OD2" Residue "E ASP 470": "OD1" <-> "OD2" Residue "E ARG 474": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 510": "OE1" <-> "OE2" Residue "E ARG 512": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E TYR 514": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 43": "OD1" <-> "OD2" Residue "F ASP 47": "OD1" <-> "OD2" Residue "F GLU 48": "OE1" <-> "OE2" Residue "F ARG 57": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F GLU 75": "OE1" <-> "OE2" Residue "F PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 103": "OE1" <-> "OE2" Residue "F ARG 105": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 117": "OD1" <-> "OD2" Residue "F ARG 136": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 146": "OE1" <-> "OE2" Residue "F ASP 164": "OD1" <-> "OD2" Residue "F ASP 170": "OD1" <-> "OD2" Residue "F GLU 177": "OE1" <-> "OE2" Residue "F ARG 182": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F GLU 184": "OE1" <-> "OE2" Residue "F ASP 214": "OD1" <-> "OD2" Residue "F GLU 217": "OE1" <-> "OE2" Residue "F TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ARG 253": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ASP 256": "OD1" <-> "OD2" Residue "F ASP 261": "OD1" <-> "OD2" Residue "F ASP 269": "OD1" <-> "OD2" Residue "F TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 319": "OD1" <-> "OD2" Residue "F GLU 335": "OE1" <-> "OE2" Residue "F ARG 355": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F PHE 357": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 402": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ARG 407": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F TYR 411": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 421": "OE1" <-> "OE2" Residue "F ASP 470": "OD1" <-> "OD2" Residue "F ARG 474": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 509": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 510": "OE1" <-> "OE2" Residue "F ARG 512": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F TYR 514": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ASP 47": "OD1" <-> "OD2" Residue "G GLU 48": "OE1" <-> "OE2" Residue "G ARG 57": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G GLU 75": "OE1" <-> "OE2" Residue "G PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 103": "OE1" <-> "OE2" Residue "G ARG 105": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ASP 117": "OD1" <-> "OD2" Residue "G ARG 136": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 146": "OE1" <-> "OE2" Residue "G ASP 164": "OD1" <-> "OD2" Residue "G GLU 168": "OE1" <-> "OE2" Residue "G GLU 177": "OE1" <-> "OE2" Residue "G ARG 182": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G GLU 184": "OE1" <-> "OE2" Residue "G GLU 199": "OE1" <-> "OE2" Residue "G TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ASP 239": "OD1" <-> "OD2" Residue "G ARG 253": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ASP 256": "OD1" <-> "OD2" Residue "G ASP 261": "OD1" <-> "OD2" Residue "G ASP 269": "OD1" <-> "OD2" Residue "G TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ASP 319": "OD1" <-> "OD2" Residue "G ARG 355": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G PHE 357": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 402": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ARG 407": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G TYR 411": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 421": "OE1" <-> "OE2" Residue "G ASP 470": "OD1" <-> "OD2" Residue "G ARG 474": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 491": "OE1" <-> "OE2" Residue "G GLU 510": "OE1" <-> "OE2" Residue "G ARG 512": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G TYR 514": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ASP 43": "OD1" <-> "OD2" Residue "H ASP 47": "OD1" <-> "OD2" Residue "H ARG 57": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H GLU 75": "OE1" <-> "OE2" Residue "H PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 103": "OE1" <-> "OE2" Residue "H ARG 105": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ASP 117": "OD1" <-> "OD2" Residue "H ARG 136": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 146": "OE1" <-> "OE2" Residue "H ASP 164": "OD1" <-> "OD2" Residue "H GLU 177": "OE1" <-> "OE2" Residue "H ARG 182": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H GLU 184": "OE1" <-> "OE2" Residue "H GLU 217": "OE1" <-> "OE2" Residue "H TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ASP 239": "OD1" <-> "OD2" Residue "H ARG 253": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ASP 255": "OD1" <-> "OD2" Residue "H ASP 256": "OD1" <-> "OD2" Residue "H ASP 261": "OD1" <-> "OD2" Residue "H ASP 269": "OD1" <-> "OD2" Residue "H TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ASP 319": "OD1" <-> "OD2" Residue "H GLU 335": "OE1" <-> "OE2" Residue "H ARG 355": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 402": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ASP 404": "OD1" <-> "OD2" Residue "H ARG 407": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H TYR 411": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 421": "OE1" <-> "OE2" Residue "H ASP 470": "OD1" <-> "OD2" Residue "H ARG 474": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 510": "OE1" <-> "OE2" Residue "H ARG 512": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H TYR 514": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 60824 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 7485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 7485 Classifications: {'peptide': 491} Link IDs: {'PTRANS': 17, 'TRANS': 473} Chain breaks: 1 Chain: "B" Number of atoms: 7485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 7485 Classifications: {'peptide': 491} Link IDs: {'PTRANS': 17, 'TRANS': 473} Chain breaks: 1 Chain: "C" Number of atoms: 7485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 7485 Classifications: {'peptide': 491} Link IDs: {'PTRANS': 17, 'TRANS': 473} Chain breaks: 1 Chain: "D" Number of atoms: 7485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 7485 Classifications: {'peptide': 491} Link IDs: {'PTRANS': 17, 'TRANS': 473} Chain breaks: 1 Chain: "E" Number of atoms: 7485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 7485 Classifications: {'peptide': 491} Link IDs: {'PTRANS': 17, 'TRANS': 473} Chain breaks: 1 Chain: "F" Number of atoms: 7485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 7485 Classifications: {'peptide': 491} Link IDs: {'PTRANS': 17, 'TRANS': 473} Chain breaks: 1 Chain: "G" Number of atoms: 7485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 7485 Classifications: {'peptide': 491} Link IDs: {'PTRANS': 17, 'TRANS': 473} Chain breaks: 1 Chain: "H" Number of atoms: 7485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 7485 Classifications: {'peptide': 491} Link IDs: {'PTRANS': 17, 'TRANS': 473} Chain breaks: 1 Chain: "A" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 118 Unusual residues: {'ATP': 1, 'GTP': 2} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "B" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 118 Unusual residues: {'ATP': 1, 'GTP': 2} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "C" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 118 Unusual residues: {'ATP': 1, 'GTP': 2} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "D" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 118 Unusual residues: {'ATP': 1, 'GTP': 2} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "E" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 118 Unusual residues: {'ATP': 1, 'GTP': 2} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "F" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 118 Unusual residues: {'ATP': 1, 'GTP': 2} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "G" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 118 Unusual residues: {'ATP': 1, 'GTP': 2} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "H" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 118 Unusual residues: {'ATP': 1, 'GTP': 2} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Time building chain proxies: 21.36, per 1000 atoms: 0.35 Number of scatterers: 60824 At special positions: 0 Unit cell: (166.95, 168, 112.35, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 192 16.00 P 80 15.00 O 6040 8.00 N 5232 7.00 C 19040 6.00 H 30240 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: 42.25 Conformation dependent library (CDL) restraints added in 4.8 seconds 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7072 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 156 helices and 51 sheets defined 35.5% alpha, 11.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.92 Creating SS restraints... Processing helix chain 'A' and resid 20 through 25 Processing helix chain 'A' and resid 32 through 34 No H-bonds generated for 'chain 'A' and resid 32 through 34' Processing helix chain 'A' and resid 46 through 48 No H-bonds generated for 'chain 'A' and resid 46 through 48' Processing helix chain 'A' and resid 76 through 84 Processing helix chain 'A' and resid 97 through 109 Processing helix chain 'A' and resid 127 through 137 Processing helix chain 'A' and resid 160 through 163 No H-bonds generated for 'chain 'A' and resid 160 through 163' Processing helix chain 'A' and resid 175 through 177 No H-bonds generated for 'chain 'A' and resid 175 through 177' Processing helix chain 'A' and resid 194 through 204 Processing helix chain 'A' and resid 224 through 232 Processing helix chain 'A' and resid 254 through 265 removed outlier: 3.629A pdb=" N LEU A 260 " --> pdb=" O LYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 293 Processing helix chain 'A' and resid 307 through 316 removed outlier: 3.636A pdb=" N ASN A 312 " --> pdb=" O ALA A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 337 Processing helix chain 'A' and resid 343 through 357 removed outlier: 4.503A pdb=" N ARG A 356 " --> pdb=" O GLU A 352 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N PHE A 357 " --> pdb=" O TYR A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 378 Processing helix chain 'A' and resid 453 through 471 Proline residue: A 458 - end of helix Processing helix chain 'A' and resid 476 through 485 Processing helix chain 'A' and resid 495 through 501 Processing helix chain 'B' and resid 20 through 25 Processing helix chain 'B' and resid 32 through 34 No H-bonds generated for 'chain 'B' and resid 32 through 34' Processing helix chain 'B' and resid 46 through 48 No H-bonds generated for 'chain 'B' and resid 46 through 48' Processing helix chain 'B' and resid 76 through 84 Processing helix chain 'B' and resid 97 through 110 Processing helix chain 'B' and resid 127 through 137 Processing helix chain 'B' and resid 160 through 163 No H-bonds generated for 'chain 'B' and resid 160 through 163' Processing helix chain 'B' and resid 175 through 177 No H-bonds generated for 'chain 'B' and resid 175 through 177' Processing helix chain 'B' and resid 194 through 204 Processing helix chain 'B' and resid 224 through 232 Processing helix chain 'B' and resid 254 through 265 removed outlier: 3.606A pdb=" N LEU B 260 " --> pdb=" O LYS B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 293 Processing helix chain 'B' and resid 307 through 316 removed outlier: 3.631A pdb=" N ASN B 312 " --> pdb=" O ALA B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 337 Processing helix chain 'B' and resid 343 through 357 removed outlier: 4.504A pdb=" N ARG B 356 " --> pdb=" O GLU B 352 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N PHE B 357 " --> pdb=" O TYR B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 378 Processing helix chain 'B' and resid 417 through 420 No H-bonds generated for 'chain 'B' and resid 417 through 420' Processing helix chain 'B' and resid 453 through 471 Proline residue: B 458 - end of helix Processing helix chain 'B' and resid 476 through 485 Processing helix chain 'B' and resid 495 through 501 Processing helix chain 'C' and resid 20 through 25 Processing helix chain 'C' and resid 32 through 34 No H-bonds generated for 'chain 'C' and resid 32 through 34' Processing helix chain 'C' and resid 46 through 48 No H-bonds generated for 'chain 'C' and resid 46 through 48' Processing helix chain 'C' and resid 76 through 84 Processing helix chain 'C' and resid 97 through 110 Processing helix chain 'C' and resid 127 through 137 Processing helix chain 'C' and resid 160 through 163 No H-bonds generated for 'chain 'C' and resid 160 through 163' Processing helix chain 'C' and resid 175 through 177 No H-bonds generated for 'chain 'C' and resid 175 through 177' Processing helix chain 'C' and resid 194 through 204 Processing helix chain 'C' and resid 224 through 232 Processing helix chain 'C' and resid 254 through 265 removed outlier: 3.601A pdb=" N LEU C 260 " --> pdb=" O LYS C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 293 Processing helix chain 'C' and resid 307 through 316 removed outlier: 3.644A pdb=" N ASN C 312 " --> pdb=" O ALA C 308 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU C 313 " --> pdb=" O GLN C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 337 Processing helix chain 'C' and resid 343 through 357 removed outlier: 4.415A pdb=" N ARG C 356 " --> pdb=" O GLU C 352 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N PHE C 357 " --> pdb=" O TYR C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 378 Processing helix chain 'C' and resid 417 through 420 No H-bonds generated for 'chain 'C' and resid 417 through 420' Processing helix chain 'C' and resid 453 through 471 Proline residue: C 458 - end of helix Processing helix chain 'C' and resid 476 through 484 Processing helix chain 'C' and resid 495 through 501 Processing helix chain 'D' and resid 20 through 25 Processing helix chain 'D' and resid 32 through 34 No H-bonds generated for 'chain 'D' and resid 32 through 34' Processing helix chain 'D' and resid 46 through 48 No H-bonds generated for 'chain 'D' and resid 46 through 48' Processing helix chain 'D' and resid 76 through 84 Processing helix chain 'D' and resid 97 through 110 Processing helix chain 'D' and resid 127 through 137 Processing helix chain 'D' and resid 160 through 163 No H-bonds generated for 'chain 'D' and resid 160 through 163' Processing helix chain 'D' and resid 175 through 177 No H-bonds generated for 'chain 'D' and resid 175 through 177' Processing helix chain 'D' and resid 194 through 204 Processing helix chain 'D' and resid 224 through 232 Processing helix chain 'D' and resid 254 through 265 removed outlier: 3.600A pdb=" N LEU D 260 " --> pdb=" O LYS D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 293 Processing helix chain 'D' and resid 307 through 316 removed outlier: 3.682A pdb=" N ASN D 312 " --> pdb=" O ALA D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 333 through 337 Processing helix chain 'D' and resid 343 through 357 removed outlier: 4.430A pdb=" N ARG D 356 " --> pdb=" O GLU D 352 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N PHE D 357 " --> pdb=" O TYR D 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 378 Processing helix chain 'D' and resid 453 through 471 Proline residue: D 458 - end of helix Processing helix chain 'D' and resid 476 through 485 Processing helix chain 'D' and resid 495 through 500 Processing helix chain 'E' and resid 20 through 25 Processing helix chain 'E' and resid 32 through 34 No H-bonds generated for 'chain 'E' and resid 32 through 34' Processing helix chain 'E' and resid 46 through 48 No H-bonds generated for 'chain 'E' and resid 46 through 48' Processing helix chain 'E' and resid 76 through 84 Processing helix chain 'E' and resid 97 through 110 Processing helix chain 'E' and resid 127 through 137 Processing helix chain 'E' and resid 160 through 163 No H-bonds generated for 'chain 'E' and resid 160 through 163' Processing helix chain 'E' and resid 175 through 177 No H-bonds generated for 'chain 'E' and resid 175 through 177' Processing helix chain 'E' and resid 194 through 204 Processing helix chain 'E' and resid 224 through 232 Processing helix chain 'E' and resid 254 through 265 removed outlier: 3.619A pdb=" N LEU E 260 " --> pdb=" O LYS E 257 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N THR E 264 " --> pdb=" O ASP E 261 " (cutoff:3.500A) Processing helix chain 'E' and resid 281 through 293 Processing helix chain 'E' and resid 307 through 316 removed outlier: 3.647A pdb=" N ASN E 312 " --> pdb=" O ALA E 308 " (cutoff:3.500A) Processing helix chain 'E' and resid 333 through 336 No H-bonds generated for 'chain 'E' and resid 333 through 336' Processing helix chain 'E' and resid 343 through 357 removed outlier: 4.449A pdb=" N ARG E 356 " --> pdb=" O GLU E 352 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N PHE E 357 " --> pdb=" O TYR E 353 " (cutoff:3.500A) Processing helix chain 'E' and resid 370 through 378 Processing helix chain 'E' and resid 417 through 420 No H-bonds generated for 'chain 'E' and resid 417 through 420' Processing helix chain 'E' and resid 453 through 471 Proline residue: E 458 - end of helix Processing helix chain 'E' and resid 476 through 484 Processing helix chain 'E' and resid 495 through 501 Processing helix chain 'F' and resid 20 through 25 Processing helix chain 'F' and resid 32 through 34 No H-bonds generated for 'chain 'F' and resid 32 through 34' Processing helix chain 'F' and resid 46 through 48 No H-bonds generated for 'chain 'F' and resid 46 through 48' Processing helix chain 'F' and resid 76 through 84 Processing helix chain 'F' and resid 97 through 110 Processing helix chain 'F' and resid 127 through 137 Processing helix chain 'F' and resid 160 through 163 No H-bonds generated for 'chain 'F' and resid 160 through 163' Processing helix chain 'F' and resid 175 through 177 No H-bonds generated for 'chain 'F' and resid 175 through 177' Processing helix chain 'F' and resid 194 through 204 Processing helix chain 'F' and resid 224 through 232 Processing helix chain 'F' and resid 254 through 265 removed outlier: 3.618A pdb=" N LEU F 260 " --> pdb=" O LYS F 257 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR F 264 " --> pdb=" O ASP F 261 " (cutoff:3.500A) Processing helix chain 'F' and resid 281 through 293 Processing helix chain 'F' and resid 307 through 316 removed outlier: 3.638A pdb=" N ASN F 312 " --> pdb=" O ALA F 308 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU F 313 " --> pdb=" O GLN F 309 " (cutoff:3.500A) Processing helix chain 'F' and resid 333 through 337 Processing helix chain 'F' and resid 343 through 357 removed outlier: 4.479A pdb=" N ARG F 356 " --> pdb=" O GLU F 352 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N PHE F 357 " --> pdb=" O TYR F 353 " (cutoff:3.500A) Processing helix chain 'F' and resid 370 through 378 Processing helix chain 'F' and resid 453 through 471 Proline residue: F 458 - end of helix Processing helix chain 'F' and resid 476 through 485 Processing helix chain 'F' and resid 495 through 501 Processing helix chain 'G' and resid 20 through 25 Processing helix chain 'G' and resid 32 through 34 No H-bonds generated for 'chain 'G' and resid 32 through 34' Processing helix chain 'G' and resid 46 through 48 No H-bonds generated for 'chain 'G' and resid 46 through 48' Processing helix chain 'G' and resid 76 through 84 Processing helix chain 'G' and resid 97 through 110 Processing helix chain 'G' and resid 127 through 137 Processing helix chain 'G' and resid 160 through 163 No H-bonds generated for 'chain 'G' and resid 160 through 163' Processing helix chain 'G' and resid 175 through 177 No H-bonds generated for 'chain 'G' and resid 175 through 177' Processing helix chain 'G' and resid 194 through 204 Processing helix chain 'G' and resid 224 through 232 Processing helix chain 'G' and resid 254 through 265 removed outlier: 3.649A pdb=" N LEU G 260 " --> pdb=" O LYS G 257 " (cutoff:3.500A) Processing helix chain 'G' and resid 281 through 293 Processing helix chain 'G' and resid 307 through 316 removed outlier: 3.657A pdb=" N ASN G 312 " --> pdb=" O ALA G 308 " (cutoff:3.500A) Processing helix chain 'G' and resid 333 through 337 Processing helix chain 'G' and resid 343 through 357 removed outlier: 4.455A pdb=" N ARG G 356 " --> pdb=" O GLU G 352 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N PHE G 357 " --> pdb=" O TYR G 353 " (cutoff:3.500A) Processing helix chain 'G' and resid 370 through 378 Processing helix chain 'G' and resid 453 through 471 Proline residue: G 458 - end of helix Processing helix chain 'G' and resid 476 through 485 Processing helix chain 'G' and resid 495 through 501 Processing helix chain 'H' and resid 20 through 25 Processing helix chain 'H' and resid 32 through 34 No H-bonds generated for 'chain 'H' and resid 32 through 34' Processing helix chain 'H' and resid 46 through 48 No H-bonds generated for 'chain 'H' and resid 46 through 48' Processing helix chain 'H' and resid 76 through 84 Processing helix chain 'H' and resid 97 through 109 Processing helix chain 'H' and resid 127 through 137 Processing helix chain 'H' and resid 160 through 163 No H-bonds generated for 'chain 'H' and resid 160 through 163' Processing helix chain 'H' and resid 175 through 177 No H-bonds generated for 'chain 'H' and resid 175 through 177' Processing helix chain 'H' and resid 194 through 204 Processing helix chain 'H' and resid 224 through 232 Processing helix chain 'H' and resid 254 through 265 removed outlier: 3.611A pdb=" N LEU H 260 " --> pdb=" O LYS H 257 " (cutoff:3.500A) Processing helix chain 'H' and resid 281 through 293 Processing helix chain 'H' and resid 307 through 316 removed outlier: 3.622A pdb=" N ASN H 312 " --> pdb=" O ALA H 308 " (cutoff:3.500A) Processing helix chain 'H' and resid 333 through 337 Processing helix chain 'H' and resid 343 through 357 removed outlier: 4.477A pdb=" N ARG H 356 " --> pdb=" O GLU H 352 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N PHE H 357 " --> pdb=" O TYR H 353 " (cutoff:3.500A) Processing helix chain 'H' and resid 370 through 378 Processing helix chain 'H' and resid 417 through 420 No H-bonds generated for 'chain 'H' and resid 417 through 420' Processing helix chain 'H' and resid 453 through 471 Proline residue: H 458 - end of helix Processing helix chain 'H' and resid 476 through 485 Processing helix chain 'H' and resid 495 through 501 Processing sheet with id= A, first strand: chain 'A' and resid 35 through 37 Processing sheet with id= B, first strand: chain 'A' and resid 65 through 67 removed outlier: 6.471A pdb=" N VAL A 384 " --> pdb=" O ILE A 66 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ASN A 303 " --> pdb=" O ARG A 322 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N GLY A 302 " --> pdb=" O LEU A 273 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 187 through 189 removed outlier: 8.061A pdb=" N ALA A 188 " --> pdb=" O LYS A 208 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 408 through 411 Processing sheet with id= E, first strand: chain 'A' and resid 53 through 56 removed outlier: 6.632A pdb=" N ILE A 59 " --> pdb=" O LEU A 55 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 142 through 145 Processing sheet with id= G, first strand: chain 'B' and resid 35 through 37 Processing sheet with id= H, first strand: chain 'B' and resid 65 through 67 removed outlier: 6.465A pdb=" N VAL B 384 " --> pdb=" O ILE B 66 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 187 through 189 removed outlier: 8.053A pdb=" N ALA B 188 " --> pdb=" O LYS B 208 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 247 through 250 removed outlier: 6.612A pdb=" N VAL B 270 " --> pdb=" O ALA B 248 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N VAL B 250 " --> pdb=" O VAL B 270 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N VAL B 272 " --> pdb=" O VAL B 250 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N GLN B 298 " --> pdb=" O ILE B 271 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N LEU B 273 " --> pdb=" O GLN B 298 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N ILE B 300 " --> pdb=" O LEU B 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'B' and resid 408 through 411 Processing sheet with id= L, first strand: chain 'B' and resid 142 through 145 Processing sheet with id= M, first strand: chain 'C' and resid 35 through 37 Processing sheet with id= N, first strand: chain 'C' and resid 65 through 67 removed outlier: 6.437A pdb=" N VAL C 384 " --> pdb=" O ILE C 66 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ASN C 303 " --> pdb=" O ARG C 322 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLY C 302 " --> pdb=" O LEU C 273 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 187 through 189 removed outlier: 8.093A pdb=" N ALA C 188 " --> pdb=" O LYS C 208 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 400 through 402 Processing sheet with id= Q, first strand: chain 'C' and resid 53 through 56 removed outlier: 6.632A pdb=" N ILE C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 142 through 145 Processing sheet with id= S, first strand: chain 'D' and resid 35 through 37 Processing sheet with id= T, first strand: chain 'D' and resid 65 through 67 removed outlier: 6.453A pdb=" N VAL D 384 " --> pdb=" O ILE D 66 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'D' and resid 187 through 189 removed outlier: 8.056A pdb=" N ALA D 188 " --> pdb=" O LYS D 208 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'D' and resid 247 through 250 removed outlier: 6.604A pdb=" N VAL D 270 " --> pdb=" O ALA D 248 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N VAL D 250 " --> pdb=" O VAL D 270 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N VAL D 272 " --> pdb=" O VAL D 250 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N GLN D 298 " --> pdb=" O ILE D 271 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N LEU D 273 " --> pdb=" O GLN D 298 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N ILE D 300 " --> pdb=" O LEU D 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= V Processing sheet with id= W, first strand: chain 'D' and resid 408 through 411 Processing sheet with id= X, first strand: chain 'D' and resid 53 through 56 removed outlier: 6.620A pdb=" N ILE D 59 " --> pdb=" O LEU D 55 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'D' and resid 142 through 145 Processing sheet with id= Z, first strand: chain 'E' and resid 35 through 37 Processing sheet with id= AA, first strand: chain 'E' and resid 65 through 67 removed outlier: 6.463A pdb=" N VAL E 384 " --> pdb=" O ILE E 66 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ASN E 303 " --> pdb=" O ARG E 322 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N GLY E 302 " --> pdb=" O LEU E 273 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'E' and resid 187 through 189 removed outlier: 8.030A pdb=" N ALA E 188 " --> pdb=" O LYS E 208 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'E' and resid 408 through 411 Processing sheet with id= AD, first strand: chain 'E' and resid 53 through 56 removed outlier: 6.622A pdb=" N ILE E 59 " --> pdb=" O LEU E 55 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'E' and resid 142 through 145 Processing sheet with id= AF, first strand: chain 'F' and resid 35 through 37 Processing sheet with id= AG, first strand: chain 'F' and resid 65 through 67 removed outlier: 6.434A pdb=" N VAL F 384 " --> pdb=" O ILE F 66 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ASN F 303 " --> pdb=" O ARG F 322 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLY F 302 " --> pdb=" O LEU F 273 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'F' and resid 187 through 189 removed outlier: 8.141A pdb=" N ALA F 188 " --> pdb=" O LYS F 208 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'F' and resid 408 through 411 Processing sheet with id= AJ, first strand: chain 'F' and resid 53 through 56 removed outlier: 6.612A pdb=" N ILE F 59 " --> pdb=" O LEU F 55 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'F' and resid 142 through 145 Processing sheet with id= AL, first strand: chain 'G' and resid 35 through 37 Processing sheet with id= AM, first strand: chain 'G' and resid 65 through 67 removed outlier: 6.423A pdb=" N VAL G 384 " --> pdb=" O ILE G 66 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'G' and resid 187 through 189 removed outlier: 8.036A pdb=" N ALA G 188 " --> pdb=" O LYS G 208 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'G' and resid 247 through 250 removed outlier: 6.606A pdb=" N VAL G 270 " --> pdb=" O ALA G 248 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N VAL G 250 " --> pdb=" O VAL G 270 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N VAL G 272 " --> pdb=" O VAL G 250 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N GLN G 298 " --> pdb=" O ILE G 271 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N LEU G 273 " --> pdb=" O GLN G 298 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N ILE G 300 " --> pdb=" O LEU G 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= AO Processing sheet with id= AP, first strand: chain 'G' and resid 408 through 411 Processing sheet with id= AQ, first strand: chain 'G' and resid 53 through 56 removed outlier: 6.622A pdb=" N ILE G 59 " --> pdb=" O LEU G 55 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'G' and resid 142 through 145 Processing sheet with id= AS, first strand: chain 'H' and resid 35 through 37 Processing sheet with id= AT, first strand: chain 'H' and resid 65 through 67 removed outlier: 6.455A pdb=" N VAL H 384 " --> pdb=" O ILE H 66 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'H' and resid 187 through 189 removed outlier: 8.071A pdb=" N ALA H 188 " --> pdb=" O LYS H 208 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'H' and resid 247 through 250 removed outlier: 6.581A pdb=" N VAL H 270 " --> pdb=" O ALA H 248 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N VAL H 250 " --> pdb=" O VAL H 270 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N VAL H 272 " --> pdb=" O VAL H 250 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N GLN H 298 " --> pdb=" O ILE H 271 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N LEU H 273 " --> pdb=" O GLN H 298 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N ILE H 300 " --> pdb=" O LEU H 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= AV Processing sheet with id= AW, first strand: chain 'H' and resid 408 through 411 Processing sheet with id= AX, first strand: chain 'H' and resid 53 through 56 removed outlier: 6.630A pdb=" N ILE H 59 " --> pdb=" O LEU H 55 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'H' and resid 142 through 145 969 hydrogen bonds defined for protein. 2616 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: 20.85 Time building geometry restraints manager: 44.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.90 - 1.09: 7965 1.09 - 1.27: 27284 1.27 - 1.45: 8171 1.45 - 1.64: 17588 1.64 - 1.82: 328 Bond restraints: 61336 Sorted by residual: bond pdb=" CB SER A 416 " pdb=" OG SER A 416 " ideal model delta sigma weight residual 1.417 1.180 0.237 2.00e-02 2.50e+03 1.41e+02 bond pdb=" CE1 HIS A 137 " pdb=" HE1 HIS A 137 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.73e+01 bond pdb=" N LYS A 349 " pdb=" H LYS A 349 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.72e+01 bond pdb=" N GLY A 405 " pdb=" H GLY A 405 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.72e+01 bond pdb=" N LYS D 153 " pdb=" H LYS D 153 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 ... (remaining 61331 not shown) Histogram of bond angle deviations from ideal: 73.28 - 85.32: 9 85.32 - 97.35: 41 97.35 - 109.39: 42641 109.39 - 121.43: 59418 121.43 - 133.47: 8923 Bond angle restraints: 111032 Sorted by residual: angle pdb=" PB ATP A 603 " pdb=" O3B ATP A 603 " pdb=" PG ATP A 603 " ideal model delta sigma weight residual 139.87 124.00 15.87 1.00e+00 1.00e+00 2.52e+02 angle pdb=" PB ATP G 603 " pdb=" O3B ATP G 603 " pdb=" PG ATP G 603 " ideal model delta sigma weight residual 139.87 124.32 15.55 1.00e+00 1.00e+00 2.42e+02 angle pdb=" PB ATP C 603 " pdb=" O3B ATP C 603 " pdb=" PG ATP C 603 " ideal model delta sigma weight residual 139.87 124.32 15.55 1.00e+00 1.00e+00 2.42e+02 angle pdb=" PB ATP B 603 " pdb=" O3B ATP B 603 " pdb=" PG ATP B 603 " ideal model delta sigma weight residual 139.87 124.33 15.54 1.00e+00 1.00e+00 2.42e+02 angle pdb=" PB ATP E 603 " pdb=" O3B ATP E 603 " pdb=" PG ATP E 603 " ideal model delta sigma weight residual 139.87 124.91 14.96 1.00e+00 1.00e+00 2.24e+02 ... (remaining 111027 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.51: 22913 34.51 - 69.03: 975 69.03 - 103.54: 82 103.54 - 138.06: 57 138.06 - 172.57: 13 Dihedral angle restraints: 24040 sinusoidal: 11592 harmonic: 12448 Sorted by residual: dihedral pdb=" CA ASP G 418 " pdb=" C ASP G 418 " pdb=" N ALA G 419 " pdb=" CA ALA G 419 " ideal model delta harmonic sigma weight residual -180.00 -143.77 -36.23 0 5.00e+00 4.00e-02 5.25e+01 dihedral pdb=" O5' GTP C 601 " pdb=" O3A GTP C 601 " pdb=" PA GTP C 601 " pdb=" PB GTP C 601 " ideal model delta sinusoidal sigma weight residual 274.12 101.55 172.57 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" C5' GTP B 601 " pdb=" O5' GTP B 601 " pdb=" PA GTP B 601 " pdb=" O3A GTP B 601 " ideal model delta sinusoidal sigma weight residual 69.27 -99.92 169.19 1 2.00e+01 2.50e-03 4.76e+01 ... (remaining 24037 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.308: 4844 0.308 - 0.617: 25 0.617 - 0.925: 0 0.925 - 1.234: 0 1.234 - 1.542: 3 Chirality restraints: 4872 Sorted by residual: chirality pdb=" CB VAL F 437 " pdb=" CA VAL F 437 " pdb=" CG1 VAL F 437 " pdb=" CG2 VAL F 437 " both_signs ideal model delta sigma weight residual False -2.63 -1.09 -1.54 2.00e-01 2.50e+01 5.95e+01 chirality pdb=" CB VAL C 437 " pdb=" CA VAL C 437 " pdb=" CG1 VAL C 437 " pdb=" CG2 VAL C 437 " both_signs ideal model delta sigma weight residual False -2.63 -1.19 -1.44 2.00e-01 2.50e+01 5.20e+01 chirality pdb=" CB VAL E 437 " pdb=" CA VAL E 437 " pdb=" CG1 VAL E 437 " pdb=" CG2 VAL E 437 " both_signs ideal model delta sigma weight residual False -2.63 -1.23 -1.40 2.00e-01 2.50e+01 4.91e+01 ... (remaining 4869 not shown) Planarity restraints: 9024 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG D 412 " 0.432 9.50e-02 1.11e+02 1.83e-01 3.10e+02 pdb=" NE ARG D 412 " 0.080 2.00e-02 2.50e+03 pdb=" CZ ARG D 412 " 0.030 2.00e-02 2.50e+03 pdb=" NH1 ARG D 412 " 0.044 2.00e-02 2.50e+03 pdb=" NH2 ARG D 412 " -0.031 2.00e-02 2.50e+03 pdb="HH11 ARG D 412 " -0.236 2.00e-02 2.50e+03 pdb="HH12 ARG D 412 " 0.203 2.00e-02 2.50e+03 pdb="HH21 ARG D 412 " -0.020 2.00e-02 2.50e+03 pdb="HH22 ARG D 412 " -0.089 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 230 " 0.143 2.00e-02 2.50e+03 1.42e-01 3.04e+02 pdb=" CG ASN B 230 " -0.061 2.00e-02 2.50e+03 pdb=" OD1 ASN B 230 " -0.085 2.00e-02 2.50e+03 pdb=" ND2 ASN B 230 " -0.160 2.00e-02 2.50e+03 pdb="HD21 ASN B 230 " -0.078 2.00e-02 2.50e+03 pdb="HD22 ASN B 230 " 0.242 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 412 " -0.419 9.50e-02 1.11e+02 1.74e-01 2.66e+02 pdb=" NE ARG A 412 " -0.073 2.00e-02 2.50e+03 pdb=" CZ ARG A 412 " -0.039 2.00e-02 2.50e+03 pdb=" NH1 ARG A 412 " -0.074 2.00e-02 2.50e+03 pdb=" NH2 ARG A 412 " 0.018 2.00e-02 2.50e+03 pdb="HH11 ARG A 412 " 0.234 2.00e-02 2.50e+03 pdb="HH12 ARG A 412 " -0.158 2.00e-02 2.50e+03 pdb="HH21 ARG A 412 " 0.047 2.00e-02 2.50e+03 pdb="HH22 ARG A 412 " 0.064 2.00e-02 2.50e+03 ... (remaining 9021 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.19: 4958 2.19 - 2.79: 115862 2.79 - 3.39: 188097 3.39 - 4.00: 259390 4.00 - 4.60: 374343 Nonbonded interactions: 942650 Sorted by model distance: nonbonded pdb=" HG1 THR D 159 " pdb=" O1B ATP D 603 " model vdw 1.587 1.850 nonbonded pdb=" HG SER D 140 " pdb=" O2G GTP D 602 " model vdw 1.604 1.850 nonbonded pdb=" HG SER E 140 " pdb=" O2G GTP E 602 " model vdw 1.604 1.850 nonbonded pdb=" HG SER H 140 " pdb=" O1G GTP H 602 " model vdw 1.605 1.850 nonbonded pdb=" HG1 THR F 159 " pdb=" O1B ATP F 603 " model vdw 1.608 1.850 ... (remaining 942645 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 80 5.49 5 S 192 5.16 5 C 19040 2.51 5 N 5232 2.21 5 O 6040 1.98 5 H 30240 0.53 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.050 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: 0.920 Extract box with map and model: 11.400 Check model and map are aligned: 0.670 Process input model: 152.270 Find NCS groups from input model: 2.280 Set up NCS constraints: 0.270 Set refine NCS operators: 0.000 Set scattering table: 0.430 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 178.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 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 : 0.013 0.237 31096 Z= 0.830 Angle : 2.031 23.065 42200 Z= 1.299 Chirality : 0.110 1.542 4872 Planarity : 0.017 0.161 5248 Dihedral : 18.661 172.571 11496 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 1.16 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.18 % Favored : 95.64 % Rotamer Outliers : 1.84 % Cbeta Deviations : 0.76 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.12), residues: 3896 helix: -0.43 (0.12), residues: 1504 sheet: -1.14 (0.29), residues: 296 loop : 0.04 (0.13), residues: 2096 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 868 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 809 time to evaluate : 3.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 59 outliers final: 27 residues processed: 844 average time/residue: 2.6566 time to fit residues: 2646.6449 Evaluate side-chains 723 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 696 time to evaluate : 3.703 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 27 outliers final: 19 residues processed: 10 average time/residue: 1.4042 time to fit residues: 23.3587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 331 optimal weight: 0.9980 chunk 297 optimal weight: 1.9990 chunk 164 optimal weight: 0.9980 chunk 101 optimal weight: 0.7980 chunk 200 optimal weight: 0.9980 chunk 158 optimal weight: 2.9990 chunk 307 optimal weight: 1.9990 chunk 118 optimal weight: 0.9990 chunk 186 optimal weight: 0.9980 chunk 228 optimal weight: 1.9990 chunk 355 optimal weight: 0.9980 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 ASN B 202 GLN B 283 GLN C 303 ASN D 202 GLN E 94 ASN ** E 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 303 ASN F 94 ASN F 112 GLN F 198 ASN F 243 GLN F 303 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 31096 Z= 0.216 Angle : 0.673 10.667 42200 Z= 0.345 Chirality : 0.061 1.585 4872 Planarity : 0.005 0.048 5248 Dihedral : 18.486 179.350 4520 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.85 % Favored : 97.10 % Rotamer Outliers : 3.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: 0.14 (0.13), residues: 3896 helix: 0.46 (0.13), residues: 1456 sheet: -0.30 (0.24), residues: 448 loop : 0.06 (0.13), residues: 1992 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 866 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 763 time to evaluate : 3.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 103 outliers final: 42 residues processed: 796 average time/residue: 2.5773 time to fit residues: 2450.6767 Evaluate side-chains 756 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 714 time to evaluate : 3.776 Switching outliers to nearest non-outliers outliers start: 42 outliers final: 23 residues processed: 20 average time/residue: 1.2188 time to fit residues: 38.6644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 197 optimal weight: 2.9990 chunk 110 optimal weight: 0.9980 chunk 296 optimal weight: 0.8980 chunk 242 optimal weight: 0.9980 chunk 98 optimal weight: 0.7980 chunk 356 optimal weight: 3.9990 chunk 385 optimal weight: 5.9990 chunk 317 optimal weight: 1.9990 chunk 353 optimal weight: 1.9990 chunk 121 optimal weight: 3.9990 chunk 286 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN A 112 GLN B 198 ASN C 94 ASN C 454 GLN D 94 ASN D 283 GLN E 94 ASN E 498 GLN F 94 ASN ** F 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 498 GLN G 283 GLN H 94 ASN H 303 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.2871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 31096 Z= 0.190 Angle : 0.601 11.714 42200 Z= 0.304 Chirality : 0.061 1.709 4872 Planarity : 0.004 0.047 5248 Dihedral : 17.824 177.436 4520 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.03 % Favored : 97.95 % Rotamer Outliers : 2.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.13), residues: 3896 helix: 0.57 (0.14), residues: 1512 sheet: -0.23 (0.26), residues: 408 loop : 0.10 (0.14), residues: 1976 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 792 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 724 time to evaluate : 3.814 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 68 outliers final: 39 residues processed: 759 average time/residue: 2.7231 time to fit residues: 2490.6752 Evaluate side-chains 747 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 708 time to evaluate : 3.749 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 25 residues processed: 14 average time/residue: 1.1317 time to fit residues: 27.9130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 352 optimal weight: 2.9990 chunk 268 optimal weight: 3.9990 chunk 185 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 170 optimal weight: 3.9990 chunk 239 optimal weight: 1.9990 chunk 357 optimal weight: 2.9990 chunk 378 optimal weight: 0.9980 chunk 186 optimal weight: 2.9990 chunk 339 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 94 ASN B 198 ASN C 94 ASN D 94 ASN D 283 GLN D 498 GLN E 94 ASN F 94 ASN ** F 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 441 GLN G 94 ASN G 283 GLN G 498 GLN H 94 ASN ** H 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 368 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.3090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.050 31096 Z= 0.364 Angle : 0.665 11.376 42200 Z= 0.342 Chirality : 0.064 1.709 4872 Planarity : 0.005 0.057 5248 Dihedral : 18.248 176.746 4520 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.64 % Favored : 97.33 % Rotamer Outliers : 2.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -0.04 (0.13), residues: 3896 helix: 0.27 (0.13), residues: 1568 sheet: -0.45 (0.32), residues: 272 loop : -0.07 (0.13), residues: 2056 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 836 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 749 time to evaluate : 3.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 87 outliers final: 48 residues processed: 786 average time/residue: 2.6015 time to fit residues: 2425.0164 Evaluate side-chains 766 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 718 time to evaluate : 3.671 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 26 residues processed: 23 average time/residue: 1.1035 time to fit residues: 40.9275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 315 optimal weight: 2.9990 chunk 215 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 282 optimal weight: 2.9990 chunk 156 optimal weight: 2.9990 chunk 323 optimal weight: 0.3980 chunk 261 optimal weight: 5.9990 chunk 0 optimal weight: 2.9990 chunk 193 optimal weight: 1.9990 chunk 340 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 ASN A 202 GLN ** B 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 202 GLN B 283 GLN C 112 GLN ** C 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 94 ASN D 198 ASN D 303 ASN E 94 ASN ** E 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 94 ASN ** F 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN H 94 ASN ** H 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 298 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.3245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 31096 Z= 0.260 Angle : 0.612 11.050 42200 Z= 0.310 Chirality : 0.062 1.702 4872 Planarity : 0.005 0.062 5248 Dihedral : 17.927 176.253 4520 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.64 % Favored : 97.33 % Rotamer Outliers : 2.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.13), residues: 3896 helix: 0.45 (0.13), residues: 1520 sheet: -0.21 (0.27), residues: 392 loop : -0.07 (0.14), residues: 1984 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 782 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 717 time to evaluate : 3.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 65 outliers final: 43 residues processed: 758 average time/residue: 2.6551 time to fit residues: 2404.3026 Evaluate side-chains 751 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 708 time to evaluate : 3.772 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 29 residues processed: 15 average time/residue: 0.7435 time to fit residues: 23.4112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 127 optimal weight: 0.6980 chunk 341 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 222 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 379 optimal weight: 1.9990 chunk 314 optimal weight: 3.9990 chunk 175 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 125 optimal weight: 1.9990 chunk 199 optimal weight: 2.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 ASN A 202 GLN ** B 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 202 GLN D 94 ASN E 94 ASN E 198 ASN ** F 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 303 ASN G 94 ASN ** G 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.3356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.045 31096 Z= 0.324 Angle : 0.637 11.008 42200 Z= 0.324 Chirality : 0.063 1.724 4872 Planarity : 0.005 0.067 5248 Dihedral : 17.942 176.407 4520 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.85 % Favored : 97.13 % Rotamer Outliers : 2.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.13), residues: 3896 helix: 0.39 (0.13), residues: 1520 sheet: -0.28 (0.27), residues: 392 loop : -0.14 (0.14), residues: 1984 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 769 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 700 time to evaluate : 3.812 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 outliers start: 69 outliers final: 48 residues processed: 743 average time/residue: 2.6756 time to fit residues: 2361.1272 Evaluate side-chains 754 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 706 time to evaluate : 3.736 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 33 residues processed: 15 average time/residue: 1.1224 time to fit residues: 28.6714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 365 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 216 optimal weight: 2.9990 chunk 276 optimal weight: 2.9990 chunk 214 optimal weight: 0.7980 chunk 319 optimal weight: 2.9990 chunk 211 optimal weight: 3.9990 chunk 377 optimal weight: 1.9990 chunk 236 optimal weight: 4.9990 chunk 230 optimal weight: 0.9980 chunk 174 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 ASN A 202 GLN ** B 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 372 HIS D 94 ASN D 303 ASN D 372 HIS E 94 ASN ** F 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.3430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 31096 Z= 0.295 Angle : 0.624 11.314 42200 Z= 0.316 Chirality : 0.062 1.719 4872 Planarity : 0.005 0.077 5248 Dihedral : 17.855 179.815 4520 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.00 % Favored : 96.97 % Rotamer Outliers : 1.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.13), residues: 3896 helix: 0.44 (0.13), residues: 1520 sheet: -0.32 (0.27), residues: 392 loop : -0.15 (0.14), residues: 1984 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 764 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 702 time to evaluate : 3.651 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 outliers start: 62 outliers final: 48 residues processed: 745 average time/residue: 2.6136 time to fit residues: 2301.3966 Evaluate side-chains 738 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 690 time to evaluate : 3.680 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 38 residues processed: 13 average time/residue: 0.7259 time to fit residues: 20.1174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 233 optimal weight: 2.9990 chunk 150 optimal weight: 1.9990 chunk 225 optimal weight: 2.9990 chunk 113 optimal weight: 5.9990 chunk 74 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 240 optimal weight: 2.9990 chunk 257 optimal weight: 3.9990 chunk 186 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 296 optimal weight: 0.9980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 ASN A 202 GLN ** B 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 33 ASN D 33 ASN D 198 ASN E 94 ASN ** F 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 202 GLN ** H 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.3513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 31096 Z= 0.238 Angle : 0.600 11.303 42200 Z= 0.301 Chirality : 0.061 1.720 4872 Planarity : 0.005 0.092 5248 Dihedral : 17.536 178.869 4520 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.85 % Favored : 97.13 % Rotamer Outliers : 1.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.13), residues: 3896 helix: 0.56 (0.14), residues: 1520 sheet: -0.34 (0.26), residues: 392 loop : -0.12 (0.14), residues: 1984 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 747 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 692 time to evaluate : 3.834 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 outliers start: 55 outliers final: 45 residues processed: 735 average time/residue: 2.6606 time to fit residues: 2315.4514 Evaluate side-chains 731 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 686 time to evaluate : 3.692 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 38 residues processed: 8 average time/residue: 0.6972 time to fit residues: 13.9782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 343 optimal weight: 1.9990 chunk 361 optimal weight: 5.9990 chunk 330 optimal weight: 1.9990 chunk 352 optimal weight: 1.9990 chunk 211 optimal weight: 3.9990 chunk 153 optimal weight: 3.9990 chunk 276 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 318 optimal weight: 1.9990 chunk 332 optimal weight: 2.9990 chunk 350 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 ASN A 202 GLN ** B 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 303 ASN D 94 ASN D 198 ASN ** F 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 198 ASN ** H 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.3564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.038 31096 Z= 0.333 Angle : 0.642 11.404 42200 Z= 0.325 Chirality : 0.063 1.731 4872 Planarity : 0.005 0.102 5248 Dihedral : 17.790 179.959 4520 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.18 % Favored : 96.79 % Rotamer Outliers : 1.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.13), residues: 3896 helix: 0.35 (0.13), residues: 1568 sheet: -0.65 (0.25), residues: 392 loop : -0.14 (0.14), residues: 1936 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 737 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 684 time to evaluate : 3.812 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 outliers start: 53 outliers final: 43 residues processed: 729 average time/residue: 2.6769 time to fit residues: 2324.6707 Evaluate side-chains 717 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 674 time to evaluate : 3.683 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 37 residues processed: 8 average time/residue: 1.0541 time to fit residues: 16.9095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 231 optimal weight: 0.9980 chunk 372 optimal weight: 2.9990 chunk 227 optimal weight: 0.5980 chunk 176 optimal weight: 1.9990 chunk 258 optimal weight: 1.9990 chunk 390 optimal weight: 0.6980 chunk 359 optimal weight: 4.9990 chunk 310 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 240 optimal weight: 2.9990 chunk 190 optimal weight: 0.6980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 ASN A 202 GLN ** B 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 198 ASN ** H 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.3623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 31096 Z= 0.198 Angle : 0.586 11.475 42200 Z= 0.291 Chirality : 0.061 1.718 4872 Planarity : 0.005 0.091 5248 Dihedral : 17.113 178.568 4520 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.87 % Favored : 97.10 % Rotamer Outliers : 1.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.13), residues: 3896 helix: 0.67 (0.14), residues: 1520 sheet: -0.38 (0.26), residues: 392 loop : -0.10 (0.14), residues: 1984 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 732 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 692 time to evaluate : 3.739 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 outliers start: 40 outliers final: 32 residues processed: 730 average time/residue: 2.6662 time to fit residues: 2316.4132 Evaluate side-chains 711 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 679 time to evaluate : 3.719 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 32 residues processed: 0 time to fit residues: 4.6274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 247 optimal weight: 1.9990 chunk 331 optimal weight: 3.9990 chunk 95 optimal weight: 0.8980 chunk 286 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 311 optimal weight: 0.4980 chunk 130 optimal weight: 3.9990 chunk 319 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 57 optimal weight: 0.0870 overall best weight: 0.8760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 ASN A 202 GLN ** B 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 198 ASN D 303 ASN ** F 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 198 ASN ** H 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.135966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.103217 restraints weight = 87583.733| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 1.45 r_work: 0.2870 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2745 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.3681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 31096 Z= 0.183 Angle : 0.580 11.279 42200 Z= 0.287 Chirality : 0.061 1.712 4872 Planarity : 0.005 0.092 5248 Dihedral : 16.711 177.401 4520 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.82 % Favored : 97.15 % Rotamer Outliers : 1.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.13), residues: 3896 helix: 0.75 (0.14), residues: 1520 sheet: -0.40 (0.26), residues: 392 loop : -0.06 (0.14), residues: 1984 =============================================================================== Job complete usr+sys time: 29649.48 seconds wall clock time: 507 minutes 10.12 seconds (30430.12 seconds total)