Starting phenix.real_space_refine (version: dev) on Thu Feb 23 04:55:32 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rfe_24439/02_2023/7rfe_24439_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rfe_24439/02_2023/7rfe_24439.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/7rfe_24439/02_2023/7rfe_24439.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rfe_24439/02_2023/7rfe_24439.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rfe_24439/02_2023/7rfe_24439_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rfe_24439/02_2023/7rfe_24439_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= -0.001 sd= 0.009 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 GLU 15": "OE1" <-> "OE2" Residue "A ASP 16": "OD1" <-> "OD2" Residue "A PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 28": "OD1" <-> "OD2" Residue "A GLU 48": "OE1" <-> "OE2" Residue "A ASP 50": "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 110": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 117": "OD1" <-> "OD2" Residue "A ASP 129": "OD1" <-> "OD2" 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 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 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 GLU 399": "OE1" <-> "OE2" Residue "A PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 404": "OD1" <-> "OD2" 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 449": "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 GLU 510": "OE1" <-> "OE2" 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 ASP 28": "OD1" <-> "OD2" Residue "B ASP 47": "OD1" <-> "OD2" Residue "B GLU 48": "OE1" <-> "OE2" Residue "B ASP 50": "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 110": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 117": "OD1" <-> "OD2" Residue "B ARG 136": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 146": "OE1" <-> "OE2" Residue "B ARG 182": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 184": "OE1" <-> "OE2" 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 ASP 255": "OD1" <-> "OD2" Residue "B ASP 256": "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 GLU 335": "OE1" <-> "OE2" Residue "B ARG 355": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 357": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 399": "OE1" <-> "OE2" Residue "B PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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 449": "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 TYR 509": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 510": "OE1" <-> "OE2" 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 GLU 15": "OE1" <-> "OE2" Residue "C ASP 16": "OD1" <-> "OD2" Residue "C PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 28": "OD1" <-> "OD2" Residue "C ASP 47": "OD1" <-> "OD2" Residue "C GLU 48": "OE1" <-> "OE2" Residue "C ASP 50": "OD1" <-> "OD2" 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 110": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 129": "OD1" <-> "OD2" Residue "C ARG 136": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 146": "OE1" <-> "OE2" Residue "C ARG 182": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 184": "OE1" <-> "OE2" Residue "C ASP 226": "OD1" <-> "OD2" 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 255": "OD1" <-> "OD2" 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 GLU 399": "OE1" <-> "OE2" Residue "C PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 404": "OD1" <-> "OD2" Residue "C ARG 407": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 411": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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 GLU 15": "OE1" <-> "OE2" Residue "D ASP 16": "OD1" <-> "OD2" Residue "D PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 28": "OD1" <-> "OD2" Residue "D ASP 47": "OD1" <-> "OD2" Residue "D ASP 50": "OD1" <-> "OD2" 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 110": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 117": "OD1" <-> "OD2" Residue "D ASP 129": "OD1" <-> "OD2" 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 ARG 182": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D GLU 184": "OE1" <-> "OE2" Residue "D GLU 196": "OE1" <-> "OE2" Residue "D ASP 216": "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 ASP 255": "OD1" <-> "OD2" Residue "D ASP 256": "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 GLU 335": "OE1" <-> "OE2" Residue "D ARG 355": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D PHE 357": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 399": "OE1" <-> "OE2" Residue "D PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 404": "OD1" <-> "OD2" Residue "D ARG 407": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D TYR 411": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 449": "OD1" <-> "OD2" 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 TYR 509": "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 GLU 15": "OE1" <-> "OE2" Residue "E ASP 16": "OD1" <-> "OD2" Residue "E PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 28": "OD1" <-> "OD2" Residue "E ASP 50": "OD1" <-> "OD2" Residue "E ARG 57": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E GLU 75": "OE1" <-> "OE2" Residue "E ASP 77": "OD1" <-> "OD2" 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 110": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 136": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 182": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E GLU 184": "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 255": "OD1" <-> "OD2" Residue "E ASP 256": "OD1" <-> "OD2" Residue "E ASP 261": "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 GLU 335": "OE1" <-> "OE2" Residue "E ARG 355": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E PHE 357": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 399": "OE1" <-> "OE2" Residue "E PHE 401": "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 449": "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 TYR 509": "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 GLU 15": "OE1" <-> "OE2" Residue "F ASP 16": "OD1" <-> "OD2" Residue "F PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 28": "OD1" <-> "OD2" Residue "F ASP 47": "OD1" <-> "OD2" Residue "F GLU 48": "OE1" <-> "OE2" Residue "F ASP 50": "OD1" <-> "OD2" 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 110": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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 ARG 182": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F GLU 184": "OE1" <-> "OE2" Residue "F GLU 196": "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 ASP 239": "OD1" <-> "OD2" Residue "F ARG 253": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ASP 255": "OD1" <-> "OD2" Residue "F ASP 256": "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 GLU 399": "OE1" <-> "OE2" Residue "F PHE 401": "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 ASP 449": "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 "G TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ASP 16": "OD1" <-> "OD2" Residue "G PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ASP 28": "OD1" <-> "OD2" Residue "G ASP 47": "OD1" <-> "OD2" Residue "G GLU 48": "OE1" <-> "OE2" Residue "G ASP 50": "OD1" <-> "OD2" Residue "G ARG 57": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G GLU 75": "OE1" <-> "OE2" Residue "G ASP 77": "OD1" <-> "OD2" 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 ASP 129": "OD1" <-> "OD2" Residue "G GLU 132": "OE1" <-> "OE2" 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 ARG 182": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G GLU 184": "OE1" <-> "OE2" Residue "G GLU 217": "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 255": "OD1" <-> "OD2" Residue "G ASP 256": "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 GLU 335": "OE1" <-> "OE2" Residue "G ARG 355": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G PHE 357": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 399": "OE1" <-> "OE2" Residue "G PHE 401": "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 ASP 449": "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 TYR 509": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 510": "OE1" <-> "OE2" Residue "G ARG 512": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 15": "OE1" <-> "OE2" Residue "H ASP 16": "OD1" <-> "OD2" Residue "H PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ASP 28": "OD1" <-> "OD2" Residue "H ASP 47": "OD1" <-> "OD2" Residue "H ASP 50": "OD1" <-> "OD2" Residue "H ARG 57": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H GLU 75": "OE1" <-> "OE2" Residue "H ASP 77": "OD1" <-> "OD2" 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 ASP 129": "OD1" <-> "OD2" Residue "H GLU 132": "OE1" <-> "OE2" Residue "H ARG 136": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ARG 182": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ASP 216": "OD1" <-> "OD2" 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 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 357": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 399": "OE1" <-> "OE2" Residue "H PHE 401": "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 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 TYR 509": "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: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 58720 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 7222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 7222 Classifications: {'peptide': 475} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 17, 'TRANS': 457} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 7222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 7222 Classifications: {'peptide': 475} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 17, 'TRANS': 457} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 7222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 7222 Classifications: {'peptide': 475} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 17, 'TRANS': 457} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 7222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 7222 Classifications: {'peptide': 475} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 17, 'TRANS': 457} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 7222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 7222 Classifications: {'peptide': 475} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 17, 'TRANS': 457} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 7222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 7222 Classifications: {'peptide': 475} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 17, 'TRANS': 457} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 7222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 7222 Classifications: {'peptide': 475} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 17, 'TRANS': 457} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 7222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 7222 Classifications: {'peptide': 475} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 17, 'TRANS': 457} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 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: 19.43, per 1000 atoms: 0.33 Number of scatterers: 58720 At special positions: 0 Unit cell: (169.05, 169.05, 128.1, 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 5808 8.00 N 5072 7.00 C 18368 6.00 H 29200 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: 39.52 Conformation dependent library (CDL) restraints added in 4.5 seconds 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6816 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 139 helices and 52 sheets defined 34.8% alpha, 11.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.91 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 110 Processing helix chain 'A' and resid 127 through 137 Processing helix chain 'A' and resid 160 through 162 No H-bonds generated for 'chain 'A' and resid 160 through 162' Processing helix chain 'A' and resid 194 through 204 Processing helix chain 'A' and resid 224 through 232 Processing helix chain 'A' and resid 255 through 265 removed outlier: 3.528A pdb=" N ARG A 259 " --> pdb=" O ASP A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 293 Processing helix chain 'A' and resid 307 through 316 removed outlier: 3.639A pdb=" N ASN A 312 " --> pdb=" O ALA A 308 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU A 313 " --> pdb=" O GLN A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 336 No H-bonds generated for 'chain 'A' and resid 333 through 336' Processing helix chain 'A' and resid 343 through 357 removed outlier: 4.427A pdb=" N ARG A 356 " --> pdb=" O GLU A 352 " (cutoff:3.500A) removed outlier: 4.237A 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 194 through 204 Processing helix chain 'B' and resid 224 through 232 Processing helix chain 'B' and resid 255 through 265 removed outlier: 3.569A pdb=" N ARG B 259 " --> pdb=" O ASP B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 293 Processing helix chain 'B' and resid 307 through 316 removed outlier: 3.607A pdb=" N ASN B 312 " --> pdb=" O ALA B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 336 No H-bonds generated for 'chain 'B' and resid 333 through 336' Processing helix chain 'B' and resid 343 through 357 removed outlier: 4.441A pdb=" N ARG B 356 " --> pdb=" O GLU B 352 " (cutoff:3.500A) removed outlier: 4.224A 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 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 162 No H-bonds generated for 'chain 'C' and resid 160 through 162' Processing helix chain 'C' and resid 194 through 204 Processing helix chain 'C' and resid 224 through 232 Processing helix chain 'C' and resid 255 through 265 removed outlier: 3.516A pdb=" N ARG C 259 " --> pdb=" O ASP C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 293 Processing helix chain 'C' and resid 307 through 316 removed outlier: 3.678A pdb=" N ASN C 312 " --> pdb=" O ALA C 308 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU C 313 " --> pdb=" O GLN C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 336 No H-bonds generated for 'chain 'C' and resid 333 through 336' Processing helix chain 'C' and resid 343 through 357 removed outlier: 4.463A pdb=" N ARG C 356 " --> pdb=" O GLU C 352 " (cutoff:3.500A) removed outlier: 4.252A 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 453 through 471 Proline residue: C 458 - end of helix Processing helix chain 'C' and resid 476 through 485 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 162 No H-bonds generated for 'chain 'D' and resid 160 through 162' Processing helix chain 'D' and resid 194 through 204 Processing helix chain 'D' and resid 224 through 232 Processing helix chain 'D' and resid 255 through 265 removed outlier: 3.581A pdb=" N ARG D 259 " --> pdb=" O ASP D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 293 Processing helix chain 'D' and resid 307 through 316 removed outlier: 3.653A pdb=" N ASN D 312 " --> pdb=" O ALA D 308 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU D 313 " --> pdb=" O GLN D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 333 through 336 No H-bonds generated for 'chain 'D' and resid 333 through 336' Processing helix chain 'D' and resid 343 through 357 removed outlier: 4.442A pdb=" N ARG D 356 " --> pdb=" O GLU D 352 " (cutoff:3.500A) removed outlier: 4.244A 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 501 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 194 through 204 Processing helix chain 'E' and resid 224 through 232 Processing helix chain 'E' and resid 255 through 265 removed outlier: 3.640A pdb=" N ARG E 259 " --> pdb=" O ASP E 255 " (cutoff:3.500A) Processing helix chain 'E' and resid 281 through 293 Processing helix chain 'E' and resid 307 through 316 removed outlier: 3.675A pdb=" N ASN E 312 " --> pdb=" O ALA E 308 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU E 313 " --> pdb=" O GLN E 309 " (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: 4.429A pdb=" N ARG E 356 " --> pdb=" O GLU E 352 " (cutoff:3.500A) removed outlier: 4.248A 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 453 through 471 Proline residue: E 458 - end of helix Processing helix chain 'E' and resid 476 through 485 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 194 through 204 Processing helix chain 'F' and resid 224 through 232 Processing helix chain 'F' and resid 255 through 265 removed outlier: 3.528A pdb=" N ARG F 259 " --> pdb=" O ASP F 255 " (cutoff:3.500A) Processing helix chain 'F' and resid 281 through 293 Processing helix chain 'F' and resid 307 through 316 removed outlier: 3.654A pdb=" N ASN F 312 " --> pdb=" O ALA F 308 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU F 313 " --> pdb=" O GLN F 309 " (cutoff:3.500A) Processing helix chain 'F' and resid 333 through 336 No H-bonds generated for 'chain 'F' and resid 333 through 336' Processing helix chain 'F' and resid 343 through 357 removed outlier: 4.414A pdb=" N ARG F 356 " --> pdb=" O GLU F 352 " (cutoff:3.500A) removed outlier: 4.225A 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 194 through 204 Processing helix chain 'G' and resid 224 through 232 Processing helix chain 'G' and resid 255 through 265 removed outlier: 3.568A pdb=" N ARG G 259 " --> pdb=" O ASP G 255 " (cutoff:3.500A) Processing helix chain 'G' and resid 281 through 293 Processing helix chain 'G' and resid 307 through 316 removed outlier: 3.662A pdb=" N ASN G 312 " --> pdb=" O ALA G 308 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU G 313 " --> pdb=" O GLN G 309 " (cutoff:3.500A) Processing helix chain 'G' and resid 333 through 336 No H-bonds generated for 'chain 'G' and resid 333 through 336' Processing helix chain 'G' and resid 343 through 357 removed outlier: 4.399A pdb=" N ARG G 356 " --> pdb=" O GLU G 352 " (cutoff:3.500A) removed outlier: 4.219A 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 110 Processing helix chain 'H' and resid 127 through 137 Processing helix chain 'H' and resid 194 through 204 Processing helix chain 'H' and resid 224 through 232 Processing helix chain 'H' and resid 255 through 265 Processing helix chain 'H' and resid 281 through 293 Processing helix chain 'H' and resid 307 through 316 removed outlier: 3.635A pdb=" N ASN H 312 " --> pdb=" O ALA H 308 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU H 313 " --> pdb=" O GLN H 309 " (cutoff:3.500A) Processing helix chain 'H' and resid 333 through 336 No H-bonds generated for 'chain 'H' and resid 333 through 336' Processing helix chain 'H' and resid 343 through 357 removed outlier: 4.440A pdb=" N ARG H 356 " --> pdb=" O GLU H 352 " (cutoff:3.500A) removed outlier: 4.217A 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 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: 6.409A pdb=" N VAL A 384 " --> pdb=" O ILE A 66 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ASN A 303 " --> pdb=" O ARG A 322 " (cutoff:3.500A) removed outlier: 4.261A 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: 8.219A pdb=" N ALA A 188 " --> pdb=" O LYS A 208 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 400 through 402 Processing sheet with id= E, first strand: chain 'A' and resid 142 through 145 Processing sheet with id= F, first strand: chain 'B' and resid 35 through 37 Processing sheet with id= G, first strand: chain 'B' and resid 65 through 67 removed outlier: 6.405A pdb=" N VAL B 384 " --> pdb=" O ILE B 66 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 187 through 189 removed outlier: 8.310A pdb=" N ALA B 188 " --> pdb=" O LYS B 208 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 247 through 250 removed outlier: 6.651A pdb=" N VAL B 270 " --> pdb=" O ALA B 248 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N VAL B 250 " --> pdb=" O VAL B 270 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N VAL B 272 " --> pdb=" O VAL B 250 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N GLN B 298 " --> pdb=" O ILE B 271 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N LEU B 273 " --> pdb=" O GLN B 298 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N ILE B 300 " --> pdb=" O LEU B 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'B' and resid 400 through 403 Processing sheet with id= K, first strand: chain 'B' and resid 142 through 145 Processing sheet with id= L, first strand: chain 'C' and resid 35 through 37 Processing sheet with id= M, first strand: chain 'C' and resid 65 through 67 removed outlier: 6.408A pdb=" N VAL C 384 " --> pdb=" O ILE C 66 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 187 through 189 removed outlier: 8.221A pdb=" N ALA C 188 " --> pdb=" O LYS C 208 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 247 through 250 removed outlier: 6.643A pdb=" N VAL C 270 " --> pdb=" O ALA C 248 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N VAL C 250 " --> pdb=" O VAL C 270 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N VAL C 272 " --> pdb=" O VAL C 250 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N GLN C 298 " --> pdb=" O ILE C 271 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N LEU C 273 " --> pdb=" O GLN C 298 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N ILE C 300 " --> pdb=" O LEU C 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= O 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 142 through 145 Processing sheet with id= R, first strand: chain 'D' and resid 35 through 37 Processing sheet with id= S, first strand: chain 'D' and resid 65 through 67 removed outlier: 6.381A pdb=" N VAL D 384 " --> pdb=" O ILE D 66 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 187 through 189 removed outlier: 8.261A pdb=" N ALA D 188 " --> pdb=" O LYS D 208 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'D' and resid 247 through 250 removed outlier: 6.638A pdb=" N VAL D 270 " --> pdb=" O ALA D 248 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N VAL D 250 " --> pdb=" O VAL D 270 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N VAL D 272 " --> pdb=" O VAL D 250 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N GLN D 298 " --> pdb=" O ILE D 271 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N LEU D 273 " --> pdb=" O GLN D 298 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N ILE D 300 " --> pdb=" O LEU D 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= U Processing sheet with id= V, first strand: chain 'D' and resid 400 through 402 Processing sheet with id= W, first strand: chain 'D' and resid 53 through 56 removed outlier: 6.604A pdb=" N ILE D 59 " --> pdb=" O LEU D 55 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'D' and resid 142 through 145 Processing sheet with id= Y, first strand: chain 'E' and resid 35 through 37 Processing sheet with id= Z, first strand: chain 'E' and resid 65 through 67 removed outlier: 6.418A pdb=" N VAL E 384 " --> pdb=" O ILE E 66 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'E' and resid 187 through 189 removed outlier: 8.183A pdb=" N ALA E 188 " --> pdb=" O LYS E 208 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'E' and resid 247 through 250 removed outlier: 6.632A pdb=" N VAL E 270 " --> pdb=" O ALA E 248 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N VAL E 250 " --> pdb=" O VAL E 270 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N VAL E 272 " --> pdb=" O VAL E 250 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N GLN E 298 " --> pdb=" O ILE E 271 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N LEU E 273 " --> pdb=" O GLN E 298 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N ILE E 300 " --> pdb=" O LEU E 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= AB Processing sheet with id= AC, first strand: chain 'E' and resid 400 through 402 Processing sheet with id= AD, first strand: chain 'E' and resid 53 through 56 removed outlier: 6.611A 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: 6.394A pdb=" N VAL F 384 " --> pdb=" O ILE F 66 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'F' and resid 187 through 189 removed outlier: 8.291A pdb=" N ALA F 188 " --> pdb=" O LYS F 208 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA F 220 " --> pdb=" O ILE F 211 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'F' and resid 247 through 250 removed outlier: 6.657A pdb=" N VAL F 270 " --> pdb=" O ALA F 248 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N VAL F 250 " --> pdb=" O VAL F 270 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N VAL F 272 " --> pdb=" O VAL F 250 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N GLN F 298 " --> pdb=" O ILE F 271 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N LEU F 273 " --> pdb=" O GLN F 298 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N ILE F 300 " --> pdb=" O LEU F 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= AI Processing sheet with id= AJ, first strand: chain 'F' and resid 400 through 402 Processing sheet with id= AK, first strand: chain 'F' and resid 53 through 56 removed outlier: 6.631A pdb=" N ILE F 59 " --> pdb=" O LEU F 55 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'F' and resid 142 through 145 Processing sheet with id= AM, first strand: chain 'G' and resid 35 through 37 Processing sheet with id= AN, first strand: chain 'G' and resid 65 through 67 removed outlier: 6.384A pdb=" N VAL G 384 " --> pdb=" O ILE G 66 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'G' and resid 187 through 189 removed outlier: 8.207A pdb=" N ALA G 188 " --> pdb=" O LYS G 208 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'G' and resid 247 through 250 removed outlier: 6.646A pdb=" N VAL G 270 " --> pdb=" O ALA G 248 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N VAL G 250 " --> pdb=" O VAL G 270 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N VAL G 272 " --> pdb=" O VAL G 250 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N GLN G 298 " --> pdb=" O ILE G 271 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N LEU G 273 " --> pdb=" O GLN G 298 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N ILE G 300 " --> pdb=" O LEU G 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= AP Processing sheet with id= AQ, first strand: chain 'G' and resid 400 through 402 Processing sheet with id= AR, first strand: chain 'G' and resid 53 through 56 removed outlier: 6.615A pdb=" N ILE G 59 " --> pdb=" O LEU G 55 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'G' and resid 142 through 145 Processing sheet with id= AT, first strand: chain 'H' and resid 35 through 37 Processing sheet with id= AU, first strand: chain 'H' and resid 65 through 67 removed outlier: 6.382A pdb=" N VAL H 384 " --> pdb=" O ILE H 66 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'H' and resid 187 through 189 removed outlier: 8.238A pdb=" N ALA H 188 " --> pdb=" O LYS H 208 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'H' and resid 247 through 250 removed outlier: 6.605A pdb=" N VAL H 270 " --> pdb=" O ALA H 248 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N VAL H 250 " --> pdb=" O VAL H 270 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N VAL H 272 " --> pdb=" O VAL H 250 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N GLN H 298 " --> pdb=" O ILE H 271 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N LEU H 273 " --> pdb=" O GLN H 298 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N ILE H 300 " --> pdb=" O LEU H 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= AW Processing sheet with id= AX, first strand: chain 'H' and resid 400 through 402 Processing sheet with id= AY, first strand: chain 'H' and resid 53 through 56 removed outlier: 6.620A pdb=" N ILE H 59 " --> pdb=" O LEU H 55 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain 'H' and resid 142 through 145 931 hydrogen bonds defined for protein. 2700 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: 19.49 Time building geometry restraints manager: 41.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.95 - 1.13: 29144 1.13 - 1.30: 5204 1.30 - 1.48: 11245 1.48 - 1.66: 13287 1.66 - 1.83: 328 Bond restraints: 59208 Sorted by residual: bond pdb=" N GLY C 501 " pdb=" H GLY C 501 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" N GLN G 292 " pdb=" H GLN G 292 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" N ASP A 71 " pdb=" H ASP A 71 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" N THR C 180 " pdb=" H THR C 180 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" N HIS C 466 " pdb=" H HIS C 466 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 ... (remaining 59203 not shown) Histogram of bond angle deviations from ideal: 93.09 - 100.92: 183 100.92 - 108.75: 28429 108.75 - 116.59: 47288 116.59 - 124.42: 29020 124.42 - 132.25: 2216 Bond angle restraints: 107136 Sorted by residual: angle pdb=" PB ATP E 603 " pdb=" O3B ATP E 603 " pdb=" PG ATP E 603 " ideal model delta sigma weight residual 139.87 122.50 17.37 1.00e+00 1.00e+00 3.02e+02 angle pdb=" PB ATP H 603 " pdb=" O3B ATP H 603 " pdb=" PG ATP H 603 " ideal model delta sigma weight residual 139.87 123.58 16.29 1.00e+00 1.00e+00 2.65e+02 angle pdb=" PB ATP A 603 " pdb=" O3B ATP A 603 " pdb=" PG ATP A 603 " ideal model delta sigma weight residual 139.87 123.66 16.21 1.00e+00 1.00e+00 2.63e+02 angle pdb=" PB ATP B 603 " pdb=" O3B ATP B 603 " pdb=" PG ATP B 603 " ideal model delta sigma weight residual 139.87 123.70 16.17 1.00e+00 1.00e+00 2.61e+02 angle pdb=" PB ATP G 603 " pdb=" O3B ATP G 603 " pdb=" PG ATP G 603 " ideal model delta sigma weight residual 139.87 123.77 16.10 1.00e+00 1.00e+00 2.59e+02 ... (remaining 107131 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.73: 22090 35.73 - 71.46: 940 71.46 - 107.19: 76 107.19 - 142.92: 42 142.92 - 178.65: 20 Dihedral angle restraints: 23168 sinusoidal: 11176 harmonic: 11992 Sorted by residual: dihedral pdb=" C8 GTP G 601 " pdb=" C1' GTP G 601 " pdb=" N9 GTP G 601 " pdb=" O4' GTP G 601 " ideal model delta sinusoidal sigma weight residual 104.59 -74.05 178.65 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C8 GTP A 601 " pdb=" C1' GTP A 601 " pdb=" N9 GTP A 601 " pdb=" O4' GTP A 601 " ideal model delta sinusoidal sigma weight residual 104.59 -73.16 177.76 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C8 GTP F 601 " pdb=" C1' GTP F 601 " pdb=" N9 GTP F 601 " pdb=" O4' GTP F 601 " ideal model delta sinusoidal sigma weight residual 104.59 -79.24 -176.16 1 2.00e+01 2.50e-03 4.79e+01 ... (remaining 23165 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 3283 0.100 - 0.200: 1215 0.200 - 0.300: 174 0.300 - 0.400: 16 0.400 - 0.501: 8 Chirality restraints: 4696 Sorted by residual: chirality pdb=" CA TYR D 514 " pdb=" N TYR D 514 " pdb=" C TYR D 514 " pdb=" CB TYR D 514 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.26e+00 chirality pdb=" CA TYR A 514 " pdb=" N TYR A 514 " pdb=" C TYR A 514 " pdb=" CB TYR A 514 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.76e+00 chirality pdb=" CA TYR F 514 " pdb=" N TYR F 514 " pdb=" C TYR F 514 " pdb=" CB TYR F 514 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.48 2.00e-01 2.50e+01 5.65e+00 ... (remaining 4693 not shown) Planarity restraints: 8704 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG F 412 " 0.569 9.50e-02 1.11e+02 2.25e-01 3.61e+02 pdb=" NE ARG F 412 " 0.079 2.00e-02 2.50e+03 pdb=" CZ ARG F 412 " 0.060 2.00e-02 2.50e+03 pdb=" NH1 ARG F 412 " 0.124 2.00e-02 2.50e+03 pdb=" NH2 ARG F 412 " -0.041 2.00e-02 2.50e+03 pdb="HH11 ARG F 412 " -0.280 2.00e-02 2.50e+03 pdb="HH12 ARG F 412 " 0.136 2.00e-02 2.50e+03 pdb="HH21 ARG F 412 " -0.071 2.00e-02 2.50e+03 pdb="HH22 ARG F 412 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 412 " 0.535 9.50e-02 1.11e+02 2.13e-01 3.36e+02 pdb=" NE ARG C 412 " 0.077 2.00e-02 2.50e+03 pdb=" CZ ARG C 412 " 0.056 2.00e-02 2.50e+03 pdb=" NH1 ARG C 412 " 0.122 2.00e-02 2.50e+03 pdb=" NH2 ARG C 412 " -0.072 2.00e-02 2.50e+03 pdb="HH11 ARG C 412 " -0.268 2.00e-02 2.50e+03 pdb="HH12 ARG C 412 " 0.134 2.00e-02 2.50e+03 pdb="HH21 ARG C 412 " -0.049 2.00e-02 2.50e+03 pdb="HH22 ARG C 412 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 412 " -0.578 9.50e-02 1.11e+02 2.24e-01 3.35e+02 pdb=" NE ARG B 412 " -0.079 2.00e-02 2.50e+03 pdb=" CZ ARG B 412 " -0.047 2.00e-02 2.50e+03 pdb=" NH1 ARG B 412 " -0.110 2.00e-02 2.50e+03 pdb=" NH2 ARG B 412 " 0.055 2.00e-02 2.50e+03 pdb="HH11 ARG B 412 " 0.266 2.00e-02 2.50e+03 pdb="HH12 ARG B 412 " -0.146 2.00e-02 2.50e+03 pdb="HH21 ARG B 412 " 0.052 2.00e-02 2.50e+03 pdb="HH22 ARG B 412 " 0.035 2.00e-02 2.50e+03 ... (remaining 8701 not shown) Histogram of nonbonded interaction distances: 1.54 - 2.16: 3897 2.16 - 2.77: 105402 2.77 - 3.38: 184205 3.38 - 3.99: 252940 3.99 - 4.60: 366032 Nonbonded interactions: 912476 Sorted by model distance: nonbonded pdb=" HH TYR D 411 " pdb=" O3P IMP D 604 " model vdw 1.544 1.850 nonbonded pdb=" HH TYR H 411 " pdb=" O1P IMP H 604 " model vdw 1.548 1.850 nonbonded pdb=" HH TYR C 411 " pdb=" O3P IMP C 604 " model vdw 1.552 1.850 nonbonded pdb=" HH TYR B 411 " pdb=" O3P IMP B 604 " model vdw 1.556 1.850 nonbonded pdb=" HH TYR G 411 " pdb=" O1P IMP G 604 " model vdw 1.558 1.850 ... (remaining 912471 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 18368 2.51 5 N 5072 2.21 5 O 5808 1.98 5 H 29200 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: 1.210 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: 0.670 Extract box with map and model: 10.450 Check model and map are aligned: 0.650 Process input model: 140.210 Find NCS groups from input model: 2.180 Set up NCS constraints: 0.260 Set refine NCS operators: 0.000 Set scattering table: 0.390 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:9.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 165.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 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 0.086 30008 Z= 0.858 Angle : 2.068 17.366 40728 Z= 1.329 Chirality : 0.099 0.501 4696 Planarity : 0.019 0.211 5064 Dihedral : 19.387 178.647 11080 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 1.13 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.54 % Favored : 96.24 % Rotamer Outliers : 2.87 % Cbeta Deviations : 0.38 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.73 (0.12), residues: 3752 helix: -0.66 (0.11), residues: 1416 sheet: -0.75 (0.29), residues: 280 loop : -0.17 (0.13), residues: 2056 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Evaluate side-chains 581 residues out of total 3080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 493 time to evaluate : 3.469 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 outliers start: 88 outliers final: 24 residues processed: 553 average time/residue: 2.4656 time to fit residues: 1619.0602 Evaluate side-chains 392 residues out of total 3080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 368 time to evaluate : 3.429 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 11 residues processed: 13 average time/residue: 0.5159 time to fit residues: 16.8849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 317 optimal weight: 0.9980 chunk 284 optimal weight: 0.9990 chunk 158 optimal weight: 5.9990 chunk 97 optimal weight: 2.9990 chunk 192 optimal weight: 1.9990 chunk 152 optimal weight: 5.9990 chunk 294 optimal weight: 7.9990 chunk 114 optimal weight: 1.9990 chunk 179 optimal weight: 5.9990 chunk 219 optimal weight: 0.9980 chunk 341 optimal weight: 5.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 GLN ** A 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 21 GLN B 202 GLN ** B 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 292 GLN C 21 GLN C 33 ASN C 202 GLN C 292 GLN D 21 GLN D 33 ASN D 292 GLN E 202 GLN F 292 GLN G 202 GLN G 292 GLN G 441 GLN H 202 GLN H 292 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 30008 Z= 0.213 Angle : 0.665 7.467 40728 Z= 0.338 Chirality : 0.044 0.215 4696 Planarity : 0.005 0.053 5064 Dihedral : 19.226 172.855 4392 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.45 % Favored : 97.52 % Rotamer Outliers : 2.02 % 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: 0.13 (0.13), residues: 3752 helix: 0.78 (0.13), residues: 1416 sheet: -0.62 (0.25), residues: 360 loop : -0.18 (0.13), residues: 1976 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Evaluate side-chains 465 residues out of total 3080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 403 time to evaluate : 3.447 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: 62 outliers final: 18 residues processed: 438 average time/residue: 2.3880 time to fit residues: 1248.9389 Evaluate side-chains 388 residues out of total 3080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 370 time to evaluate : 3.432 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 16 residues processed: 2 average time/residue: 0.4983 time to fit residues: 6.1509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 189 optimal weight: 5.9990 chunk 105 optimal weight: 7.9990 chunk 284 optimal weight: 3.9990 chunk 232 optimal weight: 3.9990 chunk 94 optimal weight: 0.9980 chunk 342 optimal weight: 7.9990 chunk 369 optimal weight: 9.9990 chunk 304 optimal weight: 5.9990 chunk 339 optimal weight: 0.6980 chunk 116 optimal weight: 8.9990 chunk 274 optimal weight: 10.0000 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN A 202 GLN A 298 GLN A 303 ASN B 94 ASN ** B 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 298 GLN C 94 ASN C 202 GLN C 292 GLN C 303 ASN C 372 HIS D 94 ASN D 202 GLN ** D 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 292 GLN D 298 GLN D 372 HIS E 94 ASN E 202 GLN E 298 GLN F 94 ASN F 202 GLN F 292 GLN F 441 GLN G 94 ASN G 202 GLN ** G 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 292 GLN G 298 GLN H 94 ASN H 202 GLN H 298 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.2961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.070 30008 Z= 0.312 Angle : 0.665 6.648 40728 Z= 0.341 Chirality : 0.045 0.172 4696 Planarity : 0.005 0.052 5064 Dihedral : 18.262 179.471 4392 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer Outliers : 2.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.13), residues: 3752 helix: 1.08 (0.14), residues: 1416 sheet: -0.81 (0.26), residues: 312 loop : -0.09 (0.13), residues: 2024 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Evaluate side-chains 468 residues out of total 3080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 399 time to evaluate : 3.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 69 outliers final: 37 residues processed: 439 average time/residue: 2.6898 time to fit residues: 1397.2888 Evaluate side-chains 399 residues out of total 3080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 362 time to evaluate : 3.473 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 25 residues processed: 12 average time/residue: 0.9208 time to fit residues: 20.9627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 337 optimal weight: 2.9990 chunk 257 optimal weight: 5.9990 chunk 177 optimal weight: 6.9990 chunk 37 optimal weight: 5.9990 chunk 163 optimal weight: 5.9990 chunk 229 optimal weight: 5.9990 chunk 343 optimal weight: 9.9990 chunk 363 optimal weight: 3.9990 chunk 179 optimal weight: 7.9990 chunk 325 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 GLN ** B 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 202 GLN C 298 GLN C 303 ASN D 202 GLN ** D 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 292 GLN D 441 GLN E 202 GLN E 303 ASN E 441 GLN E 507 HIS F 202 GLN F 298 GLN F 303 ASN ** G 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 202 GLN H 507 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.3251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.049 30008 Z= 0.408 Angle : 0.685 6.866 40728 Z= 0.351 Chirality : 0.046 0.149 4696 Planarity : 0.005 0.052 5064 Dihedral : 18.149 178.840 4392 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer Outliers : 2.90 % 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: 0.28 (0.13), residues: 3752 helix: 0.96 (0.14), residues: 1416 sheet: -0.99 (0.25), residues: 312 loop : -0.08 (0.14), residues: 2024 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Evaluate side-chains 464 residues out of total 3080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 375 time to evaluate : 3.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 89 outliers final: 55 residues processed: 429 average time/residue: 2.6159 time to fit residues: 1336.3895 Evaluate side-chains 407 residues out of total 3080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 352 time to evaluate : 3.659 Switching outliers to nearest non-outliers outliers start: 55 outliers final: 38 residues processed: 17 average time/residue: 0.8766 time to fit residues: 28.5333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 302 optimal weight: 6.9990 chunk 206 optimal weight: 7.9990 chunk 5 optimal weight: 0.9980 chunk 270 optimal weight: 3.9990 chunk 149 optimal weight: 0.9990 chunk 310 optimal weight: 4.9990 chunk 251 optimal weight: 6.9990 chunk 0 optimal weight: 4.9990 chunk 185 optimal weight: 2.9990 chunk 326 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 303 ASN B 507 HIS C 21 GLN C 202 GLN C 303 ASN C 441 GLN D 21 GLN ** D 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 292 GLN D 303 ASN E 202 GLN E 441 GLN ** G 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 441 GLN H 202 GLN H 303 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.3389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 30008 Z= 0.253 Angle : 0.601 6.692 40728 Z= 0.303 Chirality : 0.043 0.151 4696 Planarity : 0.004 0.047 5064 Dihedral : 17.532 179.482 4392 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer Outliers : 2.64 % 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: 0.52 (0.14), residues: 3752 helix: 1.25 (0.14), residues: 1416 sheet: -1.04 (0.24), residues: 312 loop : 0.02 (0.14), residues: 2024 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Evaluate side-chains 440 residues out of total 3080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 359 time to evaluate : 3.920 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: 81 outliers final: 57 residues processed: 407 average time/residue: 2.6624 time to fit residues: 1272.9607 Evaluate side-chains 403 residues out of total 3080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 346 time to evaluate : 3.508 Switching outliers to nearest non-outliers outliers start: 57 outliers final: 38 residues processed: 19 average time/residue: 0.7132 time to fit residues: 26.8267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 122 optimal weight: 4.9990 chunk 327 optimal weight: 3.9990 chunk 71 optimal weight: 0.8980 chunk 213 optimal weight: 0.6980 chunk 89 optimal weight: 5.9990 chunk 363 optimal weight: 3.9990 chunk 301 optimal weight: 0.9980 chunk 168 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 120 optimal weight: 3.9990 chunk 190 optimal weight: 3.9990 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 ASN A 507 HIS ** B 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 202 GLN C 507 HIS D 202 GLN ** D 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 202 GLN ** G 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 202 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.3487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 30008 Z= 0.236 Angle : 0.584 6.487 40728 Z= 0.291 Chirality : 0.043 0.152 4696 Planarity : 0.004 0.046 5064 Dihedral : 16.985 179.436 4392 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer Outliers : 2.45 % 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: 0.65 (0.14), residues: 3752 helix: 1.39 (0.14), residues: 1416 sheet: -1.10 (0.24), residues: 312 loop : 0.09 (0.14), residues: 2024 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Evaluate side-chains 432 residues out of total 3080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 357 time to evaluate : 3.503 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: 75 outliers final: 51 residues processed: 405 average time/residue: 2.6292 time to fit residues: 1261.3939 Evaluate side-chains 393 residues out of total 3080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 342 time to evaluate : 3.413 Switching outliers to nearest non-outliers outliers start: 51 outliers final: 37 residues processed: 14 average time/residue: 0.9561 time to fit residues: 24.1714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 350 optimal weight: 0.7980 chunk 41 optimal weight: 5.9990 chunk 207 optimal weight: 6.9990 chunk 265 optimal weight: 5.9990 chunk 205 optimal weight: 3.9990 chunk 306 optimal weight: 5.9990 chunk 203 optimal weight: 9.9990 chunk 362 optimal weight: 3.9990 chunk 226 optimal weight: 0.9990 chunk 220 optimal weight: 3.9990 chunk 167 optimal weight: 0.7980 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN ** A 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 303 ASN ** B 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 202 GLN ** D 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 202 GLN ** G 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 303 ASN H 202 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.3585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 30008 Z= 0.230 Angle : 0.580 6.648 40728 Z= 0.288 Chirality : 0.043 0.149 4696 Planarity : 0.004 0.046 5064 Dihedral : 16.482 175.886 4392 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer Outliers : 2.06 % 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: 0.72 (0.14), residues: 3752 helix: 1.46 (0.14), residues: 1416 sheet: -0.47 (0.23), residues: 392 loop : 0.04 (0.14), residues: 1944 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Evaluate side-chains 422 residues out of total 3080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 359 time to evaluate : 3.647 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 outliers start: 63 outliers final: 51 residues processed: 398 average time/residue: 2.8444 time to fit residues: 1351.5441 Evaluate side-chains 400 residues out of total 3080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 349 time to evaluate : 3.426 Switching outliers to nearest non-outliers outliers start: 51 outliers final: 35 residues processed: 16 average time/residue: 0.8266 time to fit residues: 26.1832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 224 optimal weight: 5.9990 chunk 144 optimal weight: 4.9990 chunk 216 optimal weight: 1.9990 chunk 109 optimal weight: 7.9990 chunk 71 optimal weight: 5.9990 chunk 70 optimal weight: 0.9980 chunk 230 optimal weight: 3.9990 chunk 246 optimal weight: 1.9990 chunk 179 optimal weight: 5.9990 chunk 33 optimal weight: 0.0040 chunk 284 optimal weight: 0.9980 overall best weight: 1.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 303 ASN ** B 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 202 GLN ** D 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 202 GLN ** G 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 202 GLN ** H 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.3692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.023 30008 Z= 0.161 Angle : 0.547 7.516 40728 Z= 0.265 Chirality : 0.042 0.148 4696 Planarity : 0.004 0.043 5064 Dihedral : 15.305 175.455 4392 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer Outliers : 1.83 % 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: 0.91 (0.14), residues: 3752 helix: 1.72 (0.14), residues: 1416 sheet: -0.54 (0.23), residues: 392 loop : 0.10 (0.14), residues: 1944 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Evaluate side-chains 404 residues out of total 3080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 348 time to evaluate : 3.865 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 outliers start: 56 outliers final: 40 residues processed: 386 average time/residue: 2.7544 time to fit residues: 1249.9957 Evaluate side-chains 376 residues out of total 3080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 336 time to evaluate : 3.457 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 31 residues processed: 9 average time/residue: 0.7929 time to fit residues: 15.5503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 329 optimal weight: 4.9990 chunk 347 optimal weight: 0.9990 chunk 316 optimal weight: 4.9990 chunk 337 optimal weight: 4.9990 chunk 203 optimal weight: 8.9990 chunk 147 optimal weight: 4.9990 chunk 265 optimal weight: 4.9990 chunk 103 optimal weight: 0.9980 chunk 305 optimal weight: 5.9990 chunk 319 optimal weight: 0.9980 chunk 336 optimal weight: 3.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 292 GLN ** D 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 202 GLN ** G 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 202 GLN ** H 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.3700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 30008 Z= 0.254 Angle : 0.588 7.297 40728 Z= 0.291 Chirality : 0.043 0.148 4696 Planarity : 0.004 0.047 5064 Dihedral : 15.166 177.690 4392 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer Outliers : 1.47 % 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: 0.83 (0.14), residues: 3752 helix: 1.59 (0.14), residues: 1416 sheet: -0.47 (0.23), residues: 392 loop : 0.09 (0.14), residues: 1944 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Evaluate side-chains 389 residues out of total 3080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 344 time to evaluate : 3.478 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 outliers start: 45 outliers final: 38 residues processed: 379 average time/residue: 2.7673 time to fit residues: 1233.0204 Evaluate side-chains 379 residues out of total 3080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 341 time to evaluate : 3.440 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 33 residues processed: 5 average time/residue: 0.8034 time to fit residues: 10.9760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 221 optimal weight: 1.9990 chunk 357 optimal weight: 1.9990 chunk 217 optimal weight: 2.9990 chunk 169 optimal weight: 1.9990 chunk 248 optimal weight: 10.0000 chunk 374 optimal weight: 0.8980 chunk 344 optimal weight: 10.0000 chunk 298 optimal weight: 6.9990 chunk 30 optimal weight: 0.0970 chunk 230 optimal weight: 2.9990 chunk 182 optimal weight: 6.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 292 GLN ** D 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 202 GLN ** H 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.3767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 30008 Z= 0.176 Angle : 0.552 7.554 40728 Z= 0.267 Chirality : 0.042 0.146 4696 Planarity : 0.004 0.044 5064 Dihedral : 14.490 175.640 4392 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer Outliers : 1.40 % 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: 0.97 (0.14), residues: 3752 helix: 1.76 (0.14), residues: 1416 sheet: -0.51 (0.23), residues: 392 loop : 0.15 (0.14), residues: 1944 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7504 Ramachandran restraints generated. 3752 Oldfield, 0 Emsley, 3752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Residue LYS 436 is missing expected H atoms. Skipping. Residue VAL 503 is missing expected H atoms. Skipping. Evaluate side-chains 380 residues out of total 3080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 337 time to evaluate : 3.431 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 outliers start: 43 outliers final: 38 residues processed: 371 average time/residue: 2.8093 time to fit residues: 1216.1893 Evaluate side-chains 371 residues out of total 3080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 333 time to evaluate : 3.424 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 34 residues processed: 4 average time/residue: 0.5135 time to fit residues: 8.1457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 236 optimal weight: 2.9990 chunk 317 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 275 optimal weight: 9.9990 chunk 44 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 chunk 298 optimal weight: 1.9990 chunk 125 optimal weight: 4.9990 chunk 306 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 202 GLN ** H 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.137253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.104366 restraints weight = 93225.896| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 1.29 r_work: 0.3048 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.3751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 30008 Z= 0.287 Angle : 0.607 7.569 40728 Z= 0.301 Chirality : 0.044 0.146 4696 Planarity : 0.004 0.048 5064 Dihedral : 14.483 176.570 4392 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer Outliers : 1.34 % 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: 0.82 (0.14), residues: 3752 helix: 1.55 (0.14), residues: 1416 sheet: -0.45 (0.23), residues: 392 loop : 0.10 (0.14), residues: 1944 =============================================================================== Job complete usr+sys time: 18767.62 seconds wall clock time: 323 minutes 6.30 seconds (19386.30 seconds total)