Starting phenix.real_space_refine (version: dev) on Thu Feb 23 08:11:43 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rgq_24454/02_2023/7rgq_24454_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rgq_24454/02_2023/7rgq_24454.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rgq_24454/02_2023/7rgq_24454.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rgq_24454/02_2023/7rgq_24454.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rgq_24454/02_2023/7rgq_24454_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rgq_24454/02_2023/7rgq_24454_trim_updated.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.500 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "A TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 50": "OD1" <-> "OD2" Residue "A ARG 57": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 71": "OD1" <-> "OD2" Residue "A PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 105": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 111": "OE1" <-> "OE2" Residue "A ASP 117": "OD1" <-> "OD2" Residue "A ARG 136": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 161": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 162": "OD1" <-> "OD2" Residue "A ARG 182": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 214": "OD1" <-> "OD2" Residue "A ARG 224": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 226": "OD1" <-> "OD2" 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 GLU 254": "OE1" <-> "OE2" Residue "A TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 274": "OD1" <-> "OD2" Residue "A TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 319": "OD1" <-> "OD2" Residue "A GLU 352": "OE1" <-> "OE2" Residue "A TYR 353": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 355": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 399": "OE1" <-> "OE2" Residue "A PHE 402": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 407": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 474": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 57": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ASP 71": "OD1" <-> "OD2" Residue "B PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 105": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 111": "OE1" <-> "OE2" Residue "B ASP 117": "OD1" <-> "OD2" Residue "B ARG 136": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 146": "OE1" <-> "OE2" Residue "B ARG 161": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ASP 162": "OD1" <-> "OD2" Residue "B ARG 182": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ASP 214": "OD1" <-> "OD2" Residue "B ARG 224": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 239": "OD1" <-> "OD2" Residue "B ARG 253": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 254": "OE1" <-> "OE2" Residue "B TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 261": "OD1" <-> "OD2" Residue "B ASP 269": "OD1" <-> "OD2" Residue "B ASP 274": "OD1" <-> "OD2" Residue "B TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 352": "OE1" <-> "OE2" Residue "B TYR 353": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 355": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 357": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 364": "OD1" <-> "OD2" Residue "B GLU 399": "OE1" <-> "OE2" Residue "B TYR 400": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 407": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 474": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 57": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ASP 71": "OD1" <-> "OD2" Residue "C PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 105": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 111": "OE1" <-> "OE2" Residue "C ASP 117": "OD1" <-> "OD2" Residue "C ARG 136": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 146": "OE1" <-> "OE2" Residue "C ARG 161": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ASP 162": "OD1" <-> "OD2" Residue "C ARG 182": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ASP 214": "OD1" <-> "OD2" Residue "C ARG 224": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" 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 GLU 254": "OE1" <-> "OE2" Residue "C TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 269": "OD1" <-> "OD2" Residue "C ASP 274": "OD1" <-> "OD2" Residue "C TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 352": "OE1" <-> "OE2" Residue "C TYR 353": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 355": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 399": "OE1" <-> "OE2" Residue "C TYR 400": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 407": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 474": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 514": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 57": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ASP 71": "OD1" <-> "OD2" Residue "D PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 105": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 111": "OE1" <-> "OE2" Residue "D ASP 117": "OD1" <-> "OD2" Residue "D ARG 136": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D GLU 146": "OE1" <-> "OE2" Residue "D ARG 161": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ASP 162": "OD1" <-> "OD2" Residue "D ARG 182": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ASP 214": "OD1" <-> "OD2" Residue "D ASP 216": "OD1" <-> "OD2" Residue "D ARG 224": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 239": "OD1" <-> "OD2" Residue "D ARG 253": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D GLU 254": "OE1" <-> "OE2" Residue "D TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 269": "OD1" <-> "OD2" Residue "D ASP 274": "OD1" <-> "OD2" Residue "D TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 352": "OE1" <-> "OE2" Residue "D TYR 353": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 355": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D GLU 399": "OE1" <-> "OE2" Residue "D TYR 400": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 407": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 474": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 57": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ASP 71": "OD1" <-> "OD2" Residue "E PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 105": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 111": "OE1" <-> "OE2" Residue "E ASP 117": "OD1" <-> "OD2" Residue "E ARG 136": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E GLU 146": "OE1" <-> "OE2" Residue "E ARG 161": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ASP 162": "OD1" <-> "OD2" Residue "E ARG 182": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ASP 214": "OD1" <-> "OD2" Residue "E ASP 216": "OD1" <-> "OD2" Residue "E ARG 224": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" 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 GLU 254": "OE1" <-> "OE2" Residue "E TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 269": "OD1" <-> "OD2" Residue "E ASP 274": "OD1" <-> "OD2" Residue "E TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 352": "OE1" <-> "OE2" Residue "E TYR 353": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 355": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E PHE 357": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 364": "OD1" <-> "OD2" Residue "E GLU 399": "OE1" <-> "OE2" Residue "E TYR 400": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 407": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 474": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E PHE 514": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ARG 57": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ASP 71": "OD1" <-> "OD2" Residue "F PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ARG 105": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 117": "OD1" <-> "OD2" Residue "F ARG 136": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F GLU 146": "OE1" <-> "OE2" Residue "F ARG 161": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ASP 162": "OD1" <-> "OD2" Residue "F ARG 182": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ASP 214": "OD1" <-> "OD2" Residue "F ARG 224": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" 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 GLU 254": "OE1" <-> "OE2" Residue "F TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 269": "OD1" <-> "OD2" Residue "F ASP 274": "OD1" <-> "OD2" Residue "F TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 352": "OE1" <-> "OE2" Residue "F TYR 353": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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 TYR 400": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ARG 407": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 474": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F PHE 514": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ARG 57": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ASP 71": "OD1" <-> "OD2" Residue "G PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ARG 105": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 111": "OE1" <-> "OE2" Residue "G ASP 117": "OD1" <-> "OD2" Residue "G ARG 136": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G GLU 146": "OE1" <-> "OE2" Residue "G ARG 161": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ASP 162": "OD1" <-> "OD2" Residue "G ARG 182": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ASP 214": "OD1" <-> "OD2" Residue "G ARG 224": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" 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 GLU 254": "OE1" <-> "OE2" Residue "G TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ASP 269": "OD1" <-> "OD2" Residue "G ASP 274": "OD1" <-> "OD2" Residue "G TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 352": "OE1" <-> "OE2" Residue "G TYR 353": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ARG 355": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G GLU 399": "OE1" <-> "OE2" Residue "G TYR 400": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ARG 407": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 474": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ASP 50": "OD1" <-> "OD2" Residue "H ARG 57": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ASP 71": "OD1" <-> "OD2" Residue "H PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ARG 105": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ASP 117": "OD1" <-> "OD2" Residue "H ARG 136": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H GLU 146": "OE1" <-> "OE2" Residue "H ARG 161": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ASP 162": "OD1" <-> "OD2" Residue "H ARG 182": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ASP 214": "OD1" <-> "OD2" Residue "H ARG 224": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" 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 GLU 254": "OE1" <-> "OE2" Residue "H TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ASP 274": "OD1" <-> "OD2" Residue "H TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 352": "OE1" <-> "OE2" Residue "H TYR 353": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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 TYR 400": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ARG 407": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 474": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H PHE 514": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 59832 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 7317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 7317 Classifications: {'peptide': 481} Link IDs: {'PTRANS': 18, 'TRANS': 462} Chain breaks: 2 Chain: "B" Number of atoms: 7317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 7317 Classifications: {'peptide': 481} Link IDs: {'PTRANS': 18, 'TRANS': 462} Chain breaks: 2 Chain: "C" Number of atoms: 7317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 7317 Classifications: {'peptide': 481} Link IDs: {'PTRANS': 18, 'TRANS': 462} Chain breaks: 2 Chain: "D" Number of atoms: 7317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 7317 Classifications: {'peptide': 481} Link IDs: {'PTRANS': 18, 'TRANS': 462} Chain breaks: 2 Chain: "E" Number of atoms: 7317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 7317 Classifications: {'peptide': 481} Link IDs: {'PTRANS': 18, 'TRANS': 462} Chain breaks: 2 Chain: "F" Number of atoms: 7317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 7317 Classifications: {'peptide': 481} Link IDs: {'PTRANS': 18, 'TRANS': 462} Chain breaks: 2 Chain: "G" Number of atoms: 7317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 7317 Classifications: {'peptide': 481} Link IDs: {'PTRANS': 18, 'TRANS': 462} Chain breaks: 2 Chain: "H" Number of atoms: 7317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 7317 Classifications: {'peptide': 481} Link IDs: {'PTRANS': 18, 'TRANS': 462} Chain breaks: 2 Chain: "A" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna3p': 1} Link IDs: {None: 4} Chain: "B" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna3p': 1} Link IDs: {None: 4} Chain: "C" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna3p': 1} Link IDs: {None: 4} Chain: "D" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna3p': 1} Link IDs: {None: 4} Chain: "E" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna3p': 1} Link IDs: {None: 4} Chain: "F" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna3p': 1} Link IDs: {None: 4} Chain: "G" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna3p': 1} Link IDs: {None: 4} Chain: "H" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna3p': 1} Link IDs: {None: 4} Time building chain proxies: 21.78, per 1000 atoms: 0.36 Number of scatterers: 59832 At special positions: 0 Unit cell: (151.96, 151.96, 114.84, 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 184 16.00 P 96 15.00 O 6008 8.00 N 5160 7.00 C 18840 6.00 H 29544 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: 38.71 Conformation dependent library (CDL) restraints added in 4.1 seconds 7600 Ramachandran restraints generated. 3800 Oldfield, 0 Emsley, 3800 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6912 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 147 helices and 53 sheets defined 34.1% alpha, 10.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.83 Creating SS restraints... Processing helix chain 'A' and resid 20 through 25 removed outlier: 4.160A pdb=" N PHE A 24 " --> pdb=" O ALA A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 85 removed outlier: 4.227A pdb=" N MET A 85 " --> pdb=" O ALA A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 110 removed outlier: 4.158A pdb=" N PHE A 110 " --> pdb=" O LYS A 106 " (cutoff:3.500A) 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 175 through 177 No H-bonds generated for 'chain 'A' and resid 175 through 177' Processing helix chain 'A' and resid 196 through 202 Processing helix chain 'A' and resid 224 through 232 Processing helix chain 'A' and resid 254 through 265 removed outlier: 3.987A pdb=" N LEU A 260 " --> pdb=" O LYS A 257 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU A 263 " --> pdb=" O LEU A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 293 Processing helix chain 'A' and resid 307 through 316 removed outlier: 4.845A pdb=" N ASN A 312 " --> pdb=" O ALA A 308 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU A 313 " --> pdb=" O GLN A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 337 Processing helix chain 'A' and resid 343 through 354 removed outlier: 3.591A pdb=" N TYR A 348 " --> pdb=" O GLY A 344 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N TYR A 353 " --> pdb=" O LYS A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 379 Processing helix chain 'A' and resid 414 through 416 No H-bonds generated for 'chain 'A' and resid 414 through 416' Processing helix chain 'A' and resid 453 through 471 Proline residue: A 458 - end of helix removed outlier: 3.602A pdb=" N HIS A 466 " --> pdb=" O ALA A 462 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLY A 467 " --> pdb=" O GLY A 463 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ASP A 470 " --> pdb=" O HIS A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 485 Processing helix chain 'A' and resid 495 through 498 No H-bonds generated for 'chain 'A' and resid 495 through 498' Processing helix chain 'B' and resid 20 through 25 removed outlier: 4.161A pdb=" N PHE B 24 " --> pdb=" O ALA B 20 " (cutoff:3.500A) 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 76 through 85 removed outlier: 4.227A pdb=" N MET B 85 " --> pdb=" O ALA B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 110 removed outlier: 4.214A pdb=" N PHE B 110 " --> pdb=" O LYS B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 137 Processing helix chain 'B' and resid 160 through 162 No H-bonds generated for 'chain 'B' and resid 160 through 162' Processing helix chain 'B' and resid 175 through 177 No H-bonds generated for 'chain 'B' and resid 175 through 177' Processing helix chain 'B' and resid 196 through 202 Processing helix chain 'B' and resid 224 through 232 Processing helix chain 'B' and resid 254 through 265 removed outlier: 4.000A pdb=" N LEU B 260 " --> pdb=" O LYS B 257 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU B 263 " --> pdb=" O LEU B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 293 Processing helix chain 'B' and resid 307 through 316 removed outlier: 4.961A pdb=" N ASN B 312 " --> pdb=" O ALA B 308 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LEU B 313 " --> pdb=" O GLN B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 337 Processing helix chain 'B' and resid 343 through 357 removed outlier: 3.590A pdb=" N TYR B 348 " --> pdb=" O GLY B 344 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N TYR B 353 " --> pdb=" O LYS B 349 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ARG B 356 " --> pdb=" O GLU B 352 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N PHE B 357 " --> pdb=" O TYR B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 379 Processing helix chain 'B' and resid 414 through 416 No H-bonds generated for 'chain 'B' and resid 414 through 416' Processing helix chain 'B' and resid 453 through 471 Proline residue: B 458 - end of helix removed outlier: 3.550A pdb=" N HIS B 466 " --> pdb=" O ALA B 462 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASP B 470 " --> pdb=" O HIS B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 485 Processing helix chain 'B' and resid 495 through 498 No H-bonds generated for 'chain 'B' and resid 495 through 498' Processing helix chain 'C' and resid 20 through 25 removed outlier: 4.161A pdb=" N PHE C 24 " --> pdb=" O ALA C 20 " (cutoff:3.500A) 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 76 through 85 removed outlier: 4.091A pdb=" N MET C 85 " --> pdb=" O ALA C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 110 removed outlier: 4.242A pdb=" N PHE C 110 " --> pdb=" O LYS C 106 " (cutoff:3.500A) 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 182 through 184 No H-bonds generated for 'chain 'C' and resid 182 through 184' Processing helix chain 'C' and resid 196 through 202 Processing helix chain 'C' and resid 224 through 232 Processing helix chain 'C' and resid 256 through 265 removed outlier: 4.234A pdb=" N ASP C 261 " --> pdb=" O LYS C 257 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU C 262 " --> pdb=" O TYR C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 293 Processing helix chain 'C' and resid 307 through 316 removed outlier: 4.970A pdb=" N ASN C 312 " --> pdb=" O ALA C 308 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU C 313 " --> pdb=" O GLN C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 337 Processing helix chain 'C' and resid 343 through 354 removed outlier: 3.590A pdb=" N TYR C 348 " --> pdb=" O GLY C 344 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N TYR C 353 " --> pdb=" O LYS C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 379 Processing helix chain 'C' and resid 453 through 471 Proline residue: C 458 - end of helix removed outlier: 3.552A pdb=" N HIS C 466 " --> pdb=" O ALA C 462 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLY C 467 " --> pdb=" O GLY C 463 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ASP C 470 " --> pdb=" O HIS C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 485 Processing helix chain 'C' and resid 495 through 498 No H-bonds generated for 'chain 'C' and resid 495 through 498' Processing helix chain 'D' and resid 20 through 25 removed outlier: 4.161A pdb=" N PHE D 24 " --> pdb=" O ALA D 20 " (cutoff:3.500A) 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 76 through 85 removed outlier: 4.227A pdb=" N MET D 85 " --> pdb=" O ALA D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 110 removed outlier: 4.192A pdb=" N PHE D 110 " --> pdb=" O LYS D 106 " (cutoff:3.500A) 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 175 through 177 No H-bonds generated for 'chain 'D' and resid 175 through 177' Processing helix chain 'D' and resid 196 through 203 Processing helix chain 'D' and resid 224 through 232 Processing helix chain 'D' and resid 254 through 265 removed outlier: 3.923A pdb=" N LEU D 260 " --> pdb=" O LYS D 257 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU D 263 " --> pdb=" O LEU D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 293 Processing helix chain 'D' and resid 307 through 316 removed outlier: 4.838A pdb=" N ASN D 312 " --> pdb=" O ALA D 308 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU D 313 " --> pdb=" O GLN D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 333 through 337 Processing helix chain 'D' and resid 343 through 357 removed outlier: 3.591A pdb=" N TYR D 348 " --> pdb=" O GLY D 344 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N TYR D 353 " --> pdb=" O LYS D 349 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ARG D 356 " --> pdb=" O GLU D 352 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N PHE D 357 " --> pdb=" O TYR D 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 379 Processing helix chain 'D' and resid 453 through 471 Proline residue: D 458 - end of helix removed outlier: 3.937A pdb=" N ASP D 470 " --> pdb=" O HIS D 466 " (cutoff:3.500A) Processing helix chain 'D' and resid 476 through 485 Processing helix chain 'D' and resid 495 through 497 No H-bonds generated for 'chain 'D' and resid 495 through 497' Processing helix chain 'E' and resid 20 through 25 removed outlier: 4.161A pdb=" N PHE E 24 " --> pdb=" O ALA E 20 " (cutoff:3.500A) 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 76 through 85 removed outlier: 4.227A pdb=" N MET E 85 " --> pdb=" O ALA E 81 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 110 removed outlier: 4.223A pdb=" N PHE E 110 " --> pdb=" O LYS E 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 137 Processing helix chain 'E' and resid 160 through 162 No H-bonds generated for 'chain 'E' and resid 160 through 162' Processing helix chain 'E' and resid 175 through 177 No H-bonds generated for 'chain 'E' and resid 175 through 177' Processing helix chain 'E' and resid 196 through 203 Processing helix chain 'E' and resid 224 through 232 Processing helix chain 'E' and resid 256 through 265 removed outlier: 4.250A pdb=" N ASP E 261 " --> pdb=" O LYS E 257 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU E 262 " --> pdb=" O TYR E 258 " (cutoff:3.500A) Processing helix chain 'E' and resid 281 through 293 Processing helix chain 'E' and resid 307 through 316 removed outlier: 4.917A pdb=" N ASN E 312 " --> pdb=" O ALA E 308 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LEU E 313 " --> pdb=" O GLN E 309 " (cutoff:3.500A) Processing helix chain 'E' and resid 333 through 337 Processing helix chain 'E' and resid 343 through 357 removed outlier: 3.590A pdb=" N TYR E 348 " --> pdb=" O GLY E 344 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N TYR E 353 " --> pdb=" O LYS E 349 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ARG E 356 " --> pdb=" O GLU E 352 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N PHE E 357 " --> pdb=" O TYR E 353 " (cutoff:3.500A) Processing helix chain 'E' and resid 370 through 379 Processing helix chain 'E' and resid 414 through 416 No H-bonds generated for 'chain 'E' and resid 414 through 416' Processing helix chain 'E' and resid 453 through 471 Proline residue: E 458 - end of helix removed outlier: 3.607A pdb=" N HIS E 466 " --> pdb=" O ALA E 462 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASP E 470 " --> pdb=" O HIS E 466 " (cutoff:3.500A) Processing helix chain 'E' and resid 476 through 485 Processing helix chain 'E' and resid 495 through 498 No H-bonds generated for 'chain 'E' and resid 495 through 498' Processing helix chain 'F' and resid 20 through 25 removed outlier: 4.161A pdb=" N PHE F 24 " --> pdb=" O ALA F 20 " (cutoff:3.500A) 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 76 through 85 removed outlier: 4.226A pdb=" N MET F 85 " --> pdb=" O ALA F 81 " (cutoff:3.500A) Processing helix chain 'F' and resid 97 through 110 removed outlier: 4.248A pdb=" N PHE F 110 " --> pdb=" O LYS F 106 " (cutoff:3.500A) Processing helix chain 'F' and resid 127 through 137 Processing helix chain 'F' and resid 160 through 162 No H-bonds generated for 'chain 'F' and resid 160 through 162' Processing helix chain 'F' and resid 175 through 177 No H-bonds generated for 'chain 'F' and resid 175 through 177' Processing helix chain 'F' and resid 196 through 204 Processing helix chain 'F' and resid 224 through 232 Processing helix chain 'F' and resid 254 through 265 removed outlier: 3.600A pdb=" N TYR F 258 " --> pdb=" O ASP F 255 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU F 260 " --> pdb=" O LYS F 257 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU F 263 " --> pdb=" O LEU F 260 " (cutoff:3.500A) Processing helix chain 'F' and resid 281 through 293 Processing helix chain 'F' and resid 307 through 316 removed outlier: 4.968A pdb=" N ASN F 312 " --> pdb=" O ALA F 308 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LEU F 313 " --> pdb=" O GLN F 309 " (cutoff:3.500A) Processing helix chain 'F' and resid 333 through 337 Processing helix chain 'F' and resid 343 through 357 removed outlier: 3.590A pdb=" N TYR F 348 " --> pdb=" O GLY F 344 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N TYR F 353 " --> pdb=" O LYS F 349 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ARG F 356 " --> pdb=" O GLU F 352 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N PHE F 357 " --> pdb=" O TYR F 353 " (cutoff:3.500A) Processing helix chain 'F' and resid 370 through 379 Processing helix chain 'F' and resid 414 through 416 No H-bonds generated for 'chain 'F' and resid 414 through 416' Processing helix chain 'F' and resid 453 through 471 Proline residue: F 458 - end of helix removed outlier: 3.562A pdb=" N HIS F 466 " --> pdb=" O ALA F 462 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ASP F 470 " --> pdb=" O HIS F 466 " (cutoff:3.500A) Processing helix chain 'F' and resid 476 through 485 Processing helix chain 'F' and resid 495 through 498 No H-bonds generated for 'chain 'F' and resid 495 through 498' Processing helix chain 'G' and resid 20 through 25 removed outlier: 4.161A pdb=" N PHE G 24 " --> pdb=" O ALA G 20 " (cutoff:3.500A) 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 76 through 85 removed outlier: 4.226A pdb=" N MET G 85 " --> pdb=" O ALA G 81 " (cutoff:3.500A) Processing helix chain 'G' and resid 97 through 110 removed outlier: 4.334A pdb=" N PHE G 110 " --> pdb=" O LYS G 106 " (cutoff:3.500A) Processing helix chain 'G' and resid 127 through 137 Processing helix chain 'G' and resid 160 through 162 No H-bonds generated for 'chain 'G' and resid 160 through 162' Processing helix chain 'G' and resid 194 through 203 Processing helix chain 'G' and resid 224 through 232 Processing helix chain 'G' and resid 254 through 265 removed outlier: 3.569A pdb=" N TYR G 258 " --> pdb=" O ASP G 255 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU G 260 " --> pdb=" O LYS G 257 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU G 263 " --> pdb=" O LEU G 260 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN G 265 " --> pdb=" O LEU G 262 " (cutoff:3.500A) Processing helix chain 'G' and resid 281 through 293 Processing helix chain 'G' and resid 307 through 316 removed outlier: 4.996A pdb=" N ASN G 312 " --> pdb=" O ALA G 308 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LEU G 313 " --> pdb=" O GLN G 309 " (cutoff:3.500A) Processing helix chain 'G' and resid 333 through 337 Processing helix chain 'G' and resid 343 through 354 removed outlier: 3.591A pdb=" N TYR G 348 " --> pdb=" O GLY G 344 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N TYR G 353 " --> pdb=" O LYS G 349 " (cutoff:3.500A) Processing helix chain 'G' and resid 370 through 379 Processing helix chain 'G' and resid 414 through 416 No H-bonds generated for 'chain 'G' and resid 414 through 416' Processing helix chain 'G' and resid 453 through 471 Proline residue: G 458 - end of helix removed outlier: 3.537A pdb=" N HIS G 466 " --> pdb=" O ALA G 462 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLY G 467 " --> pdb=" O GLY G 463 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ASP G 470 " --> pdb=" O HIS G 466 " (cutoff:3.500A) Processing helix chain 'G' and resid 476 through 485 Processing helix chain 'G' and resid 495 through 498 No H-bonds generated for 'chain 'G' and resid 495 through 498' Processing helix chain 'H' and resid 20 through 25 removed outlier: 4.161A pdb=" N PHE H 24 " --> pdb=" O ALA H 20 " (cutoff:3.500A) 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 76 through 85 removed outlier: 4.226A pdb=" N MET H 85 " --> pdb=" O ALA H 81 " (cutoff:3.500A) Processing helix chain 'H' and resid 97 through 110 removed outlier: 4.219A pdb=" N PHE H 110 " --> pdb=" O LYS H 106 " (cutoff:3.500A) Processing helix chain 'H' and resid 127 through 137 Processing helix chain 'H' and resid 160 through 162 No H-bonds generated for 'chain 'H' and resid 160 through 162' Processing helix chain 'H' and resid 196 through 203 Processing helix chain 'H' and resid 224 through 232 Processing helix chain 'H' and resid 254 through 265 removed outlier: 3.959A pdb=" N LEU H 260 " --> pdb=" O LYS H 257 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU H 263 " --> pdb=" O LEU H 260 " (cutoff:3.500A) Processing helix chain 'H' and resid 281 through 293 Processing helix chain 'H' and resid 307 through 316 removed outlier: 4.976A pdb=" N ASN H 312 " --> pdb=" O ALA H 308 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LEU H 313 " --> pdb=" O GLN H 309 " (cutoff:3.500A) Processing helix chain 'H' and resid 333 through 337 Processing helix chain 'H' and resid 343 through 357 removed outlier: 3.591A pdb=" N TYR H 348 " --> pdb=" O GLY H 344 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N TYR H 353 " --> pdb=" O LYS H 349 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ARG H 356 " --> pdb=" O GLU H 352 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N PHE H 357 " --> pdb=" O TYR H 353 " (cutoff:3.500A) Processing helix chain 'H' and resid 370 through 379 Processing helix chain 'H' and resid 414 through 416 No H-bonds generated for 'chain 'H' and resid 414 through 416' Processing helix chain 'H' and resid 453 through 471 Proline residue: H 458 - end of helix removed outlier: 3.535A pdb=" N HIS H 466 " --> pdb=" O ALA H 462 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASP H 470 " --> pdb=" O HIS H 466 " (cutoff:3.500A) Processing helix chain 'H' and resid 476 through 485 Processing helix chain 'H' and resid 495 through 497 No H-bonds generated for 'chain 'H' and resid 495 through 497' 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: 6.300A pdb=" N VAL A 384 " --> pdb=" O ILE A 66 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N THR A 383 " --> pdb=" O ILE A 361 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 187 through 189 removed outlier: 3.574A pdb=" N ALA A 220 " --> pdb=" O ILE A 211 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 247 through 250 removed outlier: 6.752A pdb=" N VAL A 270 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N VAL A 250 " --> pdb=" O VAL A 270 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N VAL A 272 " --> pdb=" O VAL A 250 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N GLN A 298 " --> pdb=" O ILE A 271 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N LEU A 273 " --> pdb=" O GLN A 298 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N ILE A 300 " --> pdb=" O LEU A 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'A' and resid 408 through 412 Processing sheet with id= F, first strand: chain 'A' and resid 53 through 56 removed outlier: 6.817A pdb=" N ILE A 59 " --> pdb=" O LEU A 55 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 142 through 145 Processing sheet with id= H, first strand: chain 'B' and resid 35 through 37 Processing sheet with id= I, first strand: chain 'B' and resid 187 through 189 removed outlier: 8.191A pdb=" N ALA B 188 " --> pdb=" O LYS B 208 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA B 220 " --> pdb=" O ILE B 211 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 247 through 250 removed outlier: 6.762A pdb=" N VAL B 270 " --> pdb=" O ALA B 248 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N VAL B 250 " --> pdb=" O VAL B 270 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N VAL B 272 " --> pdb=" O VAL B 250 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N GLN B 298 " --> pdb=" O ILE B 271 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N LEU B 273 " --> pdb=" O GLN B 298 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N ILE B 300 " --> pdb=" O LEU B 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'B' and resid 320 through 323 removed outlier: 7.824A pdb=" N VAL B 323 " --> pdb=" O PRO B 360 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ILE B 362 " --> pdb=" O VAL B 323 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N THR B 383 " --> pdb=" O ALA B 363 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'B' and resid 400 through 402 Processing sheet with id= M, first strand: chain 'B' and resid 53 through 56 removed outlier: 6.930A pdb=" N ILE B 59 " --> pdb=" O LEU B 55 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 141 through 145 removed outlier: 3.633A pdb=" N GLY B 156 " --> pdb=" O ILE B 144 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 35 through 37 removed outlier: 3.505A pdb=" N GLU C 491 " --> pdb=" O LEU C 36 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 65 through 67 removed outlier: 6.308A pdb=" N VAL C 384 " --> pdb=" O ILE C 66 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N THR C 383 " --> pdb=" O ILE C 361 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 187 through 189 removed outlier: 3.522A pdb=" N ALA C 220 " --> pdb=" O ILE C 211 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 247 through 250 removed outlier: 6.752A pdb=" N VAL C 270 " --> pdb=" O ALA C 248 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N VAL C 250 " --> pdb=" O VAL C 270 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N VAL C 272 " --> pdb=" O VAL C 250 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N GLN C 298 " --> pdb=" O ILE C 271 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N LEU C 273 " --> pdb=" O GLN C 298 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N ILE C 300 " --> pdb=" O LEU C 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= R Processing sheet with id= S, first strand: chain 'C' and resid 400 through 402 removed outlier: 3.690A pdb=" N LEU C 408 " --> pdb=" O PHE C 401 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'C' and resid 53 through 56 removed outlier: 6.930A pdb=" N ILE C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'C' and resid 143 through 145 removed outlier: 3.529A pdb=" N GLY C 156 " --> pdb=" O ILE C 144 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'D' and resid 65 through 67 removed outlier: 6.535A pdb=" N VAL D 384 " --> pdb=" O ILE D 66 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR D 383 " --> pdb=" O ILE D 361 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLY D 302 " --> pdb=" O LEU D 273 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'D' and resid 187 through 189 removed outlier: 3.536A pdb=" N ALA D 220 " --> pdb=" O ILE D 211 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'D' and resid 400 through 402 Processing sheet with id= Y, first strand: chain 'D' and resid 53 through 56 removed outlier: 6.891A pdb=" N ILE D 59 " --> pdb=" O LEU D 55 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'D' and resid 142 through 145 removed outlier: 3.555A pdb=" N GLY D 156 " --> pdb=" O ILE D 144 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'E' and resid 35 through 37 Processing sheet with id= AB, first strand: chain 'E' and resid 187 through 189 removed outlier: 3.592A pdb=" N ALA E 220 " --> pdb=" O ILE E 211 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'E' and resid 247 through 250 removed outlier: 6.773A pdb=" N VAL E 270 " --> pdb=" O ALA E 248 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N VAL E 250 " --> pdb=" O VAL E 270 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N VAL E 272 " --> pdb=" O VAL E 250 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N GLN E 298 " --> pdb=" O ILE E 271 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N LEU E 273 " --> pdb=" O GLN E 298 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N ILE E 300 " --> pdb=" O LEU E 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= AC Processing sheet with id= AD, first strand: chain 'E' and resid 320 through 323 removed outlier: 7.935A pdb=" N VAL E 323 " --> pdb=" O PRO E 360 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ILE E 362 " --> pdb=" O VAL E 323 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N THR E 383 " --> pdb=" O ALA E 363 " (cutoff:3.500A) No H-bonds generated for sheet with id= AD Processing sheet with id= AE, first strand: chain 'E' and resid 409 through 412 Processing sheet with id= AF, first strand: chain 'E' and resid 53 through 56 removed outlier: 6.925A pdb=" N ILE E 59 " --> pdb=" O LEU E 55 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'E' and resid 142 through 145 removed outlier: 3.536A pdb=" N GLY E 156 " --> pdb=" O ILE E 144 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'F' and resid 35 through 37 Processing sheet with id= AI, first strand: chain 'F' and resid 187 through 189 removed outlier: 7.789A pdb=" N ALA F 188 " --> pdb=" O LYS F 208 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'F' and resid 247 through 250 removed outlier: 6.764A pdb=" N VAL F 270 " --> pdb=" O ALA F 248 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N VAL F 250 " --> pdb=" O VAL F 270 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N VAL F 272 " --> pdb=" O VAL F 250 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N GLN F 298 " --> pdb=" O ILE F 271 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N LEU F 273 " --> pdb=" O GLN F 298 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N ILE F 300 " --> pdb=" O LEU F 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= AJ Processing sheet with id= AK, first strand: chain 'F' and resid 320 through 323 removed outlier: 7.829A pdb=" N VAL F 323 " --> pdb=" O PRO F 360 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ILE F 362 " --> pdb=" O VAL F 323 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N THR F 383 " --> pdb=" O ALA F 363 " (cutoff:3.500A) No H-bonds generated for sheet with id= AK Processing sheet with id= AL, first strand: chain 'F' and resid 409 through 412 Processing sheet with id= AM, first strand: chain 'F' and resid 53 through 56 removed outlier: 6.898A pdb=" N ILE F 59 " --> pdb=" O LEU F 55 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'F' and resid 142 through 145 Processing sheet with id= AO, first strand: chain 'G' and resid 35 through 37 Processing sheet with id= AP, first strand: chain 'G' and resid 65 through 67 removed outlier: 6.293A pdb=" N VAL G 384 " --> pdb=" O ILE G 66 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N THR G 383 " --> pdb=" O ILE G 361 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'G' and resid 187 through 189 removed outlier: 8.291A pdb=" N ALA G 188 " --> pdb=" O LYS G 208 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'G' and resid 247 through 250 removed outlier: 6.730A pdb=" N VAL G 270 " --> pdb=" O ALA G 248 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N VAL G 250 " --> pdb=" O VAL G 270 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N VAL G 272 " --> pdb=" O VAL G 250 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N GLN G 298 " --> pdb=" O ILE G 271 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N LEU G 273 " --> pdb=" O GLN G 298 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N ILE G 300 " --> pdb=" O LEU G 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= AR Processing sheet with id= AS, first strand: chain 'G' and resid 400 through 402 removed outlier: 3.606A pdb=" N LEU G 408 " --> pdb=" O PHE G 401 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'G' and resid 53 through 56 removed outlier: 6.900A pdb=" N ILE G 59 " --> pdb=" O LEU G 55 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'G' and resid 142 through 145 Processing sheet with id= AV, first strand: chain 'H' and resid 65 through 67 removed outlier: 6.526A pdb=" N VAL H 384 " --> pdb=" O ILE H 66 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR H 383 " --> pdb=" O ILE H 361 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'H' and resid 187 through 189 removed outlier: 8.090A pdb=" N ALA H 188 " --> pdb=" O LYS H 208 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'H' and resid 247 through 250 removed outlier: 6.778A pdb=" N VAL H 270 " --> pdb=" O ALA H 248 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N VAL H 250 " --> pdb=" O VAL H 270 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N VAL H 272 " --> pdb=" O VAL H 250 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N GLN H 298 " --> pdb=" O ILE H 271 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N LEU H 273 " --> pdb=" O GLN H 298 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N ILE H 300 " --> pdb=" O LEU H 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= AX Processing sheet with id= AY, first strand: chain 'H' and resid 400 through 402 Processing sheet with id= AZ, first strand: chain 'H' and resid 53 through 56 removed outlier: 6.870A pdb=" N ILE H 59 " --> pdb=" O LEU H 55 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'H' and resid 141 through 145 removed outlier: 3.578A pdb=" N GLY H 156 " --> pdb=" O ILE H 144 " (cutoff:3.500A) 783 hydrogen bonds defined for protein. 2184 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 20.62 Time building geometry restraints manager: 40.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.87 - 1.06: 6339 1.06 - 1.25: 27564 1.25 - 1.44: 8324 1.44 - 1.63: 17833 1.63 - 1.82: 324 Bond restraints: 60384 Sorted by residual: bond pdb=" C2' GTP D 601 " pdb=" C3' GTP D 601 " ideal model delta sigma weight residual 1.524 1.226 0.298 2.00e-02 2.50e+03 2.21e+02 bond pdb=" C2' GTP E 601 " pdb=" C3' GTP E 601 " ideal model delta sigma weight residual 1.524 1.227 0.297 2.00e-02 2.50e+03 2.21e+02 bond pdb=" C1' GTP D 601 " pdb=" N9 GTP D 601 " ideal model delta sigma weight residual 1.475 1.323 0.152 2.00e-02 2.50e+03 5.74e+01 bond pdb=" C1' GTP E 601 " pdb=" N9 GTP E 601 " ideal model delta sigma weight residual 1.475 1.323 0.152 2.00e-02 2.50e+03 5.74e+01 bond pdb=" N ILE H 330 " pdb=" H ILE H 330 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.72e+01 ... (remaining 60379 not shown) Histogram of bond angle deviations from ideal: 93.96 - 102.26: 333 102.26 - 110.57: 60833 110.57 - 118.87: 24477 118.87 - 127.18: 23133 127.18 - 135.48: 368 Bond angle restraints: 109144 Sorted by residual: angle pdb=" PB ATP E 604 " pdb=" O3B ATP E 604 " pdb=" PG ATP E 604 " ideal model delta sigma weight residual 139.87 121.11 18.76 1.00e+00 1.00e+00 3.52e+02 angle pdb=" PB ATP F 604 " pdb=" O3B ATP F 604 " pdb=" PG ATP F 604 " ideal model delta sigma weight residual 139.87 121.37 18.50 1.00e+00 1.00e+00 3.42e+02 angle pdb=" PA ATP B 604 " pdb=" O3A ATP B 604 " pdb=" PB ATP B 604 " ideal model delta sigma weight residual 136.83 118.51 18.32 1.00e+00 1.00e+00 3.36e+02 angle pdb=" PB ATP D 604 " pdb=" O3B ATP D 604 " pdb=" PG ATP D 604 " ideal model delta sigma weight residual 139.87 121.64 18.23 1.00e+00 1.00e+00 3.32e+02 angle pdb=" PB ATP H 604 " pdb=" O3B ATP H 604 " pdb=" PG ATP H 604 " ideal model delta sigma weight residual 139.87 121.65 18.22 1.00e+00 1.00e+00 3.32e+02 ... (remaining 109139 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.80: 22189 29.80 - 59.60: 982 59.60 - 89.40: 338 89.40 - 119.20: 24 119.20 - 149.00: 43 Dihedral angle restraints: 23576 sinusoidal: 11328 harmonic: 12248 Sorted by residual: dihedral pdb=" C8 GTP E 601 " pdb=" C1' GTP E 601 " pdb=" N9 GTP E 601 " pdb=" O4' GTP E 601 " ideal model delta sinusoidal sigma weight residual 104.59 -106.40 -149.00 1 2.00e+01 2.50e-03 4.46e+01 dihedral pdb=" C8 GTP D 601 " pdb=" C1' GTP D 601 " pdb=" N9 GTP D 601 " pdb=" O4' GTP D 601 " ideal model delta sinusoidal sigma weight residual 104.59 -106.43 -148.97 1 2.00e+01 2.50e-03 4.46e+01 dihedral pdb=" C4' GTP E 601 " pdb=" C5' GTP E 601 " pdb=" O5' GTP E 601 " pdb=" PA GTP E 601 " ideal model delta sinusoidal sigma weight residual 260.87 112.11 148.76 1 2.00e+01 2.50e-03 4.45e+01 ... (remaining 23573 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.102: 3596 0.102 - 0.205: 1075 0.205 - 0.307: 168 0.307 - 0.409: 16 0.409 - 0.512: 1 Chirality restraints: 4856 Sorted by residual: chirality pdb=" CA LYS F 205 " pdb=" N LYS F 205 " pdb=" C LYS F 205 " pdb=" CB LYS F 205 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.54e+00 chirality pdb=" CA THR H 172 " pdb=" N THR H 172 " pdb=" C THR H 172 " pdb=" CB THR H 172 " both_signs ideal model delta sigma weight residual False 2.53 2.13 0.40 2.00e-01 2.50e+01 4.02e+00 chirality pdb=" CA THR G 172 " pdb=" N THR G 172 " pdb=" C THR G 172 " pdb=" CB THR G 172 " both_signs ideal model delta sigma weight residual False 2.53 2.13 0.40 2.00e-01 2.50e+01 3.96e+00 ... (remaining 4853 not shown) Planarity restraints: 8840 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' IMP A 603 " -0.335 2.00e-02 2.50e+03 1.55e-01 6.00e+02 pdb=" C2 IMP A 603 " 0.081 2.00e-02 2.50e+03 pdb=" C4 IMP A 603 " 0.136 2.00e-02 2.50e+03 pdb=" C5 IMP A 603 " -0.004 2.00e-02 2.50e+03 pdb=" C6 IMP A 603 " -0.193 2.00e-02 2.50e+03 pdb=" C8 IMP A 603 " 0.143 2.00e-02 2.50e+03 pdb=" N1 IMP A 603 " -0.105 2.00e-02 2.50e+03 pdb=" N3 IMP A 603 " 0.140 2.00e-02 2.50e+03 pdb=" N7 IMP A 603 " 0.019 2.00e-02 2.50e+03 pdb=" N9 IMP A 603 " 0.118 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG G 224 " 0.226 9.50e-02 1.11e+02 1.31e-01 2.65e+02 pdb=" NE ARG G 224 " 0.028 2.00e-02 2.50e+03 pdb=" CZ ARG G 224 " -0.026 2.00e-02 2.50e+03 pdb=" NH1 ARG G 224 " -0.067 2.00e-02 2.50e+03 pdb=" NH2 ARG G 224 " -0.043 2.00e-02 2.50e+03 pdb="HH11 ARG G 224 " -0.092 2.00e-02 2.50e+03 pdb="HH12 ARG G 224 " 0.232 2.00e-02 2.50e+03 pdb="HH21 ARG G 224 " 0.107 2.00e-02 2.50e+03 pdb="HH22 ARG G 224 " -0.149 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' ATP F 604 " -0.212 2.00e-02 2.50e+03 8.92e-02 2.19e+02 pdb=" C2 ATP F 604 " 0.039 2.00e-02 2.50e+03 pdb=" C4 ATP F 604 " 0.074 2.00e-02 2.50e+03 pdb=" C5 ATP F 604 " 0.053 2.00e-02 2.50e+03 pdb=" C6 ATP F 604 " -0.022 2.00e-02 2.50e+03 pdb=" C8 ATP F 604 " 0.059 2.00e-02 2.50e+03 pdb=" N1 ATP F 604 " -0.030 2.00e-02 2.50e+03 pdb=" N3 ATP F 604 " 0.071 2.00e-02 2.50e+03 pdb=" N6 ATP F 604 " -0.134 2.00e-02 2.50e+03 pdb=" N7 ATP F 604 " 0.054 2.00e-02 2.50e+03 pdb=" N9 ATP F 604 " 0.047 2.00e-02 2.50e+03 ... (remaining 8837 not shown) Histogram of nonbonded interaction distances: 1.50 - 2.12: 2801 2.12 - 2.74: 96210 2.74 - 3.36: 172024 3.36 - 3.98: 228959 3.98 - 4.60: 347052 Nonbonded interactions: 847046 Sorted by model distance: nonbonded pdb="HD21 LEU A 38 " pdb=" HD3 ARG D 341 " model vdw 1.502 2.440 nonbonded pdb=" HD3 ARG C 341 " pdb="HD21 LEU D 38 " model vdw 1.504 2.440 nonbonded pdb=" HD3 ARG B 341 " pdb="HD21 LEU C 38 " model vdw 1.504 2.440 nonbonded pdb=" HD3 ARG A 341 " pdb="HD21 LEU B 38 " model vdw 1.504 2.440 nonbonded pdb=" HD3 ARG G 341 " pdb="HD21 LEU H 38 " model vdw 1.507 2.440 ... (remaining 847041 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 96 5.49 5 S 184 5.16 5 C 18840 2.51 5 N 5160 2.21 5 O 6008 1.98 5 H 29544 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.780 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: 0.650 Extract box with map and model: 9.950 Check model and map are aligned: 0.660 Process input model: 145.160 Find NCS groups from input model: 2.650 Set up NCS constraints: 0.310 Set refine NCS operators: 0.000 Set scattering table: 0.400 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 163.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 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 0.298 30840 Z= 0.871 Angle : 1.979 18.755 41952 Z= 1.240 Chirality : 0.094 0.512 4856 Planarity : 0.013 0.155 5160 Dihedral : 17.745 149.003 11216 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.66 % Allowed : 6.95 % Favored : 92.39 % Rotamer Outliers : 2.74 % Cbeta Deviations : 0.26 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.13), residues: 3800 helix: -1.72 (0.13), residues: 1256 sheet: -1.36 (0.23), residues: 456 loop : -0.94 (0.13), residues: 2088 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7600 Ramachandran restraints generated. 3800 Oldfield, 0 Emsley, 3800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7600 Ramachandran restraints generated. 3800 Oldfield, 0 Emsley, 3800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1182 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 1096 time to evaluate : 3.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 86 outliers final: 32 residues processed: 1160 average time/residue: 0.8182 time to fit residues: 1503.4978 Evaluate side-chains 923 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 891 time to evaluate : 3.373 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 32 outliers final: 11 residues processed: 32 average time/residue: 0.5459 time to fit residues: 37.3271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 324 optimal weight: 0.7980 chunk 291 optimal weight: 0.9990 chunk 161 optimal weight: 3.9990 chunk 99 optimal weight: 0.9980 chunk 196 optimal weight: 0.8980 chunk 155 optimal weight: 1.9990 chunk 300 optimal weight: 0.9990 chunk 116 optimal weight: 1.9990 chunk 183 optimal weight: 5.9990 chunk 224 optimal weight: 0.8980 chunk 348 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 466 HIS C 466 HIS D 466 HIS F 466 HIS H 466 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.2507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 30840 Z= 0.225 Angle : 0.680 7.690 41952 Z= 0.343 Chirality : 0.045 0.173 4856 Planarity : 0.005 0.053 5160 Dihedral : 17.289 158.200 4456 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.39 % Favored : 95.50 % Rotamer Outliers : 1.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.30 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.13), residues: 3800 helix: -0.40 (0.16), residues: 1184 sheet: -1.36 (0.22), residues: 456 loop : -0.85 (0.13), residues: 2160 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7600 Ramachandran restraints generated. 3800 Oldfield, 0 Emsley, 3800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7600 Ramachandran restraints generated. 3800 Oldfield, 0 Emsley, 3800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 951 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 910 time to evaluate : 3.452 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 outliers start: 41 outliers final: 27 residues processed: 932 average time/residue: 0.7637 time to fit residues: 1166.7154 Evaluate side-chains 875 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 848 time to evaluate : 3.348 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 2 residues processed: 27 average time/residue: 0.5926 time to fit residues: 34.0832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 193 optimal weight: 2.9990 chunk 108 optimal weight: 4.9990 chunk 290 optimal weight: 2.9990 chunk 237 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 349 optimal weight: 1.9990 chunk 377 optimal weight: 3.9990 chunk 311 optimal weight: 2.9990 chunk 346 optimal weight: 0.0040 chunk 119 optimal weight: 0.9990 chunk 280 optimal weight: 5.9990 overall best weight: 1.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 498 GLN B 466 HIS C 125 HIS C 202 GLN C 466 HIS C 498 GLN F 125 HIS ** G 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 498 GLN H 466 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.3029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 30840 Z= 0.282 Angle : 0.641 6.871 41952 Z= 0.323 Chirality : 0.045 0.163 4856 Planarity : 0.004 0.051 5160 Dihedral : 15.875 172.119 4456 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer Outliers : 1.18 % Cbeta Deviations : 0.00 % 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: -1.36 (0.13), residues: 3800 helix: -0.51 (0.15), residues: 1272 sheet: -1.49 (0.23), residues: 456 loop : -0.95 (0.13), residues: 2072 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7600 Ramachandran restraints generated. 3800 Oldfield, 0 Emsley, 3800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7600 Ramachandran restraints generated. 3800 Oldfield, 0 Emsley, 3800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 895 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 858 time to evaluate : 3.418 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 outliers start: 37 outliers final: 22 residues processed: 873 average time/residue: 0.7888 time to fit residues: 1135.9009 Evaluate side-chains 842 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 820 time to evaluate : 3.391 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 22 outliers final: 1 residues processed: 22 average time/residue: 0.5497 time to fit residues: 27.3073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 345 optimal weight: 2.9990 chunk 262 optimal weight: 3.9990 chunk 181 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 166 optimal weight: 1.9990 chunk 234 optimal weight: 0.9990 chunk 350 optimal weight: 3.9990 chunk 371 optimal weight: 1.9990 chunk 183 optimal weight: 7.9990 chunk 332 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 466 HIS C 466 HIS G 466 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.3338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 30840 Z= 0.255 Angle : 0.601 6.620 41952 Z= 0.299 Chirality : 0.044 0.163 4856 Planarity : 0.004 0.051 5160 Dihedral : 15.201 179.751 4456 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer Outliers : 1.15 % 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: -1.23 (0.13), residues: 3800 helix: -0.29 (0.15), residues: 1232 sheet: -1.60 (0.22), residues: 456 loop : -0.89 (0.13), residues: 2112 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7600 Ramachandran restraints generated. 3800 Oldfield, 0 Emsley, 3800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7600 Ramachandran restraints generated. 3800 Oldfield, 0 Emsley, 3800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 882 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 846 time to evaluate : 3.462 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 outliers start: 36 outliers final: 24 residues processed: 856 average time/residue: 0.7644 time to fit residues: 1070.9986 Evaluate side-chains 833 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 809 time to evaluate : 3.414 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 24 outliers final: 1 residues processed: 24 average time/residue: 0.5675 time to fit residues: 29.3864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 309 optimal weight: 1.9990 chunk 210 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 276 optimal weight: 1.9990 chunk 153 optimal weight: 2.9990 chunk 316 optimal weight: 2.9990 chunk 256 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 189 optimal weight: 2.9990 chunk 333 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 466 HIS C 466 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.3538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 30840 Z= 0.257 Angle : 0.591 6.870 41952 Z= 0.294 Chirality : 0.044 0.164 4856 Planarity : 0.004 0.053 5160 Dihedral : 14.195 164.662 4456 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer Outliers : 1.24 % 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: -1.29 (0.13), residues: 3800 helix: -0.21 (0.15), residues: 1232 sheet: -1.76 (0.20), residues: 536 loop : -0.93 (0.14), residues: 2032 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7600 Ramachandran restraints generated. 3800 Oldfield, 0 Emsley, 3800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7600 Ramachandran restraints generated. 3800 Oldfield, 0 Emsley, 3800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 889 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 850 time to evaluate : 3.480 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 outliers start: 39 outliers final: 17 residues processed: 874 average time/residue: 0.7604 time to fit residues: 1091.2691 Evaluate side-chains 846 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 829 time to evaluate : 3.393 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 2 residues processed: 17 average time/residue: 0.5360 time to fit residues: 21.4357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 124 optimal weight: 2.9990 chunk 334 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 chunk 217 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 371 optimal weight: 2.9990 chunk 308 optimal weight: 2.9990 chunk 172 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 195 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 466 HIS C 466 HIS G 466 HIS H 125 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.3720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.045 30840 Z= 0.392 Angle : 0.639 7.007 41952 Z= 0.323 Chirality : 0.046 0.165 4856 Planarity : 0.004 0.058 5160 Dihedral : 14.137 158.962 4456 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer Outliers : 1.15 % Cbeta Deviations : 0.00 % 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: -1.66 (0.13), residues: 3800 helix: -0.50 (0.15), residues: 1280 sheet: -2.27 (0.18), residues: 528 loop : -1.08 (0.14), residues: 1992 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7600 Ramachandran restraints generated. 3800 Oldfield, 0 Emsley, 3800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7600 Ramachandran restraints generated. 3800 Oldfield, 0 Emsley, 3800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 894 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 858 time to evaluate : 3.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 29 residues processed: 871 average time/residue: 0.8049 time to fit residues: 1161.3533 Evaluate side-chains 866 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 837 time to evaluate : 3.437 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 3 residues processed: 29 average time/residue: 0.5976 time to fit residues: 36.7041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 358 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 211 optimal weight: 2.9990 chunk 271 optimal weight: 5.9990 chunk 210 optimal weight: 1.9990 chunk 312 optimal weight: 1.9990 chunk 207 optimal weight: 4.9990 chunk 370 optimal weight: 0.6980 chunk 231 optimal weight: 8.9990 chunk 225 optimal weight: 1.9990 chunk 170 optimal weight: 3.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 466 HIS ** E 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.3833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 30840 Z= 0.273 Angle : 0.595 6.929 41952 Z= 0.297 Chirality : 0.044 0.160 4856 Planarity : 0.004 0.058 5160 Dihedral : 13.960 158.698 4456 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer Outliers : 0.64 % 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: -1.54 (0.13), residues: 3800 helix: -0.40 (0.15), residues: 1280 sheet: -2.18 (0.18), residues: 536 loop : -1.01 (0.14), residues: 1984 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7600 Ramachandran restraints generated. 3800 Oldfield, 0 Emsley, 3800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7600 Ramachandran restraints generated. 3800 Oldfield, 0 Emsley, 3800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 870 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 850 time to evaluate : 3.373 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 outliers start: 20 outliers final: 16 residues processed: 861 average time/residue: 0.7820 time to fit residues: 1106.2196 Evaluate side-chains 853 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 837 time to evaluate : 3.403 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 2 residues processed: 16 average time/residue: 0.7950 time to fit residues: 25.1710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 228 optimal weight: 0.9980 chunk 147 optimal weight: 1.9990 chunk 221 optimal weight: 0.0040 chunk 111 optimal weight: 2.9990 chunk 72 optimal weight: 0.7980 chunk 71 optimal weight: 0.6980 chunk 235 optimal weight: 1.9990 chunk 252 optimal weight: 4.9990 chunk 182 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 290 optimal weight: 2.9990 overall best weight: 0.6792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 441 GLN B 466 HIS ** F 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 498 GLN G 466 HIS ** H 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.3973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 30840 Z= 0.149 Angle : 0.556 6.990 41952 Z= 0.272 Chirality : 0.042 0.159 4856 Planarity : 0.004 0.054 5160 Dihedral : 13.589 159.971 4456 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer Outliers : 0.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.13), residues: 3800 helix: 0.08 (0.15), residues: 1224 sheet: -1.95 (0.19), residues: 536 loop : -0.83 (0.14), residues: 2040 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7600 Ramachandran restraints generated. 3800 Oldfield, 0 Emsley, 3800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7600 Ramachandran restraints generated. 3800 Oldfield, 0 Emsley, 3800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 884 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 866 time to evaluate : 3.670 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 outliers start: 18 outliers final: 11 residues processed: 876 average time/residue: 0.7521 time to fit residues: 1085.9736 Evaluate side-chains 857 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 846 time to evaluate : 3.364 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 3 residues processed: 11 average time/residue: 0.6860 time to fit residues: 17.1054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 336 optimal weight: 0.3980 chunk 354 optimal weight: 2.9990 chunk 323 optimal weight: 2.9990 chunk 344 optimal weight: 2.9990 chunk 207 optimal weight: 3.9990 chunk 150 optimal weight: 2.9990 chunk 270 optimal weight: 2.9990 chunk 105 optimal weight: 0.8980 chunk 311 optimal weight: 2.9990 chunk 326 optimal weight: 4.9990 chunk 343 optimal weight: 1.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 441 GLN ** B 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 112 GLN ** G 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.4038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 30840 Z= 0.293 Angle : 0.593 7.284 41952 Z= 0.296 Chirality : 0.044 0.160 4856 Planarity : 0.004 0.056 5160 Dihedral : 13.649 159.379 4456 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer Outliers : 0.67 % 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: -1.24 (0.13), residues: 3800 helix: -0.10 (0.15), residues: 1256 sheet: -2.05 (0.19), residues: 536 loop : -0.86 (0.14), residues: 2008 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7600 Ramachandran restraints generated. 3800 Oldfield, 0 Emsley, 3800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7600 Ramachandran restraints generated. 3800 Oldfield, 0 Emsley, 3800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 879 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 858 time to evaluate : 3.498 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 outliers start: 21 outliers final: 16 residues processed: 866 average time/residue: 0.7437 time to fit residues: 1062.4149 Evaluate side-chains 869 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 853 time to evaluate : 3.384 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 2 residues processed: 16 average time/residue: 0.6214 time to fit residues: 22.3944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 226 optimal weight: 0.0980 chunk 364 optimal weight: 0.9990 chunk 222 optimal weight: 0.9990 chunk 173 optimal weight: 0.7980 chunk 253 optimal weight: 1.9990 chunk 382 optimal weight: 3.9990 chunk 352 optimal weight: 4.9990 chunk 304 optimal weight: 0.0060 chunk 31 optimal weight: 6.9990 chunk 235 optimal weight: 2.9990 chunk 186 optimal weight: 0.6980 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 498 GLN ** G 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.4154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 30840 Z= 0.140 Angle : 0.554 7.465 41952 Z= 0.271 Chirality : 0.042 0.153 4856 Planarity : 0.004 0.053 5160 Dihedral : 13.437 161.501 4456 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer Outliers : 0.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.14), residues: 3800 helix: 0.18 (0.15), residues: 1248 sheet: -1.69 (0.20), residues: 496 loop : -0.62 (0.14), residues: 2056 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7600 Ramachandran restraints generated. 3800 Oldfield, 0 Emsley, 3800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7600 Ramachandran restraints generated. 3800 Oldfield, 0 Emsley, 3800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 863 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 854 time to evaluate : 3.390 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 outliers start: 9 outliers final: 7 residues processed: 858 average time/residue: 0.7554 time to fit residues: 1079.3057 Evaluate side-chains 851 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 844 time to evaluate : 3.381 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 2 residues processed: 7 average time/residue: 0.5778 time to fit residues: 12.1009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 241 optimal weight: 2.9990 chunk 324 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 280 optimal weight: 0.4980 chunk 44 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 305 optimal weight: 1.9990 chunk 127 optimal weight: 6.9990 chunk 313 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 56 optimal weight: 0.9990 overall best weight: 1.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.116176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.090503 restraints weight = 111206.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.095043 restraints weight = 55365.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.098031 restraints weight = 35273.975| |-----------------------------------------------------------------------------| r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.4180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 30840 Z= 0.248 Angle : 0.577 7.623 41952 Z= 0.285 Chirality : 0.043 0.159 4856 Planarity : 0.004 0.054 5160 Dihedral : 13.466 171.922 4456 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer Outliers : 0.26 % 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: -0.98 (0.14), residues: 3800 helix: 0.28 (0.16), residues: 1200 sheet: -2.00 (0.18), residues: 592 loop : -0.70 (0.14), residues: 2008 =============================================================================== Job complete usr+sys time: 15695.98 seconds wall clock time: 271 minutes 12.26 seconds (16272.26 seconds total)