Starting phenix.real_space_refine (version: dev) on Tue Mar 14 00:01:56 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rgm_24452/03_2023/7rgm_24452_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rgm_24452/03_2023/7rgm_24452.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rgm_24452/03_2023/7rgm_24452.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rgm_24452/03_2023/7rgm_24452.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rgm_24452/03_2023/7rgm_24452_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rgm_24452/03_2023/7rgm_24452_trim_updated.pdb" } resolution = 2.8 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= 0.278 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "A TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 15": "OE1" <-> "OE2" Residue "A TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 75": "OE1" <-> "OE2" Residue "A PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 103": "OE1" <-> "OE2" Residue "A PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 117": "OD1" <-> "OD2" Residue "A ARG 136": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 203": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 214": "OD1" <-> "OD2" Residue "A GLU 217": "OE1" <-> "OE2" Residue "A ASP 226": "OD1" <-> "OD2" Residue "A ARG 231": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 232": "OD1" <-> "OD2" Residue "A TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 239": "OD1" <-> "OD2" Residue "A ASP 269": "OD1" <-> "OD2" Residue "A ASP 319": "OD1" <-> "OD2" Residue "A ARG 356": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 364": "OD1" <-> "OD2" Residue "A GLU 395": "OE1" <-> "OE2" Residue "A GLU 399": "OE1" <-> "OE2" Residue "A TYR 400": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 402": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 407": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 411": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 412": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 511": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 43": "OD1" <-> "OD2" Residue "B GLU 48": "OE1" <-> "OE2" Residue "B GLU 75": "OE1" <-> "OE2" Residue "B PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 103": "OE1" <-> "OE2" Residue "B PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 117": "OD1" <-> "OD2" Residue "B ARG 136": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ASP 164": "OD1" <-> "OD2" Residue "B ARG 182": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 184": "OE1" <-> "OE2" Residue "B ARG 203": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ASP 214": "OD1" <-> "OD2" Residue "B ASP 216": "OD1" <-> "OD2" Residue "B GLU 217": "OE1" <-> "OE2" Residue "B ASP 226": "OD1" <-> "OD2" Residue "B ARG 231": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ASP 232": "OD1" <-> "OD2" Residue "B TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 239": "OD1" <-> "OD2" Residue "B GLU 254": "OE1" <-> "OE2" Residue "B ASP 261": "OD1" <-> "OD2" Residue "B ASP 269": "OD1" <-> "OD2" Residue "B ASP 319": "OD1" <-> "OD2" Residue "B ARG 356": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ASP 364": "OD1" <-> "OD2" Residue "B GLU 395": "OE1" <-> "OE2" Residue "B GLU 399": "OE1" <-> "OE2" Residue "B PHE 402": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 407": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 411": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 412": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ASP 418": "OD1" <-> "OD2" Residue "B GLU 421": "OE1" <-> "OE2" Residue "C TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 15": "OE1" <-> "OE2" Residue "C TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 47": "OD1" <-> "OD2" Residue "C GLU 75": "OE1" <-> "OE2" Residue "C PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 103": "OE1" <-> "OE2" Residue "C PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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 ASP 164": "OD1" <-> "OD2" Residue "C GLU 199": "OE1" <-> "OE2" Residue "C ARG 203": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ASP 214": "OD1" <-> "OD2" Residue "C GLU 217": "OE1" <-> "OE2" Residue "C ASP 226": "OD1" <-> "OD2" Residue "C ARG 231": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ASP 232": "OD1" <-> "OD2" Residue "C TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 239": "OD1" <-> "OD2" Residue "C ASP 261": "OD1" <-> "OD2" Residue "C ASP 269": "OD1" <-> "OD2" Residue "C ASP 319": "OD1" <-> "OD2" Residue "C ARG 356": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ASP 364": "OD1" <-> "OD2" Residue "C GLU 395": "OE1" <-> "OE2" Residue "C GLU 399": "OE1" <-> "OE2" Residue "C PHE 402": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 404": "OD1" <-> "OD2" Residue "C ARG 407": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 411": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 412": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ASP 418": "OD1" <-> "OD2" Residue "C ASP 449": "OD1" <-> "OD2" Residue "D TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 15": "OE1" <-> "OE2" Residue "D TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 47": "OD1" <-> "OD2" Residue "D GLU 75": "OE1" <-> "OE2" Residue "D PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 103": "OE1" <-> "OE2" 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 ASP 164": "OD1" <-> "OD2" Residue "D GLU 184": "OE1" <-> "OE2" Residue "D GLU 196": "OE1" <-> "OE2" Residue "D GLU 199": "OE1" <-> "OE2" Residue "D ARG 203": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ASP 214": "OD1" <-> "OD2" Residue "D ASP 226": "OD1" <-> "OD2" Residue "D ARG 231": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ASP 232": "OD1" <-> "OD2" Residue "D TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 239": "OD1" <-> "OD2" Residue "D ASP 256": "OD1" <-> "OD2" Residue "D ASP 269": "OD1" <-> "OD2" Residue "D ASP 319": "OD1" <-> "OD2" Residue "D ARG 356": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ASP 364": "OD1" <-> "OD2" Residue "D GLU 395": "OE1" <-> "OE2" Residue "D GLU 399": "OE1" <-> "OE2" Residue "D PHE 402": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 404": "OD1" <-> "OD2" Residue "D ARG 407": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D TYR 411": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 412": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ASP 418": "OD1" <-> "OD2" Residue "D ASP 470": "OD1" <-> "OD2" Residue "D PHE 511": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 48": "OE1" <-> "OE2" Residue "E GLU 75": "OE1" <-> "OE2" Residue "E PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 103": "OE1" <-> "OE2" 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 ASP 164": "OD1" <-> "OD2" Residue "E GLU 184": "OE1" <-> "OE2" Residue "E GLU 196": "OE1" <-> "OE2" Residue "E GLU 199": "OE1" <-> "OE2" Residue "E ARG 203": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ASP 214": "OD1" <-> "OD2" Residue "E ASP 216": "OD1" <-> "OD2" Residue "E GLU 217": "OE1" <-> "OE2" Residue "E ASP 226": "OD1" <-> "OD2" Residue "E ARG 231": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ASP 232": "OD1" <-> "OD2" Residue "E TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 239": "OD1" <-> "OD2" Residue "E ASP 256": "OD1" <-> "OD2" Residue "E ASP 261": "OD1" <-> "OD2" Residue "E ASP 269": "OD1" <-> "OD2" Residue "E ASP 319": "OD1" <-> "OD2" Residue "E ARG 356": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ASP 364": "OD1" <-> "OD2" Residue "E GLU 395": "OE1" <-> "OE2" Residue "E GLU 399": "OE1" <-> "OE2" Residue "E PHE 402": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 404": "OD1" <-> "OD2" Residue "E ARG 407": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E TYR 411": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 412": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E TYR 509": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 511": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 15": "OE1" <-> "OE2" Residue "F TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 47": "OD1" <-> "OD2" Residue "F GLU 75": "OE1" <-> "OE2" Residue "F PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 103": "OE1" <-> "OE2" Residue "F PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 111": "OE1" <-> "OE2" Residue "F ASP 117": "OD1" <-> "OD2" Residue "F ARG 136": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ASP 164": "OD1" <-> "OD2" Residue "F GLU 184": "OE1" <-> "OE2" Residue "F ARG 203": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ASP 214": "OD1" <-> "OD2" Residue "F ASP 216": "OD1" <-> "OD2" Residue "F GLU 217": "OE1" <-> "OE2" Residue "F ASP 226": "OD1" <-> "OD2" Residue "F ARG 231": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ASP 232": "OD1" <-> "OD2" Residue "F TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 239": "OD1" <-> "OD2" Residue "F ASP 256": "OD1" <-> "OD2" Residue "F ASP 261": "OD1" <-> "OD2" Residue "F ASP 269": "OD1" <-> "OD2" Residue "F ASP 319": "OD1" <-> "OD2" Residue "F ARG 356": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ASP 364": "OD1" <-> "OD2" Residue "F GLU 395": "OE1" <-> "OE2" Residue "F GLU 399": "OE1" <-> "OE2" Residue "F PHE 402": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ARG 407": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F TYR 411": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ARG 412": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ASP 418": "OD1" <-> "OD2" Residue "F GLU 421": "OE1" <-> "OE2" Residue "F PHE 511": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ASP 47": "OD1" <-> "OD2" Residue "G GLU 48": "OE1" <-> "OE2" Residue "G GLU 75": "OE1" <-> "OE2" Residue "G PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 103": "OE1" <-> "OE2" 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 ASP 164": "OD1" <-> "OD2" Residue "G GLU 168": "OE1" <-> "OE2" Residue "G GLU 184": "OE1" <-> "OE2" Residue "G ARG 203": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ASP 214": "OD1" <-> "OD2" Residue "G ARG 231": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ASP 232": "OD1" <-> "OD2" Residue "G TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ASP 239": "OD1" <-> "OD2" Residue "G ASP 256": "OD1" <-> "OD2" Residue "G ASP 261": "OD1" <-> "OD2" Residue "G ASP 269": "OD1" <-> "OD2" Residue "G ASP 319": "OD1" <-> "OD2" Residue "G ARG 356": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ASP 364": "OD1" <-> "OD2" Residue "G GLU 395": "OE1" <-> "OE2" Residue "G GLU 399": "OE1" <-> "OE2" Residue "G TYR 400": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 402": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ASP 404": "OD1" <-> "OD2" Residue "G ARG 407": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G TYR 411": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ARG 412": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ASP 470": "OD1" <-> "OD2" Residue "G TYR 509": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 15": "OE1" <-> "OE2" Residue "H TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 48": "OE1" <-> "OE2" Residue "H GLU 75": "OE1" <-> "OE2" Residue "H PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 103": "OE1" <-> "OE2" 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 ASP 164": "OD1" <-> "OD2" Residue "H GLU 168": "OE1" <-> "OE2" Residue "H GLU 199": "OE1" <-> "OE2" Residue "H ARG 203": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ASP 214": "OD1" <-> "OD2" Residue "H ASP 226": "OD1" <-> "OD2" Residue "H ARG 231": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ASP 232": "OD1" <-> "OD2" Residue "H TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ASP 239": "OD1" <-> "OD2" Residue "H ASP 256": "OD1" <-> "OD2" Residue "H ASP 261": "OD1" <-> "OD2" Residue "H ASP 269": "OD1" <-> "OD2" Residue "H ASP 319": "OD1" <-> "OD2" Residue "H ARG 356": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ASP 364": "OD1" <-> "OD2" Residue "H GLU 395": "OE1" <-> "OE2" Residue "H PHE 402": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ARG 407": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H TYR 411": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ARG 412": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H GLU 421": "OE1" <-> "OE2" Residue "H TYR 509": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 511": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/chem_data/mon_lib" Total number of atoms: 59928 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 7362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 7362 Classifications: {'peptide': 484} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 465} Chain breaks: 2 Chain: "B" Number of atoms: 7362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 7362 Classifications: {'peptide': 484} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 465} Chain breaks: 2 Chain: "C" Number of atoms: 7362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 7362 Classifications: {'peptide': 484} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 465} Chain breaks: 2 Chain: "D" Number of atoms: 7362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 7362 Classifications: {'peptide': 484} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 465} Chain breaks: 2 Chain: "E" Number of atoms: 7362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 7362 Classifications: {'peptide': 484} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 465} Chain breaks: 2 Chain: "F" Number of atoms: 7362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 7362 Classifications: {'peptide': 484} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 465} Chain breaks: 2 Chain: "G" Number of atoms: 7362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 7362 Classifications: {'peptide': 484} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 465} Chain breaks: 2 Chain: "H" Number of atoms: 7362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 7362 Classifications: {'peptide': 484} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 465} Chain breaks: 2 Chain: "A" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 129 Unusual residues: {'ATP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "B" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 129 Unusual residues: {'ATP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "C" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 129 Unusual residues: {'ATP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "D" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 129 Unusual residues: {'ATP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "E" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 129 Unusual residues: {'ATP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "F" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 129 Unusual residues: {'ATP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "G" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 129 Unusual residues: {'ATP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "H" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 129 Unusual residues: {'ATP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Time building chain proxies: 20.43, per 1000 atoms: 0.34 Number of scatterers: 59928 At special positions: 0 Unit cell: (146.682, 145.839, 130.665, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 192 16.00 P 72 15.00 O 5928 8.00 N 5160 7.00 C 18840 6.00 H 29736 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: 40.27 Conformation dependent library (CDL) restraints added in 4.2 seconds 7648 Ramachandran restraints generated. 3824 Oldfield, 0 Emsley, 3824 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6960 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 152 helices and 48 sheets defined 34.2% alpha, 10.5% 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 23 No H-bonds generated for 'chain 'A' and resid 20 through 23' Processing helix chain 'A' and resid 32 through 34 No H-bonds generated for 'chain 'A' and resid 32 through 34' Processing helix chain 'A' and resid 46 through 48 No H-bonds generated for 'chain 'A' and resid 46 through 48' Processing helix chain 'A' and resid 76 through 85 Processing helix chain 'A' and resid 97 through 108 Processing helix chain 'A' and resid 127 through 137 Processing helix chain 'A' and resid 160 through 163 No H-bonds generated for 'chain 'A' and resid 160 through 163' Processing helix chain 'A' and resid 194 through 204 Processing helix chain 'A' and resid 224 through 228 Processing helix chain 'A' and resid 254 through 265 removed outlier: 3.795A pdb=" N LEU A 260 " --> pdb=" O LYS A 257 " (cutoff:3.500A) removed outlier: 3.930A 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 Processing helix chain 'A' and resid 333 through 337 Processing helix chain 'A' and resid 343 through 357 removed outlier: 3.989A pdb=" N ARG A 356 " --> pdb=" O GLU A 352 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N PHE A 357 " --> pdb=" O TYR A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 378 Processing helix chain 'A' and resid 453 through 471 Proline residue: A 458 - end of helix Processing helix chain 'A' and resid 476 through 485 Processing helix chain 'A' and resid 495 through 500 Processing helix chain 'B' and resid 20 through 23 No H-bonds generated for 'chain 'B' and resid 20 through 23' Processing helix chain 'B' and resid 32 through 34 No H-bonds generated for 'chain 'B' and resid 32 through 34' Processing helix chain 'B' and resid 46 through 48 No H-bonds generated for 'chain 'B' and resid 46 through 48' Processing helix chain 'B' and resid 76 through 85 Processing helix chain 'B' and resid 97 through 108 Processing helix chain 'B' and resid 127 through 137 Processing helix chain 'B' and resid 160 through 163 No H-bonds generated for 'chain 'B' and resid 160 through 163' Processing helix chain 'B' and resid 182 through 184 No H-bonds generated for 'chain 'B' and resid 182 through 184' Processing helix chain 'B' and resid 194 through 204 Processing helix chain 'B' and resid 224 through 228 Processing helix chain 'B' and resid 254 through 265 removed outlier: 3.957A pdb=" N LEU B 260 " --> pdb=" O LYS B 257 " (cutoff:3.500A) removed outlier: 3.823A 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 Processing helix chain 'B' and resid 333 through 337 Processing helix chain 'B' and resid 343 through 357 removed outlier: 3.987A pdb=" N ARG B 356 " --> pdb=" O GLU B 352 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N PHE B 357 " --> pdb=" O TYR B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 378 Processing helix chain 'B' and resid 417 through 420 No H-bonds generated for 'chain 'B' and resid 417 through 420' Processing helix chain 'B' and resid 453 through 471 Proline residue: B 458 - end of helix Processing helix chain 'B' and resid 476 through 485 Processing helix chain 'B' and resid 495 through 500 Processing helix chain 'C' and resid 20 through 23 No H-bonds generated for 'chain 'C' and resid 20 through 23' Processing helix chain 'C' and resid 32 through 34 No H-bonds generated for 'chain 'C' and resid 32 through 34' Processing helix chain 'C' and resid 46 through 48 No H-bonds generated for 'chain 'C' and resid 46 through 48' Processing helix chain 'C' and resid 76 through 85 Processing helix chain 'C' and resid 97 through 108 Processing helix chain 'C' and resid 127 through 137 Processing helix chain 'C' and resid 160 through 163 No H-bonds generated for 'chain 'C' and resid 160 through 163' Processing helix chain 'C' and resid 182 through 184 No H-bonds generated for 'chain 'C' and resid 182 through 184' Processing helix chain 'C' and resid 194 through 204 Processing helix chain 'C' and resid 224 through 228 Processing helix chain 'C' and resid 254 through 265 removed outlier: 3.509A pdb=" N TYR C 258 " --> pdb=" O ASP C 255 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LEU C 260 " --> pdb=" O LYS C 257 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU C 263 " --> pdb=" O LEU C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 293 Processing helix chain 'C' and resid 307 through 316 Processing helix chain 'C' and resid 333 through 337 Processing helix chain 'C' and resid 343 through 357 removed outlier: 3.982A pdb=" N ARG C 356 " --> pdb=" O GLU C 352 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N PHE C 357 " --> pdb=" O TYR C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 378 Processing helix chain 'C' and resid 417 through 420 No H-bonds generated for 'chain 'C' and resid 417 through 420' Processing helix chain 'C' and resid 453 through 471 Proline residue: C 458 - end of helix Processing helix chain 'C' and resid 476 through 485 Processing helix chain 'C' and resid 495 through 500 Processing helix chain 'D' and resid 20 through 23 No H-bonds generated for 'chain 'D' and resid 20 through 23' Processing helix chain 'D' and resid 32 through 34 No H-bonds generated for 'chain 'D' and resid 32 through 34' Processing helix chain 'D' and resid 46 through 48 No H-bonds generated for 'chain 'D' and resid 46 through 48' Processing helix chain 'D' and resid 76 through 85 Processing helix chain 'D' and resid 97 through 108 Processing helix chain 'D' and resid 127 through 137 Processing helix chain 'D' and resid 160 through 163 No H-bonds generated for 'chain 'D' and resid 160 through 163' Processing helix chain 'D' and resid 182 through 184 No H-bonds generated for 'chain 'D' and resid 182 through 184' Processing helix chain 'D' and resid 194 through 204 Processing helix chain 'D' and resid 224 through 228 Processing helix chain 'D' and resid 254 through 265 removed outlier: 3.810A pdb=" N TYR D 258 " --> pdb=" O ASP D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 293 Processing helix chain 'D' and resid 307 through 316 Processing helix chain 'D' and resid 333 through 337 Processing helix chain 'D' and resid 343 through 357 removed outlier: 3.982A pdb=" N ARG D 356 " --> pdb=" O GLU D 352 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N PHE D 357 " --> pdb=" O TYR D 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 378 Processing helix chain 'D' and resid 417 through 420 No H-bonds generated for 'chain 'D' and resid 417 through 420' Processing helix chain 'D' and resid 453 through 471 Proline residue: D 458 - end of helix Processing helix chain 'D' and resid 476 through 485 Processing helix chain 'D' and resid 495 through 500 Processing helix chain 'E' and resid 20 through 23 No H-bonds generated for 'chain 'E' and resid 20 through 23' Processing helix chain 'E' and resid 32 through 34 No H-bonds generated for 'chain 'E' and resid 32 through 34' Processing helix chain 'E' and resid 46 through 48 No H-bonds generated for 'chain 'E' and resid 46 through 48' Processing helix chain 'E' and resid 76 through 85 Processing helix chain 'E' and resid 97 through 108 Processing helix chain 'E' and resid 127 through 137 Processing helix chain 'E' and resid 194 through 204 Processing helix chain 'E' and resid 224 through 228 Processing helix chain 'E' and resid 254 through 265 removed outlier: 3.727A pdb=" N TYR E 258 " --> pdb=" O ASP E 255 " (cutoff:3.500A) Processing helix chain 'E' and resid 281 through 293 Processing helix chain 'E' and resid 307 through 316 Processing helix chain 'E' and resid 333 through 337 Processing helix chain 'E' and resid 343 through 357 removed outlier: 3.991A pdb=" N ARG E 356 " --> pdb=" O GLU E 352 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N PHE E 357 " --> pdb=" O TYR E 353 " (cutoff:3.500A) Processing helix chain 'E' and resid 370 through 378 Processing helix chain 'E' and resid 417 through 420 No H-bonds generated for 'chain 'E' and resid 417 through 420' Processing helix chain 'E' and resid 453 through 471 Proline residue: E 458 - end of helix Processing helix chain 'E' and resid 476 through 485 Processing helix chain 'E' and resid 495 through 500 Processing helix chain 'F' and resid 20 through 23 No H-bonds generated for 'chain 'F' and resid 20 through 23' Processing helix chain 'F' and resid 32 through 34 No H-bonds generated for 'chain 'F' and resid 32 through 34' Processing helix chain 'F' and resid 46 through 48 No H-bonds generated for 'chain 'F' and resid 46 through 48' Processing helix chain 'F' and resid 76 through 85 Processing helix chain 'F' and resid 97 through 109 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 194 through 204 Processing helix chain 'F' and resid 224 through 228 Processing helix chain 'F' and resid 254 through 265 removed outlier: 3.860A pdb=" N TYR F 258 " --> pdb=" O ASP F 255 " (cutoff:3.500A) Processing helix chain 'F' and resid 281 through 293 Processing helix chain 'F' and resid 307 through 316 Processing helix chain 'F' and resid 333 through 337 Processing helix chain 'F' and resid 343 through 357 removed outlier: 3.986A pdb=" N ARG F 356 " --> pdb=" O GLU F 352 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N PHE F 357 " --> pdb=" O TYR F 353 " (cutoff:3.500A) Processing helix chain 'F' and resid 370 through 378 Processing helix chain 'F' and resid 417 through 420 No H-bonds generated for 'chain 'F' and resid 417 through 420' Processing helix chain 'F' and resid 453 through 471 Proline residue: F 458 - end of helix Processing helix chain 'F' and resid 476 through 485 Processing helix chain 'F' and resid 495 through 500 Processing helix chain 'G' and resid 20 through 23 No H-bonds generated for 'chain 'G' and resid 20 through 23' Processing helix chain 'G' and resid 32 through 34 No H-bonds generated for 'chain 'G' and resid 32 through 34' Processing helix chain 'G' and resid 46 through 48 No H-bonds generated for 'chain 'G' and resid 46 through 48' Processing helix chain 'G' and resid 76 through 85 Processing helix chain 'G' and resid 97 through 109 Processing helix chain 'G' and resid 127 through 137 Processing helix chain 'G' and resid 160 through 163 No H-bonds generated for 'chain 'G' and resid 160 through 163' Processing helix chain 'G' and resid 194 through 204 Processing helix chain 'G' and resid 224 through 228 Processing helix chain 'G' and resid 254 through 265 removed outlier: 3.818A pdb=" N TYR G 258 " --> pdb=" O ASP G 255 " (cutoff:3.500A) Processing helix chain 'G' and resid 281 through 293 Processing helix chain 'G' and resid 307 through 316 Processing helix chain 'G' and resid 333 through 337 Processing helix chain 'G' and resid 343 through 357 removed outlier: 3.983A pdb=" N ARG G 356 " --> pdb=" O GLU G 352 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N PHE G 357 " --> pdb=" O TYR G 353 " (cutoff:3.500A) Processing helix chain 'G' and resid 370 through 378 Processing helix chain 'G' and resid 453 through 471 Proline residue: G 458 - end of helix Processing helix chain 'G' and resid 476 through 485 Processing helix chain 'G' and resid 495 through 500 Processing helix chain 'H' and resid 20 through 23 No H-bonds generated for 'chain 'H' and resid 20 through 23' Processing helix chain 'H' and resid 32 through 34 No H-bonds generated for 'chain 'H' and resid 32 through 34' Processing helix chain 'H' and resid 46 through 48 No H-bonds generated for 'chain 'H' and resid 46 through 48' Processing helix chain 'H' and resid 76 through 85 Processing helix chain 'H' and resid 97 through 108 Processing helix chain 'H' and resid 127 through 137 Processing helix chain 'H' and resid 160 through 163 No H-bonds generated for 'chain 'H' and resid 160 through 163' Processing helix chain 'H' and resid 182 through 184 No H-bonds generated for 'chain 'H' and resid 182 through 184' Processing helix chain 'H' and resid 194 through 204 Processing helix chain 'H' and resid 224 through 228 Processing helix chain 'H' and resid 254 through 265 removed outlier: 4.461A pdb=" N TYR H 258 " --> pdb=" O ASP H 255 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG H 259 " --> pdb=" O ASP H 256 " (cutoff:3.500A) Processing helix chain 'H' and resid 281 through 293 Processing helix chain 'H' and resid 307 through 316 Processing helix chain 'H' and resid 333 through 337 Processing helix chain 'H' and resid 343 through 357 removed outlier: 3.984A pdb=" N ARG H 356 " --> pdb=" O GLU H 352 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N PHE H 357 " --> pdb=" O TYR H 353 " (cutoff:3.500A) Processing helix chain 'H' and resid 370 through 378 Processing helix chain 'H' and resid 453 through 471 Proline residue: H 458 - end of helix Processing helix chain 'H' and resid 476 through 485 Processing helix chain 'H' and resid 495 through 500 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: 6.504A pdb=" N VAL A 384 " --> pdb=" O ILE A 66 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR A 383 " --> pdb=" O ILE A 361 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 247 through 250 removed outlier: 6.695A pdb=" N VAL A 270 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N VAL A 250 " --> pdb=" O VAL A 270 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N VAL A 272 " --> pdb=" O VAL A 250 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N GLN A 298 " --> pdb=" O ILE A 271 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N LEU A 273 " --> pdb=" O GLN A 298 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ILE A 300 " --> pdb=" O LEU A 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 408 through 412 Processing sheet with id= E, first strand: chain 'A' and resid 142 through 145 Processing sheet with id= F, first strand: chain 'A' and resid 208 through 212 Processing sheet with id= G, first strand: chain 'B' and resid 35 through 37 Processing sheet with id= H, first strand: chain 'B' and resid 65 through 67 removed outlier: 6.471A pdb=" N VAL B 384 " --> pdb=" O ILE B 66 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR B 383 " --> pdb=" O ILE B 361 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 247 through 250 removed outlier: 6.686A pdb=" N VAL B 270 " --> pdb=" O ALA B 248 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N VAL B 250 " --> pdb=" O VAL B 270 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N VAL B 272 " --> pdb=" O VAL B 250 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N GLN B 298 " --> pdb=" O ILE B 271 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N LEU B 273 " --> pdb=" O GLN B 298 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ILE B 300 " --> pdb=" O LEU B 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'B' and resid 401 through 403 Processing sheet with id= K, first strand: chain 'B' and resid 142 through 145 Processing sheet with id= L, first strand: chain 'B' and resid 208 through 212 Processing sheet with id= M, first strand: chain 'C' and resid 35 through 37 Processing sheet with id= N, first strand: chain 'C' and resid 65 through 67 removed outlier: 6.414A pdb=" N VAL C 384 " --> pdb=" O ILE C 66 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THR C 383 " --> pdb=" O ILE C 361 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 247 through 250 removed outlier: 6.668A pdb=" N VAL C 270 " --> pdb=" O ALA C 248 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N VAL C 250 " --> pdb=" O VAL C 270 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N VAL C 272 " --> pdb=" O VAL C 250 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N GLN C 298 " --> pdb=" O ILE C 271 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N LEU C 273 " --> pdb=" O GLN C 298 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ILE C 300 " --> pdb=" O LEU C 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'C' and resid 401 through 403 Processing sheet with id= Q, first strand: chain 'C' and resid 142 through 145 Processing sheet with id= R, first strand: chain 'C' and resid 208 through 212 Processing sheet with id= S, first strand: chain 'D' and resid 35 through 37 Processing sheet with id= T, first strand: chain 'D' and resid 65 through 67 removed outlier: 6.458A pdb=" N VAL D 384 " --> pdb=" O ILE D 66 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N THR D 383 " --> pdb=" O ILE D 361 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'D' and resid 247 through 250 removed outlier: 6.708A pdb=" N VAL D 270 " --> pdb=" O ALA D 248 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N VAL D 250 " --> pdb=" O VAL D 270 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N VAL D 272 " --> pdb=" O VAL D 250 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N GLN D 298 " --> pdb=" O ILE D 271 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N LEU D 273 " --> pdb=" O GLN D 298 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ILE D 300 " --> pdb=" O LEU D 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= U Processing sheet with id= V, first strand: chain 'D' and resid 401 through 403 Processing sheet with id= W, first strand: chain 'D' and resid 142 through 145 Processing sheet with id= X, first strand: chain 'D' and resid 208 through 212 Processing sheet with id= Y, first strand: chain 'E' and resid 35 through 37 Processing sheet with id= Z, first strand: chain 'E' and resid 65 through 67 removed outlier: 6.454A pdb=" N VAL E 384 " --> pdb=" O ILE E 66 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR E 383 " --> pdb=" O ILE E 361 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'E' and resid 247 through 250 removed outlier: 6.701A pdb=" N VAL E 270 " --> pdb=" O ALA E 248 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N VAL E 250 " --> pdb=" O VAL E 270 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N VAL E 272 " --> pdb=" O VAL E 250 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N GLN E 298 " --> pdb=" O ILE E 271 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N LEU E 273 " --> pdb=" O GLN E 298 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ILE E 300 " --> pdb=" O LEU E 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= AA Processing sheet with id= AB, first strand: chain 'E' and resid 401 through 403 Processing sheet with id= AC, first strand: chain 'E' and resid 142 through 145 Processing sheet with id= AD, first strand: chain 'E' and resid 208 through 212 Processing sheet with id= AE, first strand: chain 'F' and resid 35 through 37 Processing sheet with id= AF, first strand: chain 'F' and resid 65 through 67 removed outlier: 6.472A pdb=" N VAL F 384 " --> pdb=" O ILE F 66 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR F 383 " --> pdb=" O ILE F 361 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'F' and resid 187 through 189 removed outlier: 8.173A pdb=" N ALA F 188 " --> pdb=" O LYS F 208 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'F' and resid 247 through 250 removed outlier: 6.692A pdb=" N VAL F 270 " --> pdb=" O ALA F 248 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N VAL F 250 " --> pdb=" O VAL F 270 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N VAL F 272 " --> pdb=" O VAL F 250 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N GLN F 298 " --> pdb=" O ILE F 271 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N LEU F 273 " --> pdb=" O GLN F 298 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ILE F 300 " --> pdb=" O LEU F 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= AH Processing sheet with id= AI, first strand: chain 'F' and resid 401 through 403 Processing sheet with id= AJ, first strand: chain 'F' and resid 142 through 145 Processing sheet with id= AK, first strand: chain 'G' and resid 35 through 37 Processing sheet with id= AL, first strand: chain 'G' and resid 65 through 67 removed outlier: 6.504A pdb=" N VAL G 384 " --> pdb=" O ILE G 66 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N THR G 383 " --> pdb=" O ILE G 361 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'G' and resid 247 through 250 removed outlier: 6.703A pdb=" N VAL G 270 " --> pdb=" O ALA G 248 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N VAL G 250 " --> pdb=" O VAL G 270 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N VAL G 272 " --> pdb=" O VAL G 250 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N GLN G 298 " --> pdb=" O ILE G 271 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N LEU G 273 " --> pdb=" O GLN G 298 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ILE G 300 " --> pdb=" O LEU G 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= AM Processing sheet with id= AN, first strand: chain 'G' and resid 408 through 412 Processing sheet with id= AO, first strand: chain 'G' and resid 142 through 145 removed outlier: 3.506A pdb=" N GLY G 156 " --> pdb=" O ILE G 144 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'G' and resid 208 through 212 Processing sheet with id= AQ, first strand: chain 'H' and resid 35 through 37 Processing sheet with id= AR, first strand: chain 'H' and resid 65 through 67 removed outlier: 6.518A pdb=" N VAL H 384 " --> pdb=" O ILE H 66 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR H 383 " --> pdb=" O ILE H 361 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'H' and resid 208 through 211 Processing sheet with id= AT, first strand: chain 'H' and resid 247 through 250 removed outlier: 6.699A pdb=" N VAL H 270 " --> pdb=" O ALA H 248 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N VAL H 250 " --> pdb=" O VAL H 270 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N VAL H 272 " --> pdb=" O VAL H 250 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N GLN H 298 " --> pdb=" O ILE H 271 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N LEU H 273 " --> pdb=" O GLN H 298 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ILE H 300 " --> pdb=" O LEU H 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= AT Processing sheet with id= AU, first strand: chain 'H' and resid 401 through 403 Processing sheet with id= AV, first strand: chain 'H' and resid 142 through 145 removed outlier: 3.562A pdb=" N GLY H 156 " --> pdb=" O ILE H 144 " (cutoff:3.500A) 875 hydrogen bonds defined for protein. 2385 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 19.82 Time building geometry restraints manager: 42.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.94 - 1.12: 29680 1.12 - 1.29: 5018 1.29 - 1.47: 11156 1.47 - 1.65: 14266 1.65 - 1.82: 328 Bond restraints: 60448 Sorted by residual: bond pdb=" NE ARG B 57 " pdb=" HE ARG B 57 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" N ILE C 157 " pdb=" H ILE C 157 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" N ILE F 221 " pdb=" H ILE F 221 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" N ALA A 81 " pdb=" H ALA A 81 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" NH1 ARG G 412 " pdb="HH11 ARG G 412 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 ... (remaining 60443 not shown) Histogram of bond angle deviations from ideal: 92.37 - 100.94: 143 100.94 - 109.50: 48264 109.50 - 118.07: 33280 118.07 - 126.64: 27210 126.64 - 135.21: 447 Bond angle restraints: 109344 Sorted by residual: angle pdb=" PB ATP D 601 " pdb=" O3B ATP D 601 " pdb=" PG ATP D 601 " ideal model delta sigma weight residual 139.87 121.01 18.86 1.00e+00 1.00e+00 3.56e+02 angle pdb=" PB ATP E 602 " pdb=" O3B ATP E 602 " pdb=" PG ATP E 602 " ideal model delta sigma weight residual 139.87 121.09 18.78 1.00e+00 1.00e+00 3.53e+02 angle pdb=" PB ATP F 602 " pdb=" O3B ATP F 602 " pdb=" PG ATP F 602 " ideal model delta sigma weight residual 139.87 121.66 18.21 1.00e+00 1.00e+00 3.32e+02 angle pdb=" PB ATP H 602 " pdb=" O3B ATP H 602 " pdb=" PG ATP H 602 " ideal model delta sigma weight residual 139.87 121.96 17.91 1.00e+00 1.00e+00 3.21e+02 angle pdb=" PB ATP D 602 " pdb=" O3B ATP D 602 " pdb=" PG ATP D 602 " ideal model delta sigma weight residual 139.87 122.08 17.79 1.00e+00 1.00e+00 3.17e+02 ... (remaining 109339 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.23: 21533 24.23 - 48.47: 1197 48.47 - 72.70: 669 72.70 - 96.93: 76 96.93 - 121.16: 5 Dihedral angle restraints: 23480 sinusoidal: 11208 harmonic: 12272 Sorted by residual: dihedral pdb=" C5' IMP H 603 " pdb=" O5' IMP H 603 " pdb=" P IMP H 603 " pdb=" O2P IMP H 603 " ideal model delta sinusoidal sigma weight residual 191.93 70.77 121.16 1 2.00e+01 2.50e-03 3.64e+01 dihedral pdb=" C5' IMP G 603 " pdb=" O5' IMP G 603 " pdb=" P IMP G 603 " pdb=" O2P IMP G 603 " ideal model delta sinusoidal sigma weight residual -168.07 -47.50 -120.57 1 2.00e+01 2.50e-03 3.62e+01 dihedral pdb=" C5' IMP D 603 " pdb=" O5' IMP D 603 " pdb=" P IMP D 603 " pdb=" O2P IMP D 603 " ideal model delta sinusoidal sigma weight residual -168.07 -54.66 -113.41 1 2.00e+01 2.50e-03 3.35e+01 ... (remaining 23477 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 3142 0.072 - 0.145: 1275 0.145 - 0.217: 333 0.217 - 0.290: 83 0.290 - 0.362: 7 Chirality restraints: 4840 Sorted by residual: chirality pdb=" CA ASP C 216 " pdb=" N ASP C 216 " pdb=" C ASP C 216 " pdb=" CB ASP C 216 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.28e+00 chirality pdb=" CA ASP B 216 " pdb=" N ASP B 216 " pdb=" C ASP B 216 " pdb=" CB ASP B 216 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.22e+00 chirality pdb=" CA ASP H 216 " pdb=" N ASP H 216 " pdb=" C ASP H 216 " pdb=" CB ASP H 216 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.16e+00 ... (remaining 4837 not shown) Planarity restraints: 8888 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' IMP G 603 " -0.140 2.00e-02 2.50e+03 1.08e-01 2.89e+02 pdb=" C2 IMP G 603 " 0.182 2.00e-02 2.50e+03 pdb=" C4 IMP G 603 " -0.040 2.00e-02 2.50e+03 pdb=" C5 IMP G 603 " -0.027 2.00e-02 2.50e+03 pdb=" C6 IMP G 603 " -0.158 2.00e-02 2.50e+03 pdb=" C8 IMP G 603 " 0.109 2.00e-02 2.50e+03 pdb=" N1 IMP G 603 " -0.084 2.00e-02 2.50e+03 pdb=" N3 IMP G 603 " 0.074 2.00e-02 2.50e+03 pdb=" N7 IMP G 603 " 0.105 2.00e-02 2.50e+03 pdb=" N9 IMP G 603 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 161 " 0.069 9.50e-02 1.11e+02 1.06e-01 2.39e+02 pdb=" NE ARG E 161 " 0.099 2.00e-02 2.50e+03 pdb=" CZ ARG E 161 " 0.083 2.00e-02 2.50e+03 pdb=" NH1 ARG E 161 " 0.043 2.00e-02 2.50e+03 pdb=" NH2 ARG E 161 " 0.074 2.00e-02 2.50e+03 pdb="HH11 ARG E 161 " -0.173 2.00e-02 2.50e+03 pdb="HH12 ARG E 161 " 0.033 2.00e-02 2.50e+03 pdb="HH21 ARG E 161 " -0.198 2.00e-02 2.50e+03 pdb="HH22 ARG E 161 " 0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG G 161 " -0.040 9.50e-02 1.11e+02 8.87e-02 1.73e+02 pdb=" NE ARG G 161 " 0.054 2.00e-02 2.50e+03 pdb=" CZ ARG G 161 " 0.085 2.00e-02 2.50e+03 pdb=" NH1 ARG G 161 " 0.071 2.00e-02 2.50e+03 pdb=" NH2 ARG G 161 " 0.088 2.00e-02 2.50e+03 pdb="HH11 ARG G 161 " -0.143 2.00e-02 2.50e+03 pdb="HH12 ARG G 161 " 0.001 2.00e-02 2.50e+03 pdb="HH21 ARG G 161 " -0.161 2.00e-02 2.50e+03 pdb="HH22 ARG G 161 " 0.006 2.00e-02 2.50e+03 ... (remaining 8885 not shown) Histogram of nonbonded interaction distances: 1.42 - 2.05: 2253 2.05 - 2.69: 84720 2.69 - 3.33: 183298 3.33 - 3.96: 247116 3.96 - 4.60: 368255 Nonbonded interactions: 885642 Sorted by model distance: nonbonded pdb=" HA LYS G 455 " pdb=" HD3 LYS G 455 " model vdw 1.417 2.440 nonbonded pdb=" HA LYS A 455 " pdb=" HD3 LYS A 455 " model vdw 1.424 2.440 nonbonded pdb=" HA LYS C 455 " pdb=" HD3 LYS C 455 " model vdw 1.425 2.440 nonbonded pdb=" HB2 GLN A 283 " pdb="HE21 GLN A 283 " model vdw 1.476 2.270 nonbonded pdb=" HB2 GLN B 283 " pdb="HE21 GLN B 283 " model vdw 1.480 2.270 ... (remaining 885637 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 72 5.49 5 S 192 5.16 5 C 18840 2.51 5 N 5160 2.21 5 O 5928 1.98 5 H 29736 0.53 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.670 Extract box with map and model: 15.790 Check model and map are aligned: 0.660 Process input model: 144.080 Find NCS groups from input model: 2.390 Set up NCS constraints: 0.280 Set refine NCS operators: 0.000 Set scattering table: 0.430 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 177.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 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 : 0.014 0.102 30712 Z= 0.914 Angle : 1.699 18.864 41680 Z= 1.129 Chirality : 0.084 0.362 4840 Planarity : 0.011 0.108 5176 Dihedral : 15.747 121.163 11104 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 1.94 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.18 % Favored : 94.56 % Rotamer Outliers : 3.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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: -1.77 (0.12), residues: 3824 helix: -1.38 (0.11), residues: 1496 sheet: -0.26 (0.30), residues: 192 loop : -1.05 (0.12), residues: 2136 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7648 Ramachandran restraints generated. 3824 Oldfield, 0 Emsley, 3824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7648 Ramachandran restraints generated. 3824 Oldfield, 0 Emsley, 3824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 753 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 639 time to evaluate : 3.610 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: 114 outliers final: 63 residues processed: 738 average time/residue: 2.2518 time to fit residues: 2001.0050 Evaluate side-chains 566 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 503 time to evaluate : 3.537 Switching outliers to nearest non-outliers outliers start: 63 outliers final: 61 residues processed: 6 average time/residue: 0.9369 time to fit residues: 12.8127 ------------------------------------------------------------------------------- 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: 0.6980 chunk 161 optimal weight: 3.9990 chunk 99 optimal weight: 0.8980 chunk 196 optimal weight: 0.9990 chunk 155 optimal weight: 5.9990 chunk 300 optimal weight: 4.9990 chunk 116 optimal weight: 0.9990 chunk 183 optimal weight: 2.9990 chunk 224 optimal weight: 0.7980 chunk 348 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 GLN ** A 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 498 GLN B 277 GLN B 498 GLN C 277 GLN C 498 GLN D 265 GLN D 277 GLN D 498 GLN E 265 GLN E 277 GLN E 498 GLN F 265 GLN F 277 GLN F 441 GLN F 498 GLN G 243 GLN G 265 GLN G 277 GLN G 441 GLN G 498 GLN H 265 GLN H 277 GLN ** H 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 30712 Z= 0.220 Angle : 0.589 6.378 41680 Z= 0.313 Chirality : 0.043 0.166 4840 Planarity : 0.005 0.041 5176 Dihedral : 9.578 96.491 4280 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.69 % Favored : 97.04 % Rotamer Outliers : 2.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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: -0.80 (0.13), residues: 3824 helix: -0.21 (0.13), residues: 1504 sheet: 0.51 (0.29), residues: 272 loop : -0.86 (0.13), residues: 2048 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7648 Ramachandran restraints generated. 3824 Oldfield, 0 Emsley, 3824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7648 Ramachandran restraints generated. 3824 Oldfield, 0 Emsley, 3824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 625 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 532 time to evaluate : 3.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 93 outliers final: 65 residues processed: 590 average time/residue: 2.2653 time to fit residues: 1610.7104 Evaluate side-chains 558 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 493 time to evaluate : 3.531 Switching outliers to nearest non-outliers outliers start: 65 outliers final: 48 residues processed: 20 average time/residue: 0.9438 time to fit residues: 32.4695 ------------------------------------------------------------------------------- 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: 1.9990 chunk 108 optimal weight: 4.9990 chunk 290 optimal weight: 0.6980 chunk 237 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 349 optimal weight: 3.9990 chunk 377 optimal weight: 7.9990 chunk 311 optimal weight: 4.9990 chunk 346 optimal weight: 0.0030 chunk 119 optimal weight: 3.9990 chunk 280 optimal weight: 7.9990 overall best weight: 1.3396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 GLN C 94 ASN F 441 GLN G 441 GLN G 498 GLN ** H 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 30712 Z= 0.241 Angle : 0.522 5.566 41680 Z= 0.273 Chirality : 0.043 0.171 4840 Planarity : 0.004 0.036 5176 Dihedral : 8.560 77.501 4280 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.84 % Favored : 96.08 % Rotamer Outliers : 2.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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: -0.36 (0.13), residues: 3824 helix: 0.28 (0.14), residues: 1496 sheet: 0.56 (0.29), residues: 272 loop : -0.70 (0.13), residues: 2056 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7648 Ramachandran restraints generated. 3824 Oldfield, 0 Emsley, 3824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7648 Ramachandran restraints generated. 3824 Oldfield, 0 Emsley, 3824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 609 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 523 time to evaluate : 3.610 Fit side-chains outliers start: 86 outliers final: 64 residues processed: 575 average time/residue: 2.2861 time to fit residues: 1605.3712 Evaluate side-chains 565 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 501 time to evaluate : 3.572 Switching outliers to nearest non-outliers outliers start: 64 outliers final: 54 residues processed: 20 average time/residue: 1.0989 time to fit residues: 36.2427 ------------------------------------------------------------------------------- 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: 4.9990 chunk 181 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 166 optimal weight: 2.9990 chunk 234 optimal weight: 5.9990 chunk 350 optimal weight: 4.9990 chunk 371 optimal weight: 2.9990 chunk 183 optimal weight: 5.9990 chunk 332 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN A 265 GLN ** A 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 GLN C 265 GLN D 94 ASN E 94 ASN F 94 ASN F 441 GLN G 94 ASN G 441 GLN ** H 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.2637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.059 30712 Z= 0.499 Angle : 0.593 5.664 41680 Z= 0.313 Chirality : 0.048 0.170 4840 Planarity : 0.005 0.054 5176 Dihedral : 8.721 89.731 4280 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.63 % Favored : 95.19 % Rotamer Outliers : 3.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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: -0.65 (0.13), residues: 3824 helix: 0.12 (0.14), residues: 1504 sheet: 0.16 (0.26), residues: 352 loop : -0.94 (0.13), residues: 1968 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7648 Ramachandran restraints generated. 3824 Oldfield, 0 Emsley, 3824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7648 Ramachandran restraints generated. 3824 Oldfield, 0 Emsley, 3824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 636 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 511 time to evaluate : 3.643 Fit side-chains revert: symmetry clash outliers start: 125 outliers final: 83 residues processed: 582 average time/residue: 2.1972 time to fit residues: 1549.6536 Evaluate side-chains 580 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 497 time to evaluate : 3.571 Switching outliers to nearest non-outliers outliers start: 83 outliers final: 62 residues processed: 21 average time/residue: 0.9950 time to fit residues: 34.8650 ------------------------------------------------------------------------------- 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: 6.9990 chunk 210 optimal weight: 5.9990 chunk 5 optimal weight: 0.8980 chunk 276 optimal weight: 1.9990 chunk 153 optimal weight: 1.9990 chunk 316 optimal weight: 1.9990 chunk 256 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 189 optimal weight: 1.9990 chunk 333 optimal weight: 0.9990 chunk 93 optimal weight: 0.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN A 265 GLN ** A 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 GLN C 265 GLN E 112 GLN F 94 ASN F 441 GLN G 441 GLN ** H 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 30712 Z= 0.220 Angle : 0.502 6.451 41680 Z= 0.260 Chirality : 0.042 0.170 4840 Planarity : 0.004 0.039 5176 Dihedral : 8.079 87.273 4280 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.53 % Favored : 96.42 % Rotamer Outliers : 2.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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: -0.19 (0.14), residues: 3824 helix: 0.52 (0.14), residues: 1504 sheet: 0.36 (0.28), residues: 272 loop : -0.63 (0.13), residues: 2048 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7648 Ramachandran restraints generated. 3824 Oldfield, 0 Emsley, 3824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7648 Ramachandran restraints generated. 3824 Oldfield, 0 Emsley, 3824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 600 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 508 time to evaluate : 3.594 Fit side-chains revert: symmetry clash outliers start: 92 outliers final: 73 residues processed: 576 average time/residue: 2.2375 time to fit residues: 1573.0090 Evaluate side-chains 562 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 489 time to evaluate : 3.573 Switching outliers to nearest non-outliers outliers start: 73 outliers final: 69 residues processed: 11 average time/residue: 1.0990 time to fit residues: 22.1836 ------------------------------------------------------------------------------- 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: 1.9990 chunk 73 optimal weight: 1.9990 chunk 217 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 371 optimal weight: 2.9990 chunk 308 optimal weight: 0.1980 chunk 172 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 122 optimal weight: 0.8980 chunk 195 optimal weight: 1.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN A 265 GLN ** A 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 GLN C 265 GLN G 441 GLN ** H 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.2909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 30712 Z= 0.259 Angle : 0.502 4.955 41680 Z= 0.260 Chirality : 0.043 0.161 4840 Planarity : 0.004 0.038 5176 Dihedral : 7.914 85.658 4280 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.00 % Favored : 95.92 % Rotamer Outliers : 3.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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: -0.07 (0.14), residues: 3824 helix: 0.63 (0.14), residues: 1504 sheet: 0.35 (0.28), residues: 272 loop : -0.57 (0.13), residues: 2048 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7648 Ramachandran restraints generated. 3824 Oldfield, 0 Emsley, 3824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7648 Ramachandran restraints generated. 3824 Oldfield, 0 Emsley, 3824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 607 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 508 time to evaluate : 3.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 99 outliers final: 86 residues processed: 578 average time/residue: 2.2522 time to fit residues: 1591.8179 Evaluate side-chains 584 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 498 time to evaluate : 3.640 Switching outliers to nearest non-outliers outliers start: 86 outliers final: 75 residues processed: 19 average time/residue: 1.0689 time to fit residues: 35.1463 ------------------------------------------------------------------------------- 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: 4.9990 chunk 41 optimal weight: 6.9990 chunk 211 optimal weight: 1.9990 chunk 271 optimal weight: 3.9990 chunk 210 optimal weight: 0.7980 chunk 312 optimal weight: 1.9990 chunk 207 optimal weight: 0.0970 chunk 370 optimal weight: 1.9990 chunk 231 optimal weight: 5.9990 chunk 225 optimal weight: 1.9990 chunk 170 optimal weight: 1.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 GLN ** A 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 ASN B 265 GLN C 265 GLN G 441 GLN ** H 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.2977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 30712 Z= 0.239 Angle : 0.496 5.555 41680 Z= 0.257 Chirality : 0.042 0.160 4840 Planarity : 0.004 0.037 5176 Dihedral : 7.726 80.781 4280 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.84 % Favored : 96.08 % Rotamer Outliers : 3.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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: 0.03 (0.14), residues: 3824 helix: 0.71 (0.14), residues: 1504 sheet: 0.41 (0.28), residues: 272 loop : -0.50 (0.14), residues: 2048 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7648 Ramachandran restraints generated. 3824 Oldfield, 0 Emsley, 3824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7648 Ramachandran restraints generated. 3824 Oldfield, 0 Emsley, 3824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 599 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 500 time to evaluate : 3.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 99 outliers final: 85 residues processed: 575 average time/residue: 2.1955 time to fit residues: 1531.4420 Evaluate side-chains 577 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 492 time to evaluate : 3.567 Switching outliers to nearest non-outliers outliers start: 85 outliers final: 75 residues processed: 14 average time/residue: 1.0060 time to fit residues: 24.9792 ------------------------------------------------------------------------------- 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: 1.9990 chunk 147 optimal weight: 1.9990 chunk 221 optimal weight: 0.9980 chunk 111 optimal weight: 3.9990 chunk 72 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 235 optimal weight: 0.7980 chunk 252 optimal weight: 2.9990 chunk 182 optimal weight: 4.9990 chunk 34 optimal weight: 0.9980 chunk 290 optimal weight: 0.6980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 GLN ** A 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 GLN C 265 GLN C 441 GLN E 441 GLN G 441 GLN ** H 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.3086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 30712 Z= 0.177 Angle : 0.473 5.166 41680 Z= 0.243 Chirality : 0.041 0.162 4840 Planarity : 0.003 0.034 5176 Dihedral : 7.448 78.338 4280 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.74 % Favored : 96.21 % Rotamer Outliers : 3.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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: 0.31 (0.14), residues: 3824 helix: 0.96 (0.15), residues: 1488 sheet: 0.49 (0.29), residues: 272 loop : -0.33 (0.14), residues: 2064 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7648 Ramachandran restraints generated. 3824 Oldfield, 0 Emsley, 3824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7648 Ramachandran restraints generated. 3824 Oldfield, 0 Emsley, 3824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 614 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 516 time to evaluate : 3.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 98 outliers final: 78 residues processed: 587 average time/residue: 2.2493 time to fit residues: 1612.2832 Evaluate side-chains 584 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 506 time to evaluate : 3.586 Switching outliers to nearest non-outliers outliers start: 78 outliers final: 74 residues processed: 9 average time/residue: 0.9348 time to fit residues: 17.3497 ------------------------------------------------------------------------------- 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: 0.4980 chunk 354 optimal weight: 3.9990 chunk 323 optimal weight: 2.9990 chunk 344 optimal weight: 0.5980 chunk 207 optimal weight: 0.6980 chunk 150 optimal weight: 2.9990 chunk 270 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 311 optimal weight: 3.9990 chunk 326 optimal weight: 4.9990 chunk 343 optimal weight: 2.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 ASN A 265 GLN ** A 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN B 265 GLN C 265 GLN E 441 GLN G 94 ASN G 441 GLN ** H 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.3119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.053 30712 Z= 0.246 Angle : 0.493 5.175 41680 Z= 0.255 Chirality : 0.042 0.157 4840 Planarity : 0.004 0.034 5176 Dihedral : 7.477 72.981 4280 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.26 % Favored : 95.66 % Rotamer Outliers : 3.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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: 0.32 (0.14), residues: 3824 helix: 1.05 (0.15), residues: 1440 sheet: 0.48 (0.29), residues: 272 loop : -0.37 (0.14), residues: 2112 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7648 Ramachandran restraints generated. 3824 Oldfield, 0 Emsley, 3824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7648 Ramachandran restraints generated. 3824 Oldfield, 0 Emsley, 3824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 596 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 496 time to evaluate : 4.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 100 outliers final: 80 residues processed: 566 average time/residue: 2.2475 time to fit residues: 1562.3153 Evaluate side-chains 574 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 494 time to evaluate : 3.575 Switching outliers to nearest non-outliers outliers start: 80 outliers final: 74 residues processed: 10 average time/residue: 0.7883 time to fit residues: 17.2956 ------------------------------------------------------------------------------- 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: 1.9990 chunk 364 optimal weight: 2.9990 chunk 222 optimal weight: 0.9980 chunk 173 optimal weight: 0.9990 chunk 253 optimal weight: 1.9990 chunk 382 optimal weight: 0.0980 chunk 352 optimal weight: 0.8980 chunk 304 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 chunk 235 optimal weight: 1.9990 chunk 186 optimal weight: 5.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 GLN ** A 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 GLN B 441 GLN C 265 GLN C 441 GLN D 265 GLN E 265 GLN E 441 GLN G 94 ASN G 441 GLN H 265 GLN ** H 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.3216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 30712 Z= 0.189 Angle : 0.477 5.393 41680 Z= 0.245 Chirality : 0.042 0.166 4840 Planarity : 0.003 0.033 5176 Dihedral : 7.261 72.160 4280 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.84 % Favored : 96.10 % Rotamer Outliers : 2.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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: 0.49 (0.14), residues: 3824 helix: 1.17 (0.15), residues: 1440 sheet: 0.57 (0.29), residues: 272 loop : -0.25 (0.14), residues: 2112 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7648 Ramachandran restraints generated. 3824 Oldfield, 0 Emsley, 3824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7648 Ramachandran restraints generated. 3824 Oldfield, 0 Emsley, 3824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 588 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 501 time to evaluate : 3.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 87 outliers final: 74 residues processed: 570 average time/residue: 2.1919 time to fit residues: 1519.0142 Evaluate side-chains 567 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 493 time to evaluate : 3.568 Switching outliers to nearest non-outliers outliers start: 74 outliers final: 71 residues processed: 6 average time/residue: 1.2336 time to fit residues: 14.6857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/cctbx_project/iotbx/cli_parser.py", line 865, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.3954 > 50: distance: 68 - 90: 21.993 distance: 90 - 91: 40.824 distance: 90 - 98: 8.480 distance: 91 - 92: 47.336 distance: 91 - 94: 11.284 distance: 91 - 99: 33.425 distance: 92 - 93: 5.548 distance: 92 - 109: 43.518 distance: 94 - 95: 9.509 distance: 94 - 96: 6.716 distance: 94 - 100: 16.334 distance: 95 - 97: 25.834 distance: 95 - 101: 23.393 distance: 95 - 102: 12.119 distance: 96 - 103: 13.773 distance: 96 - 104: 5.601 distance: 96 - 105: 6.446 distance: 97 - 107: 12.426 distance: 97 - 108: 7.385 distance: 109 - 110: 24.060 distance: 109 - 118: 22.051 distance: 110 - 111: 33.959 distance: 110 - 113: 46.064 distance: 110 - 119: 33.168 distance: 111 - 112: 45.321 distance: 111 - 124: 35.672 distance: 113 - 114: 36.997 distance: 113 - 120: 14.830 distance: 113 - 121: 20.859 distance: 114 - 115: 13.073 distance: 114 - 122: 15.040 distance: 114 - 123: 22.371 distance: 115 - 116: 28.807 distance: 115 - 117: 14.436 distance: 124 - 125: 16.990 distance: 124 - 132: 24.407 distance: 125 - 126: 30.610 distance: 125 - 128: 19.303 distance: 125 - 133: 12.291 distance: 126 - 127: 8.798 distance: 126 - 143: 37.540 distance: 128 - 129: 9.642 distance: 128 - 134: 25.246 distance: 128 - 135: 26.930 distance: 129 - 130: 7.750 distance: 129 - 131: 9.475 distance: 129 - 136: 6.009 distance: 130 - 137: 8.217 distance: 130 - 138: 5.010 distance: 131 - 140: 3.903 distance: 131 - 141: 4.604 distance: 131 - 142: 11.511 distance: 143 - 144: 16.125 distance: 143 - 150: 23.335 distance: 144 - 145: 13.001 distance: 144 - 147: 18.299 distance: 144 - 151: 28.025 distance: 145 - 146: 22.400 distance: 145 - 159: 52.899 distance: 147 - 148: 38.151 distance: 147 - 149: 19.731 distance: 147 - 152: 45.681 distance: 148 - 153: 17.587 distance: 148 - 154: 15.017 distance: 148 - 155: 6.395 distance: 149 - 156: 14.280 distance: 149 - 157: 3.843 distance: 149 - 158: 6.352 distance: 159 - 160: 35.894 distance: 159 - 166: 8.096 distance: 160 - 161: 25.315 distance: 160 - 163: 38.803 distance: 160 - 167: 22.634 distance: 161 - 175: 46.629 distance: 163 - 164: 19.188 distance: 163 - 165: 3.155 distance: 163 - 168: 14.370 distance: 164 - 169: 12.975 distance: 165 - 172: 7.627 distance: 165 - 173: 16.122 distance: 165 - 174: 8.296 distance: 175 - 176: 44.246 distance: 175 - 180: 40.465 distance: 176 - 177: 42.020 distance: 176 - 179: 69.159 distance: 176 - 181: 32.852 distance: 177 - 178: 38.520 distance: 177 - 185: 10.436 distance: 179 - 182: 10.114 distance: 179 - 183: 19.652 distance: 179 - 184: 11.823 distance: 185 - 186: 6.491 distance: 185 - 191: 16.017 distance: 186 - 187: 19.884 distance: 186 - 189: 16.777 distance: 186 - 192: 29.369 distance: 187 - 188: 38.562 distance: 187 - 199: 46.148 distance: 189 - 190: 11.959 distance: 189 - 193: 6.190 distance: 189 - 194: 15.134 distance: 190 - 191: 5.943 distance: 190 - 195: 21.988 distance: 190 - 196: 19.327 distance: 191 - 197: 20.387 distance: 191 - 198: 9.913 distance: 199 - 204: 10.833 distance: 200 - 201: 57.508 distance: 200 - 203: 15.578 distance: 200 - 205: 10.825 distance: 201 - 202: 35.535 distance: 201 - 209: 44.263 distance: 203 - 206: 9.364 distance: 203 - 207: 5.980 distance: 209 - 210: 44.722 distance: 209 - 213: 15.154 distance: 210 - 211: 19.397 distance: 210 - 214: 19.142 distance: 210 - 215: 22.370 distance: 211 - 212: 32.099 distance: 211 - 216: 45.599 distance: 216 - 217: 36.346 distance: 216 - 223: 14.119 distance: 217 - 218: 27.292 distance: 217 - 220: 30.478 distance: 217 - 224: 29.486 distance: 218 - 219: 23.181 distance: 218 - 232: 24.302 distance: 220 - 221: 26.099 distance: 220 - 222: 25.525 distance: 220 - 225: 27.370 distance: 221 - 226: 26.491 distance: 221 - 227: 25.009 distance: 221 - 228: 18.219 distance: 222 - 229: 11.918 distance: 222 - 230: 3.650 distance: 222 - 231: 17.821