Starting phenix.real_space_refine (version: 1.21rc1) on Thu May 4 22:51:41 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rgm_24452/05_2023/7rgm_24452_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rgm_24452/05_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_24452/05_2023/7rgm_24452.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rgm_24452/05_2023/7rgm_24452.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rgm_24452/05_2023/7rgm_24452_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rgm_24452/05_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 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. 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: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/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: 20.29, 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: 41.25 Conformation dependent library (CDL) restraints added in 4.0 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: 2.81 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: 21.18 Time building geometry restraints manager: 43.30 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 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: 2.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.650 Extract box with map and model: 15.710 Check model and map are aligned: 0.650 Set scattering table: 0.400 Process input model: 146.760 Find NCS groups from input model: 3.100 Set up NCS constraints: 0.390 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 183.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 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 : 3.487 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: 2.2401 time to fit residues: 1989.4482 Evaluate side-chains 566 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 503 time to evaluate : 3.463 Switching outliers to nearest non-outliers outliers start: 63 outliers final: 61 residues processed: 6 average time/residue: 0.9589 time to fit residues: 13.1048 ------------------------------------------------------------------------------- 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: 0.8457 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 30712 Z= 0.217 Angle : 0.587 6.361 41680 Z= 0.311 Chirality : 0.043 0.164 4840 Planarity : 0.005 0.041 5176 Dihedral : 9.561 96.098 4280 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.69 % Favored : 97.04 % Rotamer Outliers : 2.99 % 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: -0.79 (0.13), residues: 3824 helix: -0.21 (0.13), residues: 1504 sheet: 0.52 (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 626 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 532 time to evaluate : 3.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 94 outliers final: 65 residues processed: 591 average time/residue: 2.2782 time to fit residues: 1625.9218 Evaluate side-chains 557 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 492 time to evaluate : 3.491 Switching outliers to nearest non-outliers outliers start: 65 outliers final: 49 residues processed: 19 average time/residue: 0.9804 time to fit residues: 31.8385 ------------------------------------------------------------------------------- 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: 5.9990 chunk 290 optimal weight: 0.9990 chunk 237 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 349 optimal weight: 2.9990 chunk 377 optimal weight: 6.9990 chunk 311 optimal weight: 4.9990 chunk 346 optimal weight: 0.9990 chunk 119 optimal weight: 3.9990 chunk 280 optimal weight: 7.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- 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: 0.8482 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 30712 Z= 0.277 Angle : 0.536 7.607 41680 Z= 0.281 Chirality : 0.043 0.172 4840 Planarity : 0.004 0.036 5176 Dihedral : 8.582 81.658 4280 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.87 % Favored : 96.08 % Rotamer Outliers : 3.09 % 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: -0.42 (0.13), residues: 3824 helix: 0.25 (0.14), residues: 1496 sheet: 0.54 (0.29), residues: 272 loop : -0.76 (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 626 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 529 time to evaluate : 3.550 Fit side-chains revert: symmetry clash outliers start: 97 outliers final: 70 residues processed: 585 average time/residue: 2.2399 time to fit residues: 1603.7161 Evaluate side-chains 569 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 499 time to evaluate : 3.452 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 70 outliers final: 56 residues processed: 25 average time/residue: 1.0998 time to fit residues: 43.9590 ------------------------------------------------------------------------------- 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: 2.9990 chunk 181 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 166 optimal weight: 3.9990 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: 1.9990 chunk 100 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN A 265 GLN ** A 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 GLN C 94 ASN 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: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.053 30712 Z= 0.461 Angle : 0.581 6.505 41680 Z= 0.306 Chirality : 0.047 0.168 4840 Planarity : 0.005 0.051 5176 Dihedral : 8.612 87.316 4280 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.34 % Favored : 95.45 % Rotamer Outliers : 3.91 % 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: -0.60 (0.13), residues: 3824 helix: 0.18 (0.14), residues: 1504 sheet: 0.16 (0.26), residues: 352 loop : -0.92 (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 627 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 504 time to evaluate : 3.567 Fit side-chains outliers start: 123 outliers final: 84 residues processed: 574 average time/residue: 2.1794 time to fit residues: 1515.4241 Evaluate side-chains 577 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 493 time to evaluate : 3.432 Switching outliers to nearest non-outliers outliers start: 84 outliers final: 66 residues processed: 19 average time/residue: 0.9541 time to fit residues: 31.0300 ------------------------------------------------------------------------------- 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: 0.4980 chunk 210 optimal weight: 4.9990 chunk 5 optimal weight: 0.5980 chunk 276 optimal weight: 1.9990 chunk 153 optimal weight: 2.9990 chunk 316 optimal weight: 1.9990 chunk 256 optimal weight: 5.9990 chunk 0 optimal weight: 1.9990 chunk 189 optimal weight: 1.9990 chunk 333 optimal weight: 1.9990 chunk 93 optimal weight: 0.9980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN A 265 GLN ** A 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 GLN C 94 ASN C 265 GLN E 112 GLN 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: 0.8483 moved from start: 0.2844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 30712 Z= 0.214 Angle : 0.502 6.867 41680 Z= 0.260 Chirality : 0.042 0.168 4840 Planarity : 0.004 0.039 5176 Dihedral : 8.032 88.959 4280 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.84 % Favored : 96.10 % 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: -0.19 (0.14), residues: 3824 helix: 0.52 (0.14), residues: 1504 sheet: 0.37 (0.28), residues: 272 loop : -0.65 (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 608 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 515 time to evaluate : 3.508 Fit side-chains revert: symmetry clash outliers start: 93 outliers final: 79 residues processed: 582 average time/residue: 2.2537 time to fit residues: 1603.1043 Evaluate side-chains 568 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 489 time to evaluate : 3.440 Switching outliers to nearest non-outliers outliers start: 79 outliers final: 74 residues processed: 14 average time/residue: 0.9872 time to fit residues: 24.9214 ------------------------------------------------------------------------------- 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: 1.9990 chunk 334 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 217 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 371 optimal weight: 3.9990 chunk 308 optimal weight: 3.9990 chunk 172 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 122 optimal weight: 0.9980 chunk 195 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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 G 441 GLN ** H 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.2947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.038 30712 Z= 0.308 Angle : 0.516 4.905 41680 Z= 0.269 Chirality : 0.043 0.164 4840 Planarity : 0.004 0.041 5176 Dihedral : 7.948 78.435 4280 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.58 % Favored : 95.32 % Rotamer Outliers : 3.66 % 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: -0.18 (0.13), residues: 3824 helix: 0.55 (0.14), residues: 1504 sheet: 0.35 (0.28), residues: 272 loop : -0.65 (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 614 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 499 time to evaluate : 3.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 115 outliers final: 88 residues processed: 577 average time/residue: 2.2347 time to fit residues: 1579.5533 Evaluate side-chains 579 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 491 time to evaluate : 3.443 Switching outliers to nearest non-outliers outliers start: 88 outliers final: 75 residues processed: 15 average time/residue: 1.2107 time to fit residues: 29.8587 ------------------------------------------------------------------------------- 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: 3.9990 chunk 41 optimal weight: 5.9990 chunk 211 optimal weight: 0.6980 chunk 271 optimal weight: 2.9990 chunk 210 optimal weight: 0.9990 chunk 312 optimal weight: 1.9990 chunk 207 optimal weight: 4.9990 chunk 370 optimal weight: 0.9980 chunk 231 optimal weight: 6.9990 chunk 225 optimal weight: 1.9990 chunk 170 optimal weight: 0.9980 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 G 441 GLN H 94 ASN ** 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: 0.8477 moved from start: 0.3044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 30712 Z= 0.205 Angle : 0.484 5.046 41680 Z= 0.250 Chirality : 0.042 0.164 4840 Planarity : 0.004 0.035 5176 Dihedral : 7.573 77.553 4280 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.40 % Favored : 96.55 % Rotamer Outliers : 3.24 % 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: 0.13 (0.14), residues: 3824 helix: 0.81 (0.15), residues: 1496 sheet: 0.44 (0.28), residues: 272 loop : -0.45 (0.14), residues: 2056 *********************** 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 605 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 503 time to evaluate : 3.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 102 outliers final: 85 residues processed: 577 average time/residue: 2.2116 time to fit residues: 1543.8781 Evaluate side-chains 574 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 489 time to evaluate : 3.437 Switching outliers to nearest non-outliers outliers start: 85 outliers final: 72 residues processed: 14 average time/residue: 0.8997 time to fit residues: 23.2596 ------------------------------------------------------------------------------- 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: 0.6980 chunk 221 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 235 optimal weight: 0.6980 chunk 252 optimal weight: 5.9990 chunk 182 optimal weight: 4.9990 chunk 34 optimal weight: 0.9980 chunk 290 optimal weight: 0.7980 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 C 441 GLN 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: 0.8473 moved from start: 0.3134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 30712 Z= 0.200 Angle : 0.478 5.015 41680 Z= 0.247 Chirality : 0.042 0.157 4840 Planarity : 0.004 0.034 5176 Dihedral : 7.428 72.550 4280 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.87 % Favored : 96.05 % Rotamer Outliers : 3.44 % 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: 0.24 (0.14), residues: 3824 helix: 0.90 (0.15), residues: 1496 sheet: 0.45 (0.28), residues: 272 loop : -0.37 (0.14), residues: 2056 *********************** 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 610 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 502 time to evaluate : 3.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 108 outliers final: 82 residues processed: 576 average time/residue: 2.2213 time to fit residues: 1561.3231 Evaluate side-chains 575 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 493 time to evaluate : 3.498 Switching outliers to nearest non-outliers outliers start: 82 outliers final: 73 residues processed: 11 average time/residue: 0.8589 time to fit residues: 19.2443 ------------------------------------------------------------------------------- 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: 0.8980 chunk 354 optimal weight: 3.9990 chunk 323 optimal weight: 2.9990 chunk 344 optimal weight: 2.9990 chunk 207 optimal weight: 4.9990 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: 0.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 GLN ** A 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 ASN B 265 GLN B 441 GLN C 265 GLN C 441 GLN D 265 GLN E 441 GLN F 265 GLN F 441 GLN G 441 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: 0.8497 moved from start: 0.3138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.046 30712 Z= 0.333 Angle : 0.517 5.038 41680 Z= 0.270 Chirality : 0.044 0.161 4840 Planarity : 0.004 0.038 5176 Dihedral : 7.652 70.366 4280 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.73 % Favored : 95.19 % Rotamer Outliers : 3.53 % 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: 0.09 (0.14), residues: 3824 helix: 0.89 (0.15), residues: 1448 sheet: 0.39 (0.29), residues: 272 loop : -0.53 (0.13), residues: 2104 *********************** 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 594 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 483 time to evaluate : 3.564 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: 111 outliers final: 94 residues processed: 559 average time/residue: 2.3159 time to fit residues: 1576.6221 Evaluate side-chains 574 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 480 time to evaluate : 3.553 Switching outliers to nearest non-outliers outliers start: 94 outliers final: 73 residues processed: 23 average time/residue: 0.9814 time to fit residues: 38.2420 ------------------------------------------------------------------------------- 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: 0.9980 chunk 222 optimal weight: 0.9980 chunk 173 optimal weight: 0.8980 chunk 253 optimal weight: 1.9990 chunk 382 optimal weight: 0.7980 chunk 352 optimal weight: 0.7980 chunk 304 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 235 optimal weight: 0.9990 chunk 186 optimal weight: 3.9990 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 B 441 GLN C 265 GLN D 265 GLN E 265 GLN E 441 GLN F 265 GLN G 441 GLN H 265 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: 0.8468 moved from start: 0.3219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 30712 Z= 0.174 Angle : 0.478 5.326 41680 Z= 0.246 Chirality : 0.041 0.165 4840 Planarity : 0.003 0.035 5176 Dihedral : 7.297 73.030 4280 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.82 % Favored : 96.13 % Rotamer Outliers : 2.67 % 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: 0.43 (0.14), residues: 3824 helix: 1.14 (0.15), residues: 1440 sheet: 0.53 (0.29), residues: 272 loop : -0.31 (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 579 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 495 time to evaluate : 3.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 84 outliers final: 73 residues processed: 567 average time/residue: 2.2134 time to fit residues: 1522.4595 Evaluate side-chains 564 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 491 time to evaluate : 3.495 Switching outliers to nearest non-outliers outliers start: 73 outliers final: 72 residues processed: 3 average time/residue: 0.6775 time to fit residues: 7.8244 ------------------------------------------------------------------------------- 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-1.21rc1-4953/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-1.21rc1-4953/modules/cctbx_project/iotbx/cli_parser.py", line 872, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/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-1.21rc1-4953/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/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-1.21rc1-4953/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-1.21rc1-4953/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-1.21rc1-4953/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-1.21rc1-4953/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-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/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-1.21rc1-4953/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-1.21rc1-4953/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/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-1.21rc1-4953/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-1.21rc1-4953/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-1.21rc1-4953/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-1.21rc1-4953/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: 63.3141 > 50: distance: 68 - 90: 7.180 distance: 90 - 91: 11.916 distance: 90 - 98: 9.801 distance: 91 - 92: 8.537 distance: 91 - 94: 5.011 distance: 91 - 99: 9.548 distance: 92 - 93: 17.575 distance: 92 - 109: 11.905 distance: 94 - 95: 4.102 distance: 94 - 96: 5.575 distance: 94 - 100: 5.166 distance: 95 - 97: 9.747 distance: 95 - 101: 7.406 distance: 95 - 102: 7.684 distance: 96 - 105: 3.426 distance: 97 - 107: 4.963 distance: 97 - 108: 3.151 distance: 109 - 110: 15.715 distance: 109 - 118: 12.046 distance: 110 - 111: 7.183 distance: 110 - 113: 8.028 distance: 110 - 119: 14.040 distance: 111 - 112: 18.081 distance: 111 - 124: 6.345 distance: 113 - 114: 7.437 distance: 113 - 120: 4.679 distance: 113 - 121: 8.720 distance: 114 - 115: 10.675 distance: 114 - 122: 3.949 distance: 114 - 123: 5.300 distance: 115 - 117: 3.062 distance: 124 - 125: 5.381 distance: 124 - 132: 18.972 distance: 125 - 126: 6.292 distance: 125 - 128: 7.232 distance: 126 - 127: 21.142 distance: 126 - 143: 13.924 distance: 128 - 129: 3.498 distance: 128 - 134: 4.923 distance: 128 - 135: 5.637 distance: 143 - 144: 4.345 distance: 143 - 150: 12.375 distance: 144 - 145: 14.147 distance: 144 - 147: 7.477 distance: 144 - 151: 6.778 distance: 145 - 146: 13.685 distance: 145 - 159: 14.561 distance: 147 - 148: 6.097 distance: 147 - 149: 3.900 distance: 147 - 152: 3.902 distance: 148 - 153: 5.443 distance: 148 - 154: 4.388 distance: 159 - 160: 10.655 distance: 159 - 166: 17.637 distance: 160 - 163: 8.006 distance: 160 - 167: 9.867 distance: 161 - 162: 18.940 distance: 161 - 175: 3.812 distance: 163 - 164: 9.839 distance: 163 - 165: 9.935 distance: 163 - 168: 6.157 distance: 164 - 170: 3.167 distance: 164 - 171: 3.679 distance: 165 - 172: 3.754 distance: 165 - 173: 3.678 distance: 165 - 174: 4.581 distance: 175 - 180: 21.037 distance: 176 - 177: 3.329 distance: 176 - 179: 8.118 distance: 176 - 181: 14.902 distance: 177 - 178: 9.296 distance: 179 - 182: 14.652 distance: 179 - 183: 17.813 distance: 179 - 184: 16.459 distance: 185 - 191: 7.070 distance: 186 - 187: 6.449 distance: 186 - 189: 8.934 distance: 186 - 192: 4.494 distance: 187 - 188: 27.885 distance: 187 - 199: 11.178 distance: 189 - 190: 3.349 distance: 189 - 194: 4.524 distance: 190 - 191: 5.565 distance: 190 - 195: 5.038 distance: 191 - 197: 4.050 distance: 199 - 200: 5.238 distance: 199 - 204: 29.246 distance: 200 - 201: 8.508 distance: 200 - 203: 12.902 distance: 200 - 205: 19.836 distance: 201 - 202: 17.574 distance: 201 - 209: 10.508 distance: 203 - 206: 12.022 distance: 203 - 207: 5.893 distance: 203 - 208: 4.092 distance: 209 - 210: 4.289 distance: 209 - 213: 22.206 distance: 210 - 211: 5.112 distance: 210 - 214: 13.329 distance: 210 - 215: 13.142 distance: 211 - 212: 24.306 distance: 211 - 216: 17.708 distance: 216 - 217: 3.360 distance: 216 - 223: 18.279 distance: 217 - 218: 7.330 distance: 217 - 220: 14.388 distance: 217 - 224: 10.795 distance: 218 - 219: 9.917 distance: 218 - 232: 13.733 distance: 220 - 222: 8.779 distance: 220 - 225: 13.220 distance: 221 - 227: 9.516 distance: 221 - 228: 3.966 distance: 222 - 230: 4.251 distance: 222 - 231: 6.888