Starting phenix.real_space_refine on Wed Feb 14 10:25:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rgm_24452/02_2024/7rgm_24452_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rgm_24452/02_2024/7rgm_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_24452/02_2024/7rgm_24452.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rgm_24452/02_2024/7rgm_24452.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rgm_24452/02_2024/7rgm_24452_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rgm_24452/02_2024/7rgm_24452_trim_updated.pdb" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- 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: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 19.49, per 1000 atoms: 0.33 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: 37.34 Conformation dependent library (CDL) restraints added in 4.6 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: 6.76 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: 18.88 Time building geometry restraints manager: 39.42 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: 25890 24.23 - 48.47: 1855 48.47 - 72.70: 916 72.70 - 96.93: 94 96.93 - 121.16: 5 Dihedral angle restraints: 28760 sinusoidal: 16488 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 28757 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: 2.970 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: 0.640 Extract box with map and model: 13.930 Check model and map are aligned: 0.650 Set scattering table: 0.410 Process input model: 141.410 Find NCS groups from input model: 2.880 Set up NCS constraints: 0.340 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: 0.000 Load rotamer database and sin/cos tables:11.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 174.750 ------------------------------------------------------------------------------- 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 : 17.170 121.163 12000 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 % Allowed : 9.48 % Favored : 86.90 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS B 466 PHE 0.081 0.011 PHE B 44 TYR 0.143 0.011 TYR E 400 ARG 0.012 0.001 ARG B 161 *********************** 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 : 3.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 THR cc_start: 0.9067 (OUTLIER) cc_final: 0.8803 (m) REVERT: A 105 ARG cc_start: 0.8238 (ttp80) cc_final: 0.7953 (ttp80) REVERT: A 140 SER cc_start: 0.7979 (t) cc_final: 0.7777 (p) REVERT: A 292 GLN cc_start: 0.8012 (tm-30) cc_final: 0.7281 (tm130) REVERT: A 293 LYS cc_start: 0.8303 (tttp) cc_final: 0.8080 (tttm) REVERT: A 325 MET cc_start: 0.9333 (ttt) cc_final: 0.9031 (ttt) REVERT: A 412 ARG cc_start: 0.7319 (ptt180) cc_final: 0.7067 (ptt-90) REVERT: A 456 PHE cc_start: 0.8765 (t80) cc_final: 0.8522 (t80) REVERT: A 459 TYR cc_start: 0.7874 (t80) cc_final: 0.7472 (t80) REVERT: B 62 LYS cc_start: 0.8423 (mmtp) cc_final: 0.8171 (mmmt) REVERT: B 63 THR cc_start: 0.9086 (OUTLIER) cc_final: 0.8838 (m) REVERT: B 112 GLN cc_start: 0.6915 (tt0) cc_final: 0.6705 (mp10) REVERT: B 206 LYS cc_start: 0.8012 (mmtt) cc_final: 0.7731 (mmmt) REVERT: B 269 ASP cc_start: 0.7769 (m-30) cc_final: 0.7559 (m-30) REVERT: B 292 GLN cc_start: 0.8024 (tm-30) cc_final: 0.7300 (tm130) REVERT: B 293 LYS cc_start: 0.8302 (tttp) cc_final: 0.8093 (tttm) REVERT: B 325 MET cc_start: 0.9307 (ttt) cc_final: 0.8995 (ttt) REVERT: B 330 ILE cc_start: 0.8710 (OUTLIER) cc_final: 0.8507 (pp) REVERT: B 412 ARG cc_start: 0.7896 (ptt180) cc_final: 0.7507 (ptt180) REVERT: B 459 TYR cc_start: 0.7934 (t80) cc_final: 0.7493 (t80) REVERT: C 63 THR cc_start: 0.9117 (OUTLIER) cc_final: 0.8844 (m) REVERT: C 292 GLN cc_start: 0.7999 (tm-30) cc_final: 0.7287 (tm130) REVERT: C 293 LYS cc_start: 0.8261 (tttp) cc_final: 0.8030 (tttm) REVERT: C 325 MET cc_start: 0.9313 (ttt) cc_final: 0.8998 (ttt) REVERT: C 412 ARG cc_start: 0.8006 (ptt180) cc_final: 0.7584 (ptt180) REVERT: C 456 PHE cc_start: 0.8843 (t80) cc_final: 0.8606 (t80) REVERT: C 459 TYR cc_start: 0.7835 (t80) cc_final: 0.7562 (t80) REVERT: D 63 THR cc_start: 0.9091 (OUTLIER) cc_final: 0.8828 (m) REVERT: D 112 GLN cc_start: 0.6988 (tt0) cc_final: 0.6704 (mp10) REVERT: D 269 ASP cc_start: 0.7755 (m-30) cc_final: 0.7512 (m-30) REVERT: D 292 GLN cc_start: 0.8080 (tm-30) cc_final: 0.7351 (tm130) REVERT: D 325 MET cc_start: 0.9323 (ttt) cc_final: 0.9012 (ttt) REVERT: D 412 ARG cc_start: 0.8065 (ptt180) cc_final: 0.7754 (ptt180) REVERT: D 456 PHE cc_start: 0.8799 (t80) cc_final: 0.8503 (t80) REVERT: D 459 TYR cc_start: 0.7958 (t80) cc_final: 0.7529 (t80) REVERT: D 470 ASP cc_start: 0.7979 (OUTLIER) cc_final: 0.7779 (m-30) REVERT: E 52 THR cc_start: 0.8963 (t) cc_final: 0.8716 (m) REVERT: E 62 LYS cc_start: 0.8404 (mmtp) cc_final: 0.8065 (mmmt) REVERT: E 63 THR cc_start: 0.9115 (OUTLIER) cc_final: 0.8847 (m) REVERT: E 206 LYS cc_start: 0.7978 (mmpt) cc_final: 0.7667 (mmmt) REVERT: E 269 ASP cc_start: 0.7762 (m-30) cc_final: 0.7549 (m-30) REVERT: E 291 LYS cc_start: 0.8364 (mmmt) cc_final: 0.8136 (mttp) REVERT: E 292 GLN cc_start: 0.8062 (tm-30) cc_final: 0.7317 (tm130) REVERT: E 325 MET cc_start: 0.9327 (ttt) cc_final: 0.8994 (ttt) REVERT: E 412 ARG cc_start: 0.8043 (ptt180) cc_final: 0.7698 (ptt180) REVERT: E 456 PHE cc_start: 0.8728 (t80) cc_final: 0.8405 (t80) REVERT: E 459 TYR cc_start: 0.7919 (t80) cc_final: 0.7507 (t80) REVERT: F 63 THR cc_start: 0.9102 (OUTLIER) cc_final: 0.8820 (m) REVERT: F 292 GLN cc_start: 0.8051 (tm-30) cc_final: 0.7322 (tm130) REVERT: F 325 MET cc_start: 0.9318 (ttt) cc_final: 0.9012 (ttt) REVERT: F 459 TYR cc_start: 0.7898 (t80) cc_final: 0.7660 (t80) REVERT: G 52 THR cc_start: 0.8925 (t) cc_final: 0.8718 (m) REVERT: G 62 LYS cc_start: 0.8439 (mmtp) cc_final: 0.8084 (mmmt) REVERT: G 63 THR cc_start: 0.9112 (OUTLIER) cc_final: 0.8825 (m) REVERT: G 292 GLN cc_start: 0.8052 (tm-30) cc_final: 0.7325 (tm130) REVERT: G 325 MET cc_start: 0.9334 (ttt) cc_final: 0.9040 (ttt) REVERT: G 412 ARG cc_start: 0.7824 (ptt180) cc_final: 0.7362 (ptt180) REVERT: G 456 PHE cc_start: 0.8765 (t80) cc_final: 0.8499 (t80) REVERT: G 459 TYR cc_start: 0.8008 (t80) cc_final: 0.7562 (t80) REVERT: G 470 ASP cc_start: 0.7930 (OUTLIER) cc_final: 0.7719 (m-30) REVERT: H 52 THR cc_start: 0.8963 (t) cc_final: 0.8683 (m) REVERT: H 62 LYS cc_start: 0.8423 (mmtp) cc_final: 0.8155 (mmmt) REVERT: H 63 THR cc_start: 0.9106 (OUTLIER) cc_final: 0.8833 (m) REVERT: H 162 ASP cc_start: 0.7661 (m-30) cc_final: 0.7452 (m-30) REVERT: H 217 GLU cc_start: 0.6237 (mp0) cc_final: 0.5718 (pm20) REVERT: H 269 ASP cc_start: 0.7792 (m-30) cc_final: 0.7556 (m-30) REVERT: H 292 GLN cc_start: 0.8052 (tm-30) cc_final: 0.7326 (tm130) REVERT: H 325 MET cc_start: 0.9312 (ttt) cc_final: 0.8977 (ttt) REVERT: H 420 MET cc_start: 0.8012 (mtm) cc_final: 0.7743 (mtp) REVERT: H 459 TYR cc_start: 0.7827 (t80) cc_final: 0.7547 (t80) outliers start: 114 outliers final: 63 residues processed: 738 average time/residue: 2.2245 time to fit residues: 1974.7175 Evaluate side-chains 595 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 521 time to evaluate : 3.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 327 CYS Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 339 CYS Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 438 LYS Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 327 CYS Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 339 CYS Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 327 CYS Chi-restraints excluded: chain C residue 339 CYS Chi-restraints excluded: chain C residue 361 ILE Chi-restraints excluded: chain C residue 450 LYS Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 77 ASP Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 327 CYS Chi-restraints excluded: chain D residue 339 CYS Chi-restraints excluded: chain D residue 361 ILE Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 470 ASP Chi-restraints excluded: chain E residue 45 ILE Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 264 THR Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 327 CYS Chi-restraints excluded: chain E residue 339 CYS Chi-restraints excluded: chain E residue 361 ILE Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 77 ASP Chi-restraints excluded: chain F residue 264 THR Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 327 CYS Chi-restraints excluded: chain F residue 339 CYS Chi-restraints excluded: chain F residue 361 ILE Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain G residue 45 ILE Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 264 THR Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 327 CYS Chi-restraints excluded: chain G residue 339 CYS Chi-restraints excluded: chain G residue 361 ILE Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 438 LYS Chi-restraints excluded: chain G residue 443 VAL Chi-restraints excluded: chain G residue 447 ILE Chi-restraints excluded: chain G residue 470 ASP Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 264 THR Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 327 CYS Chi-restraints excluded: chain H residue 333 THR Chi-restraints excluded: chain H residue 339 CYS Chi-restraints excluded: chain H residue 361 ILE Chi-restraints excluded: chain H residue 438 LYS 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: 5.9990 chunk 99 optimal weight: 0.7980 chunk 196 optimal weight: 0.9990 chunk 155 optimal weight: 5.9990 chunk 300 optimal weight: 2.9990 chunk 116 optimal weight: 0.9980 chunk 183 optimal weight: 0.9990 chunk 224 optimal weight: 0.8980 chunk 348 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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: 0.8461 moved from start: 0.1979 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= 0.221 Angle : 0.585 6.256 41680 Z= 0.313 Chirality : 0.043 0.164 4840 Planarity : 0.005 0.044 5176 Dihedral : 14.770 94.993 5297 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.75 % Favored : 96.99 % Rotamer: Outliers : 3.09 % Allowed : 14.76 % Favored : 82.16 % 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: -0.77 (0.13), residues: 3824 helix: -0.20 (0.13), residues: 1504 sheet: 0.53 (0.29), residues: 272 loop : -0.84 (0.13), residues: 2048 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 466 PHE 0.010 0.001 PHE D 357 TYR 0.013 0.001 TYR C 282 ARG 0.004 0.000 ARG B 136 *********************** 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 649 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 552 time to evaluate : 4.361 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: A 140 SER cc_start: 0.8491 (t) cc_final: 0.8204 (p) REVERT: A 292 GLN cc_start: 0.7947 (tm-30) cc_final: 0.7339 (tm-30) REVERT: A 293 LYS cc_start: 0.8284 (tttp) cc_final: 0.8045 (ttpp) REVERT: A 456 PHE cc_start: 0.8714 (t80) cc_final: 0.8483 (t80) REVERT: A 459 TYR cc_start: 0.7846 (t80) cc_final: 0.7479 (t80) REVERT: B 62 LYS cc_start: 0.8494 (mmtp) cc_final: 0.8179 (mmmt) REVERT: B 202 GLN cc_start: 0.8443 (tt0) cc_final: 0.8186 (tt0) REVERT: B 292 GLN cc_start: 0.7950 (tm-30) cc_final: 0.7340 (tm-30) REVERT: B 293 LYS cc_start: 0.8303 (tttp) cc_final: 0.7999 (ttpp) REVERT: B 330 ILE cc_start: 0.8611 (OUTLIER) cc_final: 0.8411 (pp) REVERT: B 412 ARG cc_start: 0.7897 (ptt180) cc_final: 0.7684 (ptt180) REVERT: B 459 TYR cc_start: 0.7866 (t80) cc_final: 0.7464 (t80) REVERT: B 474 ARG cc_start: 0.8210 (OUTLIER) cc_final: 0.7295 (ptp90) REVERT: C 63 THR cc_start: 0.9081 (OUTLIER) cc_final: 0.8874 (m) REVERT: C 292 GLN cc_start: 0.7902 (tm-30) cc_final: 0.7328 (tm-30) REVERT: C 325 MET cc_start: 0.9232 (ttt) cc_final: 0.8953 (ttt) REVERT: C 412 ARG cc_start: 0.7981 (ptt180) cc_final: 0.7764 (ptt90) REVERT: C 459 TYR cc_start: 0.7813 (t80) cc_final: 0.7544 (t80) REVERT: D 292 GLN cc_start: 0.7996 (tm-30) cc_final: 0.7395 (tm-30) REVERT: D 412 ARG cc_start: 0.8088 (ptt180) cc_final: 0.7784 (ptt90) REVERT: D 456 PHE cc_start: 0.8742 (t80) cc_final: 0.8425 (t80) REVERT: E 62 LYS cc_start: 0.8497 (mmtp) cc_final: 0.8162 (mmmt) REVERT: E 63 THR cc_start: 0.9059 (OUTLIER) cc_final: 0.8853 (m) REVERT: E 150 MET cc_start: 0.7083 (tpp) cc_final: 0.6880 (tpt) REVERT: E 206 LYS cc_start: 0.8044 (mmpt) cc_final: 0.7822 (mmmt) REVERT: E 292 GLN cc_start: 0.7988 (tm-30) cc_final: 0.7375 (tm-30) REVERT: E 325 MET cc_start: 0.9247 (ttt) cc_final: 0.8942 (ttt) REVERT: E 330 ILE cc_start: 0.8559 (OUTLIER) cc_final: 0.8325 (pp) REVERT: E 456 PHE cc_start: 0.8660 (t80) cc_final: 0.8339 (t80) REVERT: F 63 THR cc_start: 0.9029 (OUTLIER) cc_final: 0.8821 (m) REVERT: F 217 GLU cc_start: 0.6364 (mp0) cc_final: 0.5922 (mp0) REVERT: F 291 LYS cc_start: 0.8309 (mmmt) cc_final: 0.8106 (mttp) REVERT: F 292 GLN cc_start: 0.7977 (tm-30) cc_final: 0.7374 (tm-30) REVERT: F 325 MET cc_start: 0.9242 (ttt) cc_final: 0.8939 (ttt) REVERT: F 330 ILE cc_start: 0.8631 (OUTLIER) cc_final: 0.8344 (pp) REVERT: F 459 TYR cc_start: 0.7857 (t80) cc_final: 0.7614 (t80) REVERT: G 63 THR cc_start: 0.9026 (OUTLIER) cc_final: 0.8794 (m) REVERT: G 112 GLN cc_start: 0.6781 (mp10) cc_final: 0.6437 (mp10) REVERT: G 202 GLN cc_start: 0.8465 (tt0) cc_final: 0.8185 (tt0) REVERT: G 292 GLN cc_start: 0.7979 (tm-30) cc_final: 0.7367 (tm-30) REVERT: G 412 ARG cc_start: 0.7920 (ptt180) cc_final: 0.7414 (ptt180) REVERT: G 456 PHE cc_start: 0.8700 (t80) cc_final: 0.8484 (t80) REVERT: G 459 TYR cc_start: 0.7946 (t80) cc_final: 0.7537 (t80) REVERT: G 470 ASP cc_start: 0.7778 (OUTLIER) cc_final: 0.7565 (m-30) REVERT: H 52 THR cc_start: 0.8937 (t) cc_final: 0.8703 (m) REVERT: H 63 THR cc_start: 0.9009 (OUTLIER) cc_final: 0.8793 (m) REVERT: H 217 GLU cc_start: 0.6222 (mp0) cc_final: 0.5644 (pm20) REVERT: H 291 LYS cc_start: 0.8300 (mmmt) cc_final: 0.8099 (mttp) REVERT: H 292 GLN cc_start: 0.7974 (tm-30) cc_final: 0.7371 (tm-30) REVERT: H 420 MET cc_start: 0.8056 (mtm) cc_final: 0.7776 (mtp) REVERT: H 459 TYR cc_start: 0.7812 (t80) cc_final: 0.7541 (t80) outliers start: 97 outliers final: 59 residues processed: 616 average time/residue: 2.2678 time to fit residues: 1694.4826 Evaluate side-chains 575 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 506 time to evaluate : 3.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 339 CYS Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 470 ASP Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 339 CYS Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 470 ASP Chi-restraints excluded: chain B residue 474 ARG Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 135 MET Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 339 CYS Chi-restraints excluded: chain C residue 361 ILE Chi-restraints excluded: chain C residue 388 SER Chi-restraints excluded: chain C residue 447 ILE Chi-restraints excluded: chain C residue 450 LYS Chi-restraints excluded: chain C residue 470 ASP Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 339 CYS Chi-restraints excluded: chain D residue 361 ILE Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 135 MET Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain E residue 264 THR Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 339 CYS Chi-restraints excluded: chain E residue 361 ILE Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 470 ASP Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 135 MET Chi-restraints excluded: chain F residue 264 THR Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 339 CYS Chi-restraints excluded: chain F residue 361 ILE Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 443 VAL Chi-restraints excluded: chain F residue 470 ASP Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 226 ASP Chi-restraints excluded: chain G residue 264 THR Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 339 CYS Chi-restraints excluded: chain G residue 361 ILE Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 443 VAL Chi-restraints excluded: chain G residue 470 ASP Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 179 MET Chi-restraints excluded: chain H residue 264 THR Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 339 CYS Chi-restraints excluded: chain H residue 361 ILE Chi-restraints excluded: chain H residue 470 ASP 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: 0.8980 chunk 237 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 349 optimal weight: 3.9990 chunk 377 optimal weight: 7.9990 chunk 311 optimal weight: 4.9990 chunk 346 optimal weight: 0.9980 chunk 119 optimal weight: 3.9990 chunk 280 optimal weight: 7.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 30712 Z= 0.271 Angle : 0.531 5.546 41680 Z= 0.282 Chirality : 0.044 0.170 4840 Planarity : 0.004 0.038 5176 Dihedral : 13.877 87.977 5252 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.84 % Favored : 96.05 % Rotamer: Outliers : 2.96 % Allowed : 14.25 % Favored : 82.79 % 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 (0.13), residues: 3824 helix: 0.22 (0.14), residues: 1496 sheet: 0.59 (0.29), residues: 272 loop : -0.74 (0.13), residues: 2056 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 296 PHE 0.010 0.001 PHE E 110 TYR 0.009 0.001 TYR C 282 ARG 0.004 0.001 ARG B 136 *********************** 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 630 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 537 time to evaluate : 3.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 GLN cc_start: 0.7939 (tm-30) cc_final: 0.7292 (tm-30) REVERT: A 293 LYS cc_start: 0.8301 (tttp) cc_final: 0.7975 (ttpp) REVERT: A 325 MET cc_start: 0.9264 (ttt) cc_final: 0.9010 (ttt) REVERT: A 330 ILE cc_start: 0.8773 (OUTLIER) cc_final: 0.8566 (pp) REVERT: A 495 MET cc_start: 0.6430 (OUTLIER) cc_final: 0.6051 (tmm) REVERT: B 202 GLN cc_start: 0.8468 (tt0) cc_final: 0.8174 (tt0) REVERT: B 217 GLU cc_start: 0.5931 (mp0) cc_final: 0.5612 (mp0) REVERT: B 291 LYS cc_start: 0.8318 (mmmt) cc_final: 0.8111 (mttp) REVERT: B 292 GLN cc_start: 0.7984 (tm-30) cc_final: 0.7346 (tm-30) REVERT: B 293 LYS cc_start: 0.8345 (tttp) cc_final: 0.8045 (ttpp) REVERT: B 325 MET cc_start: 0.9268 (ttt) cc_final: 0.9005 (ttt) REVERT: C 150 MET cc_start: 0.7453 (tpp) cc_final: 0.7206 (tpt) REVERT: C 217 GLU cc_start: 0.6176 (mp0) cc_final: 0.5803 (mp0) REVERT: C 292 GLN cc_start: 0.7899 (tm-30) cc_final: 0.7317 (tm-30) REVERT: C 293 LYS cc_start: 0.8332 (tttp) cc_final: 0.8009 (ttpp) REVERT: C 412 ARG cc_start: 0.8013 (ptt180) cc_final: 0.7748 (ptt90) REVERT: C 459 TYR cc_start: 0.7814 (t80) cc_final: 0.7465 (t80) REVERT: D 217 GLU cc_start: 0.6186 (mp0) cc_final: 0.5787 (mp0) REVERT: D 292 GLN cc_start: 0.7989 (tm-30) cc_final: 0.7291 (tm130) REVERT: D 325 MET cc_start: 0.9245 (ttt) cc_final: 0.8995 (ttt) REVERT: D 412 ARG cc_start: 0.8056 (ptt180) cc_final: 0.7800 (ptt90) REVERT: D 456 PHE cc_start: 0.8772 (t80) cc_final: 0.8480 (t80) REVERT: E 150 MET cc_start: 0.7052 (tpp) cc_final: 0.6735 (tpt) REVERT: E 292 GLN cc_start: 0.7977 (tm-30) cc_final: 0.7358 (tm-30) REVERT: E 325 MET cc_start: 0.9247 (ttt) cc_final: 0.9011 (ttt) REVERT: E 456 PHE cc_start: 0.8703 (t80) cc_final: 0.8432 (t80) REVERT: F 217 GLU cc_start: 0.6449 (mp0) cc_final: 0.5952 (mp0) REVERT: F 292 GLN cc_start: 0.8008 (tm-30) cc_final: 0.7301 (tm130) REVERT: F 325 MET cc_start: 0.9255 (ttt) cc_final: 0.9045 (ttt) REVERT: F 455 LYS cc_start: 0.7846 (mmtm) cc_final: 0.7580 (mmmt) REVERT: G 112 GLN cc_start: 0.6855 (mp10) cc_final: 0.6442 (mp10) REVERT: G 202 GLN cc_start: 0.8451 (tt0) cc_final: 0.8153 (tt0) REVERT: G 292 GLN cc_start: 0.7981 (tm-30) cc_final: 0.7299 (tm130) REVERT: G 325 MET cc_start: 0.9261 (ttt) cc_final: 0.8992 (ttt) REVERT: G 412 ARG cc_start: 0.8010 (ptt180) cc_final: 0.7720 (ptt180) REVERT: H 52 THR cc_start: 0.8980 (t) cc_final: 0.8736 (m) REVERT: H 111 GLU cc_start: 0.7435 (tp30) cc_final: 0.7174 (mm-30) REVERT: H 217 GLU cc_start: 0.6320 (mp0) cc_final: 0.6012 (mp0) REVERT: H 291 LYS cc_start: 0.8306 (mmmt) cc_final: 0.8098 (mttp) REVERT: H 292 GLN cc_start: 0.7979 (tm-30) cc_final: 0.7280 (tm130) REVERT: H 325 MET cc_start: 0.9272 (ttt) cc_final: 0.8993 (ttt) REVERT: H 420 MET cc_start: 0.8172 (mtm) cc_final: 0.7864 (mtp) REVERT: H 459 TYR cc_start: 0.7804 (t80) cc_final: 0.7507 (t80) outliers start: 93 outliers final: 64 residues processed: 596 average time/residue: 2.2445 time to fit residues: 1612.2674 Evaluate side-chains 575 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 509 time to evaluate : 3.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 ASP Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 339 CYS Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 470 ASP Chi-restraints excluded: chain A residue 495 MET Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 339 CYS Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain C residue 135 MET Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 339 CYS Chi-restraints excluded: chain C residue 361 ILE Chi-restraints excluded: chain C residue 388 SER Chi-restraints excluded: chain C residue 450 LYS Chi-restraints excluded: chain C residue 470 ASP Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 339 CYS Chi-restraints excluded: chain D residue 361 ILE Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 470 ASP Chi-restraints excluded: chain E residue 135 MET Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain E residue 264 THR Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 339 CYS Chi-restraints excluded: chain E residue 361 ILE Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 443 VAL Chi-restraints excluded: chain E residue 470 ASP Chi-restraints excluded: chain F residue 135 MET Chi-restraints excluded: chain F residue 179 MET Chi-restraints excluded: chain F residue 264 THR Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 339 CYS Chi-restraints excluded: chain F residue 361 ILE Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 443 VAL Chi-restraints excluded: chain F residue 470 ASP Chi-restraints excluded: chain G residue 179 MET Chi-restraints excluded: chain G residue 226 ASP Chi-restraints excluded: chain G residue 264 THR Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 339 CYS Chi-restraints excluded: chain G residue 361 ILE Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 443 VAL Chi-restraints excluded: chain H residue 77 ASP Chi-restraints excluded: chain H residue 135 MET Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 264 THR Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 339 CYS Chi-restraints excluded: chain H residue 361 ILE Chi-restraints excluded: chain H residue 470 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 345 optimal weight: 2.9990 chunk 262 optimal weight: 4.9990 chunk 181 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 166 optimal weight: 1.9990 chunk 234 optimal weight: 4.9990 chunk 350 optimal weight: 3.9990 chunk 371 optimal weight: 2.9990 chunk 183 optimal weight: 5.9990 chunk 332 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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 265 GLN D 94 ASN E 94 ASN F 94 ASN F 441 GLN G 94 ASN G 441 GLN ** H 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.2513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 30712 Z= 0.451 Angle : 0.574 5.476 41680 Z= 0.307 Chirality : 0.047 0.166 4840 Planarity : 0.005 0.049 5176 Dihedral : 14.053 89.385 5242 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.58 % Favored : 95.24 % Rotamer: Outliers : 3.63 % Allowed : 15.46 % Favored : 80.92 % 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: -0.58 (0.13), residues: 3824 helix: 0.17 (0.14), residues: 1496 sheet: 0.24 (0.26), residues: 352 loop : -0.89 (0.13), residues: 1976 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 296 PHE 0.015 0.002 PHE C 44 TYR 0.010 0.002 TYR E 233 ARG 0.004 0.001 ARG A 259 *********************** 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 625 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 511 time to evaluate : 3.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 GLN cc_start: 0.7992 (tm-30) cc_final: 0.7322 (tm-30) REVERT: A 325 MET cc_start: 0.9275 (ttt) cc_final: 0.9007 (ttt) REVERT: A 455 LYS cc_start: 0.7837 (mmtm) cc_final: 0.7572 (mmmt) REVERT: B 202 GLN cc_start: 0.8478 (tt0) cc_final: 0.8156 (tt0) REVERT: B 217 GLU cc_start: 0.5958 (mp0) cc_final: 0.5615 (mp0) REVERT: B 292 GLN cc_start: 0.8003 (tm-30) cc_final: 0.7438 (tm-30) REVERT: B 459 TYR cc_start: 0.7817 (t80) cc_final: 0.7428 (t80) REVERT: C 111 GLU cc_start: 0.7416 (tp30) cc_final: 0.7165 (mm-30) REVERT: C 217 GLU cc_start: 0.6082 (mp0) cc_final: 0.5777 (mp0) REVERT: C 292 GLN cc_start: 0.7938 (tm-30) cc_final: 0.7356 (tm-30) REVERT: D 292 GLN cc_start: 0.8040 (tm-30) cc_final: 0.7314 (tm130) REVERT: D 325 MET cc_start: 0.9301 (ttt) cc_final: 0.9052 (ttt) REVERT: D 412 ARG cc_start: 0.8098 (ptt180) cc_final: 0.7844 (ptt90) REVERT: D 456 PHE cc_start: 0.8794 (t80) cc_final: 0.8534 (t80) REVERT: E 111 GLU cc_start: 0.7484 (tp30) cc_final: 0.7203 (mm-30) REVERT: E 112 GLN cc_start: 0.7645 (OUTLIER) cc_final: 0.7203 (tm-30) REVERT: E 150 MET cc_start: 0.6984 (tpp) cc_final: 0.6593 (tpt) REVERT: E 292 GLN cc_start: 0.8005 (tm-30) cc_final: 0.7259 (tm130) REVERT: E 325 MET cc_start: 0.9283 (ttt) cc_final: 0.9044 (ttt) REVERT: E 456 PHE cc_start: 0.8726 (t80) cc_final: 0.8481 (t80) REVERT: F 111 GLU cc_start: 0.7472 (tp30) cc_final: 0.7258 (mm-30) REVERT: F 217 GLU cc_start: 0.6480 (mp0) cc_final: 0.5975 (mp0) REVERT: F 292 GLN cc_start: 0.8014 (tm-30) cc_final: 0.7288 (tm130) REVERT: F 325 MET cc_start: 0.9280 (ttt) cc_final: 0.9058 (ttt) REVERT: F 455 LYS cc_start: 0.7845 (mmtm) cc_final: 0.7579 (mmmt) REVERT: G 112 GLN cc_start: 0.6887 (mp10) cc_final: 0.6434 (mp10) REVERT: G 121 LEU cc_start: 0.7174 (OUTLIER) cc_final: 0.6928 (mp) REVERT: G 202 GLN cc_start: 0.8412 (tt0) cc_final: 0.8088 (tt0) REVERT: G 292 GLN cc_start: 0.8004 (tm-30) cc_final: 0.7306 (tm130) REVERT: G 412 ARG cc_start: 0.8023 (ptt180) cc_final: 0.7486 (ptt180) REVERT: G 414 MET cc_start: 0.7845 (mmm) cc_final: 0.7590 (mmm) REVERT: G 455 LYS cc_start: 0.7832 (mmtm) cc_final: 0.7577 (mmmt) REVERT: H 111 GLU cc_start: 0.7476 (tp30) cc_final: 0.7213 (mm-30) REVERT: H 140 SER cc_start: 0.8019 (m) cc_final: 0.7289 (p) REVERT: H 217 GLU cc_start: 0.6282 (mp0) cc_final: 0.5911 (mp0) REVERT: H 292 GLN cc_start: 0.8018 (tm-30) cc_final: 0.7244 (tm130) REVERT: H 325 MET cc_start: 0.9279 (ttt) cc_final: 0.9004 (ttt) REVERT: H 420 MET cc_start: 0.8243 (mtm) cc_final: 0.7949 (mtp) REVERT: H 459 TYR cc_start: 0.7785 (t80) cc_final: 0.7461 (t80) REVERT: H 495 MET cc_start: 0.6457 (OUTLIER) cc_final: 0.6237 (tpt) outliers start: 114 outliers final: 80 residues processed: 570 average time/residue: 2.2624 time to fit residues: 1551.7571 Evaluate side-chains 585 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 502 time to evaluate : 3.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 339 CYS Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 339 CYS Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain C residue 77 ASP Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 135 MET Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 339 CYS Chi-restraints excluded: chain C residue 361 ILE Chi-restraints excluded: chain C residue 388 SER Chi-restraints excluded: chain C residue 450 LYS Chi-restraints excluded: chain D residue 77 ASP Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 268 VAL Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 339 CYS Chi-restraints excluded: chain D residue 361 ILE Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 112 GLN Chi-restraints excluded: chain E residue 135 MET Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain E residue 255 ASP Chi-restraints excluded: chain E residue 264 THR Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 339 CYS Chi-restraints excluded: chain E residue 361 ILE Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 443 VAL Chi-restraints excluded: chain E residue 470 ASP Chi-restraints excluded: chain F residue 77 ASP Chi-restraints excluded: chain F residue 135 MET Chi-restraints excluded: chain F residue 179 MET Chi-restraints excluded: chain F residue 264 THR Chi-restraints excluded: chain F residue 268 VAL Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 339 CYS Chi-restraints excluded: chain F residue 361 ILE Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 443 VAL Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 121 LEU Chi-restraints excluded: chain G residue 179 MET Chi-restraints excluded: chain G residue 226 ASP Chi-restraints excluded: chain G residue 255 ASP Chi-restraints excluded: chain G residue 264 THR Chi-restraints excluded: chain G residue 268 VAL Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 339 CYS Chi-restraints excluded: chain G residue 361 ILE Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 443 VAL Chi-restraints excluded: chain H residue 77 ASP Chi-restraints excluded: chain H residue 135 MET Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 179 MET Chi-restraints excluded: chain H residue 221 ILE Chi-restraints excluded: chain H residue 264 THR Chi-restraints excluded: chain H residue 268 VAL Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 339 CYS Chi-restraints excluded: chain H residue 361 ILE Chi-restraints excluded: chain H residue 443 VAL Chi-restraints excluded: chain H residue 495 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 309 optimal weight: 5.9990 chunk 210 optimal weight: 0.0980 chunk 5 optimal weight: 0.8980 chunk 276 optimal weight: 1.9990 chunk 153 optimal weight: 2.9990 chunk 316 optimal weight: 0.8980 chunk 256 optimal weight: 3.9990 chunk 0 optimal weight: 1.9990 chunk 189 optimal weight: 1.9990 chunk 333 optimal weight: 0.9990 chunk 93 optimal weight: 0.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- 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 230 ASN B 265 GLN C 265 GLN C 441 GLN F 94 ASN F 441 GLN G 441 GLN ** H 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 30712 Z= 0.176 Angle : 0.492 6.319 41680 Z= 0.259 Chirality : 0.042 0.170 4840 Planarity : 0.004 0.039 5176 Dihedral : 13.421 89.837 5241 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.61 % Favored : 96.34 % Rotamer: Outliers : 2.70 % Allowed : 16.73 % Favored : 80.57 % 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: -0.10 (0.14), residues: 3824 helix: 0.57 (0.14), residues: 1496 sheet: 0.47 (0.28), residues: 272 loop : -0.57 (0.13), residues: 2056 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.000 HIS C 296 PHE 0.012 0.001 PHE G 99 TYR 0.009 0.001 TYR G 353 ARG 0.002 0.000 ARG A 259 *********************** 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 604 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 519 time to evaluate : 3.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 GLN cc_start: 0.7934 (tm-30) cc_final: 0.7279 (tm-30) REVERT: A 325 MET cc_start: 0.9212 (ttt) cc_final: 0.9002 (ttt) REVERT: A 455 LYS cc_start: 0.7796 (mmtm) cc_final: 0.7534 (mmmt) REVERT: A 459 TYR cc_start: 0.7757 (t80) cc_final: 0.7426 (t80) REVERT: B 202 GLN cc_start: 0.8492 (tt0) cc_final: 0.8156 (tt0) REVERT: B 217 GLU cc_start: 0.5910 (mp0) cc_final: 0.5582 (mp0) REVERT: B 243 GLN cc_start: 0.7502 (mm-40) cc_final: 0.7277 (mm-40) REVERT: B 292 GLN cc_start: 0.7946 (tm-30) cc_final: 0.7396 (tm-30) REVERT: B 293 LYS cc_start: 0.8316 (tttp) cc_final: 0.8016 (ttpp) REVERT: B 325 MET cc_start: 0.9234 (ttt) cc_final: 0.8989 (ttt) REVERT: B 459 TYR cc_start: 0.7779 (t80) cc_final: 0.7417 (t80) REVERT: C 111 GLU cc_start: 0.7375 (tp30) cc_final: 0.7135 (mm-30) REVERT: C 150 MET cc_start: 0.7451 (tpp) cc_final: 0.7230 (tpt) REVERT: C 217 GLU cc_start: 0.6152 (mp0) cc_final: 0.5808 (mp0) REVERT: C 226 ASP cc_start: 0.7930 (OUTLIER) cc_final: 0.7622 (m-30) REVERT: C 292 GLN cc_start: 0.7882 (tm-30) cc_final: 0.7315 (tm-30) REVERT: C 293 LYS cc_start: 0.8271 (tttp) cc_final: 0.7948 (ttpp) REVERT: C 459 TYR cc_start: 0.7780 (t80) cc_final: 0.7436 (t80) REVERT: D 292 GLN cc_start: 0.7973 (tm-30) cc_final: 0.7262 (tm130) REVERT: D 325 MET cc_start: 0.9215 (ttt) cc_final: 0.8996 (ttt) REVERT: D 412 ARG cc_start: 0.8042 (ptt180) cc_final: 0.7790 (ptt90) REVERT: D 456 PHE cc_start: 0.8755 (t80) cc_final: 0.8499 (t80) REVERT: E 111 GLU cc_start: 0.7497 (tp30) cc_final: 0.7212 (mm-30) REVERT: E 112 GLN cc_start: 0.7576 (OUTLIER) cc_final: 0.7168 (tm-30) REVERT: E 217 GLU cc_start: 0.6151 (mp0) cc_final: 0.5734 (mp0) REVERT: E 292 GLN cc_start: 0.7959 (tm-30) cc_final: 0.7327 (tm-30) REVERT: E 325 MET cc_start: 0.9195 (ttt) cc_final: 0.8977 (ttt) REVERT: E 456 PHE cc_start: 0.8719 (t80) cc_final: 0.8455 (t80) REVERT: F 111 GLU cc_start: 0.7426 (tp30) cc_final: 0.7147 (mm-30) REVERT: F 217 GLU cc_start: 0.6433 (mp0) cc_final: 0.5953 (mp0) REVERT: F 292 GLN cc_start: 0.7950 (tm-30) cc_final: 0.7301 (tm-30) REVERT: F 455 LYS cc_start: 0.7819 (mmtm) cc_final: 0.7582 (mmmt) REVERT: G 112 GLN cc_start: 0.6870 (mp10) cc_final: 0.6373 (mp10) REVERT: G 121 LEU cc_start: 0.7052 (OUTLIER) cc_final: 0.6820 (mp) REVERT: G 202 GLN cc_start: 0.8409 (tt0) cc_final: 0.8084 (tt0) REVERT: G 292 GLN cc_start: 0.7943 (tm-30) cc_final: 0.7350 (tm-30) REVERT: G 325 MET cc_start: 0.9264 (ttt) cc_final: 0.8968 (ttt) REVERT: G 412 ARG cc_start: 0.8021 (ptt180) cc_final: 0.7486 (ptt180) REVERT: G 455 LYS cc_start: 0.7793 (mmtm) cc_final: 0.7535 (mmmt) REVERT: H 111 GLU cc_start: 0.7454 (tp30) cc_final: 0.7226 (mm-30) REVERT: H 140 SER cc_start: 0.7944 (m) cc_final: 0.7216 (p) REVERT: H 217 GLU cc_start: 0.6347 (mp0) cc_final: 0.5994 (mp0) REVERT: H 292 GLN cc_start: 0.7957 (tm-30) cc_final: 0.7309 (tm-30) REVERT: H 325 MET cc_start: 0.9212 (ttt) cc_final: 0.8981 (ttt) REVERT: H 420 MET cc_start: 0.8194 (mtm) cc_final: 0.7880 (mtp) REVERT: H 459 TYR cc_start: 0.7776 (t80) cc_final: 0.7445 (t80) outliers start: 85 outliers final: 67 residues processed: 571 average time/residue: 2.2349 time to fit residues: 1539.0452 Evaluate side-chains 579 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 509 time to evaluate : 3.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 339 CYS Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 470 ASP Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 339 CYS Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 470 ASP Chi-restraints excluded: chain C residue 135 MET Chi-restraints excluded: chain C residue 226 ASP Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 339 CYS Chi-restraints excluded: chain C residue 361 ILE Chi-restraints excluded: chain C residue 388 SER Chi-restraints excluded: chain C residue 450 LYS Chi-restraints excluded: chain C residue 470 ASP Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 268 VAL Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 339 CYS Chi-restraints excluded: chain D residue 361 ILE Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain E residue 112 GLN Chi-restraints excluded: chain E residue 135 MET Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain E residue 179 MET Chi-restraints excluded: chain E residue 264 THR Chi-restraints excluded: chain E residue 268 VAL Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 339 CYS Chi-restraints excluded: chain E residue 361 ILE Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 443 VAL Chi-restraints excluded: chain E residue 470 ASP Chi-restraints excluded: chain F residue 135 MET Chi-restraints excluded: chain F residue 179 MET Chi-restraints excluded: chain F residue 264 THR Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 339 CYS Chi-restraints excluded: chain F residue 361 ILE Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 443 VAL Chi-restraints excluded: chain F residue 470 ASP Chi-restraints excluded: chain G residue 121 LEU Chi-restraints excluded: chain G residue 179 MET Chi-restraints excluded: chain G residue 226 ASP Chi-restraints excluded: chain G residue 264 THR Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 339 CYS Chi-restraints excluded: chain G residue 361 ILE Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 393 THR Chi-restraints excluded: chain G residue 443 VAL Chi-restraints excluded: chain G residue 470 ASP Chi-restraints excluded: chain H residue 264 THR Chi-restraints excluded: chain H residue 268 VAL Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 339 CYS Chi-restraints excluded: chain H residue 361 ILE 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: 2.9990 chunk 91 optimal weight: 1.9990 chunk 371 optimal weight: 3.9990 chunk 308 optimal weight: 3.9990 chunk 172 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 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 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 30712 Z= 0.317 Angle : 0.518 5.300 41680 Z= 0.275 Chirality : 0.044 0.164 4840 Planarity : 0.005 0.043 5176 Dihedral : 13.333 89.980 5241 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.58 % Favored : 95.32 % Rotamer: Outliers : 3.31 % Allowed : 16.51 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.14), residues: 3824 helix: 0.58 (0.14), residues: 1496 sheet: 0.35 (0.29), residues: 272 loop : -0.61 (0.13), residues: 2056 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS H 466 PHE 0.016 0.002 PHE A 99 TYR 0.009 0.001 TYR G 353 ARG 0.003 0.001 ARG A 322 *********************** 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 618 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 514 time to evaluate : 3.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 GLN cc_start: 0.7943 (tm-30) cc_final: 0.7281 (tm-30) REVERT: A 455 LYS cc_start: 0.7797 (mmtm) cc_final: 0.7540 (mmmt) REVERT: A 459 TYR cc_start: 0.7763 (t80) cc_final: 0.7410 (t80) REVERT: B 202 GLN cc_start: 0.8522 (tt0) cc_final: 0.8192 (tt0) REVERT: B 217 GLU cc_start: 0.5914 (mp0) cc_final: 0.5606 (mp0) REVERT: B 292 GLN cc_start: 0.7962 (tm-30) cc_final: 0.7337 (tm-30) REVERT: B 325 MET cc_start: 0.9276 (ttt) cc_final: 0.9038 (ttt) REVERT: B 459 TYR cc_start: 0.7811 (t80) cc_final: 0.7445 (t80) REVERT: C 111 GLU cc_start: 0.7426 (tp30) cc_final: 0.7181 (mm-30) REVERT: C 132 GLU cc_start: 0.6928 (OUTLIER) cc_final: 0.6632 (tm-30) REVERT: C 150 MET cc_start: 0.7453 (tpp) cc_final: 0.7237 (tpt) REVERT: C 217 GLU cc_start: 0.6045 (mp0) cc_final: 0.5772 (mp0) REVERT: C 292 GLN cc_start: 0.7920 (tm-30) cc_final: 0.7343 (tm-30) REVERT: D 292 GLN cc_start: 0.8011 (tm-30) cc_final: 0.7286 (tm130) REVERT: D 412 ARG cc_start: 0.8085 (ptt180) cc_final: 0.7841 (ptt90) REVERT: D 456 PHE cc_start: 0.8790 (t80) cc_final: 0.8507 (t80) REVERT: E 111 GLU cc_start: 0.7534 (tp30) cc_final: 0.7265 (mm-30) REVERT: E 112 GLN cc_start: 0.7592 (OUTLIER) cc_final: 0.7228 (tm-30) REVERT: E 217 GLU cc_start: 0.6238 (mp0) cc_final: 0.5830 (mp0) REVERT: E 292 GLN cc_start: 0.8011 (tm-30) cc_final: 0.7292 (tm130) REVERT: E 325 MET cc_start: 0.9245 (ttt) cc_final: 0.9044 (ttt) REVERT: F 111 GLU cc_start: 0.7484 (tp30) cc_final: 0.7217 (mm-30) REVERT: F 217 GLU cc_start: 0.6332 (mp0) cc_final: 0.5918 (mp0) REVERT: F 292 GLN cc_start: 0.7994 (tm-30) cc_final: 0.7272 (tm130) REVERT: F 455 LYS cc_start: 0.7811 (mmtm) cc_final: 0.7604 (mmmt) REVERT: G 112 GLN cc_start: 0.6865 (mp10) cc_final: 0.6374 (mp10) REVERT: G 121 LEU cc_start: 0.7094 (OUTLIER) cc_final: 0.6856 (mp) REVERT: G 202 GLN cc_start: 0.8434 (tt0) cc_final: 0.8214 (tt0) REVERT: G 217 GLU cc_start: 0.6555 (mp0) cc_final: 0.6320 (mp0) REVERT: G 292 GLN cc_start: 0.7987 (tm-30) cc_final: 0.7281 (tm130) REVERT: G 325 MET cc_start: 0.9287 (ttt) cc_final: 0.9019 (ttt) REVERT: G 412 ARG cc_start: 0.8029 (ptt180) cc_final: 0.7497 (ptt180) REVERT: G 455 LYS cc_start: 0.7820 (mmtm) cc_final: 0.7556 (mmmt) REVERT: H 140 SER cc_start: 0.7932 (m) cc_final: 0.7264 (p) REVERT: H 217 GLU cc_start: 0.6394 (mp0) cc_final: 0.6067 (mp0) REVERT: H 292 GLN cc_start: 0.7974 (tm-30) cc_final: 0.7253 (tm130) REVERT: H 325 MET cc_start: 0.9268 (ttt) cc_final: 0.9047 (ttt) REVERT: H 420 MET cc_start: 0.8248 (mtm) cc_final: 0.7938 (mtp) REVERT: H 455 LYS cc_start: 0.7780 (mmtm) cc_final: 0.7507 (mmmt) REVERT: H 459 TYR cc_start: 0.7775 (t80) cc_final: 0.7422 (t80) outliers start: 104 outliers final: 80 residues processed: 573 average time/residue: 2.2128 time to fit residues: 1529.6813 Evaluate side-chains 589 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 506 time to evaluate : 3.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 339 CYS Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain B residue 112 GLN Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 339 CYS Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 470 ASP Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 135 MET Chi-restraints excluded: chain C residue 255 ASP Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 339 CYS Chi-restraints excluded: chain C residue 361 ILE Chi-restraints excluded: chain C residue 388 SER Chi-restraints excluded: chain C residue 450 LYS Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 77 ASP Chi-restraints excluded: chain D residue 135 MET Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 268 VAL Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 339 CYS Chi-restraints excluded: chain D residue 361 ILE Chi-restraints excluded: chain E residue 112 GLN Chi-restraints excluded: chain E residue 135 MET Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain E residue 179 MET Chi-restraints excluded: chain E residue 255 ASP Chi-restraints excluded: chain E residue 264 THR Chi-restraints excluded: chain E residue 268 VAL Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 339 CYS Chi-restraints excluded: chain E residue 361 ILE Chi-restraints excluded: chain E residue 443 VAL Chi-restraints excluded: chain E residue 450 LYS Chi-restraints excluded: chain E residue 470 ASP Chi-restraints excluded: chain F residue 135 MET Chi-restraints excluded: chain F residue 179 MET Chi-restraints excluded: chain F residue 264 THR Chi-restraints excluded: chain F residue 268 VAL Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 339 CYS Chi-restraints excluded: chain F residue 361 ILE Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 443 VAL Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 121 LEU Chi-restraints excluded: chain G residue 179 MET Chi-restraints excluded: chain G residue 226 ASP Chi-restraints excluded: chain G residue 255 ASP Chi-restraints excluded: chain G residue 264 THR Chi-restraints excluded: chain G residue 268 VAL Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 339 CYS Chi-restraints excluded: chain G residue 361 ILE Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 393 THR Chi-restraints excluded: chain G residue 443 VAL Chi-restraints excluded: chain G residue 470 ASP Chi-restraints excluded: chain H residue 77 ASP Chi-restraints excluded: chain H residue 179 MET Chi-restraints excluded: chain H residue 221 ILE Chi-restraints excluded: chain H residue 264 THR Chi-restraints excluded: chain H residue 268 VAL Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 339 CYS Chi-restraints excluded: chain H residue 361 ILE Chi-restraints excluded: chain H residue 443 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 358 optimal weight: 0.0980 chunk 41 optimal weight: 7.9990 chunk 211 optimal weight: 0.8980 chunk 271 optimal weight: 3.9990 chunk 210 optimal weight: 0.7980 chunk 312 optimal weight: 1.9990 chunk 207 optimal weight: 4.9990 chunk 370 optimal weight: 1.9990 chunk 231 optimal weight: 6.9990 chunk 225 optimal weight: 1.9990 chunk 170 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 GLN B 94 ASN B 265 GLN C 265 GLN C 441 GLN G 94 ASN G 441 GLN H 94 ASN ** 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: 0.2903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 30712 Z= 0.181 Angle : 0.480 5.056 41680 Z= 0.252 Chirality : 0.042 0.166 4840 Planarity : 0.004 0.036 5176 Dihedral : 12.875 89.980 5239 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.45 % Favored : 96.50 % Rotamer: Outliers : 2.77 % Allowed : 17.08 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.14), residues: 3824 helix: 0.85 (0.15), residues: 1488 sheet: 0.44 (0.28), residues: 272 loop : -0.41 (0.14), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS C 296 PHE 0.016 0.001 PHE A 99 TYR 0.009 0.001 TYR G 353 ARG 0.003 0.000 ARG B 412 *********************** 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 609 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 522 time to evaluate : 3.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 ASN cc_start: 0.8096 (t0) cc_final: 0.7870 (t0) REVERT: A 292 GLN cc_start: 0.7942 (tm-30) cc_final: 0.7302 (tm-30) REVERT: A 455 LYS cc_start: 0.7815 (mmtm) cc_final: 0.7561 (mmmt) REVERT: A 459 TYR cc_start: 0.7772 (t80) cc_final: 0.7435 (t80) REVERT: B 202 GLN cc_start: 0.8487 (tt0) cc_final: 0.8177 (tt0) REVERT: B 217 GLU cc_start: 0.5876 (mp0) cc_final: 0.5539 (mp0) REVERT: B 243 GLN cc_start: 0.7486 (mm-40) cc_final: 0.7262 (mm-40) REVERT: B 292 GLN cc_start: 0.7922 (tm-30) cc_final: 0.7395 (tm-30) REVERT: B 293 LYS cc_start: 0.8320 (tttp) cc_final: 0.8008 (ttpp) REVERT: B 325 MET cc_start: 0.9202 (ttt) cc_final: 0.8965 (ttt) REVERT: B 459 TYR cc_start: 0.7787 (t80) cc_final: 0.7436 (t80) REVERT: C 111 GLU cc_start: 0.7423 (tp30) cc_final: 0.7187 (mm-30) REVERT: C 132 GLU cc_start: 0.6908 (OUTLIER) cc_final: 0.6622 (tm-30) REVERT: C 150 MET cc_start: 0.7461 (tpp) cc_final: 0.7261 (tpt) REVERT: C 217 GLU cc_start: 0.6169 (mp0) cc_final: 0.5862 (mp0) REVERT: C 292 GLN cc_start: 0.7900 (tm-30) cc_final: 0.7342 (tm-30) REVERT: C 330 ILE cc_start: 0.8726 (OUTLIER) cc_final: 0.8488 (pp) REVERT: C 459 TYR cc_start: 0.7782 (t80) cc_final: 0.7433 (t80) REVERT: D 217 GLU cc_start: 0.6280 (mp0) cc_final: 0.5910 (mp0) REVERT: D 292 GLN cc_start: 0.7963 (tm-30) cc_final: 0.7249 (tm130) REVERT: D 412 ARG cc_start: 0.8050 (ptt180) cc_final: 0.7797 (ptt90) REVERT: D 456 PHE cc_start: 0.8770 (t80) cc_final: 0.8517 (t80) REVERT: E 111 GLU cc_start: 0.7519 (tp30) cc_final: 0.7263 (mm-30) REVERT: E 112 GLN cc_start: 0.7587 (OUTLIER) cc_final: 0.7248 (tm-30) REVERT: E 132 GLU cc_start: 0.6887 (OUTLIER) cc_final: 0.6597 (tm-30) REVERT: E 217 GLU cc_start: 0.6249 (mp0) cc_final: 0.5852 (mp0) REVERT: E 292 GLN cc_start: 0.7961 (tm-30) cc_final: 0.7315 (tm-30) REVERT: E 325 MET cc_start: 0.9185 (ttt) cc_final: 0.8965 (ttt) REVERT: F 111 GLU cc_start: 0.7465 (tp30) cc_final: 0.7213 (mm-30) REVERT: F 217 GLU cc_start: 0.6247 (mp0) cc_final: 0.5887 (mp0) REVERT: F 292 GLN cc_start: 0.7965 (tm-30) cc_final: 0.7322 (tm-30) REVERT: G 112 GLN cc_start: 0.6867 (mp10) cc_final: 0.6386 (mp10) REVERT: G 121 LEU cc_start: 0.7075 (OUTLIER) cc_final: 0.6844 (mp) REVERT: G 202 GLN cc_start: 0.8436 (tt0) cc_final: 0.8217 (tt0) REVERT: G 217 GLU cc_start: 0.6524 (mp0) cc_final: 0.6319 (mp0) REVERT: G 292 GLN cc_start: 0.7953 (tm-30) cc_final: 0.7370 (tm-30) REVERT: G 325 MET cc_start: 0.9234 (ttt) cc_final: 0.8949 (ttt) REVERT: G 412 ARG cc_start: 0.8016 (ptt180) cc_final: 0.7494 (ptt180) REVERT: G 455 LYS cc_start: 0.7784 (mmtm) cc_final: 0.7533 (mmmt) REVERT: H 140 SER cc_start: 0.7845 (m) cc_final: 0.7168 (p) REVERT: H 217 GLU cc_start: 0.6285 (mp0) cc_final: 0.5863 (pm20) REVERT: H 292 GLN cc_start: 0.7948 (tm-30) cc_final: 0.7337 (tm-30) REVERT: H 325 MET cc_start: 0.9183 (ttt) cc_final: 0.8966 (ttt) REVERT: H 420 MET cc_start: 0.8266 (mtm) cc_final: 0.7931 (mtp) REVERT: H 455 LYS cc_start: 0.7762 (mmtm) cc_final: 0.7483 (mmmt) REVERT: H 459 TYR cc_start: 0.7767 (t80) cc_final: 0.7436 (t80) outliers start: 87 outliers final: 65 residues processed: 569 average time/residue: 2.3189 time to fit residues: 1603.6085 Evaluate side-chains 576 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 506 time to evaluate : 3.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 339 CYS Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 470 ASP Chi-restraints excluded: chain B residue 112 GLN Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 226 ASP Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 339 CYS Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 470 ASP Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 135 MET Chi-restraints excluded: chain C residue 255 ASP Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 339 CYS Chi-restraints excluded: chain C residue 361 ILE Chi-restraints excluded: chain C residue 388 SER Chi-restraints excluded: chain C residue 450 LYS Chi-restraints excluded: chain C residue 470 ASP Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 268 VAL Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 339 CYS Chi-restraints excluded: chain D residue 361 ILE Chi-restraints excluded: chain E residue 112 GLN Chi-restraints excluded: chain E residue 132 GLU Chi-restraints excluded: chain E residue 135 MET Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain E residue 226 ASP Chi-restraints excluded: chain E residue 264 THR Chi-restraints excluded: chain E residue 268 VAL Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 339 CYS Chi-restraints excluded: chain E residue 361 ILE Chi-restraints excluded: chain E residue 443 VAL Chi-restraints excluded: chain E residue 450 LYS Chi-restraints excluded: chain E residue 470 ASP Chi-restraints excluded: chain F residue 135 MET Chi-restraints excluded: chain F residue 179 MET Chi-restraints excluded: chain F residue 264 THR Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 339 CYS Chi-restraints excluded: chain F residue 361 ILE Chi-restraints excluded: chain F residue 443 VAL Chi-restraints excluded: chain F residue 470 ASP Chi-restraints excluded: chain G residue 121 LEU Chi-restraints excluded: chain G residue 135 MET Chi-restraints excluded: chain G residue 179 MET Chi-restraints excluded: chain G residue 226 ASP Chi-restraints excluded: chain G residue 264 THR Chi-restraints excluded: chain G residue 268 VAL Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 339 CYS Chi-restraints excluded: chain G residue 361 ILE Chi-restraints excluded: chain G residue 393 THR Chi-restraints excluded: chain G residue 443 VAL Chi-restraints excluded: chain H residue 226 ASP Chi-restraints excluded: chain H residue 264 THR Chi-restraints excluded: chain H residue 268 VAL Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 339 CYS Chi-restraints excluded: chain H residue 361 ILE Chi-restraints excluded: chain H residue 443 VAL 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: 0.3980 chunk 221 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 chunk 72 optimal weight: 0.3980 chunk 71 optimal weight: 0.9990 chunk 235 optimal weight: 1.9990 chunk 252 optimal weight: 2.9990 chunk 182 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 chunk 290 optimal weight: 0.7980 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN A 265 GLN ** A 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 GLN C 265 GLN G 94 ASN G 441 GLN H 94 ASN ** H 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.2986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 30712 Z= 0.159 Angle : 0.470 5.085 41680 Z= 0.246 Chirality : 0.041 0.163 4840 Planarity : 0.004 0.035 5176 Dihedral : 12.582 89.279 5235 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.58 % Favored : 96.37 % Rotamer: Outliers : 2.54 % Allowed : 17.72 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.14), residues: 3824 helix: 0.97 (0.15), residues: 1488 sheet: 0.49 (0.29), residues: 272 loop : -0.32 (0.14), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 137 PHE 0.017 0.001 PHE D 99 TYR 0.009 0.001 TYR G 353 ARG 0.002 0.000 ARG B 412 *********************** 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 597 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 517 time to evaluate : 3.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 GLU cc_start: 0.7715 (OUTLIER) cc_final: 0.7444 (mt-10) REVERT: A 230 ASN cc_start: 0.8092 (t0) cc_final: 0.7872 (t0) REVERT: A 292 GLN cc_start: 0.7944 (tm-30) cc_final: 0.7306 (tm-30) REVERT: A 455 LYS cc_start: 0.7810 (mmtm) cc_final: 0.7549 (mmmt) REVERT: A 459 TYR cc_start: 0.7766 (t80) cc_final: 0.7431 (t80) REVERT: B 202 GLN cc_start: 0.8489 (tt0) cc_final: 0.8181 (tt0) REVERT: B 217 GLU cc_start: 0.5785 (mp0) cc_final: 0.5466 (mp0) REVERT: B 292 GLN cc_start: 0.7917 (tm-30) cc_final: 0.7402 (tm-30) REVERT: B 325 MET cc_start: 0.9213 (ttt) cc_final: 0.9005 (ttt) REVERT: B 459 TYR cc_start: 0.7788 (t80) cc_final: 0.7437 (t80) REVERT: C 111 GLU cc_start: 0.7417 (tp30) cc_final: 0.7215 (mm-30) REVERT: C 132 GLU cc_start: 0.6904 (OUTLIER) cc_final: 0.6617 (tm-30) REVERT: C 217 GLU cc_start: 0.6158 (mp0) cc_final: 0.5908 (mp0) REVERT: C 292 GLN cc_start: 0.7893 (tm-30) cc_final: 0.7337 (tm-30) REVERT: C 330 ILE cc_start: 0.8704 (OUTLIER) cc_final: 0.8471 (pp) REVERT: C 459 TYR cc_start: 0.7779 (t80) cc_final: 0.7433 (t80) REVERT: D 217 GLU cc_start: 0.6149 (mp0) cc_final: 0.5822 (mp0) REVERT: D 292 GLN cc_start: 0.7960 (tm-30) cc_final: 0.7250 (tm130) REVERT: D 412 ARG cc_start: 0.8050 (ptt180) cc_final: 0.7787 (ptt90) REVERT: D 456 PHE cc_start: 0.8768 (t80) cc_final: 0.8516 (t80) REVERT: E 75 GLU cc_start: 0.7695 (mt-10) cc_final: 0.7448 (mt-10) REVERT: E 111 GLU cc_start: 0.7526 (tp30) cc_final: 0.7281 (mm-30) REVERT: E 112 GLN cc_start: 0.7578 (OUTLIER) cc_final: 0.7237 (tm-30) REVERT: E 132 GLU cc_start: 0.6889 (OUTLIER) cc_final: 0.6601 (tm-30) REVERT: E 217 GLU cc_start: 0.6199 (mp0) cc_final: 0.5818 (mp0) REVERT: E 292 GLN cc_start: 0.7954 (tm-30) cc_final: 0.7316 (tm-30) REVERT: F 111 GLU cc_start: 0.7465 (tp30) cc_final: 0.7221 (mm-30) REVERT: F 217 GLU cc_start: 0.6170 (mp0) cc_final: 0.5816 (mp0) REVERT: F 292 GLN cc_start: 0.7956 (tm-30) cc_final: 0.7317 (tm-30) REVERT: F 330 ILE cc_start: 0.8753 (OUTLIER) cc_final: 0.8531 (pp) REVERT: G 112 GLN cc_start: 0.6859 (mp10) cc_final: 0.6386 (mp10) REVERT: G 121 LEU cc_start: 0.7044 (OUTLIER) cc_final: 0.6814 (mp) REVERT: G 202 GLN cc_start: 0.8431 (tt0) cc_final: 0.8217 (tt0) REVERT: G 217 GLU cc_start: 0.6530 (mp0) cc_final: 0.6327 (mp0) REVERT: G 292 GLN cc_start: 0.7948 (tm-30) cc_final: 0.7365 (tm-30) REVERT: G 325 MET cc_start: 0.9237 (ttt) cc_final: 0.8973 (ttt) REVERT: G 412 ARG cc_start: 0.8014 (ptt180) cc_final: 0.7496 (ptt180) REVERT: G 455 LYS cc_start: 0.7799 (mmtm) cc_final: 0.7541 (mmmt) REVERT: H 140 SER cc_start: 0.7875 (m) cc_final: 0.7199 (p) REVERT: H 217 GLU cc_start: 0.6297 (mp0) cc_final: 0.5875 (pm20) REVERT: H 292 GLN cc_start: 0.7938 (tm-30) cc_final: 0.7347 (tm-30) REVERT: H 325 MET cc_start: 0.9191 (ttt) cc_final: 0.8988 (ttt) REVERT: H 420 MET cc_start: 0.8250 (mtm) cc_final: 0.7974 (mtp) REVERT: H 455 LYS cc_start: 0.7727 (mmtm) cc_final: 0.7453 (mmmt) REVERT: H 459 TYR cc_start: 0.7776 (t80) cc_final: 0.7448 (t80) outliers start: 80 outliers final: 61 residues processed: 564 average time/residue: 2.2432 time to fit residues: 1526.4325 Evaluate side-chains 579 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 511 time to evaluate : 3.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 339 CYS Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 470 ASP Chi-restraints excluded: chain B residue 112 GLN Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 226 ASP Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 339 CYS Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 470 ASP Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 135 MET Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 339 CYS Chi-restraints excluded: chain C residue 361 ILE Chi-restraints excluded: chain C residue 450 LYS Chi-restraints excluded: chain C residue 470 ASP Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 268 VAL Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 339 CYS Chi-restraints excluded: chain D residue 361 ILE Chi-restraints excluded: chain E residue 112 GLN Chi-restraints excluded: chain E residue 132 GLU Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain E residue 226 ASP Chi-restraints excluded: chain E residue 264 THR Chi-restraints excluded: chain E residue 268 VAL Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 339 CYS Chi-restraints excluded: chain E residue 361 ILE Chi-restraints excluded: chain E residue 443 VAL Chi-restraints excluded: chain E residue 450 LYS Chi-restraints excluded: chain E residue 470 ASP Chi-restraints excluded: chain F residue 135 MET Chi-restraints excluded: chain F residue 179 MET Chi-restraints excluded: chain F residue 226 ASP Chi-restraints excluded: chain F residue 264 THR Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 339 CYS Chi-restraints excluded: chain F residue 361 ILE Chi-restraints excluded: chain F residue 443 VAL Chi-restraints excluded: chain F residue 470 ASP Chi-restraints excluded: chain G residue 121 LEU Chi-restraints excluded: chain G residue 135 MET Chi-restraints excluded: chain G residue 179 MET Chi-restraints excluded: chain G residue 264 THR Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 339 CYS Chi-restraints excluded: chain G residue 361 ILE Chi-restraints excluded: chain G residue 393 THR Chi-restraints excluded: chain G residue 443 VAL Chi-restraints excluded: chain G residue 470 ASP Chi-restraints excluded: chain H residue 221 ILE Chi-restraints excluded: chain H residue 226 ASP Chi-restraints excluded: chain H residue 254 GLU Chi-restraints excluded: chain H residue 264 THR Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 339 CYS Chi-restraints excluded: chain H residue 361 ILE Chi-restraints excluded: chain H residue 443 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 336 optimal weight: 0.2980 chunk 354 optimal weight: 0.4980 chunk 323 optimal weight: 3.9990 chunk 344 optimal weight: 1.9990 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: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN A 265 GLN ** A 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 GLN C 265 GLN D 441 GLN G 441 GLN ** H 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.3009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 30712 Z= 0.242 Angle : 0.488 5.117 41680 Z= 0.256 Chirality : 0.042 0.157 4840 Planarity : 0.004 0.036 5176 Dihedral : 12.594 88.627 5235 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.87 % Favored : 96.08 % Rotamer: Outliers : 2.77 % Allowed : 17.81 % Favored : 79.42 % 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: 0.27 (0.14), residues: 3824 helix: 0.93 (0.15), residues: 1488 sheet: 0.49 (0.29), residues: 272 loop : -0.37 (0.14), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 296 PHE 0.020 0.001 PHE A 99 TYR 0.009 0.001 TYR G 353 ARG 0.002 0.000 ARG A 322 *********************** 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: 87 poor density : 507 time to evaluate : 3.398 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: A 75 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.7466 (mt-10) REVERT: A 230 ASN cc_start: 0.8203 (t0) cc_final: 0.7988 (t0) REVERT: A 292 GLN cc_start: 0.7952 (tm-30) cc_final: 0.7408 (tm-30) REVERT: A 459 TYR cc_start: 0.7757 (t80) cc_final: 0.7414 (t80) REVERT: B 202 GLN cc_start: 0.8498 (tt0) cc_final: 0.8220 (tt0) REVERT: B 217 GLU cc_start: 0.5756 (mp0) cc_final: 0.5463 (mp0) REVERT: B 292 GLN cc_start: 0.7927 (tm-30) cc_final: 0.7405 (tm-30) REVERT: B 325 MET cc_start: 0.9233 (ttt) cc_final: 0.9026 (ttt) REVERT: B 459 TYR cc_start: 0.7803 (t80) cc_final: 0.7450 (t80) REVERT: C 111 GLU cc_start: 0.7502 (tp30) cc_final: 0.7277 (mm-30) REVERT: C 132 GLU cc_start: 0.6923 (OUTLIER) cc_final: 0.6630 (tm-30) REVERT: C 217 GLU cc_start: 0.6165 (mp0) cc_final: 0.5892 (mp0) REVERT: C 226 ASP cc_start: 0.7834 (OUTLIER) cc_final: 0.7577 (m-30) REVERT: C 292 GLN cc_start: 0.7903 (tm-30) cc_final: 0.7341 (tm-30) REVERT: C 330 ILE cc_start: 0.8723 (OUTLIER) cc_final: 0.8506 (pp) REVERT: C 459 TYR cc_start: 0.7776 (t80) cc_final: 0.7429 (t80) REVERT: D 217 GLU cc_start: 0.6188 (mp0) cc_final: 0.5852 (mp0) REVERT: D 292 GLN cc_start: 0.7971 (tm-30) cc_final: 0.7252 (tm130) REVERT: D 412 ARG cc_start: 0.8077 (ptt180) cc_final: 0.7742 (ptt180) REVERT: D 456 PHE cc_start: 0.8776 (t80) cc_final: 0.8506 (t80) REVERT: E 111 GLU cc_start: 0.7561 (tp30) cc_final: 0.7324 (mm-30) REVERT: E 112 GLN cc_start: 0.7575 (OUTLIER) cc_final: 0.7273 (tm-30) REVERT: E 132 GLU cc_start: 0.6901 (OUTLIER) cc_final: 0.6602 (tm-30) REVERT: E 217 GLU cc_start: 0.6230 (mp0) cc_final: 0.5841 (mp0) REVERT: E 292 GLN cc_start: 0.7966 (tm-30) cc_final: 0.7322 (tm-30) REVERT: F 111 GLU cc_start: 0.7471 (tp30) cc_final: 0.7234 (mm-30) REVERT: F 217 GLU cc_start: 0.6187 (mp0) cc_final: 0.5835 (mp0) REVERT: F 292 GLN cc_start: 0.7959 (tm-30) cc_final: 0.7313 (tm-30) REVERT: G 112 GLN cc_start: 0.6865 (mp10) cc_final: 0.6399 (mp10) REVERT: G 121 LEU cc_start: 0.7069 (OUTLIER) cc_final: 0.6837 (mp) REVERT: G 202 GLN cc_start: 0.8435 (tt0) cc_final: 0.8219 (tt0) REVERT: G 217 GLU cc_start: 0.6552 (mp0) cc_final: 0.6347 (mp0) REVERT: G 292 GLN cc_start: 0.7960 (tm-30) cc_final: 0.7372 (tm-30) REVERT: G 325 MET cc_start: 0.9255 (ttt) cc_final: 0.8991 (ttt) REVERT: G 412 ARG cc_start: 0.8021 (ptt180) cc_final: 0.7508 (ptt180) REVERT: H 75 GLU cc_start: 0.7828 (mt-10) cc_final: 0.7581 (mt-10) REVERT: H 217 GLU cc_start: 0.6328 (mp0) cc_final: 0.5841 (pm20) REVERT: H 292 GLN cc_start: 0.7962 (tm-30) cc_final: 0.7311 (tm-30) REVERT: H 325 MET cc_start: 0.9217 (ttt) cc_final: 0.9011 (ttt) REVERT: H 420 MET cc_start: 0.8250 (mtm) cc_final: 0.7965 (mtp) REVERT: H 455 LYS cc_start: 0.7764 (mmtm) cc_final: 0.7484 (mmmt) REVERT: H 459 TYR cc_start: 0.7803 (t80) cc_final: 0.7502 (t80) outliers start: 87 outliers final: 64 residues processed: 560 average time/residue: 2.2720 time to fit residues: 1527.3448 Evaluate side-chains 568 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 497 time to evaluate : 3.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 339 CYS Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 470 ASP Chi-restraints excluded: chain B residue 112 GLN Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 226 ASP Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 339 CYS Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 470 ASP Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 135 MET Chi-restraints excluded: chain C residue 226 ASP Chi-restraints excluded: chain C residue 255 ASP Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 339 CYS Chi-restraints excluded: chain C residue 361 ILE Chi-restraints excluded: chain C residue 450 LYS Chi-restraints excluded: chain D residue 226 ASP Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 268 VAL Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 339 CYS Chi-restraints excluded: chain D residue 361 ILE Chi-restraints excluded: chain E residue 112 GLN Chi-restraints excluded: chain E residue 132 GLU Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain E residue 264 THR Chi-restraints excluded: chain E residue 268 VAL Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 339 CYS Chi-restraints excluded: chain E residue 361 ILE Chi-restraints excluded: chain E residue 443 VAL Chi-restraints excluded: chain E residue 450 LYS Chi-restraints excluded: chain E residue 470 ASP Chi-restraints excluded: chain F residue 135 MET Chi-restraints excluded: chain F residue 179 MET Chi-restraints excluded: chain F residue 226 ASP Chi-restraints excluded: chain F residue 264 THR Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 339 CYS Chi-restraints excluded: chain F residue 361 ILE Chi-restraints excluded: chain F residue 443 VAL Chi-restraints excluded: chain F residue 470 ASP Chi-restraints excluded: chain G residue 121 LEU Chi-restraints excluded: chain G residue 135 MET Chi-restraints excluded: chain G residue 179 MET Chi-restraints excluded: chain G residue 226 ASP Chi-restraints excluded: chain G residue 264 THR Chi-restraints excluded: chain G residue 268 VAL Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 339 CYS Chi-restraints excluded: chain G residue 361 ILE Chi-restraints excluded: chain G residue 393 THR Chi-restraints excluded: chain H residue 221 ILE Chi-restraints excluded: chain H residue 226 ASP Chi-restraints excluded: chain H residue 254 GLU Chi-restraints excluded: chain H residue 264 THR Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 339 CYS Chi-restraints excluded: chain H residue 361 ILE Chi-restraints excluded: chain H residue 443 VAL 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: 0.6980 chunk 222 optimal weight: 0.9980 chunk 173 optimal weight: 0.5980 chunk 253 optimal weight: 2.9990 chunk 382 optimal weight: 1.9990 chunk 352 optimal weight: 0.0060 chunk 304 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 235 optimal weight: 1.9990 chunk 186 optimal weight: 4.9990 overall best weight: 0.8598 ------------------------------------------------------------------------------- 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 D 265 GLN E 265 GLN G 441 GLN ** H 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.3104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 30712 Z= 0.170 Angle : 0.469 5.682 41680 Z= 0.245 Chirality : 0.041 0.161 4840 Planarity : 0.004 0.035 5176 Dihedral : 12.261 88.734 5233 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.58 % Favored : 96.37 % Rotamer: Outliers : 2.19 % Allowed : 18.64 % Favored : 79.17 % 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: 0.52 (0.14), residues: 3824 helix: 1.20 (0.15), residues: 1440 sheet: 0.59 (0.29), residues: 272 loop : -0.24 (0.14), residues: 2112 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.000 HIS B 137 PHE 0.018 0.001 PHE D 99 TYR 0.008 0.001 TYR F 353 ARG 0.002 0.000 ARG A 203 ********************** 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 586 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 517 time to evaluate : 3.402 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: A 230 ASN cc_start: 0.8199 (t0) cc_final: 0.7983 (t0) REVERT: A 292 GLN cc_start: 0.7935 (tm-30) cc_final: 0.7300 (tm-30) REVERT: A 459 TYR cc_start: 0.7773 (t80) cc_final: 0.7445 (t80) REVERT: B 202 GLN cc_start: 0.8490 (tt0) cc_final: 0.8218 (tt0) REVERT: B 217 GLU cc_start: 0.5787 (mp0) cc_final: 0.5496 (mp0) REVERT: B 292 GLN cc_start: 0.7914 (tm-30) cc_final: 0.7325 (tm-30) REVERT: B 325 MET cc_start: 0.9211 (ttt) cc_final: 0.8995 (ttt) REVERT: B 459 TYR cc_start: 0.7787 (t80) cc_final: 0.7444 (t80) REVERT: C 111 GLU cc_start: 0.7473 (tp30) cc_final: 0.7271 (mm-30) REVERT: C 132 GLU cc_start: 0.6900 (OUTLIER) cc_final: 0.6614 (tm-30) REVERT: C 217 GLU cc_start: 0.6159 (mp0) cc_final: 0.5898 (mp0) REVERT: C 226 ASP cc_start: 0.7817 (OUTLIER) cc_final: 0.7580 (m-30) REVERT: C 292 GLN cc_start: 0.7892 (tm-30) cc_final: 0.7347 (tm-30) REVERT: C 330 ILE cc_start: 0.8714 (OUTLIER) cc_final: 0.8472 (pp) REVERT: C 459 TYR cc_start: 0.7772 (t80) cc_final: 0.7428 (t80) REVERT: D 217 GLU cc_start: 0.6004 (mp0) cc_final: 0.5696 (mp0) REVERT: D 292 GLN cc_start: 0.7952 (tm-30) cc_final: 0.7240 (tm130) REVERT: D 412 ARG cc_start: 0.8080 (ptt180) cc_final: 0.7739 (ptt180) REVERT: D 456 PHE cc_start: 0.8767 (t80) cc_final: 0.8499 (t80) REVERT: E 111 GLU cc_start: 0.7539 (tp30) cc_final: 0.7296 (mm-30) REVERT: E 112 GLN cc_start: 0.7554 (OUTLIER) cc_final: 0.7247 (tm-30) REVERT: E 132 GLU cc_start: 0.6892 (OUTLIER) cc_final: 0.6603 (tm-30) REVERT: E 206 LYS cc_start: 0.7888 (mmpt) cc_final: 0.7599 (mmmt) REVERT: E 217 GLU cc_start: 0.6190 (mp0) cc_final: 0.5843 (mp0) REVERT: E 292 GLN cc_start: 0.7947 (tm-30) cc_final: 0.7304 (tm-30) REVERT: F 111 GLU cc_start: 0.7488 (tp30) cc_final: 0.7261 (mm-30) REVERT: F 217 GLU cc_start: 0.6153 (mp0) cc_final: 0.5816 (mp0) REVERT: F 292 GLN cc_start: 0.7941 (tm-30) cc_final: 0.7333 (tm-30) REVERT: G 112 GLN cc_start: 0.6865 (mp10) cc_final: 0.6404 (mp10) REVERT: G 121 LEU cc_start: 0.7014 (OUTLIER) cc_final: 0.6797 (mp) REVERT: G 202 GLN cc_start: 0.8425 (tt0) cc_final: 0.8212 (tt0) REVERT: G 217 GLU cc_start: 0.6493 (mp0) cc_final: 0.6058 (mp0) REVERT: G 292 GLN cc_start: 0.7921 (tm-30) cc_final: 0.7339 (tm-30) REVERT: G 325 MET cc_start: 0.9236 (ttt) cc_final: 0.8966 (ttt) REVERT: G 412 ARG cc_start: 0.8018 (ptt180) cc_final: 0.7526 (ptt180) REVERT: H 217 GLU cc_start: 0.6200 (mp0) cc_final: 0.5808 (pm20) REVERT: H 292 GLN cc_start: 0.7942 (tm-30) cc_final: 0.7351 (tm-30) REVERT: H 325 MET cc_start: 0.9202 (ttt) cc_final: 0.8994 (ttt) REVERT: H 420 MET cc_start: 0.8258 (mtm) cc_final: 0.7971 (mtp) REVERT: H 455 LYS cc_start: 0.7768 (mmtm) cc_final: 0.7480 (mmmt) REVERT: H 459 TYR cc_start: 0.7785 (t80) cc_final: 0.7451 (t80) outliers start: 69 outliers final: 53 residues processed: 559 average time/residue: 2.2862 time to fit residues: 1545.8631 Evaluate side-chains 570 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 511 time to evaluate : 3.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 339 CYS Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 470 ASP Chi-restraints excluded: chain B residue 112 GLN Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 339 CYS Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 470 ASP Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 226 ASP Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 339 CYS Chi-restraints excluded: chain C residue 361 ILE Chi-restraints excluded: chain C residue 450 LYS Chi-restraints excluded: chain D residue 226 ASP Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 268 VAL Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 339 CYS Chi-restraints excluded: chain D residue 361 ILE Chi-restraints excluded: chain E residue 112 GLN Chi-restraints excluded: chain E residue 132 GLU Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain E residue 264 THR Chi-restraints excluded: chain E residue 268 VAL Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 339 CYS Chi-restraints excluded: chain E residue 361 ILE Chi-restraints excluded: chain E residue 443 VAL Chi-restraints excluded: chain E residue 450 LYS Chi-restraints excluded: chain E residue 470 ASP Chi-restraints excluded: chain F residue 179 MET Chi-restraints excluded: chain F residue 226 ASP Chi-restraints excluded: chain F residue 264 THR Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 339 CYS Chi-restraints excluded: chain F residue 361 ILE Chi-restraints excluded: chain F residue 470 ASP Chi-restraints excluded: chain G residue 121 LEU Chi-restraints excluded: chain G residue 226 ASP Chi-restraints excluded: chain G residue 264 THR Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 339 CYS Chi-restraints excluded: chain G residue 361 ILE Chi-restraints excluded: chain G residue 393 THR Chi-restraints excluded: chain G residue 470 ASP Chi-restraints excluded: chain H residue 221 ILE Chi-restraints excluded: chain H residue 226 ASP Chi-restraints excluded: chain H residue 264 THR Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 339 CYS Chi-restraints excluded: chain H residue 361 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 241 optimal weight: 0.8980 chunk 324 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 280 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 305 optimal weight: 0.0020 chunk 127 optimal weight: 2.9990 chunk 313 optimal weight: 0.0670 chunk 38 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 overall best weight: 0.9930 ------------------------------------------------------------------------------- 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 D 265 GLN E 265 GLN F 265 GLN G 94 ASN G 441 GLN ** H 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.153256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.111616 restraints weight = 98141.764| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 2.02 r_work: 0.3055 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.3141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 30712 Z= 0.191 Angle : 0.474 5.698 41680 Z= 0.248 Chirality : 0.042 0.153 4840 Planarity : 0.004 0.035 5176 Dihedral : 12.193 88.026 5233 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.82 % Favored : 96.13 % Rotamer: Outliers : 2.10 % Allowed : 18.92 % Favored : 78.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.14), residues: 3824 helix: 1.19 (0.15), residues: 1440 sheet: 0.16 (0.27), residues: 312 loop : -0.23 (0.14), residues: 2072 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 137 PHE 0.020 0.001 PHE D 99 TYR 0.009 0.001 TYR E 353 ARG 0.004 0.000 ARG E 412 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 22368.17 seconds wall clock time: 383 minutes 47.98 seconds (23027.98 seconds total)