Starting phenix.real_space_refine on Fri Mar 22 10:44:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j0c_9761/03_2024/6j0c_9761.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j0c_9761/03_2024/6j0c_9761.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j0c_9761/03_2024/6j0c_9761.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j0c_9761/03_2024/6j0c_9761.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j0c_9761/03_2024/6j0c_9761.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j0c_9761/03_2024/6j0c_9761.pdb" } resolution = 3.7 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= 0.003 sd= 0.025 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: 4 Type Number sf(0) Gaussians S 108 5.16 5 C 21120 2.51 5 N 5484 2.21 5 O 6396 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 44": "OD1" <-> "OD2" Residue "A ASP 66": "OD1" <-> "OD2" Residue "A ARG 73": "NH1" <-> "NH2" Residue "A GLU 92": "OE1" <-> "OE2" Residue "A ASP 100": "OD1" <-> "OD2" Residue "A ASP 110": "OD1" <-> "OD2" Residue "A GLU 133": "OE1" <-> "OE2" Residue "A GLU 135": "OE1" <-> "OE2" Residue "A GLU 142": "OE1" <-> "OE2" Residue "A TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 164": "OD1" <-> "OD2" Residue "A TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 210": "OD1" <-> "OD2" Residue "A GLU 215": "OE1" <-> "OE2" Residue "A TYR 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 243": "OD1" <-> "OD2" Residue "A ARG 254": "NH1" <-> "NH2" Residue "A ASP 262": "OD1" <-> "OD2" Residue "A PHE 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 273": "OE1" <-> "OE2" Residue "A GLU 281": "OE1" <-> "OE2" Residue "A TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 342": "OE1" <-> "OE2" Residue "A ASP 351": "OD1" <-> "OD2" Residue "A GLU 353": "OE1" <-> "OE2" Residue "A ARG 355": "NH1" <-> "NH2" Residue "B TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 44": "OD1" <-> "OD2" Residue "B ASP 66": "OD1" <-> "OD2" Residue "B ARG 73": "NH1" <-> "NH2" Residue "B GLU 92": "OE1" <-> "OE2" Residue "B ASP 100": "OD1" <-> "OD2" Residue "B ASP 110": "OD1" <-> "OD2" Residue "B GLU 133": "OE1" <-> "OE2" Residue "B GLU 135": "OE1" <-> "OE2" Residue "B GLU 142": "OE1" <-> "OE2" Residue "B TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 164": "OD1" <-> "OD2" Residue "B TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 210": "OD1" <-> "OD2" Residue "B GLU 215": "OE1" <-> "OE2" Residue "B TYR 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 243": "OD1" <-> "OD2" Residue "B ARG 254": "NH1" <-> "NH2" Residue "B ASP 262": "OD1" <-> "OD2" Residue "B PHE 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 273": "OE1" <-> "OE2" Residue "B GLU 281": "OE1" <-> "OE2" Residue "B TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 342": "OE1" <-> "OE2" Residue "B ASP 351": "OD1" <-> "OD2" Residue "B GLU 353": "OE1" <-> "OE2" Residue "B ARG 355": "NH1" <-> "NH2" Residue "C TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 44": "OD1" <-> "OD2" Residue "C ASP 66": "OD1" <-> "OD2" Residue "C ARG 73": "NH1" <-> "NH2" Residue "C GLU 92": "OE1" <-> "OE2" Residue "C ASP 100": "OD1" <-> "OD2" Residue "C ASP 110": "OD1" <-> "OD2" Residue "C GLU 133": "OE1" <-> "OE2" Residue "C GLU 135": "OE1" <-> "OE2" Residue "C GLU 142": "OE1" <-> "OE2" Residue "C TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 164": "OD1" <-> "OD2" Residue "C TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 210": "OD1" <-> "OD2" Residue "C GLU 215": "OE1" <-> "OE2" Residue "C TYR 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 243": "OD1" <-> "OD2" Residue "C ARG 254": "NH1" <-> "NH2" Residue "C ASP 262": "OD1" <-> "OD2" Residue "C PHE 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 273": "OE1" <-> "OE2" Residue "C GLU 281": "OE1" <-> "OE2" Residue "C TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 342": "OE1" <-> "OE2" Residue "C ASP 351": "OD1" <-> "OD2" Residue "C GLU 353": "OE1" <-> "OE2" Residue "C ARG 355": "NH1" <-> "NH2" Residue "D TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 44": "OD1" <-> "OD2" Residue "D ASP 66": "OD1" <-> "OD2" Residue "D ARG 73": "NH1" <-> "NH2" Residue "D GLU 92": "OE1" <-> "OE2" Residue "D ASP 100": "OD1" <-> "OD2" Residue "D ASP 110": "OD1" <-> "OD2" Residue "D GLU 133": "OE1" <-> "OE2" Residue "D GLU 135": "OE1" <-> "OE2" Residue "D GLU 142": "OE1" <-> "OE2" Residue "D TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 164": "OD1" <-> "OD2" Residue "D TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 210": "OD1" <-> "OD2" Residue "D GLU 215": "OE1" <-> "OE2" Residue "D TYR 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 243": "OD1" <-> "OD2" Residue "D ARG 254": "NH1" <-> "NH2" Residue "D ASP 262": "OD1" <-> "OD2" Residue "D PHE 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 273": "OE1" <-> "OE2" Residue "D GLU 281": "OE1" <-> "OE2" Residue "D TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 342": "OE1" <-> "OE2" Residue "D ASP 351": "OD1" <-> "OD2" Residue "D GLU 353": "OE1" <-> "OE2" Residue "D ARG 355": "NH1" <-> "NH2" Residue "E TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 44": "OD1" <-> "OD2" Residue "E ASP 66": "OD1" <-> "OD2" Residue "E ARG 73": "NH1" <-> "NH2" Residue "E GLU 92": "OE1" <-> "OE2" Residue "E ASP 100": "OD1" <-> "OD2" Residue "E ASP 110": "OD1" <-> "OD2" Residue "E GLU 133": "OE1" <-> "OE2" Residue "E GLU 135": "OE1" <-> "OE2" Residue "E GLU 142": "OE1" <-> "OE2" Residue "E TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 164": "OD1" <-> "OD2" Residue "E TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 210": "OD1" <-> "OD2" Residue "E GLU 215": "OE1" <-> "OE2" Residue "E TYR 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 243": "OD1" <-> "OD2" Residue "E ARG 254": "NH1" <-> "NH2" Residue "E ASP 262": "OD1" <-> "OD2" Residue "E PHE 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 273": "OE1" <-> "OE2" Residue "E GLU 281": "OE1" <-> "OE2" Residue "E TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 342": "OE1" <-> "OE2" Residue "E ASP 351": "OD1" <-> "OD2" Residue "E GLU 353": "OE1" <-> "OE2" Residue "E ARG 355": "NH1" <-> "NH2" Residue "F TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 44": "OD1" <-> "OD2" Residue "F ASP 66": "OD1" <-> "OD2" Residue "F ARG 73": "NH1" <-> "NH2" Residue "F GLU 92": "OE1" <-> "OE2" Residue "F ASP 100": "OD1" <-> "OD2" Residue "F ASP 110": "OD1" <-> "OD2" Residue "F GLU 133": "OE1" <-> "OE2" Residue "F GLU 135": "OE1" <-> "OE2" Residue "F GLU 142": "OE1" <-> "OE2" Residue "F TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 164": "OD1" <-> "OD2" Residue "F TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 210": "OD1" <-> "OD2" Residue "F GLU 215": "OE1" <-> "OE2" Residue "F TYR 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 243": "OD1" <-> "OD2" Residue "F ARG 254": "NH1" <-> "NH2" Residue "F ASP 262": "OD1" <-> "OD2" Residue "F PHE 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 273": "OE1" <-> "OE2" Residue "F GLU 281": "OE1" <-> "OE2" Residue "F TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 342": "OE1" <-> "OE2" Residue "F ASP 351": "OD1" <-> "OD2" Residue "F GLU 353": "OE1" <-> "OE2" Residue "F ARG 355": "NH1" <-> "NH2" Residue "a TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 44": "OD1" <-> "OD2" Residue "a ASP 66": "OD1" <-> "OD2" Residue "a ARG 73": "NH1" <-> "NH2" Residue "a GLU 92": "OE1" <-> "OE2" Residue "a ASP 100": "OD1" <-> "OD2" Residue "a ASP 110": "OD1" <-> "OD2" Residue "a GLU 133": "OE1" <-> "OE2" Residue "a GLU 135": "OE1" <-> "OE2" Residue "a GLU 142": "OE1" <-> "OE2" Residue "a TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 164": "OD1" <-> "OD2" Residue "a TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 210": "OD1" <-> "OD2" Residue "a GLU 215": "OE1" <-> "OE2" Residue "a TYR 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 243": "OD1" <-> "OD2" Residue "a ARG 254": "NH1" <-> "NH2" Residue "a ASP 262": "OD1" <-> "OD2" Residue "a PHE 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 273": "OE1" <-> "OE2" Residue "a GLU 281": "OE1" <-> "OE2" Residue "a TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 342": "OE1" <-> "OE2" Residue "a ASP 351": "OD1" <-> "OD2" Residue "a GLU 353": "OE1" <-> "OE2" Residue "a ARG 355": "NH1" <-> "NH2" Residue "b TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 44": "OD1" <-> "OD2" Residue "b ASP 66": "OD1" <-> "OD2" Residue "b ARG 73": "NH1" <-> "NH2" Residue "b GLU 92": "OE1" <-> "OE2" Residue "b ASP 100": "OD1" <-> "OD2" Residue "b ASP 110": "OD1" <-> "OD2" Residue "b GLU 133": "OE1" <-> "OE2" Residue "b GLU 135": "OE1" <-> "OE2" Residue "b GLU 142": "OE1" <-> "OE2" Residue "b TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 164": "OD1" <-> "OD2" Residue "b TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 210": "OD1" <-> "OD2" Residue "b GLU 215": "OE1" <-> "OE2" Residue "b TYR 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 243": "OD1" <-> "OD2" Residue "b ARG 254": "NH1" <-> "NH2" Residue "b ASP 262": "OD1" <-> "OD2" Residue "b PHE 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 273": "OE1" <-> "OE2" Residue "b GLU 281": "OE1" <-> "OE2" Residue "b TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 342": "OE1" <-> "OE2" Residue "b ASP 351": "OD1" <-> "OD2" Residue "b GLU 353": "OE1" <-> "OE2" Residue "b ARG 355": "NH1" <-> "NH2" Residue "c TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ASP 44": "OD1" <-> "OD2" Residue "c ASP 66": "OD1" <-> "OD2" Residue "c ARG 73": "NH1" <-> "NH2" Residue "c GLU 92": "OE1" <-> "OE2" Residue "c ASP 100": "OD1" <-> "OD2" Residue "c ASP 110": "OD1" <-> "OD2" Residue "c GLU 133": "OE1" <-> "OE2" Residue "c GLU 135": "OE1" <-> "OE2" Residue "c GLU 142": "OE1" <-> "OE2" Residue "c TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ASP 164": "OD1" <-> "OD2" Residue "c TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ASP 210": "OD1" <-> "OD2" Residue "c GLU 215": "OE1" <-> "OE2" Residue "c TYR 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ASP 243": "OD1" <-> "OD2" Residue "c ARG 254": "NH1" <-> "NH2" Residue "c ASP 262": "OD1" <-> "OD2" Residue "c PHE 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 273": "OE1" <-> "OE2" Residue "c GLU 281": "OE1" <-> "OE2" Residue "c TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 342": "OE1" <-> "OE2" Residue "c ASP 351": "OD1" <-> "OD2" Residue "c GLU 353": "OE1" <-> "OE2" Residue "c ARG 355": "NH1" <-> "NH2" Residue "d TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 44": "OD1" <-> "OD2" Residue "d ASP 66": "OD1" <-> "OD2" Residue "d ARG 73": "NH1" <-> "NH2" Residue "d GLU 92": "OE1" <-> "OE2" Residue "d ASP 100": "OD1" <-> "OD2" Residue "d ASP 110": "OD1" <-> "OD2" Residue "d GLU 133": "OE1" <-> "OE2" Residue "d GLU 135": "OE1" <-> "OE2" Residue "d GLU 142": "OE1" <-> "OE2" Residue "d TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 164": "OD1" <-> "OD2" Residue "d TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 210": "OD1" <-> "OD2" Residue "d GLU 215": "OE1" <-> "OE2" Residue "d TYR 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 243": "OD1" <-> "OD2" Residue "d ARG 254": "NH1" <-> "NH2" Residue "d ASP 262": "OD1" <-> "OD2" Residue "d PHE 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 273": "OE1" <-> "OE2" Residue "d GLU 281": "OE1" <-> "OE2" Residue "d TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 342": "OE1" <-> "OE2" Residue "d ASP 351": "OD1" <-> "OD2" Residue "d GLU 353": "OE1" <-> "OE2" Residue "d ARG 355": "NH1" <-> "NH2" Residue "e TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ASP 44": "OD1" <-> "OD2" Residue "e ASP 66": "OD1" <-> "OD2" Residue "e ARG 73": "NH1" <-> "NH2" Residue "e GLU 92": "OE1" <-> "OE2" Residue "e ASP 100": "OD1" <-> "OD2" Residue "e ASP 110": "OD1" <-> "OD2" Residue "e GLU 133": "OE1" <-> "OE2" Residue "e GLU 135": "OE1" <-> "OE2" Residue "e GLU 142": "OE1" <-> "OE2" Residue "e TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ASP 164": "OD1" <-> "OD2" Residue "e TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ASP 210": "OD1" <-> "OD2" Residue "e GLU 215": "OE1" <-> "OE2" Residue "e TYR 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ASP 243": "OD1" <-> "OD2" Residue "e ARG 254": "NH1" <-> "NH2" Residue "e ASP 262": "OD1" <-> "OD2" Residue "e PHE 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 273": "OE1" <-> "OE2" Residue "e GLU 281": "OE1" <-> "OE2" Residue "e TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 342": "OE1" <-> "OE2" Residue "e ASP 351": "OD1" <-> "OD2" Residue "e GLU 353": "OE1" <-> "OE2" Residue "e ARG 355": "NH1" <-> "NH2" Residue "f TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ASP 44": "OD1" <-> "OD2" Residue "f ASP 66": "OD1" <-> "OD2" Residue "f ARG 73": "NH1" <-> "NH2" Residue "f GLU 92": "OE1" <-> "OE2" Residue "f ASP 100": "OD1" <-> "OD2" Residue "f ASP 110": "OD1" <-> "OD2" Residue "f GLU 133": "OE1" <-> "OE2" Residue "f GLU 135": "OE1" <-> "OE2" Residue "f GLU 142": "OE1" <-> "OE2" Residue "f TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ASP 164": "OD1" <-> "OD2" Residue "f TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f PHE 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ASP 210": "OD1" <-> "OD2" Residue "f GLU 215": "OE1" <-> "OE2" Residue "f TYR 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f PHE 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ASP 243": "OD1" <-> "OD2" Residue "f ARG 254": "NH1" <-> "NH2" Residue "f ASP 262": "OD1" <-> "OD2" Residue "f PHE 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 273": "OE1" <-> "OE2" Residue "f GLU 281": "OE1" <-> "OE2" Residue "f TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 342": "OE1" <-> "OE2" Residue "f ASP 351": "OD1" <-> "OD2" Residue "f GLU 353": "OE1" <-> "OE2" Residue "f ARG 355": "NH1" <-> "NH2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 33108 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 2759 Classifications: {'peptide': 354} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 15, 'TRANS': 338} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 2759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 2759 Classifications: {'peptide': 354} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 15, 'TRANS': 338} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "C" Number of atoms: 2759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 2759 Classifications: {'peptide': 354} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 15, 'TRANS': 338} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "D" Number of atoms: 2759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 2759 Classifications: {'peptide': 354} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 15, 'TRANS': 338} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "E" Number of atoms: 2759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 2759 Classifications: {'peptide': 354} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 15, 'TRANS': 338} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "F" Number of atoms: 2759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 2759 Classifications: {'peptide': 354} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 15, 'TRANS': 338} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "a" Number of atoms: 2759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 2759 Classifications: {'peptide': 354} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 15, 'TRANS': 338} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "b" Number of atoms: 2759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 2759 Classifications: {'peptide': 354} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 15, 'TRANS': 338} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "c" Number of atoms: 2759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 2759 Classifications: {'peptide': 354} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 15, 'TRANS': 338} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "d" Number of atoms: 2759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 2759 Classifications: {'peptide': 354} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 15, 'TRANS': 338} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "e" Number of atoms: 2759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 2759 Classifications: {'peptide': 354} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 15, 'TRANS': 338} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "f" Number of atoms: 2759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 2759 Classifications: {'peptide': 354} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 15, 'TRANS': 338} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Time building chain proxies: 16.48, per 1000 atoms: 0.50 Number of scatterers: 33108 At special positions: 0 Unit cell: (232.047, 233.168, 78.47, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 108 16.00 O 6396 8.00 N 5484 7.00 C 21120 6.00 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: 11.49 Conformation dependent library (CDL) restraints added in 6.1 seconds 8448 Ramachandran restraints generated. 4224 Oldfield, 0 Emsley, 4224 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7896 Finding SS restraints... Secondary structure from input PDB file: 132 helices and 66 sheets defined 31.6% alpha, 11.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.44 Creating SS restraints... Processing helix chain 'A' and resid 51 through 56 Processing helix chain 'A' and resid 66 through 79 removed outlier: 3.526A pdb=" N ARG A 73 " --> pdb=" O ASP A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 95 removed outlier: 3.580A pdb=" N ILE A 94 " --> pdb=" O SER A 90 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE A 95 " --> pdb=" O LEU A 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 90 through 95' Processing helix chain 'A' and resid 96 through 98 No H-bonds generated for 'chain 'A' and resid 96 through 98' Processing helix chain 'A' and resid 111 through 119 Processing helix chain 'A' and resid 140 through 145 Processing helix chain 'A' and resid 171 through 187 removed outlier: 3.825A pdb=" N VAL A 175 " --> pdb=" O PRO A 171 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLY A 178 " --> pdb=" O ALA A 174 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL A 179 " --> pdb=" O VAL A 175 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA A 181 " --> pdb=" O ALA A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 267 removed outlier: 4.046A pdb=" N PHE A 256 " --> pdb=" O VAL A 252 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLU A 260 " --> pdb=" O PHE A 256 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N LYS A 264 " --> pdb=" O GLU A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 297 removed outlier: 3.825A pdb=" N ARG A 282 " --> pdb=" O PRO A 278 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG A 284 " --> pdb=" O TRP A 280 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TYR A 290 " --> pdb=" O ALA A 286 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TRP A 295 " --> pdb=" O LEU A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 308 Processing helix chain 'A' and resid 320 through 326 removed outlier: 3.603A pdb=" N ILE A 324 " --> pdb=" O THR A 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 56 Processing helix chain 'B' and resid 66 through 79 removed outlier: 3.525A pdb=" N ARG B 73 " --> pdb=" O ASP B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 95 removed outlier: 3.580A pdb=" N ILE B 94 " --> pdb=" O SER B 90 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE B 95 " --> pdb=" O LEU B 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 90 through 95' Processing helix chain 'B' and resid 96 through 98 No H-bonds generated for 'chain 'B' and resid 96 through 98' Processing helix chain 'B' and resid 111 through 119 Processing helix chain 'B' and resid 140 through 145 Processing helix chain 'B' and resid 171 through 187 removed outlier: 3.826A pdb=" N VAL B 175 " --> pdb=" O PRO B 171 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLY B 178 " --> pdb=" O ALA B 174 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL B 179 " --> pdb=" O VAL B 175 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA B 181 " --> pdb=" O ALA B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 267 removed outlier: 4.046A pdb=" N PHE B 256 " --> pdb=" O VAL B 252 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N GLU B 260 " --> pdb=" O PHE B 256 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N LYS B 264 " --> pdb=" O GLU B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 297 removed outlier: 3.825A pdb=" N ARG B 282 " --> pdb=" O PRO B 278 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG B 284 " --> pdb=" O TRP B 280 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TYR B 290 " --> pdb=" O ALA B 286 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N TRP B 295 " --> pdb=" O LEU B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 308 Processing helix chain 'B' and resid 320 through 326 removed outlier: 3.603A pdb=" N ILE B 324 " --> pdb=" O THR B 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 56 Processing helix chain 'C' and resid 66 through 79 removed outlier: 3.526A pdb=" N ARG C 73 " --> pdb=" O ASP C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 95 removed outlier: 3.581A pdb=" N ILE C 94 " --> pdb=" O SER C 90 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE C 95 " --> pdb=" O LEU C 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 90 through 95' Processing helix chain 'C' and resid 96 through 98 No H-bonds generated for 'chain 'C' and resid 96 through 98' Processing helix chain 'C' and resid 111 through 119 Processing helix chain 'C' and resid 140 through 145 Processing helix chain 'C' and resid 171 through 187 removed outlier: 3.826A pdb=" N VAL C 175 " --> pdb=" O PRO C 171 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLY C 178 " --> pdb=" O ALA C 174 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL C 179 " --> pdb=" O VAL C 175 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA C 181 " --> pdb=" O ALA C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 267 removed outlier: 4.046A pdb=" N PHE C 256 " --> pdb=" O VAL C 252 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N GLU C 260 " --> pdb=" O PHE C 256 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N LYS C 264 " --> pdb=" O GLU C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 297 removed outlier: 3.825A pdb=" N ARG C 282 " --> pdb=" O PRO C 278 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG C 284 " --> pdb=" O TRP C 280 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TYR C 290 " --> pdb=" O ALA C 286 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TRP C 295 " --> pdb=" O LEU C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 304 through 308 Processing helix chain 'C' and resid 320 through 326 removed outlier: 3.603A pdb=" N ILE C 324 " --> pdb=" O THR C 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 56 Processing helix chain 'D' and resid 66 through 79 removed outlier: 3.526A pdb=" N ARG D 73 " --> pdb=" O ASP D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 95 removed outlier: 3.581A pdb=" N ILE D 94 " --> pdb=" O SER D 90 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE D 95 " --> pdb=" O LEU D 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 90 through 95' Processing helix chain 'D' and resid 96 through 98 No H-bonds generated for 'chain 'D' and resid 96 through 98' Processing helix chain 'D' and resid 111 through 119 Processing helix chain 'D' and resid 140 through 145 Processing helix chain 'D' and resid 171 through 187 removed outlier: 3.825A pdb=" N VAL D 175 " --> pdb=" O PRO D 171 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY D 178 " --> pdb=" O ALA D 174 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL D 179 " --> pdb=" O VAL D 175 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA D 181 " --> pdb=" O ALA D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 267 removed outlier: 4.046A pdb=" N PHE D 256 " --> pdb=" O VAL D 252 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLU D 260 " --> pdb=" O PHE D 256 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N LYS D 264 " --> pdb=" O GLU D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 278 through 297 removed outlier: 3.825A pdb=" N ARG D 282 " --> pdb=" O PRO D 278 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG D 284 " --> pdb=" O TRP D 280 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N TYR D 290 " --> pdb=" O ALA D 286 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TRP D 295 " --> pdb=" O LEU D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 304 through 308 Processing helix chain 'D' and resid 320 through 326 removed outlier: 3.603A pdb=" N ILE D 324 " --> pdb=" O THR D 320 " (cutoff:3.500A) Processing helix chain 'E' and resid 51 through 56 Processing helix chain 'E' and resid 66 through 79 removed outlier: 3.525A pdb=" N ARG E 73 " --> pdb=" O ASP E 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 95 removed outlier: 3.580A pdb=" N ILE E 94 " --> pdb=" O SER E 90 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE E 95 " --> pdb=" O LEU E 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 90 through 95' Processing helix chain 'E' and resid 96 through 98 No H-bonds generated for 'chain 'E' and resid 96 through 98' Processing helix chain 'E' and resid 111 through 119 Processing helix chain 'E' and resid 140 through 145 Processing helix chain 'E' and resid 171 through 187 removed outlier: 3.826A pdb=" N VAL E 175 " --> pdb=" O PRO E 171 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY E 178 " --> pdb=" O ALA E 174 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL E 179 " --> pdb=" O VAL E 175 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA E 181 " --> pdb=" O ALA E 177 " (cutoff:3.500A) Processing helix chain 'E' and resid 249 through 267 removed outlier: 4.045A pdb=" N PHE E 256 " --> pdb=" O VAL E 252 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLU E 260 " --> pdb=" O PHE E 256 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N LYS E 264 " --> pdb=" O GLU E 260 " (cutoff:3.500A) Processing helix chain 'E' and resid 278 through 297 removed outlier: 3.825A pdb=" N ARG E 282 " --> pdb=" O PRO E 278 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG E 284 " --> pdb=" O TRP E 280 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TYR E 290 " --> pdb=" O ALA E 286 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TRP E 295 " --> pdb=" O LEU E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 304 through 308 Processing helix chain 'E' and resid 320 through 326 removed outlier: 3.602A pdb=" N ILE E 324 " --> pdb=" O THR E 320 " (cutoff:3.500A) Processing helix chain 'F' and resid 51 through 56 Processing helix chain 'F' and resid 66 through 79 removed outlier: 3.526A pdb=" N ARG F 73 " --> pdb=" O ASP F 69 " (cutoff:3.500A) Processing helix chain 'F' and resid 90 through 95 removed outlier: 3.581A pdb=" N ILE F 94 " --> pdb=" O SER F 90 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE F 95 " --> pdb=" O LEU F 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 90 through 95' Processing helix chain 'F' and resid 96 through 98 No H-bonds generated for 'chain 'F' and resid 96 through 98' Processing helix chain 'F' and resid 111 through 119 Processing helix chain 'F' and resid 140 through 145 Processing helix chain 'F' and resid 171 through 187 removed outlier: 3.826A pdb=" N VAL F 175 " --> pdb=" O PRO F 171 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY F 178 " --> pdb=" O ALA F 174 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL F 179 " --> pdb=" O VAL F 175 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA F 181 " --> pdb=" O ALA F 177 " (cutoff:3.500A) Processing helix chain 'F' and resid 249 through 267 removed outlier: 4.045A pdb=" N PHE F 256 " --> pdb=" O VAL F 252 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N GLU F 260 " --> pdb=" O PHE F 256 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N LYS F 264 " --> pdb=" O GLU F 260 " (cutoff:3.500A) Processing helix chain 'F' and resid 278 through 297 removed outlier: 3.826A pdb=" N ARG F 282 " --> pdb=" O PRO F 278 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG F 284 " --> pdb=" O TRP F 280 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TYR F 290 " --> pdb=" O ALA F 286 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N TRP F 295 " --> pdb=" O LEU F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 304 through 308 Processing helix chain 'F' and resid 320 through 326 removed outlier: 3.603A pdb=" N ILE F 324 " --> pdb=" O THR F 320 " (cutoff:3.500A) Processing helix chain 'a' and resid 51 through 56 Processing helix chain 'a' and resid 66 through 79 removed outlier: 3.526A pdb=" N ARG a 73 " --> pdb=" O ASP a 69 " (cutoff:3.500A) Processing helix chain 'a' and resid 90 through 95 removed outlier: 3.581A pdb=" N ILE a 94 " --> pdb=" O SER a 90 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE a 95 " --> pdb=" O LEU a 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 90 through 95' Processing helix chain 'a' and resid 96 through 98 No H-bonds generated for 'chain 'a' and resid 96 through 98' Processing helix chain 'a' and resid 111 through 119 Processing helix chain 'a' and resid 140 through 145 Processing helix chain 'a' and resid 171 through 187 removed outlier: 3.826A pdb=" N VAL a 175 " --> pdb=" O PRO a 171 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY a 178 " --> pdb=" O ALA a 174 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL a 179 " --> pdb=" O VAL a 175 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA a 181 " --> pdb=" O ALA a 177 " (cutoff:3.500A) Processing helix chain 'a' and resid 249 through 267 removed outlier: 4.045A pdb=" N PHE a 256 " --> pdb=" O VAL a 252 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLU a 260 " --> pdb=" O PHE a 256 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N LYS a 264 " --> pdb=" O GLU a 260 " (cutoff:3.500A) Processing helix chain 'a' and resid 278 through 297 removed outlier: 3.826A pdb=" N ARG a 282 " --> pdb=" O PRO a 278 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG a 284 " --> pdb=" O TRP a 280 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TYR a 290 " --> pdb=" O ALA a 286 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N TRP a 295 " --> pdb=" O LEU a 291 " (cutoff:3.500A) Processing helix chain 'a' and resid 304 through 308 Processing helix chain 'a' and resid 320 through 326 removed outlier: 3.603A pdb=" N ILE a 324 " --> pdb=" O THR a 320 " (cutoff:3.500A) Processing helix chain 'b' and resid 51 through 56 Processing helix chain 'b' and resid 66 through 79 removed outlier: 3.525A pdb=" N ARG b 73 " --> pdb=" O ASP b 69 " (cutoff:3.500A) Processing helix chain 'b' and resid 90 through 95 removed outlier: 3.580A pdb=" N ILE b 94 " --> pdb=" O SER b 90 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE b 95 " --> pdb=" O LEU b 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 90 through 95' Processing helix chain 'b' and resid 96 through 98 No H-bonds generated for 'chain 'b' and resid 96 through 98' Processing helix chain 'b' and resid 111 through 119 Processing helix chain 'b' and resid 140 through 145 Processing helix chain 'b' and resid 171 through 187 removed outlier: 3.827A pdb=" N VAL b 175 " --> pdb=" O PRO b 171 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLY b 178 " --> pdb=" O ALA b 174 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL b 179 " --> pdb=" O VAL b 175 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA b 181 " --> pdb=" O ALA b 177 " (cutoff:3.500A) Processing helix chain 'b' and resid 249 through 267 removed outlier: 4.045A pdb=" N PHE b 256 " --> pdb=" O VAL b 252 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLU b 260 " --> pdb=" O PHE b 256 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N LYS b 264 " --> pdb=" O GLU b 260 " (cutoff:3.500A) Processing helix chain 'b' and resid 278 through 297 removed outlier: 3.825A pdb=" N ARG b 282 " --> pdb=" O PRO b 278 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG b 284 " --> pdb=" O TRP b 280 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TYR b 290 " --> pdb=" O ALA b 286 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N TRP b 295 " --> pdb=" O LEU b 291 " (cutoff:3.500A) Processing helix chain 'b' and resid 304 through 308 Processing helix chain 'b' and resid 320 through 326 removed outlier: 3.604A pdb=" N ILE b 324 " --> pdb=" O THR b 320 " (cutoff:3.500A) Processing helix chain 'c' and resid 51 through 56 Processing helix chain 'c' and resid 66 through 79 removed outlier: 3.526A pdb=" N ARG c 73 " --> pdb=" O ASP c 69 " (cutoff:3.500A) Processing helix chain 'c' and resid 90 through 95 removed outlier: 3.581A pdb=" N ILE c 94 " --> pdb=" O SER c 90 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE c 95 " --> pdb=" O LEU c 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 90 through 95' Processing helix chain 'c' and resid 96 through 98 No H-bonds generated for 'chain 'c' and resid 96 through 98' Processing helix chain 'c' and resid 111 through 119 Processing helix chain 'c' and resid 140 through 145 Processing helix chain 'c' and resid 171 through 187 removed outlier: 3.825A pdb=" N VAL c 175 " --> pdb=" O PRO c 171 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY c 178 " --> pdb=" O ALA c 174 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL c 179 " --> pdb=" O VAL c 175 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA c 181 " --> pdb=" O ALA c 177 " (cutoff:3.500A) Processing helix chain 'c' and resid 249 through 267 removed outlier: 4.045A pdb=" N PHE c 256 " --> pdb=" O VAL c 252 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLU c 260 " --> pdb=" O PHE c 256 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N LYS c 264 " --> pdb=" O GLU c 260 " (cutoff:3.500A) Processing helix chain 'c' and resid 278 through 297 removed outlier: 3.826A pdb=" N ARG c 282 " --> pdb=" O PRO c 278 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG c 284 " --> pdb=" O TRP c 280 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TYR c 290 " --> pdb=" O ALA c 286 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TRP c 295 " --> pdb=" O LEU c 291 " (cutoff:3.500A) Processing helix chain 'c' and resid 304 through 308 Processing helix chain 'c' and resid 320 through 326 removed outlier: 3.603A pdb=" N ILE c 324 " --> pdb=" O THR c 320 " (cutoff:3.500A) Processing helix chain 'd' and resid 51 through 56 Processing helix chain 'd' and resid 66 through 79 removed outlier: 3.526A pdb=" N ARG d 73 " --> pdb=" O ASP d 69 " (cutoff:3.500A) Processing helix chain 'd' and resid 90 through 95 removed outlier: 3.581A pdb=" N ILE d 94 " --> pdb=" O SER d 90 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE d 95 " --> pdb=" O LEU d 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 90 through 95' Processing helix chain 'd' and resid 96 through 98 No H-bonds generated for 'chain 'd' and resid 96 through 98' Processing helix chain 'd' and resid 111 through 119 Processing helix chain 'd' and resid 140 through 145 Processing helix chain 'd' and resid 171 through 187 removed outlier: 3.825A pdb=" N VAL d 175 " --> pdb=" O PRO d 171 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLY d 178 " --> pdb=" O ALA d 174 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL d 179 " --> pdb=" O VAL d 175 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA d 181 " --> pdb=" O ALA d 177 " (cutoff:3.500A) Processing helix chain 'd' and resid 249 through 267 removed outlier: 4.045A pdb=" N PHE d 256 " --> pdb=" O VAL d 252 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLU d 260 " --> pdb=" O PHE d 256 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N LYS d 264 " --> pdb=" O GLU d 260 " (cutoff:3.500A) Processing helix chain 'd' and resid 278 through 297 removed outlier: 3.825A pdb=" N ARG d 282 " --> pdb=" O PRO d 278 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG d 284 " --> pdb=" O TRP d 280 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TYR d 290 " --> pdb=" O ALA d 286 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TRP d 295 " --> pdb=" O LEU d 291 " (cutoff:3.500A) Processing helix chain 'd' and resid 304 through 308 Processing helix chain 'd' and resid 320 through 326 removed outlier: 3.603A pdb=" N ILE d 324 " --> pdb=" O THR d 320 " (cutoff:3.500A) Processing helix chain 'e' and resid 51 through 56 Processing helix chain 'e' and resid 66 through 79 removed outlier: 3.526A pdb=" N ARG e 73 " --> pdb=" O ASP e 69 " (cutoff:3.500A) Processing helix chain 'e' and resid 90 through 95 removed outlier: 3.580A pdb=" N ILE e 94 " --> pdb=" O SER e 90 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE e 95 " --> pdb=" O LEU e 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 90 through 95' Processing helix chain 'e' and resid 96 through 98 No H-bonds generated for 'chain 'e' and resid 96 through 98' Processing helix chain 'e' and resid 111 through 119 Processing helix chain 'e' and resid 140 through 145 Processing helix chain 'e' and resid 171 through 187 removed outlier: 3.825A pdb=" N VAL e 175 " --> pdb=" O PRO e 171 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY e 178 " --> pdb=" O ALA e 174 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL e 179 " --> pdb=" O VAL e 175 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA e 181 " --> pdb=" O ALA e 177 " (cutoff:3.500A) Processing helix chain 'e' and resid 249 through 267 removed outlier: 4.045A pdb=" N PHE e 256 " --> pdb=" O VAL e 252 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N GLU e 260 " --> pdb=" O PHE e 256 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N LYS e 264 " --> pdb=" O GLU e 260 " (cutoff:3.500A) Processing helix chain 'e' and resid 278 through 297 removed outlier: 3.824A pdb=" N ARG e 282 " --> pdb=" O PRO e 278 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG e 284 " --> pdb=" O TRP e 280 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TYR e 290 " --> pdb=" O ALA e 286 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N TRP e 295 " --> pdb=" O LEU e 291 " (cutoff:3.500A) Processing helix chain 'e' and resid 304 through 308 Processing helix chain 'e' and resid 320 through 326 removed outlier: 3.603A pdb=" N ILE e 324 " --> pdb=" O THR e 320 " (cutoff:3.500A) Processing helix chain 'f' and resid 51 through 56 Processing helix chain 'f' and resid 66 through 79 removed outlier: 3.525A pdb=" N ARG f 73 " --> pdb=" O ASP f 69 " (cutoff:3.500A) Processing helix chain 'f' and resid 90 through 95 removed outlier: 3.581A pdb=" N ILE f 94 " --> pdb=" O SER f 90 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE f 95 " --> pdb=" O LEU f 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 90 through 95' Processing helix chain 'f' and resid 96 through 98 No H-bonds generated for 'chain 'f' and resid 96 through 98' Processing helix chain 'f' and resid 111 through 119 Processing helix chain 'f' and resid 140 through 145 Processing helix chain 'f' and resid 171 through 187 removed outlier: 3.826A pdb=" N VAL f 175 " --> pdb=" O PRO f 171 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY f 178 " --> pdb=" O ALA f 174 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL f 179 " --> pdb=" O VAL f 175 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA f 181 " --> pdb=" O ALA f 177 " (cutoff:3.500A) Processing helix chain 'f' and resid 249 through 267 removed outlier: 4.045A pdb=" N PHE f 256 " --> pdb=" O VAL f 252 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N GLU f 260 " --> pdb=" O PHE f 256 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N LYS f 264 " --> pdb=" O GLU f 260 " (cutoff:3.500A) Processing helix chain 'f' and resid 278 through 297 removed outlier: 3.825A pdb=" N ARG f 282 " --> pdb=" O PRO f 278 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ARG f 284 " --> pdb=" O TRP f 280 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TYR f 290 " --> pdb=" O ALA f 286 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TRP f 295 " --> pdb=" O LEU f 291 " (cutoff:3.500A) Processing helix chain 'f' and resid 304 through 308 Processing helix chain 'f' and resid 320 through 326 removed outlier: 3.603A pdb=" N ILE f 324 " --> pdb=" O THR f 320 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 13 removed outlier: 6.315A pdb=" N GLY A 9 " --> pdb=" O ILE B 344 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N LEU B 346 " --> pdb=" O GLY A 9 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N TYR A 11 " --> pdb=" O LEU B 346 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 49 Processing sheet with id=AA3, first strand: chain 'A' and resid 127 through 128 removed outlier: 7.462A pdb=" N ALA A 127 " --> pdb=" O ALA A 155 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 161 through 162 Processing sheet with id=AA5, first strand: chain 'A' and resid 225 through 228 Processing sheet with id=AA6, first strand: chain 'A' and resid 309 through 312 removed outlier: 3.671A pdb=" N PHE A 310 " --> pdb=" O GLY A 334 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N VAL A 331 " --> pdb=" O GLN a 347 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N THR a 349 " --> pdb=" O VAL A 331 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N VAL A 333 " --> pdb=" O THR a 349 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 343 through 347 Processing sheet with id=AA8, first strand: chain 'B' and resid 9 through 13 removed outlier: 6.318A pdb=" N GLY B 9 " --> pdb=" O ILE C 344 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N LEU C 346 " --> pdb=" O GLY B 9 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N TYR B 11 " --> pdb=" O LEU C 346 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 47 through 49 Processing sheet with id=AB1, first strand: chain 'B' and resid 127 through 128 removed outlier: 7.462A pdb=" N ALA B 127 " --> pdb=" O ALA B 155 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 161 through 162 Processing sheet with id=AB3, first strand: chain 'B' and resid 225 through 228 Processing sheet with id=AB4, first strand: chain 'B' and resid 309 through 312 removed outlier: 3.670A pdb=" N PHE B 310 " --> pdb=" O GLY B 334 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N VAL B 331 " --> pdb=" O GLN b 347 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N THR b 349 " --> pdb=" O VAL B 331 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N VAL B 333 " --> pdb=" O THR b 349 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N GLY a 9 " --> pdb=" O ILE b 344 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N LEU b 346 " --> pdb=" O GLY a 9 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N TYR a 11 " --> pdb=" O LEU b 346 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N PHE b 348 " --> pdb=" O TYR a 11 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N GLU a 13 " --> pdb=" O PHE b 348 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 9 through 13 removed outlier: 6.324A pdb=" N GLY C 9 " --> pdb=" O ILE D 344 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N LEU D 346 " --> pdb=" O GLY C 9 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N TYR C 11 " --> pdb=" O LEU D 346 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'C' and resid 47 through 49 Processing sheet with id=AB7, first strand: chain 'C' and resid 127 through 128 removed outlier: 7.461A pdb=" N ALA C 127 " --> pdb=" O ALA C 155 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'C' and resid 161 through 162 Processing sheet with id=AB9, first strand: chain 'C' and resid 225 through 228 Processing sheet with id=AC1, first strand: chain 'C' and resid 309 through 312 removed outlier: 3.670A pdb=" N PHE C 310 " --> pdb=" O GLY C 334 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LYS C 332 " --> pdb=" O GLN C 312 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N VAL C 331 " --> pdb=" O GLN c 347 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N THR c 349 " --> pdb=" O VAL C 331 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N VAL C 333 " --> pdb=" O THR c 349 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N GLY b 9 " --> pdb=" O ILE c 344 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N LEU c 346 " --> pdb=" O GLY b 9 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N TYR b 11 " --> pdb=" O LEU c 346 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N PHE c 348 " --> pdb=" O TYR b 11 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N GLU b 13 " --> pdb=" O PHE c 348 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 9 through 13 removed outlier: 6.348A pdb=" N GLY D 9 " --> pdb=" O ILE E 344 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N LEU E 346 " --> pdb=" O GLY D 9 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N TYR D 11 " --> pdb=" O LEU E 346 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'D' and resid 47 through 49 Processing sheet with id=AC4, first strand: chain 'D' and resid 127 through 128 removed outlier: 7.461A pdb=" N ALA D 127 " --> pdb=" O ALA D 155 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'D' and resid 161 through 162 Processing sheet with id=AC6, first strand: chain 'D' and resid 225 through 228 Processing sheet with id=AC7, first strand: chain 'D' and resid 309 through 312 removed outlier: 3.671A pdb=" N PHE D 310 " --> pdb=" O GLY D 334 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N VAL D 331 " --> pdb=" O GLN d 347 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N THR d 349 " --> pdb=" O VAL D 331 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N VAL D 333 " --> pdb=" O THR d 349 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N GLY c 9 " --> pdb=" O ILE d 344 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N LEU d 346 " --> pdb=" O GLY c 9 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N TYR c 11 " --> pdb=" O LEU d 346 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N PHE d 348 " --> pdb=" O TYR c 11 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N GLU c 13 " --> pdb=" O PHE d 348 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 9 through 13 removed outlier: 6.309A pdb=" N GLY E 9 " --> pdb=" O ILE F 344 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N LEU F 346 " --> pdb=" O GLY E 9 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N TYR E 11 " --> pdb=" O LEU F 346 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'E' and resid 47 through 49 Processing sheet with id=AD1, first strand: chain 'E' and resid 127 through 128 removed outlier: 7.461A pdb=" N ALA E 127 " --> pdb=" O ALA E 155 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'E' and resid 161 through 162 Processing sheet with id=AD3, first strand: chain 'E' and resid 225 through 228 Processing sheet with id=AD4, first strand: chain 'E' and resid 309 through 312 removed outlier: 3.671A pdb=" N PHE E 310 " --> pdb=" O GLY E 334 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N VAL E 331 " --> pdb=" O GLN e 347 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N THR e 349 " --> pdb=" O VAL E 331 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N VAL E 333 " --> pdb=" O THR e 349 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N GLY d 9 " --> pdb=" O ILE e 344 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N LEU e 346 " --> pdb=" O GLY d 9 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N TYR d 11 " --> pdb=" O LEU e 346 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N PHE e 348 " --> pdb=" O TYR d 11 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N GLU d 13 " --> pdb=" O PHE e 348 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 47 through 49 Processing sheet with id=AD6, first strand: chain 'F' and resid 127 through 128 removed outlier: 7.462A pdb=" N ALA F 127 " --> pdb=" O ALA F 155 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'F' and resid 161 through 162 Processing sheet with id=AD8, first strand: chain 'F' and resid 225 through 228 Processing sheet with id=AD9, first strand: chain 'F' and resid 309 through 312 removed outlier: 3.670A pdb=" N PHE F 310 " --> pdb=" O GLY F 334 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N VAL F 331 " --> pdb=" O GLN f 347 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N THR f 349 " --> pdb=" O VAL F 331 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N VAL F 333 " --> pdb=" O THR f 349 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N GLY e 9 " --> pdb=" O ILE f 344 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N LEU f 346 " --> pdb=" O GLY e 9 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N TYR e 11 " --> pdb=" O LEU f 346 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N PHE f 348 " --> pdb=" O TYR e 11 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N GLU e 13 " --> pdb=" O PHE f 348 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'a' and resid 47 through 49 Processing sheet with id=AE2, first strand: chain 'a' and resid 127 through 128 removed outlier: 7.462A pdb=" N ALA a 127 " --> pdb=" O ALA a 155 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'a' and resid 161 through 162 Processing sheet with id=AE4, first strand: chain 'a' and resid 225 through 228 Processing sheet with id=AE5, first strand: chain 'a' and resid 309 through 312 removed outlier: 3.670A pdb=" N PHE a 310 " --> pdb=" O GLY a 334 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'b' and resid 47 through 49 Processing sheet with id=AE7, first strand: chain 'b' and resid 127 through 128 removed outlier: 7.461A pdb=" N ALA b 127 " --> pdb=" O ALA b 155 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'b' and resid 161 through 162 Processing sheet with id=AE9, first strand: chain 'b' and resid 225 through 228 Processing sheet with id=AF1, first strand: chain 'b' and resid 309 through 312 removed outlier: 3.671A pdb=" N PHE b 310 " --> pdb=" O GLY b 334 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'c' and resid 47 through 49 Processing sheet with id=AF3, first strand: chain 'c' and resid 127 through 128 removed outlier: 7.461A pdb=" N ALA c 127 " --> pdb=" O ALA c 155 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF3 Processing sheet with id=AF4, first strand: chain 'c' and resid 161 through 162 Processing sheet with id=AF5, first strand: chain 'c' and resid 225 through 228 Processing sheet with id=AF6, first strand: chain 'c' and resid 309 through 312 removed outlier: 3.671A pdb=" N PHE c 310 " --> pdb=" O GLY c 334 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'd' and resid 47 through 49 Processing sheet with id=AF8, first strand: chain 'd' and resid 127 through 128 removed outlier: 7.462A pdb=" N ALA d 127 " --> pdb=" O ALA d 155 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF8 Processing sheet with id=AF9, first strand: chain 'd' and resid 161 through 162 Processing sheet with id=AG1, first strand: chain 'd' and resid 225 through 228 Processing sheet with id=AG2, first strand: chain 'd' and resid 309 through 312 removed outlier: 3.670A pdb=" N PHE d 310 " --> pdb=" O GLY d 334 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'e' and resid 47 through 49 Processing sheet with id=AG4, first strand: chain 'e' and resid 127 through 128 removed outlier: 7.462A pdb=" N ALA e 127 " --> pdb=" O ALA e 155 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG4 Processing sheet with id=AG5, first strand: chain 'e' and resid 161 through 162 Processing sheet with id=AG6, first strand: chain 'e' and resid 225 through 228 Processing sheet with id=AG7, first strand: chain 'e' and resid 309 through 312 removed outlier: 3.670A pdb=" N PHE e 310 " --> pdb=" O GLY e 334 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'f' and resid 47 through 49 Processing sheet with id=AG9, first strand: chain 'f' and resid 127 through 128 removed outlier: 7.462A pdb=" N ALA f 127 " --> pdb=" O ALA f 155 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG9 Processing sheet with id=AH1, first strand: chain 'f' and resid 161 through 162 Processing sheet with id=AH2, first strand: chain 'f' and resid 225 through 228 Processing sheet with id=AH3, first strand: chain 'f' and resid 309 through 312 removed outlier: 3.671A pdb=" N PHE f 310 " --> pdb=" O GLY f 334 " (cutoff:3.500A) 896 hydrogen bonds defined for protein. 2526 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: 10.24 Time building geometry restraints manager: 12.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 9102 1.33 - 1.45: 5898 1.45 - 1.57: 18636 1.57 - 1.68: 0 1.68 - 1.80: 192 Bond restraints: 33828 Sorted by residual: bond pdb=" C ILE E 95 " pdb=" N PRO E 96 " ideal model delta sigma weight residual 1.335 1.352 -0.018 1.28e-02 6.10e+03 1.91e+00 bond pdb=" C ILE f 95 " pdb=" N PRO f 96 " ideal model delta sigma weight residual 1.335 1.352 -0.018 1.28e-02 6.10e+03 1.88e+00 bond pdb=" C ILE D 95 " pdb=" N PRO D 96 " ideal model delta sigma weight residual 1.335 1.352 -0.018 1.28e-02 6.10e+03 1.88e+00 bond pdb=" C ILE d 95 " pdb=" N PRO d 96 " ideal model delta sigma weight residual 1.335 1.352 -0.017 1.28e-02 6.10e+03 1.87e+00 bond pdb=" CB THR d 240 " pdb=" CG2 THR d 240 " ideal model delta sigma weight residual 1.521 1.477 0.044 3.30e-02 9.18e+02 1.76e+00 ... (remaining 33823 not shown) Histogram of bond angle deviations from ideal: 99.19 - 106.17: 774 106.17 - 113.14: 18027 113.14 - 120.11: 12262 120.11 - 127.08: 14631 127.08 - 134.06: 410 Bond angle restraints: 46104 Sorted by residual: angle pdb=" CA LEU e 125 " pdb=" CB LEU e 125 " pdb=" CG LEU e 125 " ideal model delta sigma weight residual 116.30 131.99 -15.69 3.50e+00 8.16e-02 2.01e+01 angle pdb=" CA LEU F 125 " pdb=" CB LEU F 125 " pdb=" CG LEU F 125 " ideal model delta sigma weight residual 116.30 131.99 -15.69 3.50e+00 8.16e-02 2.01e+01 angle pdb=" CA LEU b 125 " pdb=" CB LEU b 125 " pdb=" CG LEU b 125 " ideal model delta sigma weight residual 116.30 131.98 -15.68 3.50e+00 8.16e-02 2.01e+01 angle pdb=" CA LEU D 125 " pdb=" CB LEU D 125 " pdb=" CG LEU D 125 " ideal model delta sigma weight residual 116.30 131.98 -15.68 3.50e+00 8.16e-02 2.01e+01 angle pdb=" CA LEU A 125 " pdb=" CB LEU A 125 " pdb=" CG LEU A 125 " ideal model delta sigma weight residual 116.30 131.97 -15.67 3.50e+00 8.16e-02 2.00e+01 ... (remaining 46099 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.55: 17593 16.55 - 33.09: 1703 33.09 - 49.64: 504 49.64 - 66.18: 132 66.18 - 82.73: 84 Dihedral angle restraints: 20016 sinusoidal: 7692 harmonic: 12324 Sorted by residual: dihedral pdb=" CA PHE f 228 " pdb=" C PHE f 228 " pdb=" N SER f 229 " pdb=" CA SER f 229 " ideal model delta harmonic sigma weight residual 180.00 -157.88 -22.12 0 5.00e+00 4.00e-02 1.96e+01 dihedral pdb=" CA PHE B 228 " pdb=" C PHE B 228 " pdb=" N SER B 229 " pdb=" CA SER B 229 " ideal model delta harmonic sigma weight residual -180.00 -157.89 -22.11 0 5.00e+00 4.00e-02 1.96e+01 dihedral pdb=" CA PHE d 228 " pdb=" C PHE d 228 " pdb=" N SER d 229 " pdb=" CA SER d 229 " ideal model delta harmonic sigma weight residual 180.00 -157.90 -22.10 0 5.00e+00 4.00e-02 1.95e+01 ... (remaining 20013 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 3073 0.038 - 0.075: 1373 0.075 - 0.113: 453 0.113 - 0.151: 219 0.151 - 0.188: 66 Chirality restraints: 5184 Sorted by residual: chirality pdb=" CA TYR F 158 " pdb=" N TYR F 158 " pdb=" C TYR F 158 " pdb=" CB TYR F 158 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.86e-01 chirality pdb=" CA TYR d 158 " pdb=" N TYR d 158 " pdb=" C TYR d 158 " pdb=" CB TYR d 158 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.84e-01 chirality pdb=" CA TYR c 158 " pdb=" N TYR c 158 " pdb=" C TYR c 158 " pdb=" CB TYR c 158 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.80e-01 ... (remaining 5181 not shown) Planarity restraints: 5988 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN a 120 " 0.046 5.00e-02 4.00e+02 6.89e-02 7.61e+00 pdb=" N PRO a 121 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO a 121 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO a 121 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN C 120 " -0.046 5.00e-02 4.00e+02 6.89e-02 7.59e+00 pdb=" N PRO C 121 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO C 121 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO C 121 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN E 120 " 0.046 5.00e-02 4.00e+02 6.89e-02 7.59e+00 pdb=" N PRO E 121 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO E 121 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO E 121 " 0.038 5.00e-02 4.00e+02 ... (remaining 5985 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 10761 2.83 - 3.35: 29211 3.35 - 3.87: 53646 3.87 - 4.38: 58039 4.38 - 4.90: 101511 Nonbonded interactions: 253168 Sorted by model distance: nonbonded pdb=" O LYS d 67 " pdb=" OG SER d 71 " model vdw 2.313 2.440 nonbonded pdb=" O LYS A 67 " pdb=" OG SER A 71 " model vdw 2.313 2.440 nonbonded pdb=" O LYS B 67 " pdb=" OG SER B 71 " model vdw 2.313 2.440 nonbonded pdb=" O LYS F 67 " pdb=" OG SER F 71 " model vdw 2.313 2.440 nonbonded pdb=" O LYS f 67 " pdb=" OG SER f 71 " model vdw 2.313 2.440 ... (remaining 253163 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 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.010 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: 0.030 Extract box with map and model: 14.510 Check model and map are aligned: 0.470 Set scattering table: 0.290 Process input model: 78.810 Find NCS groups from input model: 2.150 Set up NCS constraints: 0.210 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 102.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 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 : 0.006 0.063 33828 Z= 0.422 Angle : 0.893 15.693 46104 Z= 0.464 Chirality : 0.053 0.188 5184 Planarity : 0.007 0.069 5988 Dihedral : 15.992 82.726 12120 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 3.09 % Allowed : 13.23 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.56 (0.09), residues: 4224 helix: -4.41 (0.05), residues: 1284 sheet: -1.70 (0.24), residues: 504 loop : -2.58 (0.09), residues: 2436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP e 280 PHE 0.013 0.002 PHE D 348 TYR 0.015 0.003 TYR c 40 ARG 0.006 0.001 ARG f 48 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8448 Ramachandran restraints generated. 4224 Oldfield, 0 Emsley, 4224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8448 Ramachandran restraints generated. 4224 Oldfield, 0 Emsley, 4224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1322 residues out of total 3516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 1214 time to evaluate : 3.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ILE cc_start: 0.9091 (tp) cc_final: 0.8718 (mt) REVERT: A 248 ARG cc_start: 0.9005 (ttm170) cc_final: 0.8740 (ttm-80) REVERT: A 264 LYS cc_start: 0.8941 (OUTLIER) cc_final: 0.8707 (ttpt) REVERT: B 47 ILE cc_start: 0.9069 (tp) cc_final: 0.8656 (mt) REVERT: B 118 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8483 (tm) REVERT: B 243 ASP cc_start: 0.7427 (t0) cc_final: 0.7199 (t0) REVERT: B 264 LYS cc_start: 0.8836 (OUTLIER) cc_final: 0.8573 (ttpt) REVERT: C 47 ILE cc_start: 0.9002 (tp) cc_final: 0.8628 (mt) REVERT: C 73 ARG cc_start: 0.8727 (tpt-90) cc_final: 0.8369 (tmt-80) REVERT: C 118 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8349 (tm) REVERT: C 264 LYS cc_start: 0.8751 (OUTLIER) cc_final: 0.8414 (ttpp) REVERT: C 309 TYR cc_start: 0.8529 (p90) cc_final: 0.8263 (p90) REVERT: C 329 MET cc_start: 0.8885 (ptt) cc_final: 0.8419 (ptm) REVERT: C 345 ILE cc_start: 0.8747 (pt) cc_final: 0.8530 (mt) REVERT: D 180 TYR cc_start: 0.9054 (m-10) cc_final: 0.8597 (m-10) REVERT: D 267 MET cc_start: 0.8828 (mmt) cc_final: 0.8564 (mmp) REVERT: D 345 ILE cc_start: 0.8908 (pt) cc_final: 0.8596 (mt) REVERT: E 47 ILE cc_start: 0.8985 (tp) cc_final: 0.8607 (mt) REVERT: E 73 ARG cc_start: 0.8744 (tpt-90) cc_final: 0.8519 (tpt170) REVERT: E 118 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8622 (tm) REVERT: E 136 LEU cc_start: 0.6655 (mp) cc_final: 0.6387 (tp) REVERT: E 243 ASP cc_start: 0.7446 (t0) cc_final: 0.7201 (t0) REVERT: E 264 LYS cc_start: 0.8830 (OUTLIER) cc_final: 0.8590 (ttpt) REVERT: F 47 ILE cc_start: 0.9071 (tp) cc_final: 0.8701 (mt) REVERT: F 65 GLU cc_start: 0.7826 (tp30) cc_final: 0.7540 (mm-30) REVERT: F 73 ARG cc_start: 0.8682 (tpt-90) cc_final: 0.8441 (tpt170) REVERT: F 118 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8415 (tm) REVERT: F 180 TYR cc_start: 0.8978 (m-10) cc_final: 0.8530 (m-10) REVERT: F 184 ASP cc_start: 0.7421 (m-30) cc_final: 0.6981 (m-30) REVERT: F 264 LYS cc_start: 0.8867 (OUTLIER) cc_final: 0.8522 (ttpp) REVERT: F 329 MET cc_start: 0.8761 (ptt) cc_final: 0.8344 (ptm) REVERT: a 143 GLU cc_start: 0.8035 (tm-30) cc_final: 0.7597 (tm-30) REVERT: a 205 LYS cc_start: 0.8257 (tttt) cc_final: 0.7905 (tttt) REVERT: a 210 ASP cc_start: 0.8383 (t70) cc_final: 0.8137 (t0) REVERT: a 220 ARG cc_start: 0.8741 (ptt-90) cc_final: 0.8322 (mtm180) REVERT: a 252 VAL cc_start: 0.9243 (OUTLIER) cc_final: 0.9021 (p) REVERT: a 281 GLU cc_start: 0.7828 (tp30) cc_final: 0.7161 (tp30) REVERT: b 116 ASP cc_start: 0.6264 (t0) cc_final: 0.5606 (m-30) REVERT: b 143 GLU cc_start: 0.7779 (tm-30) cc_final: 0.7459 (tm-30) REVERT: b 220 ARG cc_start: 0.8629 (ptt-90) cc_final: 0.8362 (mtm180) REVERT: b 235 VAL cc_start: 0.9500 (m) cc_final: 0.9299 (t) REVERT: b 281 GLU cc_start: 0.7771 (tp30) cc_final: 0.7194 (tp30) REVERT: b 292 TYR cc_start: 0.8902 (t80) cc_final: 0.8559 (t80) REVERT: c 205 LYS cc_start: 0.8437 (tttt) cc_final: 0.8082 (tttt) REVERT: c 220 ARG cc_start: 0.8381 (ptt-90) cc_final: 0.7856 (mtm180) REVERT: c 276 ASN cc_start: 0.8708 (p0) cc_final: 0.8414 (p0) REVERT: c 278 PRO cc_start: 0.9195 (Cg_exo) cc_final: 0.8836 (Cg_endo) REVERT: c 281 GLU cc_start: 0.7904 (tp30) cc_final: 0.7569 (tp30) REVERT: c 332 LYS cc_start: 0.8366 (mtpp) cc_final: 0.8085 (mmtt) REVERT: d 143 GLU cc_start: 0.7845 (tm-30) cc_final: 0.7399 (tm-30) REVERT: d 210 ASP cc_start: 0.8460 (t70) cc_final: 0.8047 (t0) REVERT: d 220 ARG cc_start: 0.8741 (ptt-90) cc_final: 0.8373 (mtm180) REVERT: d 252 VAL cc_start: 0.9319 (OUTLIER) cc_final: 0.9102 (p) REVERT: d 281 GLU cc_start: 0.7960 (tp30) cc_final: 0.7396 (tp30) REVERT: d 325 ASP cc_start: 0.7663 (m-30) cc_final: 0.7405 (m-30) REVERT: e 116 ASP cc_start: 0.6137 (t0) cc_final: 0.5571 (m-30) REVERT: e 143 GLU cc_start: 0.7754 (tm-30) cc_final: 0.7440 (tm-30) REVERT: e 220 ARG cc_start: 0.8664 (ptt-90) cc_final: 0.8447 (mtm180) REVERT: e 281 GLU cc_start: 0.7819 (tp30) cc_final: 0.7235 (tp30) REVERT: e 292 TYR cc_start: 0.8908 (t80) cc_final: 0.8557 (t80) REVERT: f 205 LYS cc_start: 0.8383 (tttt) cc_final: 0.8022 (tttt) REVERT: f 220 ARG cc_start: 0.8435 (ptt-90) cc_final: 0.7981 (mtm180) REVERT: f 276 ASN cc_start: 0.8754 (p0) cc_final: 0.8470 (p0) REVERT: f 278 PRO cc_start: 0.9212 (Cg_exo) cc_final: 0.8882 (Cg_endo) REVERT: f 281 GLU cc_start: 0.7864 (tp30) cc_final: 0.7456 (tp30) REVERT: f 332 LYS cc_start: 0.8363 (mtpp) cc_final: 0.8092 (mmtt) outliers start: 108 outliers final: 32 residues processed: 1281 average time/residue: 0.4885 time to fit residues: 962.1857 Evaluate side-chains 620 residues out of total 3516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 577 time to evaluate : 3.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 264 LYS Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 264 LYS Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 264 LYS Chi-restraints excluded: chain C residue 344 ILE Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 344 ILE Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 264 LYS Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 344 ILE Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 264 LYS Chi-restraints excluded: chain F residue 344 ILE Chi-restraints excluded: chain a residue 118 LEU Chi-restraints excluded: chain a residue 125 LEU Chi-restraints excluded: chain a residue 252 VAL Chi-restraints excluded: chain a residue 318 THR Chi-restraints excluded: chain a residue 344 ILE Chi-restraints excluded: chain b residue 118 LEU Chi-restraints excluded: chain b residue 344 ILE Chi-restraints excluded: chain c residue 118 LEU Chi-restraints excluded: chain c residue 252 VAL Chi-restraints excluded: chain c residue 318 THR Chi-restraints excluded: chain d residue 118 LEU Chi-restraints excluded: chain d residue 125 LEU Chi-restraints excluded: chain d residue 252 VAL Chi-restraints excluded: chain d residue 318 THR Chi-restraints excluded: chain d residue 344 ILE Chi-restraints excluded: chain e residue 118 LEU Chi-restraints excluded: chain e residue 344 ILE Chi-restraints excluded: chain f residue 118 LEU Chi-restraints excluded: chain f residue 252 VAL Chi-restraints excluded: chain f residue 318 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 354 optimal weight: 0.0980 chunk 318 optimal weight: 5.9990 chunk 176 optimal weight: 7.9990 chunk 108 optimal weight: 0.9990 chunk 214 optimal weight: 5.9990 chunk 170 optimal weight: 2.9990 chunk 329 optimal weight: 0.7980 chunk 127 optimal weight: 7.9990 chunk 200 optimal weight: 0.7980 chunk 245 optimal weight: 0.0040 chunk 381 optimal weight: 7.9990 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 ASN A 78 ASN A 195 ASN A 246 ASN B 57 ASN B 78 ASN B 195 ASN B 246 ASN C 57 ASN C 78 ASN C 195 ASN C 246 ASN C 321 GLN D 57 ASN D 78 ASN D 195 ASN D 246 ASN D 321 GLN E 57 ASN E 78 ASN E 195 ASN E 246 ASN E 321 GLN F 57 ASN F 78 ASN F 195 ASN F 246 ASN a 78 ASN a 195 ASN b 78 ASN b 195 ASN c 45 ASN c 78 ASN c 195 ASN d 78 ASN d 195 ASN d 246 ASN e 78 ASN e 195 ASN f 45 ASN f 78 ASN f 195 ASN Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.2870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 33828 Z= 0.168 Angle : 0.633 13.169 46104 Z= 0.320 Chirality : 0.044 0.171 5184 Planarity : 0.005 0.046 5988 Dihedral : 6.316 49.873 4690 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 3.84 % Allowed : 19.56 % Favored : 76.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.54 (0.11), residues: 4224 helix: -2.57 (0.11), residues: 1428 sheet: -2.18 (0.25), residues: 384 loop : -2.27 (0.10), residues: 2412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 280 PHE 0.017 0.001 PHE d 348 TYR 0.022 0.001 TYR a 82 ARG 0.007 0.001 ARG d 284 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8448 Ramachandran restraints generated. 4224 Oldfield, 0 Emsley, 4224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8448 Ramachandran restraints generated. 4224 Oldfield, 0 Emsley, 4224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 827 residues out of total 3516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 693 time to evaluate : 3.895 Fit side-chains revert: symmetry clash REVERT: A 47 ILE cc_start: 0.8835 (tp) cc_final: 0.8614 (mt) REVERT: A 345 ILE cc_start: 0.8787 (pt) cc_final: 0.8554 (mt) REVERT: B 47 ILE cc_start: 0.8764 (tp) cc_final: 0.8514 (mt) REVERT: B 264 LYS cc_start: 0.8967 (OUTLIER) cc_final: 0.8680 (ttpt) REVERT: B 304 LYS cc_start: 0.8203 (ptmm) cc_final: 0.7738 (ptmm) REVERT: C 47 ILE cc_start: 0.8818 (tp) cc_final: 0.8599 (mt) REVERT: C 118 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8332 (tm) REVERT: C 264 LYS cc_start: 0.8955 (OUTLIER) cc_final: 0.8730 (ttmt) REVERT: C 329 MET cc_start: 0.8880 (ptt) cc_final: 0.8548 (ptm) REVERT: D 180 TYR cc_start: 0.8897 (m-10) cc_final: 0.8470 (m-10) REVERT: D 325 ASP cc_start: 0.8320 (m-30) cc_final: 0.7970 (m-30) REVERT: D 345 ILE cc_start: 0.8831 (pt) cc_final: 0.8588 (mt) REVERT: E 47 ILE cc_start: 0.8860 (tp) cc_final: 0.8598 (mt) REVERT: E 209 THR cc_start: 0.8040 (OUTLIER) cc_final: 0.7716 (p) REVERT: E 243 ASP cc_start: 0.7563 (t0) cc_final: 0.7354 (t0) REVERT: E 264 LYS cc_start: 0.8960 (OUTLIER) cc_final: 0.8588 (ttpp) REVERT: E 277 GLN cc_start: 0.8738 (tp40) cc_final: 0.8528 (tp40) REVERT: F 37 GLN cc_start: 0.7909 (tm-30) cc_final: 0.7665 (pp30) REVERT: F 118 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8337 (tm) REVERT: F 180 TYR cc_start: 0.8907 (m-10) cc_final: 0.8460 (m-10) REVERT: F 264 LYS cc_start: 0.9011 (OUTLIER) cc_final: 0.8611 (ttpp) REVERT: F 329 MET cc_start: 0.8807 (ptt) cc_final: 0.8502 (ptm) REVERT: a 260 GLU cc_start: 0.6162 (mm-30) cc_final: 0.5409 (mm-30) REVERT: a 292 TYR cc_start: 0.8658 (t80) cc_final: 0.8348 (t80) REVERT: b 72 VAL cc_start: 0.9028 (p) cc_final: 0.8680 (t) REVERT: b 82 TYR cc_start: 0.8351 (p90) cc_final: 0.8031 (p90) REVERT: b 116 ASP cc_start: 0.6015 (t0) cc_final: 0.5574 (m-30) REVERT: b 260 GLU cc_start: 0.7079 (mm-30) cc_final: 0.6717 (mm-30) REVERT: b 271 MET cc_start: 0.8577 (tpt) cc_final: 0.8341 (tpt) REVERT: b 329 MET cc_start: 0.8471 (ptt) cc_final: 0.8035 (ptm) REVERT: c 271 MET cc_start: 0.8032 (tpt) cc_final: 0.7713 (tpt) REVERT: c 321 GLN cc_start: 0.8573 (tm-30) cc_final: 0.8146 (tm-30) REVERT: c 332 LYS cc_start: 0.8251 (mtpp) cc_final: 0.8004 (mmtt) REVERT: d 72 VAL cc_start: 0.9106 (p) cc_final: 0.8898 (t) REVERT: d 260 GLU cc_start: 0.6207 (mm-30) cc_final: 0.5948 (mm-30) REVERT: e 72 VAL cc_start: 0.8991 (p) cc_final: 0.8666 (t) REVERT: e 116 ASP cc_start: 0.6288 (t0) cc_final: 0.5964 (m-30) REVERT: e 169 ASP cc_start: 0.7740 (OUTLIER) cc_final: 0.7262 (t0) REVERT: e 224 MET cc_start: 0.8448 (mmm) cc_final: 0.8246 (mmt) REVERT: e 260 GLU cc_start: 0.7092 (mm-30) cc_final: 0.6162 (mm-30) REVERT: e 329 MET cc_start: 0.8452 (ptt) cc_final: 0.8178 (ptm) REVERT: f 210 ASP cc_start: 0.8527 (t0) cc_final: 0.8325 (t0) REVERT: f 260 GLU cc_start: 0.6465 (mm-30) cc_final: 0.6085 (mm-30) REVERT: f 271 MET cc_start: 0.8027 (tpt) cc_final: 0.7757 (tpt) REVERT: f 276 ASN cc_start: 0.8680 (p0) cc_final: 0.8471 (p0) REVERT: f 332 LYS cc_start: 0.8277 (mtpp) cc_final: 0.8071 (mmtt) outliers start: 134 outliers final: 64 residues processed: 789 average time/residue: 0.4091 time to fit residues: 531.4660 Evaluate side-chains 620 residues out of total 3516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 548 time to evaluate : 3.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 228 PHE Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 264 LYS Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 228 PHE Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 264 LYS Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 164 ASP Chi-restraints excluded: chain C residue 228 PHE Chi-restraints excluded: chain C residue 264 LYS Chi-restraints excluded: chain C residue 344 ILE Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 164 ASP Chi-restraints excluded: chain D residue 228 PHE Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 344 ILE Chi-restraints excluded: chain E residue 164 ASP Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 228 PHE Chi-restraints excluded: chain E residue 264 LYS Chi-restraints excluded: chain E residue 317 ILE Chi-restraints excluded: chain E residue 344 ILE Chi-restraints excluded: chain F residue 13 GLU Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 53 MET Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 164 ASP Chi-restraints excluded: chain F residue 228 PHE Chi-restraints excluded: chain F residue 264 LYS Chi-restraints excluded: chain F residue 344 ILE Chi-restraints excluded: chain a residue 49 ILE Chi-restraints excluded: chain a residue 97 THR Chi-restraints excluded: chain a residue 118 LEU Chi-restraints excluded: chain a residue 207 LEU Chi-restraints excluded: chain b residue 97 THR Chi-restraints excluded: chain b residue 113 THR Chi-restraints excluded: chain b residue 118 LEU Chi-restraints excluded: chain b residue 169 ASP Chi-restraints excluded: chain b residue 344 ILE Chi-restraints excluded: chain c residue 97 THR Chi-restraints excluded: chain c residue 113 THR Chi-restraints excluded: chain c residue 118 LEU Chi-restraints excluded: chain c residue 137 THR Chi-restraints excluded: chain c residue 250 VAL Chi-restraints excluded: chain d residue 97 THR Chi-restraints excluded: chain d residue 118 LEU Chi-restraints excluded: chain d residue 202 LEU Chi-restraints excluded: chain d residue 235 VAL Chi-restraints excluded: chain d residue 344 ILE Chi-restraints excluded: chain e residue 97 THR Chi-restraints excluded: chain e residue 118 LEU Chi-restraints excluded: chain e residue 169 ASP Chi-restraints excluded: chain e residue 344 ILE Chi-restraints excluded: chain f residue 97 THR Chi-restraints excluded: chain f residue 113 THR Chi-restraints excluded: chain f residue 118 LEU Chi-restraints excluded: chain f residue 137 THR Chi-restraints excluded: chain f residue 250 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 211 optimal weight: 10.0000 chunk 118 optimal weight: 10.0000 chunk 317 optimal weight: 6.9990 chunk 259 optimal weight: 0.9990 chunk 105 optimal weight: 10.0000 chunk 382 optimal weight: 10.0000 chunk 412 optimal weight: 4.9990 chunk 340 optimal weight: 6.9990 chunk 378 optimal weight: 6.9990 chunk 130 optimal weight: 0.9990 chunk 306 optimal weight: 9.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN ** A 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 61 ASN B 63 ASN ** B 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 223 ASN C 61 ASN C 63 ASN ** C 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 61 ASN ** D 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 321 GLN E 61 ASN E 63 ASN ** E 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 223 ASN F 61 ASN F 63 ASN ** F 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 63 ASN a 223 ASN b 45 ASN b 57 ASN b 63 ASN b 223 ASN c 45 ASN c 63 ASN c 223 ASN c 350 GLN d 63 ASN d 223 ASN e 45 ASN e 57 ASN e 63 ASN e 223 ASN f 45 ASN f 57 ASN f 63 ASN f 223 ASN f 350 GLN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.3612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 33828 Z= 0.416 Angle : 0.716 15.188 46104 Z= 0.355 Chirality : 0.048 0.159 5184 Planarity : 0.005 0.046 5988 Dihedral : 6.056 52.420 4664 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 6.04 % Allowed : 20.76 % Favored : 73.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.68 (0.11), residues: 4224 helix: -1.31 (0.13), residues: 1428 sheet: -2.39 (0.24), residues: 408 loop : -1.98 (0.11), residues: 2388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 280 PHE 0.020 0.002 PHE c 348 TYR 0.019 0.002 TYR c 40 ARG 0.007 0.001 ARG a 284 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8448 Ramachandran restraints generated. 4224 Oldfield, 0 Emsley, 4224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8448 Ramachandran restraints generated. 4224 Oldfield, 0 Emsley, 4224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 738 residues out of total 3516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 211 poor density : 527 time to evaluate : 3.390 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 ILE cc_start: 0.8808 (tp) cc_final: 0.8574 (mt) REVERT: A 180 TYR cc_start: 0.8777 (m-10) cc_final: 0.8458 (m-10) REVERT: A 209 THR cc_start: 0.8562 (OUTLIER) cc_final: 0.8355 (p) REVERT: B 94 ILE cc_start: 0.9158 (mm) cc_final: 0.8887 (mt) REVERT: B 209 THR cc_start: 0.8523 (OUTLIER) cc_final: 0.8294 (p) REVERT: B 264 LYS cc_start: 0.9007 (OUTLIER) cc_final: 0.8675 (ttpp) REVERT: C 7 TYR cc_start: 0.8630 (p90) cc_final: 0.8358 (p90) REVERT: C 37 GLN cc_start: 0.7991 (tm-30) cc_final: 0.7787 (tm-30) REVERT: C 118 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8651 (tm) REVERT: C 135 GLU cc_start: 0.8068 (tt0) cc_final: 0.7761 (mt-10) REVERT: C 209 THR cc_start: 0.8607 (OUTLIER) cc_final: 0.8004 (p) REVERT: C 211 GLU cc_start: 0.7423 (OUTLIER) cc_final: 0.7158 (pm20) REVERT: C 264 LYS cc_start: 0.8990 (OUTLIER) cc_final: 0.8622 (ttpp) REVERT: C 329 MET cc_start: 0.8963 (ptt) cc_final: 0.8553 (ptm) REVERT: C 344 ILE cc_start: 0.9471 (OUTLIER) cc_final: 0.9203 (mt) REVERT: D 180 TYR cc_start: 0.8859 (m-10) cc_final: 0.8600 (m-10) REVERT: D 209 THR cc_start: 0.8509 (OUTLIER) cc_final: 0.8287 (p) REVERT: D 216 TYR cc_start: 0.8906 (m-80) cc_final: 0.8600 (m-10) REVERT: D 271 MET cc_start: 0.9383 (tpt) cc_final: 0.9133 (tpp) REVERT: D 305 GLU cc_start: 0.7753 (pt0) cc_final: 0.7035 (tt0) REVERT: E 47 ILE cc_start: 0.8768 (tp) cc_final: 0.8550 (mt) REVERT: E 264 LYS cc_start: 0.8976 (OUTLIER) cc_final: 0.8731 (ttpt) REVERT: E 271 MET cc_start: 0.9218 (tpt) cc_final: 0.8979 (tpt) REVERT: F 37 GLN cc_start: 0.7954 (tm-30) cc_final: 0.7749 (tm-30) REVERT: F 118 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8567 (tm) REVERT: F 264 LYS cc_start: 0.9009 (OUTLIER) cc_final: 0.8593 (ttpp) REVERT: F 304 LYS cc_start: 0.8386 (pttm) cc_final: 0.7931 (pttm) REVERT: F 306 GLU cc_start: 0.7917 (pt0) cc_final: 0.7512 (pt0) REVERT: a 260 GLU cc_start: 0.6887 (mm-30) cc_final: 0.5908 (mm-30) REVERT: a 271 MET cc_start: 0.8788 (tpt) cc_final: 0.8522 (tpt) REVERT: a 281 GLU cc_start: 0.7616 (mt-10) cc_final: 0.7396 (mt-10) REVERT: a 292 TYR cc_start: 0.8796 (t80) cc_final: 0.8500 (t80) REVERT: b 116 ASP cc_start: 0.6211 (t0) cc_final: 0.5762 (m-30) REVERT: b 260 GLU cc_start: 0.6847 (mm-30) cc_final: 0.6294 (mm-30) REVERT: b 329 MET cc_start: 0.8682 (ptt) cc_final: 0.8471 (ptm) REVERT: c 260 GLU cc_start: 0.6968 (mm-30) cc_final: 0.6552 (mm-30) REVERT: c 332 LYS cc_start: 0.8268 (mtpp) cc_final: 0.7939 (mmtt) REVERT: d 260 GLU cc_start: 0.6818 (mm-30) cc_final: 0.6521 (mm-30) REVERT: d 271 MET cc_start: 0.8840 (tpt) cc_final: 0.8584 (tpt) REVERT: d 281 GLU cc_start: 0.7593 (mt-10) cc_final: 0.7377 (mt-10) REVERT: d 292 TYR cc_start: 0.8823 (t80) cc_final: 0.8449 (t80) REVERT: e 116 ASP cc_start: 0.6291 (t0) cc_final: 0.5960 (m-30) REVERT: e 260 GLU cc_start: 0.6912 (mm-30) cc_final: 0.6341 (mm-30) REVERT: e 329 MET cc_start: 0.8622 (ptt) cc_final: 0.8408 (ptm) REVERT: f 260 GLU cc_start: 0.6791 (mm-30) cc_final: 0.6330 (mm-30) REVERT: f 332 LYS cc_start: 0.8279 (mtpp) cc_final: 0.7897 (mmtt) outliers start: 211 outliers final: 126 residues processed: 686 average time/residue: 0.3969 time to fit residues: 454.2511 Evaluate side-chains 598 residues out of total 3516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 460 time to evaluate : 3.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 228 PHE Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 264 LYS Chi-restraints excluded: chain A residue 267 MET Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain B residue 13 GLU Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 228 PHE Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 264 LYS Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 164 ASP Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 211 GLU Chi-restraints excluded: chain C residue 228 PHE Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 264 LYS Chi-restraints excluded: chain C residue 344 ILE Chi-restraints excluded: chain C residue 349 THR Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 164 ASP Chi-restraints excluded: chain D residue 209 THR Chi-restraints excluded: chain D residue 228 PHE Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 267 MET Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 344 ILE Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 65 GLU Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 164 ASP Chi-restraints excluded: chain E residue 228 PHE Chi-restraints excluded: chain E residue 234 THR Chi-restraints excluded: chain E residue 264 LYS Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 344 ILE Chi-restraints excluded: chain E residue 345 ILE Chi-restraints excluded: chain F residue 13 GLU Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 164 ASP Chi-restraints excluded: chain F residue 228 PHE Chi-restraints excluded: chain F residue 234 THR Chi-restraints excluded: chain F residue 264 LYS Chi-restraints excluded: chain F residue 344 ILE Chi-restraints excluded: chain a residue 34 VAL Chi-restraints excluded: chain a residue 97 THR Chi-restraints excluded: chain a residue 118 LEU Chi-restraints excluded: chain a residue 185 LEU Chi-restraints excluded: chain a residue 207 LEU Chi-restraints excluded: chain a residue 234 THR Chi-restraints excluded: chain a residue 235 VAL Chi-restraints excluded: chain a residue 294 LEU Chi-restraints excluded: chain a residue 344 ILE Chi-restraints excluded: chain a residue 349 THR Chi-restraints excluded: chain b residue 34 VAL Chi-restraints excluded: chain b residue 97 THR Chi-restraints excluded: chain b residue 113 THR Chi-restraints excluded: chain b residue 118 LEU Chi-restraints excluded: chain b residue 125 LEU Chi-restraints excluded: chain b residue 169 ASP Chi-restraints excluded: chain b residue 306 GLU Chi-restraints excluded: chain b residue 344 ILE Chi-restraints excluded: chain c residue 34 VAL Chi-restraints excluded: chain c residue 97 THR Chi-restraints excluded: chain c residue 113 THR Chi-restraints excluded: chain c residue 118 LEU Chi-restraints excluded: chain c residue 137 THR Chi-restraints excluded: chain c residue 185 LEU Chi-restraints excluded: chain c residue 234 THR Chi-restraints excluded: chain c residue 250 VAL Chi-restraints excluded: chain c residue 252 VAL Chi-restraints excluded: chain c residue 294 LEU Chi-restraints excluded: chain d residue 13 GLU Chi-restraints excluded: chain d residue 34 VAL Chi-restraints excluded: chain d residue 97 THR Chi-restraints excluded: chain d residue 118 LEU Chi-restraints excluded: chain d residue 185 LEU Chi-restraints excluded: chain d residue 202 LEU Chi-restraints excluded: chain d residue 234 THR Chi-restraints excluded: chain d residue 294 LEU Chi-restraints excluded: chain d residue 344 ILE Chi-restraints excluded: chain e residue 34 VAL Chi-restraints excluded: chain e residue 97 THR Chi-restraints excluded: chain e residue 113 THR Chi-restraints excluded: chain e residue 118 LEU Chi-restraints excluded: chain e residue 125 LEU Chi-restraints excluded: chain e residue 169 ASP Chi-restraints excluded: chain e residue 234 THR Chi-restraints excluded: chain e residue 250 VAL Chi-restraints excluded: chain e residue 306 GLU Chi-restraints excluded: chain e residue 344 ILE Chi-restraints excluded: chain f residue 34 VAL Chi-restraints excluded: chain f residue 97 THR Chi-restraints excluded: chain f residue 99 ASP Chi-restraints excluded: chain f residue 113 THR Chi-restraints excluded: chain f residue 118 LEU Chi-restraints excluded: chain f residue 137 THR Chi-restraints excluded: chain f residue 185 LEU Chi-restraints excluded: chain f residue 234 THR Chi-restraints excluded: chain f residue 250 VAL Chi-restraints excluded: chain f residue 252 VAL Chi-restraints excluded: chain f residue 294 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 377 optimal weight: 0.7980 chunk 287 optimal weight: 3.9990 chunk 198 optimal weight: 9.9990 chunk 42 optimal weight: 5.9990 chunk 182 optimal weight: 5.9990 chunk 256 optimal weight: 9.9990 chunk 383 optimal weight: 0.9980 chunk 405 optimal weight: 0.0570 chunk 200 optimal weight: 0.7980 chunk 363 optimal weight: 6.9990 chunk 109 optimal weight: 0.9980 overall best weight: 0.7298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 ASN F 321 GLN f 350 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.3911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 33828 Z= 0.147 Angle : 0.582 14.646 46104 Z= 0.284 Chirality : 0.043 0.154 5184 Planarity : 0.004 0.038 5988 Dihedral : 5.478 52.066 4664 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 4.61 % Allowed : 23.00 % Favored : 72.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.10 (0.12), residues: 4224 helix: -0.48 (0.14), residues: 1428 sheet: -2.32 (0.25), residues: 408 loop : -1.83 (0.11), residues: 2388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 52 PHE 0.010 0.001 PHE c 348 TYR 0.021 0.001 TYR e 292 ARG 0.005 0.000 ARG a 284 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8448 Ramachandran restraints generated. 4224 Oldfield, 0 Emsley, 4224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8448 Ramachandran restraints generated. 4224 Oldfield, 0 Emsley, 4224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 709 residues out of total 3516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 548 time to evaluate : 3.632 Fit side-chains revert: symmetry clash REVERT: A 209 THR cc_start: 0.8485 (OUTLIER) cc_final: 0.8241 (p) REVERT: A 264 LYS cc_start: 0.8936 (OUTLIER) cc_final: 0.8641 (ttpp) REVERT: B 94 ILE cc_start: 0.9059 (mm) cc_final: 0.8846 (mt) REVERT: B 264 LYS cc_start: 0.8897 (OUTLIER) cc_final: 0.8503 (ttpp) REVERT: C 118 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8597 (tm) REVERT: C 211 GLU cc_start: 0.7371 (OUTLIER) cc_final: 0.7162 (pm20) REVERT: C 264 LYS cc_start: 0.8856 (OUTLIER) cc_final: 0.8518 (ttpp) REVERT: C 329 MET cc_start: 0.8933 (ptt) cc_final: 0.8570 (ptm) REVERT: D 180 TYR cc_start: 0.8789 (m-10) cc_final: 0.8510 (m-10) REVERT: D 209 THR cc_start: 0.8403 (OUTLIER) cc_final: 0.8178 (p) REVERT: D 305 GLU cc_start: 0.7659 (pt0) cc_final: 0.7027 (tt0) REVERT: D 345 ILE cc_start: 0.8703 (pt) cc_final: 0.8485 (mt) REVERT: E 264 LYS cc_start: 0.8799 (OUTLIER) cc_final: 0.8486 (ttpp) REVERT: E 273 GLU cc_start: 0.8290 (tp30) cc_final: 0.8004 (mm-30) REVERT: F 264 LYS cc_start: 0.8836 (OUTLIER) cc_final: 0.8440 (ttpp) REVERT: a 260 GLU cc_start: 0.6693 (mm-30) cc_final: 0.6164 (mm-30) REVERT: a 271 MET cc_start: 0.8641 (tpt) cc_final: 0.8435 (tpt) REVERT: b 72 VAL cc_start: 0.8944 (p) cc_final: 0.8682 (t) REVERT: b 116 ASP cc_start: 0.6374 (t0) cc_final: 0.6147 (m-30) REVERT: b 235 VAL cc_start: 0.9580 (m) cc_final: 0.9297 (t) REVERT: b 260 GLU cc_start: 0.6727 (mm-30) cc_final: 0.6147 (mm-30) REVERT: c 44 ASP cc_start: 0.7666 (t70) cc_final: 0.7453 (t0) REVERT: c 209 THR cc_start: 0.8150 (m) cc_final: 0.7846 (p) REVERT: c 235 VAL cc_start: 0.9592 (m) cc_final: 0.9348 (t) REVERT: c 260 GLU cc_start: 0.6597 (mm-30) cc_final: 0.6223 (mm-30) REVERT: c 332 LYS cc_start: 0.8286 (mtpp) cc_final: 0.7942 (mmtm) REVERT: d 260 GLU cc_start: 0.6675 (mm-30) cc_final: 0.6132 (mm-30) REVERT: d 281 GLU cc_start: 0.7442 (mt-10) cc_final: 0.7226 (mt-10) REVERT: e 72 VAL cc_start: 0.8951 (p) cc_final: 0.8702 (t) REVERT: e 224 MET cc_start: 0.8275 (mmm) cc_final: 0.8023 (mmt) REVERT: e 260 GLU cc_start: 0.6707 (mm-30) cc_final: 0.6112 (mm-30) REVERT: f 235 VAL cc_start: 0.9565 (m) cc_final: 0.9313 (t) REVERT: f 260 GLU cc_start: 0.6427 (mm-30) cc_final: 0.5932 (mm-30) REVERT: f 332 LYS cc_start: 0.8184 (mtpp) cc_final: 0.7831 (mmtt) outliers start: 161 outliers final: 86 residues processed: 679 average time/residue: 0.3805 time to fit residues: 438.3703 Evaluate side-chains 567 residues out of total 3516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 472 time to evaluate : 3.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 228 PHE Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 264 LYS Chi-restraints excluded: chain A residue 267 MET Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 145 LYS Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 211 GLU Chi-restraints excluded: chain B residue 228 PHE Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 264 LYS Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 306 GLU Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 164 ASP Chi-restraints excluded: chain C residue 211 GLU Chi-restraints excluded: chain C residue 228 PHE Chi-restraints excluded: chain C residue 264 LYS Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 164 ASP Chi-restraints excluded: chain D residue 209 THR Chi-restraints excluded: chain D residue 228 PHE Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 267 MET Chi-restraints excluded: chain D residue 344 ILE Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 164 ASP Chi-restraints excluded: chain E residue 228 PHE Chi-restraints excluded: chain E residue 264 LYS Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 306 GLU Chi-restraints excluded: chain E residue 317 ILE Chi-restraints excluded: chain E residue 344 ILE Chi-restraints excluded: chain E residue 349 THR Chi-restraints excluded: chain F residue 13 GLU Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 164 ASP Chi-restraints excluded: chain F residue 211 GLU Chi-restraints excluded: chain F residue 228 PHE Chi-restraints excluded: chain F residue 264 LYS Chi-restraints excluded: chain F residue 317 ILE Chi-restraints excluded: chain F residue 344 ILE Chi-restraints excluded: chain F residue 349 THR Chi-restraints excluded: chain a residue 13 GLU Chi-restraints excluded: chain a residue 97 THR Chi-restraints excluded: chain a residue 118 LEU Chi-restraints excluded: chain a residue 228 PHE Chi-restraints excluded: chain a residue 305 GLU Chi-restraints excluded: chain b residue 97 THR Chi-restraints excluded: chain b residue 113 THR Chi-restraints excluded: chain b residue 118 LEU Chi-restraints excluded: chain b residue 169 ASP Chi-restraints excluded: chain b residue 228 PHE Chi-restraints excluded: chain c residue 34 VAL Chi-restraints excluded: chain c residue 97 THR Chi-restraints excluded: chain c residue 113 THR Chi-restraints excluded: chain c residue 118 LEU Chi-restraints excluded: chain c residue 250 VAL Chi-restraints excluded: chain d residue 97 THR Chi-restraints excluded: chain d residue 118 LEU Chi-restraints excluded: chain d residue 202 LEU Chi-restraints excluded: chain d residue 228 PHE Chi-restraints excluded: chain d residue 344 ILE Chi-restraints excluded: chain e residue 97 THR Chi-restraints excluded: chain e residue 113 THR Chi-restraints excluded: chain e residue 118 LEU Chi-restraints excluded: chain e residue 169 ASP Chi-restraints excluded: chain e residue 228 PHE Chi-restraints excluded: chain e residue 306 GLU Chi-restraints excluded: chain f residue 53 MET Chi-restraints excluded: chain f residue 113 THR Chi-restraints excluded: chain f residue 118 LEU Chi-restraints excluded: chain f residue 137 THR Chi-restraints excluded: chain f residue 250 VAL Chi-restraints excluded: chain f residue 252 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 338 optimal weight: 10.0000 chunk 230 optimal weight: 7.9990 chunk 5 optimal weight: 7.9990 chunk 302 optimal weight: 9.9990 chunk 167 optimal weight: 1.9990 chunk 346 optimal weight: 7.9990 chunk 280 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 207 optimal weight: 9.9990 chunk 364 optimal weight: 10.0000 chunk 102 optimal weight: 1.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 223 ASN B 78 ASN ** C 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 223 ASN F 321 GLN a 45 ASN c 350 GLN f 350 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.4203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 33828 Z= 0.426 Angle : 0.716 16.229 46104 Z= 0.348 Chirality : 0.048 0.207 5184 Planarity : 0.005 0.049 5988 Dihedral : 5.788 51.967 4656 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 5.67 % Allowed : 22.82 % Favored : 71.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.12), residues: 4224 helix: -0.35 (0.14), residues: 1440 sheet: -2.16 (0.26), residues: 384 loop : -1.66 (0.11), residues: 2400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP F 280 PHE 0.016 0.002 PHE f 228 TYR 0.024 0.002 TYR D 216 ARG 0.006 0.001 ARG a 284 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8448 Ramachandran restraints generated. 4224 Oldfield, 0 Emsley, 4224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8448 Ramachandran restraints generated. 4224 Oldfield, 0 Emsley, 4224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 650 residues out of total 3516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 198 poor density : 452 time to evaluate : 3.389 Fit side-chains REVERT: A 47 ILE cc_start: 0.8781 (tp) cc_final: 0.8580 (mt) REVERT: B 94 ILE cc_start: 0.9050 (mm) cc_final: 0.8837 (mt) REVERT: B 168 ILE cc_start: 0.7773 (OUTLIER) cc_final: 0.7543 (tp) REVERT: B 264 LYS cc_start: 0.8929 (OUTLIER) cc_final: 0.8616 (ttpt) REVERT: B 329 MET cc_start: 0.8807 (ptm) cc_final: 0.8550 (ptm) REVERT: C 118 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8628 (tm) REVERT: C 209 THR cc_start: 0.8638 (OUTLIER) cc_final: 0.8244 (p) REVERT: C 211 GLU cc_start: 0.7438 (OUTLIER) cc_final: 0.7158 (pm20) REVERT: C 264 LYS cc_start: 0.8911 (OUTLIER) cc_final: 0.8490 (ttpp) REVERT: C 304 LYS cc_start: 0.8520 (OUTLIER) cc_final: 0.8292 (pttm) REVERT: C 306 GLU cc_start: 0.7972 (pt0) cc_final: 0.7733 (pt0) REVERT: D 271 MET cc_start: 0.9419 (tpt) cc_final: 0.9177 (tpp) REVERT: D 304 LYS cc_start: 0.8498 (pttm) cc_final: 0.7955 (pttm) REVERT: D 306 GLU cc_start: 0.8067 (pt0) cc_final: 0.7679 (pm20) REVERT: D 345 ILE cc_start: 0.8763 (pt) cc_final: 0.8544 (mt) REVERT: E 13 GLU cc_start: 0.7396 (OUTLIER) cc_final: 0.7182 (pp20) REVERT: E 264 LYS cc_start: 0.8861 (OUTLIER) cc_final: 0.8475 (ttpp) REVERT: E 273 GLU cc_start: 0.8279 (tp30) cc_final: 0.7998 (mm-30) REVERT: F 264 LYS cc_start: 0.8907 (OUTLIER) cc_final: 0.8455 (ttpp) REVERT: a 260 GLU cc_start: 0.6784 (mm-30) cc_final: 0.5994 (mm-30) REVERT: a 304 LYS cc_start: 0.8812 (pttm) cc_final: 0.8526 (pttm) REVERT: b 116 ASP cc_start: 0.6257 (t0) cc_final: 0.5891 (m-30) REVERT: b 260 GLU cc_start: 0.6549 (mm-30) cc_final: 0.5800 (mm-30) REVERT: c 235 VAL cc_start: 0.9584 (m) cc_final: 0.9353 (t) REVERT: c 260 GLU cc_start: 0.7031 (mm-30) cc_final: 0.6578 (mm-30) REVERT: c 332 LYS cc_start: 0.8250 (mtpp) cc_final: 0.7812 (mmtm) REVERT: d 260 GLU cc_start: 0.7006 (mm-30) cc_final: 0.6377 (mm-30) REVERT: d 281 GLU cc_start: 0.7569 (mt-10) cc_final: 0.7318 (mt-10) REVERT: d 339 ARG cc_start: 0.8494 (OUTLIER) cc_final: 0.7275 (mtt90) REVERT: e 224 MET cc_start: 0.8340 (mmm) cc_final: 0.8057 (mmt) REVERT: e 260 GLU cc_start: 0.6587 (mm-30) cc_final: 0.5837 (mm-30) REVERT: f 260 GLU cc_start: 0.6678 (mm-30) cc_final: 0.6001 (mm-30) REVERT: f 332 LYS cc_start: 0.8226 (mtpp) cc_final: 0.7785 (mmtt) outliers start: 198 outliers final: 128 residues processed: 600 average time/residue: 0.3794 time to fit residues: 388.3190 Evaluate side-chains 558 residues out of total 3516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 419 time to evaluate : 3.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 228 PHE Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 264 LYS Chi-restraints excluded: chain A residue 267 MET Chi-restraints excluded: chain B residue 13 GLU Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 41 ILE Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 228 PHE Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 264 LYS Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 164 ASP Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 211 GLU Chi-restraints excluded: chain C residue 228 PHE Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 264 LYS Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 319 MET Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 164 ASP Chi-restraints excluded: chain D residue 228 PHE Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 267 MET Chi-restraints excluded: chain D residue 344 ILE Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain E residue 13 GLU Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain E residue 65 GLU Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 164 ASP Chi-restraints excluded: chain E residue 176 MET Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 228 PHE Chi-restraints excluded: chain E residue 234 THR Chi-restraints excluded: chain E residue 264 LYS Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 306 GLU Chi-restraints excluded: chain E residue 344 ILE Chi-restraints excluded: chain E residue 349 THR Chi-restraints excluded: chain E residue 352 VAL Chi-restraints excluded: chain F residue 13 GLU Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 164 ASP Chi-restraints excluded: chain F residue 228 PHE Chi-restraints excluded: chain F residue 234 THR Chi-restraints excluded: chain F residue 264 LYS Chi-restraints excluded: chain F residue 344 ILE Chi-restraints excluded: chain F residue 345 ILE Chi-restraints excluded: chain F residue 349 THR Chi-restraints excluded: chain a residue 13 GLU Chi-restraints excluded: chain a residue 34 VAL Chi-restraints excluded: chain a residue 97 THR Chi-restraints excluded: chain a residue 118 LEU Chi-restraints excluded: chain a residue 185 LEU Chi-restraints excluded: chain a residue 207 LEU Chi-restraints excluded: chain a residue 228 PHE Chi-restraints excluded: chain a residue 234 THR Chi-restraints excluded: chain a residue 235 VAL Chi-restraints excluded: chain a residue 349 THR Chi-restraints excluded: chain b residue 34 VAL Chi-restraints excluded: chain b residue 97 THR Chi-restraints excluded: chain b residue 113 THR Chi-restraints excluded: chain b residue 169 ASP Chi-restraints excluded: chain b residue 234 THR Chi-restraints excluded: chain b residue 250 VAL Chi-restraints excluded: chain b residue 306 GLU Chi-restraints excluded: chain c residue 34 VAL Chi-restraints excluded: chain c residue 113 THR Chi-restraints excluded: chain c residue 137 THR Chi-restraints excluded: chain c residue 176 MET Chi-restraints excluded: chain c residue 185 LEU Chi-restraints excluded: chain c residue 203 GLU Chi-restraints excluded: chain c residue 205 LYS Chi-restraints excluded: chain c residue 234 THR Chi-restraints excluded: chain c residue 250 VAL Chi-restraints excluded: chain d residue 13 GLU Chi-restraints excluded: chain d residue 34 VAL Chi-restraints excluded: chain d residue 97 THR Chi-restraints excluded: chain d residue 118 LEU Chi-restraints excluded: chain d residue 185 LEU Chi-restraints excluded: chain d residue 202 LEU Chi-restraints excluded: chain d residue 203 GLU Chi-restraints excluded: chain d residue 228 PHE Chi-restraints excluded: chain d residue 234 THR Chi-restraints excluded: chain d residue 339 ARG Chi-restraints excluded: chain d residue 344 ILE Chi-restraints excluded: chain e residue 34 VAL Chi-restraints excluded: chain e residue 97 THR Chi-restraints excluded: chain e residue 113 THR Chi-restraints excluded: chain e residue 161 LEU Chi-restraints excluded: chain e residue 169 ASP Chi-restraints excluded: chain e residue 203 GLU Chi-restraints excluded: chain e residue 234 THR Chi-restraints excluded: chain e residue 250 VAL Chi-restraints excluded: chain e residue 306 GLU Chi-restraints excluded: chain e residue 349 THR Chi-restraints excluded: chain f residue 34 VAL Chi-restraints excluded: chain f residue 113 THR Chi-restraints excluded: chain f residue 137 THR Chi-restraints excluded: chain f residue 176 MET Chi-restraints excluded: chain f residue 185 LEU Chi-restraints excluded: chain f residue 234 THR Chi-restraints excluded: chain f residue 250 VAL Chi-restraints excluded: chain f residue 252 VAL Chi-restraints excluded: chain f residue 350 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 136 optimal weight: 1.9990 chunk 365 optimal weight: 0.9980 chunk 80 optimal weight: 0.9990 chunk 238 optimal weight: 0.9990 chunk 100 optimal weight: 9.9990 chunk 406 optimal weight: 9.9990 chunk 337 optimal weight: 7.9990 chunk 188 optimal weight: 9.9990 chunk 33 optimal weight: 9.9990 chunk 134 optimal weight: 5.9990 chunk 213 optimal weight: 0.9980 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 321 GLN ** E 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 321 GLN ** e 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 350 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.4378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 33828 Z= 0.175 Angle : 0.614 15.357 46104 Z= 0.291 Chirality : 0.044 0.233 5184 Planarity : 0.004 0.041 5988 Dihedral : 5.302 51.918 4648 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 4.27 % Allowed : 23.97 % Favored : 71.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.13), residues: 4224 helix: 0.16 (0.15), residues: 1320 sheet: -2.13 (0.26), residues: 384 loop : -1.48 (0.12), residues: 2520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 280 PHE 0.011 0.001 PHE f 348 TYR 0.020 0.001 TYR c 292 ARG 0.004 0.000 ARG a 284 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8448 Ramachandran restraints generated. 4224 Oldfield, 0 Emsley, 4224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8448 Ramachandran restraints generated. 4224 Oldfield, 0 Emsley, 4224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 622 residues out of total 3516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 473 time to evaluate : 3.571 Fit side-chains REVERT: A 245 ASP cc_start: 0.8011 (t70) cc_final: 0.7781 (t70) REVERT: A 304 LYS cc_start: 0.8578 (pttm) cc_final: 0.8061 (pttm) REVERT: A 306 GLU cc_start: 0.8011 (pt0) cc_final: 0.7749 (pm20) REVERT: B 264 LYS cc_start: 0.8846 (OUTLIER) cc_final: 0.8466 (ttpp) REVERT: C 118 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8655 (tm) REVERT: C 209 THR cc_start: 0.8506 (OUTLIER) cc_final: 0.8155 (p) REVERT: C 211 GLU cc_start: 0.7416 (OUTLIER) cc_final: 0.7185 (pm20) REVERT: C 264 LYS cc_start: 0.8809 (OUTLIER) cc_final: 0.8437 (ttpp) REVERT: C 304 LYS cc_start: 0.8547 (OUTLIER) cc_final: 0.8234 (pttm) REVERT: D 245 ASP cc_start: 0.7988 (t70) cc_final: 0.7734 (t70) REVERT: D 304 LYS cc_start: 0.8490 (pttm) cc_final: 0.7925 (pttm) REVERT: D 306 GLU cc_start: 0.8003 (pt0) cc_final: 0.7717 (pm20) REVERT: E 264 LYS cc_start: 0.8840 (OUTLIER) cc_final: 0.8448 (ttpp) REVERT: a 260 GLU cc_start: 0.6582 (mm-30) cc_final: 0.5888 (mm-30) REVERT: a 304 LYS cc_start: 0.8712 (pttm) cc_final: 0.8417 (pttm) REVERT: b 72 VAL cc_start: 0.8981 (p) cc_final: 0.8661 (t) REVERT: b 235 VAL cc_start: 0.9564 (m) cc_final: 0.9312 (t) REVERT: b 260 GLU cc_start: 0.6382 (mm-30) cc_final: 0.4950 (pt0) REVERT: c 235 VAL cc_start: 0.9579 (m) cc_final: 0.9321 (t) REVERT: c 260 GLU cc_start: 0.6873 (mm-30) cc_final: 0.6494 (mm-30) REVERT: c 332 LYS cc_start: 0.8238 (mtpp) cc_final: 0.7828 (mmtm) REVERT: d 260 GLU cc_start: 0.6566 (mm-30) cc_final: 0.5929 (mm-30) REVERT: d 281 GLU cc_start: 0.7504 (mt-10) cc_final: 0.7244 (mt-10) REVERT: e 72 VAL cc_start: 0.8948 (p) cc_final: 0.8630 (t) REVERT: e 168 ILE cc_start: 0.7676 (OUTLIER) cc_final: 0.7305 (mp) REVERT: e 235 VAL cc_start: 0.9553 (m) cc_final: 0.9301 (t) REVERT: e 260 GLU cc_start: 0.6692 (mm-30) cc_final: 0.5219 (pt0) REVERT: f 235 VAL cc_start: 0.9580 (m) cc_final: 0.9345 (t) REVERT: f 260 GLU cc_start: 0.6509 (mm-30) cc_final: 0.5810 (mm-30) REVERT: f 332 LYS cc_start: 0.8167 (mtpp) cc_final: 0.7785 (mmtm) outliers start: 149 outliers final: 101 residues processed: 586 average time/residue: 0.3800 time to fit residues: 377.2645 Evaluate side-chains 541 residues out of total 3516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 432 time to evaluate : 3.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain A residue 228 PHE Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 267 MET Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 41 ILE Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 145 LYS Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 228 PHE Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 264 LYS Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 164 ASP Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 211 GLU Chi-restraints excluded: chain C residue 228 PHE Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 264 LYS Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 317 ILE Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 164 ASP Chi-restraints excluded: chain D residue 228 PHE Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 267 MET Chi-restraints excluded: chain D residue 317 ILE Chi-restraints excluded: chain D residue 344 ILE Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 164 ASP Chi-restraints excluded: chain E residue 228 PHE Chi-restraints excluded: chain E residue 264 LYS Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 306 GLU Chi-restraints excluded: chain E residue 317 ILE Chi-restraints excluded: chain E residue 344 ILE Chi-restraints excluded: chain E residue 345 ILE Chi-restraints excluded: chain F residue 13 GLU Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 164 ASP Chi-restraints excluded: chain F residue 228 PHE Chi-restraints excluded: chain F residue 234 THR Chi-restraints excluded: chain F residue 317 ILE Chi-restraints excluded: chain F residue 344 ILE Chi-restraints excluded: chain a residue 13 GLU Chi-restraints excluded: chain a residue 34 VAL Chi-restraints excluded: chain a residue 97 THR Chi-restraints excluded: chain a residue 185 LEU Chi-restraints excluded: chain a residue 203 GLU Chi-restraints excluded: chain a residue 207 LEU Chi-restraints excluded: chain a residue 235 VAL Chi-restraints excluded: chain b residue 97 THR Chi-restraints excluded: chain b residue 113 THR Chi-restraints excluded: chain b residue 169 ASP Chi-restraints excluded: chain b residue 234 THR Chi-restraints excluded: chain b residue 306 GLU Chi-restraints excluded: chain c residue 34 VAL Chi-restraints excluded: chain c residue 113 THR Chi-restraints excluded: chain c residue 137 THR Chi-restraints excluded: chain c residue 185 LEU Chi-restraints excluded: chain c residue 205 LYS Chi-restraints excluded: chain c residue 250 VAL Chi-restraints excluded: chain c residue 318 THR Chi-restraints excluded: chain d residue 12 ILE Chi-restraints excluded: chain d residue 13 GLU Chi-restraints excluded: chain d residue 97 THR Chi-restraints excluded: chain d residue 118 LEU Chi-restraints excluded: chain d residue 202 LEU Chi-restraints excluded: chain d residue 203 GLU Chi-restraints excluded: chain d residue 228 PHE Chi-restraints excluded: chain d residue 267 MET Chi-restraints excluded: chain e residue 97 THR Chi-restraints excluded: chain e residue 113 THR Chi-restraints excluded: chain e residue 168 ILE Chi-restraints excluded: chain e residue 169 ASP Chi-restraints excluded: chain e residue 250 VAL Chi-restraints excluded: chain e residue 306 GLU Chi-restraints excluded: chain f residue 34 VAL Chi-restraints excluded: chain f residue 113 THR Chi-restraints excluded: chain f residue 176 MET Chi-restraints excluded: chain f residue 185 LEU Chi-restraints excluded: chain f residue 203 GLU Chi-restraints excluded: chain f residue 215 GLU Chi-restraints excluded: chain f residue 250 VAL Chi-restraints excluded: chain f residue 252 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 391 optimal weight: 2.9990 chunk 45 optimal weight: 7.9990 chunk 231 optimal weight: 9.9990 chunk 296 optimal weight: 10.0000 chunk 229 optimal weight: 10.0000 chunk 342 optimal weight: 0.7980 chunk 226 optimal weight: 10.0000 chunk 404 optimal weight: 4.9990 chunk 253 optimal weight: 9.9990 chunk 246 optimal weight: 10.0000 chunk 186 optimal weight: 7.9990 overall best weight: 4.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 ASN ** D 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 321 GLN f 350 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.4567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 33828 Z= 0.456 Angle : 0.730 15.628 46104 Z= 0.354 Chirality : 0.048 0.236 5184 Planarity : 0.005 0.051 5988 Dihedral : 5.580 51.368 4636 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 5.15 % Allowed : 23.17 % Favored : 71.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.13), residues: 4224 helix: -0.03 (0.14), residues: 1440 sheet: -2.20 (0.26), residues: 384 loop : -1.56 (0.12), residues: 2400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP D 280 PHE 0.015 0.002 PHE f 228 TYR 0.026 0.002 TYR A 216 ARG 0.006 0.001 ARG a 284 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8448 Ramachandran restraints generated. 4224 Oldfield, 0 Emsley, 4224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8448 Ramachandran restraints generated. 4224 Oldfield, 0 Emsley, 4224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 594 residues out of total 3516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 414 time to evaluate : 3.138 Fit side-chains REVERT: A 306 GLU cc_start: 0.8037 (pt0) cc_final: 0.7836 (pm20) REVERT: A 325 ASP cc_start: 0.8383 (m-30) cc_final: 0.8040 (m-30) REVERT: B 168 ILE cc_start: 0.7819 (OUTLIER) cc_final: 0.7594 (tp) REVERT: B 264 LYS cc_start: 0.8840 (OUTLIER) cc_final: 0.8482 (ttpp) REVERT: C 118 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8618 (tm) REVERT: C 209 THR cc_start: 0.8631 (OUTLIER) cc_final: 0.8311 (p) REVERT: C 211 GLU cc_start: 0.7494 (OUTLIER) cc_final: 0.7201 (pm20) REVERT: C 224 MET cc_start: 0.8430 (mtt) cc_final: 0.8114 (mtt) REVERT: C 264 LYS cc_start: 0.8871 (OUTLIER) cc_final: 0.8452 (ttpp) REVERT: D 304 LYS cc_start: 0.8531 (pttm) cc_final: 0.7842 (pttm) REVERT: D 306 GLU cc_start: 0.8075 (pt0) cc_final: 0.7792 (pm20) REVERT: E 264 LYS cc_start: 0.8877 (OUTLIER) cc_final: 0.8452 (ttpp) REVERT: F 264 LYS cc_start: 0.8909 (OUTLIER) cc_final: 0.8518 (ttpp) REVERT: F 304 LYS cc_start: 0.8724 (pttm) cc_final: 0.8523 (pttp) REVERT: a 260 GLU cc_start: 0.6898 (mm-30) cc_final: 0.6101 (mm-30) REVERT: b 260 GLU cc_start: 0.6561 (mm-30) cc_final: 0.5766 (mm-30) REVERT: c 135 GLU cc_start: 0.8006 (tp30) cc_final: 0.7716 (tp30) REVERT: c 235 VAL cc_start: 0.9590 (m) cc_final: 0.9354 (t) REVERT: c 260 GLU cc_start: 0.7043 (mm-30) cc_final: 0.6525 (mm-30) REVERT: c 332 LYS cc_start: 0.8213 (mtpp) cc_final: 0.7792 (mmtm) REVERT: d 260 GLU cc_start: 0.6851 (mm-30) cc_final: 0.6068 (mm-30) REVERT: d 281 GLU cc_start: 0.7599 (mt-10) cc_final: 0.7331 (mt-10) REVERT: e 235 VAL cc_start: 0.9584 (OUTLIER) cc_final: 0.9384 (t) REVERT: e 260 GLU cc_start: 0.6571 (mm-30) cc_final: 0.5809 (mm-30) REVERT: f 209 THR cc_start: 0.8725 (OUTLIER) cc_final: 0.8482 (p) REVERT: f 260 GLU cc_start: 0.6633 (mm-30) cc_final: 0.5883 (mm-30) REVERT: f 332 LYS cc_start: 0.8231 (mtpp) cc_final: 0.7766 (mmtt) outliers start: 180 outliers final: 146 residues processed: 551 average time/residue: 0.3876 time to fit residues: 361.3777 Evaluate side-chains 561 residues out of total 3516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 405 time to evaluate : 3.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 228 PHE Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 267 MET Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 41 ILE Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 228 PHE Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 264 LYS Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 164 ASP Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 211 GLU Chi-restraints excluded: chain C residue 228 PHE Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 264 LYS Chi-restraints excluded: chain C residue 319 MET Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 164 ASP Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 228 PHE Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 267 MET Chi-restraints excluded: chain D residue 344 ILE Chi-restraints excluded: chain D residue 346 LEU Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain E residue 65 GLU Chi-restraints excluded: chain E residue 69 ASP Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 164 ASP Chi-restraints excluded: chain E residue 169 ASP Chi-restraints excluded: chain E residue 176 MET Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 228 PHE Chi-restraints excluded: chain E residue 233 THR Chi-restraints excluded: chain E residue 264 LYS Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 344 ILE Chi-restraints excluded: chain E residue 345 ILE Chi-restraints excluded: chain E residue 349 THR Chi-restraints excluded: chain F residue 13 GLU Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 164 ASP Chi-restraints excluded: chain F residue 228 PHE Chi-restraints excluded: chain F residue 233 THR Chi-restraints excluded: chain F residue 234 THR Chi-restraints excluded: chain F residue 264 LYS Chi-restraints excluded: chain F residue 344 ILE Chi-restraints excluded: chain F residue 345 ILE Chi-restraints excluded: chain F residue 349 THR Chi-restraints excluded: chain a residue 13 GLU Chi-restraints excluded: chain a residue 34 VAL Chi-restraints excluded: chain a residue 97 THR Chi-restraints excluded: chain a residue 185 LEU Chi-restraints excluded: chain a residue 203 GLU Chi-restraints excluded: chain a residue 207 LEU Chi-restraints excluded: chain a residue 215 GLU Chi-restraints excluded: chain a residue 234 THR Chi-restraints excluded: chain a residue 235 VAL Chi-restraints excluded: chain a residue 349 THR Chi-restraints excluded: chain b residue 34 VAL Chi-restraints excluded: chain b residue 97 THR Chi-restraints excluded: chain b residue 113 THR Chi-restraints excluded: chain b residue 203 GLU Chi-restraints excluded: chain b residue 234 THR Chi-restraints excluded: chain b residue 250 VAL Chi-restraints excluded: chain b residue 306 GLU Chi-restraints excluded: chain c residue 34 VAL Chi-restraints excluded: chain c residue 61 ASN Chi-restraints excluded: chain c residue 97 THR Chi-restraints excluded: chain c residue 113 THR Chi-restraints excluded: chain c residue 128 VAL Chi-restraints excluded: chain c residue 137 THR Chi-restraints excluded: chain c residue 176 MET Chi-restraints excluded: chain c residue 185 LEU Chi-restraints excluded: chain c residue 203 GLU Chi-restraints excluded: chain c residue 205 LYS Chi-restraints excluded: chain c residue 215 GLU Chi-restraints excluded: chain c residue 234 THR Chi-restraints excluded: chain c residue 250 VAL Chi-restraints excluded: chain c residue 318 THR Chi-restraints excluded: chain d residue 12 ILE Chi-restraints excluded: chain d residue 13 GLU Chi-restraints excluded: chain d residue 34 VAL Chi-restraints excluded: chain d residue 97 THR Chi-restraints excluded: chain d residue 118 LEU Chi-restraints excluded: chain d residue 185 LEU Chi-restraints excluded: chain d residue 202 LEU Chi-restraints excluded: chain d residue 203 GLU Chi-restraints excluded: chain d residue 228 PHE Chi-restraints excluded: chain d residue 234 THR Chi-restraints excluded: chain d residue 235 VAL Chi-restraints excluded: chain d residue 267 MET Chi-restraints excluded: chain e residue 34 VAL Chi-restraints excluded: chain e residue 97 THR Chi-restraints excluded: chain e residue 113 THR Chi-restraints excluded: chain e residue 168 ILE Chi-restraints excluded: chain e residue 169 ASP Chi-restraints excluded: chain e residue 176 MET Chi-restraints excluded: chain e residue 203 GLU Chi-restraints excluded: chain e residue 235 VAL Chi-restraints excluded: chain e residue 250 VAL Chi-restraints excluded: chain e residue 306 GLU Chi-restraints excluded: chain e residue 349 THR Chi-restraints excluded: chain f residue 34 VAL Chi-restraints excluded: chain f residue 61 ASN Chi-restraints excluded: chain f residue 97 THR Chi-restraints excluded: chain f residue 113 THR Chi-restraints excluded: chain f residue 128 VAL Chi-restraints excluded: chain f residue 137 THR Chi-restraints excluded: chain f residue 176 MET Chi-restraints excluded: chain f residue 185 LEU Chi-restraints excluded: chain f residue 203 GLU Chi-restraints excluded: chain f residue 209 THR Chi-restraints excluded: chain f residue 215 GLU Chi-restraints excluded: chain f residue 234 THR Chi-restraints excluded: chain f residue 250 VAL Chi-restraints excluded: chain f residue 252 VAL Chi-restraints excluded: chain f residue 318 THR Chi-restraints excluded: chain f residue 350 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 250 optimal weight: 10.0000 chunk 161 optimal weight: 6.9990 chunk 241 optimal weight: 3.9990 chunk 121 optimal weight: 0.7980 chunk 79 optimal weight: 7.9990 chunk 78 optimal weight: 1.9990 chunk 257 optimal weight: 0.9990 chunk 275 optimal weight: 0.3980 chunk 200 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 318 optimal weight: 4.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 321 GLN ** a 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 230 ASN b 45 ASN ** e 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 45 ASN f 350 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.4659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 33828 Z= 0.169 Angle : 0.619 14.561 46104 Z= 0.293 Chirality : 0.044 0.222 5184 Planarity : 0.004 0.043 5988 Dihedral : 5.145 51.313 4636 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 4.15 % Allowed : 24.23 % Favored : 71.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.13), residues: 4224 helix: 0.38 (0.15), residues: 1320 sheet: -2.11 (0.27), residues: 384 loop : -1.40 (0.12), residues: 2520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D 280 PHE 0.009 0.001 PHE D 228 TYR 0.021 0.001 TYR A 7 ARG 0.005 0.000 ARG d 284 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8448 Ramachandran restraints generated. 4224 Oldfield, 0 Emsley, 4224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8448 Ramachandran restraints generated. 4224 Oldfield, 0 Emsley, 4224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 604 residues out of total 3516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 459 time to evaluate : 3.526 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 305 GLU cc_start: 0.7679 (pt0) cc_final: 0.7381 (tt0) REVERT: B 23 SER cc_start: 0.8710 (p) cc_final: 0.8246 (m) REVERT: B 264 LYS cc_start: 0.8861 (OUTLIER) cc_final: 0.8558 (ttpt) REVERT: C 209 THR cc_start: 0.8535 (OUTLIER) cc_final: 0.8219 (p) REVERT: C 211 GLU cc_start: 0.7441 (OUTLIER) cc_final: 0.7214 (pm20) REVERT: C 215 GLU cc_start: 0.6747 (mm-30) cc_final: 0.6440 (mm-30) REVERT: C 264 LYS cc_start: 0.8849 (OUTLIER) cc_final: 0.8393 (ttpp) REVERT: C 329 MET cc_start: 0.8954 (ptt) cc_final: 0.8661 (ptm) REVERT: D 23 SER cc_start: 0.8662 (p) cc_final: 0.8291 (m) REVERT: D 271 MET cc_start: 0.9399 (tpt) cc_final: 0.9172 (tpp) REVERT: D 304 LYS cc_start: 0.8489 (pttm) cc_final: 0.7914 (pttm) REVERT: D 306 GLU cc_start: 0.8005 (pt0) cc_final: 0.7791 (pm20) REVERT: D 344 ILE cc_start: 0.9427 (OUTLIER) cc_final: 0.9214 (mt) REVERT: E 23 SER cc_start: 0.8689 (p) cc_final: 0.8253 (m) REVERT: E 264 LYS cc_start: 0.8835 (OUTLIER) cc_final: 0.8403 (ttpp) REVERT: F 215 GLU cc_start: 0.6718 (mm-30) cc_final: 0.6429 (mm-30) REVERT: a 260 GLU cc_start: 0.6506 (mm-30) cc_final: 0.5757 (mm-30) REVERT: b 72 VAL cc_start: 0.8905 (p) cc_final: 0.8620 (t) REVERT: b 235 VAL cc_start: 0.9565 (OUTLIER) cc_final: 0.9297 (t) REVERT: b 260 GLU cc_start: 0.6381 (mm-30) cc_final: 0.4804 (pt0) REVERT: c 135 GLU cc_start: 0.7955 (tp30) cc_final: 0.7640 (tp30) REVERT: c 235 VAL cc_start: 0.9590 (m) cc_final: 0.9349 (t) REVERT: c 260 GLU cc_start: 0.6756 (mm-30) cc_final: 0.6350 (mm-30) REVERT: c 332 LYS cc_start: 0.8184 (mtpp) cc_final: 0.7787 (mmtm) REVERT: d 176 MET cc_start: 0.8343 (mmm) cc_final: 0.8056 (mmm) REVERT: d 243 ASP cc_start: 0.7621 (t0) cc_final: 0.7420 (t70) REVERT: d 260 GLU cc_start: 0.6600 (mm-30) cc_final: 0.5834 (mm-30) REVERT: e 72 VAL cc_start: 0.8941 (p) cc_final: 0.8619 (t) REVERT: e 168 ILE cc_start: 0.7760 (OUTLIER) cc_final: 0.7402 (mp) REVERT: e 235 VAL cc_start: 0.9543 (m) cc_final: 0.9271 (t) REVERT: e 260 GLU cc_start: 0.6421 (mm-30) cc_final: 0.4906 (pt0) REVERT: f 13 GLU cc_start: 0.7398 (pt0) cc_final: 0.7096 (pt0) REVERT: f 235 VAL cc_start: 0.9589 (m) cc_final: 0.9352 (t) REVERT: f 260 GLU cc_start: 0.6547 (mm-30) cc_final: 0.5885 (mm-30) REVERT: f 332 LYS cc_start: 0.8212 (mtpp) cc_final: 0.7798 (mmtm) outliers start: 145 outliers final: 112 residues processed: 571 average time/residue: 0.3810 time to fit residues: 370.4754 Evaluate side-chains 546 residues out of total 3516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 426 time to evaluate : 3.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 228 PHE Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 267 MET Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 228 PHE Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 264 LYS Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 164 ASP Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 211 GLU Chi-restraints excluded: chain C residue 228 PHE Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 264 LYS Chi-restraints excluded: chain C residue 319 MET Chi-restraints excluded: chain D residue 13 GLU Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 164 ASP Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 228 PHE Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 267 MET Chi-restraints excluded: chain D residue 344 ILE Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 164 ASP Chi-restraints excluded: chain E residue 176 MET Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 228 PHE Chi-restraints excluded: chain E residue 233 THR Chi-restraints excluded: chain E residue 264 LYS Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 306 GLU Chi-restraints excluded: chain E residue 317 ILE Chi-restraints excluded: chain E residue 344 ILE Chi-restraints excluded: chain E residue 345 ILE Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 164 ASP Chi-restraints excluded: chain F residue 228 PHE Chi-restraints excluded: chain F residue 233 THR Chi-restraints excluded: chain F residue 234 THR Chi-restraints excluded: chain F residue 344 ILE Chi-restraints excluded: chain a residue 13 GLU Chi-restraints excluded: chain a residue 34 VAL Chi-restraints excluded: chain a residue 97 THR Chi-restraints excluded: chain a residue 185 LEU Chi-restraints excluded: chain a residue 203 GLU Chi-restraints excluded: chain a residue 207 LEU Chi-restraints excluded: chain a residue 228 PHE Chi-restraints excluded: chain a residue 234 THR Chi-restraints excluded: chain a residue 235 VAL Chi-restraints excluded: chain a residue 349 THR Chi-restraints excluded: chain b residue 34 VAL Chi-restraints excluded: chain b residue 97 THR Chi-restraints excluded: chain b residue 113 THR Chi-restraints excluded: chain b residue 234 THR Chi-restraints excluded: chain b residue 235 VAL Chi-restraints excluded: chain b residue 250 VAL Chi-restraints excluded: chain b residue 291 LEU Chi-restraints excluded: chain b residue 306 GLU Chi-restraints excluded: chain c residue 34 VAL Chi-restraints excluded: chain c residue 97 THR Chi-restraints excluded: chain c residue 113 THR Chi-restraints excluded: chain c residue 137 THR Chi-restraints excluded: chain c residue 185 LEU Chi-restraints excluded: chain c residue 234 THR Chi-restraints excluded: chain c residue 250 VAL Chi-restraints excluded: chain c residue 318 THR Chi-restraints excluded: chain d residue 13 GLU Chi-restraints excluded: chain d residue 97 THR Chi-restraints excluded: chain d residue 185 LEU Chi-restraints excluded: chain d residue 202 LEU Chi-restraints excluded: chain d residue 203 GLU Chi-restraints excluded: chain d residue 228 PHE Chi-restraints excluded: chain d residue 235 VAL Chi-restraints excluded: chain d residue 267 MET Chi-restraints excluded: chain e residue 97 THR Chi-restraints excluded: chain e residue 113 THR Chi-restraints excluded: chain e residue 168 ILE Chi-restraints excluded: chain e residue 169 ASP Chi-restraints excluded: chain e residue 176 MET Chi-restraints excluded: chain e residue 203 GLU Chi-restraints excluded: chain e residue 291 LEU Chi-restraints excluded: chain e residue 306 GLU Chi-restraints excluded: chain e residue 349 THR Chi-restraints excluded: chain f residue 113 THR Chi-restraints excluded: chain f residue 185 LEU Chi-restraints excluded: chain f residue 203 GLU Chi-restraints excluded: chain f residue 215 GLU Chi-restraints excluded: chain f residue 234 THR Chi-restraints excluded: chain f residue 250 VAL Chi-restraints excluded: chain f residue 252 VAL Chi-restraints excluded: chain f residue 306 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 368 optimal weight: 3.9990 chunk 387 optimal weight: 9.9990 chunk 353 optimal weight: 4.9990 chunk 377 optimal weight: 0.9980 chunk 227 optimal weight: 1.9990 chunk 164 optimal weight: 4.9990 chunk 296 optimal weight: 0.8980 chunk 115 optimal weight: 0.3980 chunk 340 optimal weight: 5.9990 chunk 356 optimal weight: 3.9990 chunk 375 optimal weight: 5.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 297 GLN C 321 GLN ** D 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 297 GLN ** F 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 321 GLN c 57 ASN ** e 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 350 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.4736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 33828 Z= 0.201 Angle : 0.625 16.452 46104 Z= 0.293 Chirality : 0.044 0.209 5184 Planarity : 0.004 0.045 5988 Dihedral : 4.982 49.973 4632 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 3.95 % Allowed : 24.66 % Favored : 71.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.13), residues: 4224 helix: 0.56 (0.15), residues: 1308 sheet: -2.10 (0.32), residues: 264 loop : -1.43 (0.11), residues: 2652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP D 280 PHE 0.011 0.001 PHE b 269 TYR 0.022 0.001 TYR c 40 ARG 0.005 0.000 ARG d 265 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8448 Ramachandran restraints generated. 4224 Oldfield, 0 Emsley, 4224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8448 Ramachandran restraints generated. 4224 Oldfield, 0 Emsley, 4224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 584 residues out of total 3516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 446 time to evaluate : 3.820 Fit side-chains revert: symmetry clash REVERT: B 264 LYS cc_start: 0.8862 (OUTLIER) cc_final: 0.8542 (ttpt) REVERT: C 215 GLU cc_start: 0.6745 (mm-30) cc_final: 0.6419 (mm-30) REVERT: C 264 LYS cc_start: 0.8867 (OUTLIER) cc_final: 0.8445 (ttpp) REVERT: C 329 MET cc_start: 0.8925 (ptt) cc_final: 0.8703 (ptm) REVERT: D 23 SER cc_start: 0.8668 (p) cc_final: 0.8282 (m) REVERT: D 245 ASP cc_start: 0.7970 (t70) cc_final: 0.7746 (t70) REVERT: D 271 MET cc_start: 0.9420 (tpt) cc_final: 0.9189 (tpp) REVERT: E 23 SER cc_start: 0.8682 (p) cc_final: 0.8249 (m) REVERT: E 264 LYS cc_start: 0.8802 (OUTLIER) cc_final: 0.8491 (ttpt) REVERT: F 264 LYS cc_start: 0.8861 (OUTLIER) cc_final: 0.8456 (ttpp) REVERT: a 260 GLU cc_start: 0.6668 (mm-30) cc_final: 0.5925 (mm-30) REVERT: b 72 VAL cc_start: 0.8915 (p) cc_final: 0.8606 (t) REVERT: b 235 VAL cc_start: 0.9566 (OUTLIER) cc_final: 0.9270 (t) REVERT: b 260 GLU cc_start: 0.6478 (mm-30) cc_final: 0.4859 (pt0) REVERT: c 135 GLU cc_start: 0.7955 (tp30) cc_final: 0.7730 (tp30) REVERT: c 235 VAL cc_start: 0.9593 (m) cc_final: 0.9347 (t) REVERT: c 260 GLU cc_start: 0.6816 (mm-30) cc_final: 0.6393 (mm-30) REVERT: d 176 MET cc_start: 0.8471 (mmm) cc_final: 0.8255 (mmm) REVERT: d 260 GLU cc_start: 0.6666 (mm-30) cc_final: 0.5944 (mm-30) REVERT: e 72 VAL cc_start: 0.8952 (p) cc_final: 0.8614 (t) REVERT: e 235 VAL cc_start: 0.9561 (OUTLIER) cc_final: 0.9260 (t) REVERT: e 260 GLU cc_start: 0.6529 (mm-30) cc_final: 0.4961 (pt0) REVERT: f 13 GLU cc_start: 0.7405 (pt0) cc_final: 0.7119 (pt0) REVERT: f 135 GLU cc_start: 0.7912 (tp30) cc_final: 0.7599 (tp30) REVERT: f 235 VAL cc_start: 0.9593 (m) cc_final: 0.9358 (t) REVERT: f 260 GLU cc_start: 0.6499 (mm-30) cc_final: 0.5778 (mm-30) outliers start: 138 outliers final: 118 residues processed: 547 average time/residue: 0.3778 time to fit residues: 352.4732 Evaluate side-chains 556 residues out of total 3516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 432 time to evaluate : 3.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 228 PHE Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 267 MET Chi-restraints excluded: chain B residue 13 GLU Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 228 PHE Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 264 LYS Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 164 ASP Chi-restraints excluded: chain C residue 228 PHE Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 264 LYS Chi-restraints excluded: chain C residue 317 ILE Chi-restraints excluded: chain C residue 319 MET Chi-restraints excluded: chain D residue 13 GLU Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 164 ASP Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 228 PHE Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 267 MET Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 164 ASP Chi-restraints excluded: chain E residue 176 MET Chi-restraints excluded: chain E residue 228 PHE Chi-restraints excluded: chain E residue 233 THR Chi-restraints excluded: chain E residue 264 LYS Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 306 GLU Chi-restraints excluded: chain E residue 317 ILE Chi-restraints excluded: chain E residue 344 ILE Chi-restraints excluded: chain E residue 345 ILE Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 164 ASP Chi-restraints excluded: chain F residue 228 PHE Chi-restraints excluded: chain F residue 233 THR Chi-restraints excluded: chain F residue 234 THR Chi-restraints excluded: chain F residue 264 LYS Chi-restraints excluded: chain F residue 317 ILE Chi-restraints excluded: chain F residue 344 ILE Chi-restraints excluded: chain a residue 13 GLU Chi-restraints excluded: chain a residue 34 VAL Chi-restraints excluded: chain a residue 97 THR Chi-restraints excluded: chain a residue 185 LEU Chi-restraints excluded: chain a residue 203 GLU Chi-restraints excluded: chain a residue 207 LEU Chi-restraints excluded: chain a residue 234 THR Chi-restraints excluded: chain a residue 235 VAL Chi-restraints excluded: chain b residue 34 VAL Chi-restraints excluded: chain b residue 97 THR Chi-restraints excluded: chain b residue 113 THR Chi-restraints excluded: chain b residue 169 ASP Chi-restraints excluded: chain b residue 234 THR Chi-restraints excluded: chain b residue 235 VAL Chi-restraints excluded: chain b residue 250 VAL Chi-restraints excluded: chain b residue 291 LEU Chi-restraints excluded: chain b residue 306 GLU Chi-restraints excluded: chain c residue 34 VAL Chi-restraints excluded: chain c residue 97 THR Chi-restraints excluded: chain c residue 113 THR Chi-restraints excluded: chain c residue 137 THR Chi-restraints excluded: chain c residue 185 LEU Chi-restraints excluded: chain c residue 215 GLU Chi-restraints excluded: chain c residue 234 THR Chi-restraints excluded: chain c residue 250 VAL Chi-restraints excluded: chain c residue 318 THR Chi-restraints excluded: chain d residue 34 VAL Chi-restraints excluded: chain d residue 97 THR Chi-restraints excluded: chain d residue 185 LEU Chi-restraints excluded: chain d residue 202 LEU Chi-restraints excluded: chain d residue 203 GLU Chi-restraints excluded: chain d residue 228 PHE Chi-restraints excluded: chain d residue 235 VAL Chi-restraints excluded: chain d residue 267 MET Chi-restraints excluded: chain e residue 34 VAL Chi-restraints excluded: chain e residue 97 THR Chi-restraints excluded: chain e residue 113 THR Chi-restraints excluded: chain e residue 169 ASP Chi-restraints excluded: chain e residue 176 MET Chi-restraints excluded: chain e residue 203 GLU Chi-restraints excluded: chain e residue 235 VAL Chi-restraints excluded: chain e residue 250 VAL Chi-restraints excluded: chain e residue 291 LEU Chi-restraints excluded: chain e residue 306 GLU Chi-restraints excluded: chain e residue 349 THR Chi-restraints excluded: chain f residue 34 VAL Chi-restraints excluded: chain f residue 113 THR Chi-restraints excluded: chain f residue 137 THR Chi-restraints excluded: chain f residue 185 LEU Chi-restraints excluded: chain f residue 203 GLU Chi-restraints excluded: chain f residue 215 GLU Chi-restraints excluded: chain f residue 228 PHE Chi-restraints excluded: chain f residue 234 THR Chi-restraints excluded: chain f residue 250 VAL Chi-restraints excluded: chain f residue 252 VAL Chi-restraints excluded: chain f residue 306 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 247 optimal weight: 10.0000 chunk 398 optimal weight: 0.1980 chunk 243 optimal weight: 1.9990 chunk 189 optimal weight: 10.0000 chunk 277 optimal weight: 4.9990 chunk 418 optimal weight: 2.9990 chunk 385 optimal weight: 6.9990 chunk 333 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 257 optimal weight: 5.9990 chunk 204 optimal weight: 7.9990 overall best weight: 1.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 321 GLN ** D 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 321 GLN ** E 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 120 GLN ** e 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 45 ASN f 350 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.4796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 33828 Z= 0.208 Angle : 0.628 16.613 46104 Z= 0.296 Chirality : 0.044 0.201 5184 Planarity : 0.004 0.045 5988 Dihedral : 4.947 49.740 4630 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 3.78 % Allowed : 24.89 % Favored : 71.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.13), residues: 4224 helix: 0.62 (0.15), residues: 1308 sheet: -2.07 (0.32), residues: 264 loop : -1.41 (0.12), residues: 2652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 280 PHE 0.011 0.001 PHE b 269 TYR 0.018 0.001 TYR d 292 ARG 0.004 0.000 ARG d 284 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8448 Ramachandran restraints generated. 4224 Oldfield, 0 Emsley, 4224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8448 Ramachandran restraints generated. 4224 Oldfield, 0 Emsley, 4224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 575 residues out of total 3516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 443 time to evaluate : 3.511 Fit side-chains REVERT: B 264 LYS cc_start: 0.8865 (OUTLIER) cc_final: 0.8550 (ttpt) REVERT: C 215 GLU cc_start: 0.6757 (mm-30) cc_final: 0.6428 (mm-30) REVERT: C 264 LYS cc_start: 0.8840 (OUTLIER) cc_final: 0.8421 (ttpp) REVERT: C 329 MET cc_start: 0.8918 (ptt) cc_final: 0.8706 (ptm) REVERT: D 23 SER cc_start: 0.8675 (p) cc_final: 0.8306 (m) REVERT: D 245 ASP cc_start: 0.7995 (t70) cc_final: 0.7787 (t70) REVERT: D 321 GLN cc_start: 0.8444 (tp40) cc_final: 0.8146 (tp-100) REVERT: D 325 ASP cc_start: 0.8179 (m-30) cc_final: 0.7904 (m-30) REVERT: E 23 SER cc_start: 0.8693 (p) cc_final: 0.8257 (m) REVERT: E 264 LYS cc_start: 0.8810 (OUTLIER) cc_final: 0.8497 (ttpt) REVERT: F 264 LYS cc_start: 0.8875 (OUTLIER) cc_final: 0.8423 (ttpp) REVERT: F 277 GLN cc_start: 0.8666 (tp40) cc_final: 0.8402 (tp40) REVERT: a 135 GLU cc_start: 0.7855 (tp30) cc_final: 0.7474 (tp30) REVERT: a 260 GLU cc_start: 0.6620 (mm-30) cc_final: 0.5799 (mm-30) REVERT: b 72 VAL cc_start: 0.8917 (p) cc_final: 0.8596 (t) REVERT: b 235 VAL cc_start: 0.9565 (OUTLIER) cc_final: 0.9271 (t) REVERT: b 260 GLU cc_start: 0.6486 (mm-30) cc_final: 0.5748 (mm-30) REVERT: c 235 VAL cc_start: 0.9590 (m) cc_final: 0.9341 (t) REVERT: c 260 GLU cc_start: 0.6904 (mm-30) cc_final: 0.6489 (mm-30) REVERT: d 176 MET cc_start: 0.8523 (mmm) cc_final: 0.8285 (mmm) REVERT: d 260 GLU cc_start: 0.6533 (mm-30) cc_final: 0.5771 (mm-30) REVERT: e 72 VAL cc_start: 0.8952 (p) cc_final: 0.8610 (t) REVERT: e 235 VAL cc_start: 0.9565 (OUTLIER) cc_final: 0.9254 (t) REVERT: e 260 GLU cc_start: 0.6519 (mm-30) cc_final: 0.5788 (mm-30) REVERT: f 13 GLU cc_start: 0.7407 (pt0) cc_final: 0.7091 (pt0) REVERT: f 235 VAL cc_start: 0.9591 (m) cc_final: 0.9350 (t) REVERT: f 260 GLU cc_start: 0.6543 (mm-30) cc_final: 0.5827 (mm-30) outliers start: 132 outliers final: 121 residues processed: 537 average time/residue: 0.3993 time to fit residues: 365.8387 Evaluate side-chains 553 residues out of total 3516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 426 time to evaluate : 3.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 228 PHE Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 267 MET Chi-restraints excluded: chain B residue 13 GLU Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 228 PHE Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 264 LYS Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 164 ASP Chi-restraints excluded: chain C residue 228 PHE Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 264 LYS Chi-restraints excluded: chain C residue 317 ILE Chi-restraints excluded: chain C residue 319 MET Chi-restraints excluded: chain D residue 13 GLU Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 164 ASP Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 228 PHE Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 267 MET Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 164 ASP Chi-restraints excluded: chain E residue 176 MET Chi-restraints excluded: chain E residue 228 PHE Chi-restraints excluded: chain E residue 233 THR Chi-restraints excluded: chain E residue 264 LYS Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 306 GLU Chi-restraints excluded: chain E residue 317 ILE Chi-restraints excluded: chain E residue 344 ILE Chi-restraints excluded: chain E residue 345 ILE Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 164 ASP Chi-restraints excluded: chain F residue 228 PHE Chi-restraints excluded: chain F residue 233 THR Chi-restraints excluded: chain F residue 234 THR Chi-restraints excluded: chain F residue 264 LYS Chi-restraints excluded: chain F residue 304 LYS Chi-restraints excluded: chain F residue 317 ILE Chi-restraints excluded: chain F residue 344 ILE Chi-restraints excluded: chain a residue 13 GLU Chi-restraints excluded: chain a residue 34 VAL Chi-restraints excluded: chain a residue 97 THR Chi-restraints excluded: chain a residue 185 LEU Chi-restraints excluded: chain a residue 203 GLU Chi-restraints excluded: chain a residue 207 LEU Chi-restraints excluded: chain a residue 228 PHE Chi-restraints excluded: chain a residue 234 THR Chi-restraints excluded: chain a residue 235 VAL Chi-restraints excluded: chain b residue 34 VAL Chi-restraints excluded: chain b residue 97 THR Chi-restraints excluded: chain b residue 113 THR Chi-restraints excluded: chain b residue 169 ASP Chi-restraints excluded: chain b residue 234 THR Chi-restraints excluded: chain b residue 235 VAL Chi-restraints excluded: chain b residue 250 VAL Chi-restraints excluded: chain b residue 291 LEU Chi-restraints excluded: chain b residue 306 GLU Chi-restraints excluded: chain c residue 34 VAL Chi-restraints excluded: chain c residue 97 THR Chi-restraints excluded: chain c residue 113 THR Chi-restraints excluded: chain c residue 137 THR Chi-restraints excluded: chain c residue 185 LEU Chi-restraints excluded: chain c residue 215 GLU Chi-restraints excluded: chain c residue 234 THR Chi-restraints excluded: chain c residue 250 VAL Chi-restraints excluded: chain c residue 318 THR Chi-restraints excluded: chain d residue 13 GLU Chi-restraints excluded: chain d residue 34 VAL Chi-restraints excluded: chain d residue 97 THR Chi-restraints excluded: chain d residue 185 LEU Chi-restraints excluded: chain d residue 202 LEU Chi-restraints excluded: chain d residue 203 GLU Chi-restraints excluded: chain d residue 228 PHE Chi-restraints excluded: chain d residue 234 THR Chi-restraints excluded: chain d residue 235 VAL Chi-restraints excluded: chain d residue 267 MET Chi-restraints excluded: chain e residue 34 VAL Chi-restraints excluded: chain e residue 97 THR Chi-restraints excluded: chain e residue 113 THR Chi-restraints excluded: chain e residue 169 ASP Chi-restraints excluded: chain e residue 176 MET Chi-restraints excluded: chain e residue 203 GLU Chi-restraints excluded: chain e residue 235 VAL Chi-restraints excluded: chain e residue 250 VAL Chi-restraints excluded: chain e residue 291 LEU Chi-restraints excluded: chain e residue 306 GLU Chi-restraints excluded: chain e residue 349 THR Chi-restraints excluded: chain f residue 34 VAL Chi-restraints excluded: chain f residue 113 THR Chi-restraints excluded: chain f residue 137 THR Chi-restraints excluded: chain f residue 185 LEU Chi-restraints excluded: chain f residue 203 GLU Chi-restraints excluded: chain f residue 215 GLU Chi-restraints excluded: chain f residue 228 PHE Chi-restraints excluded: chain f residue 234 THR Chi-restraints excluded: chain f residue 250 VAL Chi-restraints excluded: chain f residue 252 VAL Chi-restraints excluded: chain f residue 306 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 264 optimal weight: 9.9990 chunk 354 optimal weight: 0.0570 chunk 102 optimal weight: 7.9990 chunk 307 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 chunk 92 optimal weight: 10.0000 chunk 333 optimal weight: 0.8980 chunk 139 optimal weight: 0.0170 chunk 342 optimal weight: 2.9990 chunk 42 optimal weight: 9.9990 chunk 61 optimal weight: 0.3980 overall best weight: 0.3936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 321 GLN ** F 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 120 GLN ** e 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 120 GLN f 120 GLN f 350 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.118088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.103721 restraints weight = 51109.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.106030 restraints weight = 33380.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.107690 restraints weight = 24728.592| |-----------------------------------------------------------------------------| r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.4937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 33828 Z= 0.137 Angle : 0.605 16.421 46104 Z= 0.282 Chirality : 0.043 0.186 5184 Planarity : 0.004 0.045 5988 Dihedral : 4.687 49.724 4630 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 2.78 % Allowed : 26.00 % Favored : 71.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.13), residues: 4224 helix: 0.91 (0.15), residues: 1236 sheet: -1.95 (0.32), residues: 264 loop : -1.38 (0.11), residues: 2724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 280 PHE 0.016 0.001 PHE f 206 TYR 0.020 0.001 TYR D 216 ARG 0.004 0.000 ARG a 265 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7627.75 seconds wall clock time: 137 minutes 9.41 seconds (8229.41 seconds total)