Starting phenix.real_space_refine on Tue Jun 25 07:53:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rt6_19480/06_2024/8rt6_19480.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rt6_19480/06_2024/8rt6_19480.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rt6_19480/06_2024/8rt6_19480.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rt6_19480/06_2024/8rt6_19480.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rt6_19480/06_2024/8rt6_19480.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rt6_19480/06_2024/8rt6_19480.pdb" } resolution = 3.18 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= 0.026 sd= 0.073 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 204 5.16 5 C 34862 2.51 5 N 10180 2.21 5 O 10556 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 139": "OE1" <-> "OE2" Residue "A GLU 143": "OE1" <-> "OE2" Residue "A ARG 144": "NH1" <-> "NH2" Residue "A ASP 214": "OD1" <-> "OD2" Residue "A ARG 235": "NH1" <-> "NH2" Residue "A ASP 236": "OD1" <-> "OD2" Residue "A TYR 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 243": "NH1" <-> "NH2" Residue "A ARG 249": "NH1" <-> "NH2" Residue "A PHE 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 274": "NH1" <-> "NH2" Residue "A ASP 286": "OD1" <-> "OD2" Residue "A ASP 303": "OD1" <-> "OD2" Residue "A ARG 304": "NH1" <-> "NH2" Residue "A ARG 372": "NH1" <-> "NH2" Residue "A ASP 380": "OD1" <-> "OD2" Residue "B TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 71": "OD1" <-> "OD2" Residue "B GLU 73": "OE1" <-> "OE2" Residue "B PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 91": "OE1" <-> "OE2" Residue "B PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 109": "NH1" <-> "NH2" Residue "B ARG 113": "NH1" <-> "NH2" Residue "B GLU 122": "OE1" <-> "OE2" Residue "B ARG 136": "NH1" <-> "NH2" Residue "B GLU 137": "OE1" <-> "OE2" Residue "B ARG 141": "NH1" <-> "NH2" Residue "B ARG 151": "NH1" <-> "NH2" Residue "B PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 199": "OE1" <-> "OE2" Residue "B GLU 202": "OE1" <-> "OE2" Residue "B ARG 233": "NH1" <-> "NH2" Residue "B ASP 243": "OD1" <-> "OD2" Residue "B ARG 259": "NH1" <-> "NH2" Residue "B ARG 260": "NH1" <-> "NH2" Residue "C PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 41": "OE1" <-> "OE2" Residue "D GLU 139": "OE1" <-> "OE2" Residue "D GLU 143": "OE1" <-> "OE2" Residue "D ARG 144": "NH1" <-> "NH2" Residue "D ASP 214": "OD1" <-> "OD2" Residue "D ARG 235": "NH1" <-> "NH2" Residue "D ASP 236": "OD1" <-> "OD2" Residue "D ARG 243": "NH1" <-> "NH2" Residue "D ARG 249": "NH1" <-> "NH2" Residue "D TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 274": "NH1" <-> "NH2" Residue "D ARG 304": "NH1" <-> "NH2" Residue "D ARG 372": "NH1" <-> "NH2" Residue "E TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 109": "NH1" <-> "NH2" Residue "E ARG 113": "NH1" <-> "NH2" Residue "E ASP 129": "OD1" <-> "OD2" Residue "E ARG 136": "NH1" <-> "NH2" Residue "E ARG 141": "NH1" <-> "NH2" Residue "E GLU 145": "OE1" <-> "OE2" Residue "E ASP 167": "OD1" <-> "OD2" Residue "E TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 197": "OD1" <-> "OD2" Residue "E ARG 233": "NH1" <-> "NH2" Residue "E ASP 243": "OD1" <-> "OD2" Residue "E ASP 250": "OD1" <-> "OD2" Residue "E ARG 259": "NH1" <-> "NH2" Residue "E ARG 260": "NH1" <-> "NH2" Residue "F PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 139": "OE1" <-> "OE2" Residue "G GLU 143": "OE1" <-> "OE2" Residue "G ARG 144": "NH1" <-> "NH2" Residue "G GLU 185": "OE1" <-> "OE2" Residue "G ARG 235": "NH1" <-> "NH2" Residue "G ASP 236": "OD1" <-> "OD2" Residue "G ARG 243": "NH1" <-> "NH2" Residue "G ASP 248": "OD1" <-> "OD2" Residue "G ARG 249": "NH1" <-> "NH2" Residue "G ARG 274": "NH1" <-> "NH2" Residue "G ASP 303": "OD1" <-> "OD2" Residue "G ARG 304": "NH1" <-> "NH2" Residue "G GLU 308": "OE1" <-> "OE2" Residue "G ASP 324": "OD1" <-> "OD2" Residue "G ARG 372": "NH1" <-> "NH2" Residue "G ASP 380": "OD1" <-> "OD2" Residue "H TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 62": "OE1" <-> "OE2" Residue "H TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 91": "OE1" <-> "OE2" Residue "H TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 109": "NH1" <-> "NH2" Residue "H ARG 113": "NH1" <-> "NH2" Residue "H GLU 122": "OE1" <-> "OE2" Residue "H ARG 141": "NH1" <-> "NH2" Residue "H GLU 149": "OE1" <-> "OE2" Residue "H PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 197": "OD1" <-> "OD2" Residue "H ARG 233": "NH1" <-> "NH2" Residue "H ASP 243": "OD1" <-> "OD2" Residue "H ARG 259": "NH1" <-> "NH2" Residue "H ARG 260": "NH1" <-> "NH2" Residue "I PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 32": "OE1" <-> "OE2" Residue "J GLU 139": "OE1" <-> "OE2" Residue "J GLU 143": "OE1" <-> "OE2" Residue "J ARG 144": "NH1" <-> "NH2" Residue "J ARG 235": "NH1" <-> "NH2" Residue "J ARG 243": "NH1" <-> "NH2" Residue "J ARG 249": "NH1" <-> "NH2" Residue "J ARG 274": "NH1" <-> "NH2" Residue "J ASP 303": "OD1" <-> "OD2" Residue "J ARG 304": "NH1" <-> "NH2" Residue "J ARG 372": "NH1" <-> "NH2" Residue "J ASP 382": "OD1" <-> "OD2" Residue "K TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 47": "OD1" <-> "OD2" Residue "K GLU 60": "OE1" <-> "OE2" Residue "K GLU 62": "OE1" <-> "OE2" Residue "K TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 109": "NH1" <-> "NH2" Residue "K ARG 113": "NH1" <-> "NH2" Residue "K TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 137": "OE1" <-> "OE2" Residue "K ARG 141": "NH1" <-> "NH2" Residue "K PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 197": "OD1" <-> "OD2" Residue "K GLU 202": "OE1" <-> "OE2" Residue "K ARG 233": "NH1" <-> "NH2" Residue "K GLU 240": "OE1" <-> "OE2" Residue "K ASP 243": "OD1" <-> "OD2" Residue "K ASP 250": "OD1" <-> "OD2" Residue "K ARG 259": "NH1" <-> "NH2" Residue "K ARG 260": "NH1" <-> "NH2" Residue "L PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 139": "OE1" <-> "OE2" Residue "M GLU 143": "OE1" <-> "OE2" Residue "M ARG 144": "NH1" <-> "NH2" Residue "M ASP 214": "OD1" <-> "OD2" Residue "M ARG 235": "NH1" <-> "NH2" Residue "M ARG 243": "NH1" <-> "NH2" Residue "M ARG 249": "NH1" <-> "NH2" Residue "M PHE 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 274": "NH1" <-> "NH2" Residue "M ASP 303": "OD1" <-> "OD2" Residue "M ARG 304": "NH1" <-> "NH2" Residue "M ARG 372": "NH1" <-> "NH2" Residue "M ASP 380": "OD1" <-> "OD2" Residue "M ASP 382": "OD1" <-> "OD2" Residue "N TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 62": "OE1" <-> "OE2" Residue "N TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 91": "OE1" <-> "OE2" Residue "N TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 109": "NH1" <-> "NH2" Residue "N ARG 113": "NH1" <-> "NH2" Residue "N ASP 129": "OD1" <-> "OD2" Residue "N ARG 141": "NH1" <-> "NH2" Residue "N GLU 149": "OE1" <-> "OE2" Residue "N TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 167": "OD1" <-> "OD2" Residue "N ASP 175": "OD1" <-> "OD2" Residue "N TYR 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 189": "OD1" <-> "OD2" Residue "N GLU 199": "OE1" <-> "OE2" Residue "N ARG 233": "NH1" <-> "NH2" Residue "N ASP 243": "OD1" <-> "OD2" Residue "N ASP 250": "OD1" <-> "OD2" Residue "N ARG 259": "NH1" <-> "NH2" Residue "N ARG 260": "NH1" <-> "NH2" Residue "O PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 139": "OE1" <-> "OE2" Residue "P GLU 143": "OE1" <-> "OE2" Residue "P ARG 144": "NH1" <-> "NH2" Residue "P ASP 204": "OD1" <-> "OD2" Residue "P ASP 214": "OD1" <-> "OD2" Residue "P ARG 235": "NH1" <-> "NH2" Residue "P ARG 243": "NH1" <-> "NH2" Residue "P ARG 249": "NH1" <-> "NH2" Residue "P ARG 274": "NH1" <-> "NH2" Residue "P ASP 286": "OD1" <-> "OD2" Residue "P ARG 304": "NH1" <-> "NH2" Residue "P ASP 324": "OD1" <-> "OD2" Residue "P GLU 371": "OE1" <-> "OE2" Residue "P ARG 372": "NH1" <-> "NH2" Residue "Q TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 109": "NH1" <-> "NH2" Residue "Q ARG 113": "NH1" <-> "NH2" Residue "Q GLU 122": "OE1" <-> "OE2" Residue "Q ARG 136": "NH1" <-> "NH2" Residue "Q ARG 141": "NH1" <-> "NH2" Residue "Q GLU 145": "OE1" <-> "OE2" Residue "Q GLU 149": "OE1" <-> "OE2" Residue "Q GLU 199": "OE1" <-> "OE2" Residue "Q GLU 202": "OE1" <-> "OE2" Residue "Q ARG 233": "NH1" <-> "NH2" Residue "Q ASP 243": "OD1" <-> "OD2" Residue "Q ASP 250": "OD1" <-> "OD2" Residue "Q ARG 259": "NH1" <-> "NH2" Residue "Q ARG 260": "NH1" <-> "NH2" Residue "R PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 32": "OE1" <-> "OE2" Residue "S GLU 139": "OE1" <-> "OE2" Residue "S GLU 143": "OE1" <-> "OE2" Residue "S ARG 144": "NH1" <-> "NH2" Residue "S GLU 182": "OE1" <-> "OE2" Residue "S ARG 235": "NH1" <-> "NH2" Residue "S ASP 236": "OD1" <-> "OD2" Residue "S ARG 243": "NH1" <-> "NH2" Residue "S ASP 248": "OD1" <-> "OD2" Residue "S ARG 249": "NH1" <-> "NH2" Residue "S ARG 274": "NH1" <-> "NH2" Residue "S ASP 303": "OD1" <-> "OD2" Residue "S ARG 304": "NH1" <-> "NH2" Residue "S ARG 372": "NH1" <-> "NH2" Residue "S ASP 380": "OD1" <-> "OD2" Residue "S ASP 382": "OD1" <-> "OD2" Residue "T TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 109": "NH1" <-> "NH2" Residue "T ARG 113": "NH1" <-> "NH2" Residue "T TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 129": "OD1" <-> "OD2" Residue "T GLU 137": "OE1" <-> "OE2" Residue "T ARG 141": "NH1" <-> "NH2" Residue "T PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 199": "OE1" <-> "OE2" Residue "T ARG 233": "NH1" <-> "NH2" Residue "T ASP 243": "OD1" <-> "OD2" Residue "T ASP 250": "OD1" <-> "OD2" Residue "T ARG 259": "NH1" <-> "NH2" Residue "T ARG 260": "NH1" <-> "NH2" Residue "U PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 139": "OE1" <-> "OE2" Residue "V GLU 143": "OE1" <-> "OE2" Residue "V ARG 144": "NH1" <-> "NH2" Residue "V GLU 182": "OE1" <-> "OE2" Residue "V ASP 214": "OD1" <-> "OD2" Residue "V ARG 235": "NH1" <-> "NH2" Residue "V ARG 243": "NH1" <-> "NH2" Residue "V ASP 248": "OD1" <-> "OD2" Residue "V ARG 249": "NH1" <-> "NH2" Residue "V ARG 274": "NH1" <-> "NH2" Residue "V ARG 304": "NH1" <-> "NH2" Residue "V GLU 308": "OE1" <-> "OE2" Residue "V GLU 353": "OE1" <-> "OE2" Residue "V GLU 371": "OE1" <-> "OE2" Residue "V ARG 372": "NH1" <-> "NH2" Residue "V ASP 380": "OD1" <-> "OD2" Residue "W TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 109": "NH1" <-> "NH2" Residue "W ARG 113": "NH1" <-> "NH2" Residue "W GLU 122": "OE1" <-> "OE2" Residue "W PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 137": "OE1" <-> "OE2" Residue "W ARG 141": "NH1" <-> "NH2" Residue "W GLU 145": "OE1" <-> "OE2" Residue "W ASP 167": "OD1" <-> "OD2" Residue "W ASP 197": "OD1" <-> "OD2" Residue "W GLU 199": "OE1" <-> "OE2" Residue "W GLU 202": "OE1" <-> "OE2" Residue "W ARG 233": "NH1" <-> "NH2" Residue "W GLU 240": "OE1" <-> "OE2" Residue "W ASP 243": "OD1" <-> "OD2" Residue "W ARG 259": "NH1" <-> "NH2" Residue "W ARG 260": "NH1" <-> "NH2" Residue "X PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 139": "OE1" <-> "OE2" Residue "Y GLU 143": "OE1" <-> "OE2" Residue "Y ARG 144": "NH1" <-> "NH2" Residue "Y ARG 235": "NH1" <-> "NH2" Residue "Y ARG 243": "NH1" <-> "NH2" Residue "Y ASP 248": "OD1" <-> "OD2" Residue "Y ARG 249": "NH1" <-> "NH2" Residue "Y PHE 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 274": "NH1" <-> "NH2" Residue "Y ASP 286": "OD1" <-> "OD2" Residue "Y ASP 303": "OD1" <-> "OD2" Residue "Y ARG 304": "NH1" <-> "NH2" Residue "Y GLU 353": "OE1" <-> "OE2" Residue "Y GLU 371": "OE1" <-> "OE2" Residue "Y ARG 372": "NH1" <-> "NH2" Residue "Y ASP 380": "OD1" <-> "OD2" Residue "Z ASP 47": "OD1" <-> "OD2" Residue "Z GLU 62": "OE1" <-> "OE2" Residue "Z TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 91": "OE1" <-> "OE2" Residue "Z TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 109": "NH1" <-> "NH2" Residue "Z ARG 113": "NH1" <-> "NH2" Residue "Z GLU 122": "OE1" <-> "OE2" Residue "Z PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 141": "NH1" <-> "NH2" Residue "Z TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 165": "OD1" <-> "OD2" Residue "Z ASP 167": "OD1" <-> "OD2" Residue "Z ASP 175": "OD1" <-> "OD2" Residue "Z PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 189": "OD1" <-> "OD2" Residue "Z PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 197": "OD1" <-> "OD2" Residue "Z GLU 199": "OE1" <-> "OE2" Residue "Z ARG 233": "NH1" <-> "NH2" Residue "Z GLU 240": "OE1" <-> "OE2" Residue "Z ASP 250": "OD1" <-> "OD2" Residue "Z ARG 259": "NH1" <-> "NH2" Residue "Z ARG 260": "NH1" <-> "NH2" Residue "a PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 32": "OE1" <-> "OE2" Residue "a GLU 41": "OE1" <-> "OE2" Residue "b GLU 139": "OE1" <-> "OE2" Residue "b GLU 143": "OE1" <-> "OE2" Residue "b ARG 144": "NH1" <-> "NH2" Residue "b GLU 182": "OE1" <-> "OE2" Residue "b ARG 235": "NH1" <-> "NH2" Residue "b ASP 236": "OD1" <-> "OD2" Residue "b ARG 243": "NH1" <-> "NH2" Residue "b ARG 249": "NH1" <-> "NH2" Residue "b TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 274": "NH1" <-> "NH2" Residue "b ASP 303": "OD1" <-> "OD2" Residue "b ARG 304": "NH1" <-> "NH2" Residue "b GLU 371": "OE1" <-> "OE2" Residue "b ARG 372": "NH1" <-> "NH2" Residue "b ASP 380": "OD1" <-> "OD2" Residue "b ASP 385": "OD1" <-> "OD2" Residue "c TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ASP 47": "OD1" <-> "OD2" Residue "c GLU 62": "OE1" <-> "OE2" Residue "c TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 91": "OE1" <-> "OE2" Residue "c ARG 109": "NH1" <-> "NH2" Residue "c ARG 113": "NH1" <-> "NH2" Residue "c TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 133": "NH1" <-> "NH2" Residue "c ARG 141": "NH1" <-> "NH2" Residue "c GLU 145": "OE1" <-> "OE2" Residue "c GLU 149": "OE1" <-> "OE2" Residue "c ASP 165": "OD1" <-> "OD2" Residue "c ASP 167": "OD1" <-> "OD2" Residue "c PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ASP 189": "OD1" <-> "OD2" Residue "c PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ASP 197": "OD1" <-> "OD2" Residue "c GLU 199": "OE1" <-> "OE2" Residue "c ARG 233": "NH1" <-> "NH2" Residue "c GLU 240": "OE1" <-> "OE2" Residue "c ASP 250": "OD1" <-> "OD2" Residue "c ARG 259": "NH1" <-> "NH2" Residue "c ARG 260": "NH1" <-> "NH2" Residue "d PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 139": "OE1" <-> "OE2" Residue "e GLU 143": "OE1" <-> "OE2" Residue "e ARG 144": "NH1" <-> "NH2" Residue "e GLU 182": "OE1" <-> "OE2" Residue "e ASP 214": "OD1" <-> "OD2" Residue "e ARG 235": "NH1" <-> "NH2" Residue "e ASP 236": "OD1" <-> "OD2" Residue "e ARG 243": "NH1" <-> "NH2" Residue "e ARG 249": "NH1" <-> "NH2" Residue "e TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ARG 274": "NH1" <-> "NH2" Residue "e ARG 304": "NH1" <-> "NH2" Residue "e GLU 308": "OE1" <-> "OE2" Residue "e ASP 324": "OD1" <-> "OD2" Residue "e GLU 371": "OE1" <-> "OE2" Residue "e ARG 372": "NH1" <-> "NH2" Residue "e ASP 385": "OD1" <-> "OD2" Residue "f TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ASP 47": "OD1" <-> "OD2" Residue "f ASP 71": "OD1" <-> "OD2" Residue "f GLU 73": "OE1" <-> "OE2" Residue "f TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 91": "OE1" <-> "OE2" Residue "f TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ARG 109": "NH1" <-> "NH2" Residue "f ARG 113": "NH1" <-> "NH2" Residue "f TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 137": "OE1" <-> "OE2" Residue "f ARG 141": "NH1" <-> "NH2" Residue "f PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ASP 197": "OD1" <-> "OD2" Residue "f GLU 199": "OE1" <-> "OE2" Residue "f GLU 202": "OE1" <-> "OE2" Residue "f ARG 233": "NH1" <-> "NH2" Residue "f GLU 240": "OE1" <-> "OE2" Residue "f ASP 243": "OD1" <-> "OD2" Residue "f ASP 250": "OD1" <-> "OD2" Residue "f ARG 259": "NH1" <-> "NH2" Residue "f ARG 260": "NH1" <-> "NH2" Residue "h GLU 139": "OE1" <-> "OE2" Residue "h GLU 143": "OE1" <-> "OE2" Residue "h ARG 144": "NH1" <-> "NH2" Residue "h GLU 185": "OE1" <-> "OE2" Residue "h ASP 214": "OD1" <-> "OD2" Residue "h ARG 235": "NH1" <-> "NH2" Residue "h ASP 236": "OD1" <-> "OD2" Residue "h ARG 243": "NH1" <-> "NH2" Residue "h ARG 249": "NH1" <-> "NH2" Residue "h TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ARG 274": "NH1" <-> "NH2" Residue "h ARG 304": "NH1" <-> "NH2" Residue "h ASP 324": "OD1" <-> "OD2" Residue "h ARG 372": "NH1" <-> "NH2" Residue "h ASP 382": "OD1" <-> "OD2" Residue "h GLU 390": "OE1" <-> "OE2" Residue "i TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i GLU 59": "OE1" <-> "OE2" Residue "i TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i GLU 91": "OE1" <-> "OE2" Residue "i ASP 102": "OD1" <-> "OD2" Residue "i TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ARG 109": "NH1" <-> "NH2" Residue "i ARG 113": "NH1" <-> "NH2" Residue "i TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i GLU 122": "OE1" <-> "OE2" Residue "i TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ASP 129": "OD1" <-> "OD2" Residue "i ARG 141": "NH1" <-> "NH2" Residue "i ASP 197": "OD1" <-> "OD2" Residue "i ARG 233": "NH1" <-> "NH2" Residue "i GLU 240": "OE1" <-> "OE2" Residue "i ASP 243": "OD1" <-> "OD2" Residue "i ASP 250": "OD1" <-> "OD2" Residue "i ARG 259": "NH1" <-> "NH2" Residue "i ARG 260": "NH1" <-> "NH2" Residue "j PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k GLU 139": "OE1" <-> "OE2" Residue "k GLU 143": "OE1" <-> "OE2" Residue "k ARG 144": "NH1" <-> "NH2" Residue "k GLU 185": "OE1" <-> "OE2" Residue "k ASP 214": "OD1" <-> "OD2" Residue "k GLU 218": "OE1" <-> "OE2" Residue "k ARG 235": "NH1" <-> "NH2" Residue "k ASP 236": "OD1" <-> "OD2" Residue "k ARG 243": "NH1" <-> "NH2" Residue "k ASP 248": "OD1" <-> "OD2" Residue "k ARG 249": "NH1" <-> "NH2" Residue "k TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k PHE 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ARG 274": "NH1" <-> "NH2" Residue "k ASP 303": "OD1" <-> "OD2" Residue "k ARG 304": "NH1" <-> "NH2" Residue "k ARG 372": "NH1" <-> "NH2" Residue "l TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l GLU 59": "OE1" <-> "OE2" Residue "l PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l GLU 73": "OE1" <-> "OE2" Residue "l TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ASP 102": "OD1" <-> "OD2" Residue "l TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ARG 109": "NH1" <-> "NH2" Residue "l ARG 113": "NH1" <-> "NH2" Residue "l TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ASP 129": "OD1" <-> "OD2" Residue "l GLU 137": "OE1" <-> "OE2" Residue "l ARG 141": "NH1" <-> "NH2" Residue "l GLU 149": "OE1" <-> "OE2" Residue "l ASP 167": "OD1" <-> "OD2" Residue "l ASP 197": "OD1" <-> "OD2" Residue "l ARG 233": "NH1" <-> "NH2" Residue "l ASP 243": "OD1" <-> "OD2" Residue "l ASP 250": "OD1" <-> "OD2" Residue "l ARG 259": "NH1" <-> "NH2" Residue "l ARG 260": "NH1" <-> "NH2" Residue "m PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n GLU 139": "OE1" <-> "OE2" Residue "n GLU 143": "OE1" <-> "OE2" Residue "n ARG 144": "NH1" <-> "NH2" Residue "n ARG 235": "NH1" <-> "NH2" Residue "n ARG 243": "NH1" <-> "NH2" Residue "n ARG 249": "NH1" <-> "NH2" Residue "n ARG 274": "NH1" <-> "NH2" Residue "n ASP 303": "OD1" <-> "OD2" Residue "n ARG 304": "NH1" <-> "NH2" Residue "n ARG 372": "NH1" <-> "NH2" Residue "n ASP 380": "OD1" <-> "OD2" Residue "o TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o GLU 59": "OE1" <-> "OE2" Residue "o TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o GLU 91": "OE1" <-> "OE2" Residue "o TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ARG 109": "NH1" <-> "NH2" Residue "o ARG 113": "NH1" <-> "NH2" Residue "o TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ASP 129": "OD1" <-> "OD2" Residue "o ARG 141": "NH1" <-> "NH2" Residue "o GLU 145": "OE1" <-> "OE2" Residue "o GLU 149": "OE1" <-> "OE2" Residue "o ASP 165": "OD1" <-> "OD2" Residue "o ASP 167": "OD1" <-> "OD2" Residue "o PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ASP 197": "OD1" <-> "OD2" Residue "o GLU 199": "OE1" <-> "OE2" Residue "o ARG 233": "NH1" <-> "NH2" Residue "o ASP 243": "OD1" <-> "OD2" Residue "o ARG 259": "NH1" <-> "NH2" Residue "o ARG 260": "NH1" <-> "NH2" Residue "u GLU 139": "OE1" <-> "OE2" Residue "u GLU 143": "OE1" <-> "OE2" Residue "u ARG 144": "NH1" <-> "NH2" Residue "v TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v GLU 91": "OE1" <-> "OE2" Residue "v TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v ARG 109": "NH1" <-> "NH2" Residue "v ARG 113": "NH1" <-> "NH2" Residue "y GLU 139": "OE1" <-> "OE2" Residue "y GLU 143": "OE1" <-> "OE2" Residue "y ARG 144": "NH1" <-> "NH2" Residue "z TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z GLU 91": "OE1" <-> "OE2" Residue "z TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z ARG 109": "NH1" <-> "NH2" Residue "z ARG 113": "NH1" <-> "NH2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 55802 Number of models: 1 Model: "" Number of chains: 46 Chain: "A" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1670 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 211} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 1955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1955 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 11, 'TRANS': 234} Chain: "C" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 213 Classifications: {'peptide': 28} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 22} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1670 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 211} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 1955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1955 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 11, 'TRANS': 234} Chain: "F" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 213 Classifications: {'peptide': 28} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 22} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1670 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 211} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "H" Number of atoms: 1955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1955 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 11, 'TRANS': 234} Chain: "I" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 213 Classifications: {'peptide': 28} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 22} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "J" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1670 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 211} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "K" Number of atoms: 1955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1955 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 11, 'TRANS': 234} Chain: "L" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 213 Classifications: {'peptide': 28} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 22} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "M" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1670 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 211} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "N" Number of atoms: 1955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1955 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 11, 'TRANS': 234} Chain: "O" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 213 Classifications: {'peptide': 28} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 22} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "P" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1670 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 211} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "Q" Number of atoms: 1955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1955 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 11, 'TRANS': 234} Chain: "R" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 213 Classifications: {'peptide': 28} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 22} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "S" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1670 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 211} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "T" Number of atoms: 1955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1955 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 11, 'TRANS': 234} Chain: "U" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 213 Classifications: {'peptide': 28} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 22} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "V" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1670 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 211} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "W" Number of atoms: 1955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1955 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 11, 'TRANS': 234} Chain: "X" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 213 Classifications: {'peptide': 28} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 22} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "Y" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1670 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 211} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "Z" Number of atoms: 1955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1955 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 11, 'TRANS': 234} Chain: "a" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 213 Classifications: {'peptide': 28} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 22} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "b" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1670 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 211} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "c" Number of atoms: 1955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1955 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 11, 'TRANS': 234} Chain: "d" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 213 Classifications: {'peptide': 28} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 22} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "e" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1670 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 211} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "f" Number of atoms: 1955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1955 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 11, 'TRANS': 234} Chain: "g" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 213 Classifications: {'peptide': 28} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 22} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "h" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1670 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 211} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "i" Number of atoms: 1955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1955 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 11, 'TRANS': 234} Chain: "j" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 213 Classifications: {'peptide': 28} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 22} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "k" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1670 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 211} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "l" Number of atoms: 1955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1955 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 11, 'TRANS': 234} Chain: "m" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 213 Classifications: {'peptide': 28} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 22} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "n" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1670 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 211} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "o" Number of atoms: 1955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1955 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 11, 'TRANS': 234} Chain: "p" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 213 Classifications: {'peptide': 28} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 22} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "u" Number of atoms: 149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 149 Classifications: {'peptide': 19} Link IDs: {'PTRANS': 1, 'TRANS': 17} Chain: "v" Number of atoms: 886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 886 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 4, 'TRANS': 103} Chain: "y" Number of atoms: 149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 149 Classifications: {'peptide': 19} Link IDs: {'PTRANS': 1, 'TRANS': 17} Chain: "z" Number of atoms: 886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 886 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 4, 'TRANS': 103} Time building chain proxies: 21.22, per 1000 atoms: 0.38 Number of scatterers: 55802 At special positions: 0 Unit cell: (193.127, 195.261, 154.715, 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 204 16.00 O 10556 8.00 N 10180 7.00 C 34862 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 215 " - pdb=" SG CYS A 231 " distance=2.03 Simple disulfide: pdb=" SG CYS D 215 " - pdb=" SG CYS D 231 " distance=2.03 Simple disulfide: pdb=" SG CYS G 215 " - pdb=" SG CYS G 231 " distance=2.03 Simple disulfide: pdb=" SG CYS J 215 " - pdb=" SG CYS J 231 " distance=2.03 Simple disulfide: pdb=" SG CYS M 215 " - pdb=" SG CYS M 231 " distance=2.03 Simple disulfide: pdb=" SG CYS P 215 " - pdb=" SG CYS P 231 " distance=2.03 Simple disulfide: pdb=" SG CYS S 215 " - pdb=" SG CYS S 231 " distance=2.03 Simple disulfide: pdb=" SG CYS V 215 " - pdb=" SG CYS V 231 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 215 " - pdb=" SG CYS Y 231 " distance=2.03 Simple disulfide: pdb=" SG CYS b 215 " - pdb=" SG CYS b 231 " distance=2.03 Simple disulfide: pdb=" SG CYS e 215 " - pdb=" SG CYS e 231 " distance=2.03 Simple disulfide: pdb=" SG CYS h 215 " - pdb=" SG CYS h 231 " distance=2.03 Simple disulfide: pdb=" SG CYS k 215 " - pdb=" SG CYS k 231 " distance=2.03 Simple disulfide: pdb=" SG CYS n 215 " - pdb=" SG CYS n 231 " distance=2.03 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: 15.37 Conformation dependent library (CDL) restraints added in 7.4 seconds 14072 Ramachandran restraints generated. 7036 Oldfield, 0 Emsley, 7036 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13052 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 144 sheets defined 17.0% alpha, 26.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.83 Creating SS restraints... Processing helix chain 'A' and resid 136 through 148 Processing helix chain 'A' and resid 182 through 187 Processing helix chain 'A' and resid 305 through 329 removed outlier: 5.258A pdb=" N GLY A 312 " --> pdb=" O GLU A 308 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N ALA A 313 " --> pdb=" O ARG A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 359 removed outlier: 3.505A pdb=" N ASN A 357 " --> pdb=" O GLU A 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 151 removed outlier: 3.730A pdb=" N GLN B 131 " --> pdb=" O TYR B 127 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA B 138 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ASN B 139 " --> pdb=" O THR B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 169 Processing helix chain 'D' and resid 136 through 148 Processing helix chain 'D' and resid 180 through 186 Processing helix chain 'D' and resid 305 through 329 removed outlier: 5.475A pdb=" N GLY D 312 " --> pdb=" O GLU D 308 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N ALA D 313 " --> pdb=" O ARG D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 359 removed outlier: 3.541A pdb=" N ASN D 357 " --> pdb=" O GLU D 353 " (cutoff:3.500A) Processing helix chain 'E' and resid 128 through 150 removed outlier: 3.757A pdb=" N ARG E 136 " --> pdb=" O ALA E 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 166 through 169 Processing helix chain 'F' and resid 39 through 43 Processing helix chain 'G' and resid 136 through 148 Processing helix chain 'G' and resid 180 through 187 Processing helix chain 'G' and resid 305 through 329 removed outlier: 5.554A pdb=" N GLY G 312 " --> pdb=" O GLU G 308 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N ALA G 313 " --> pdb=" O ARG G 309 " (cutoff:3.500A) Processing helix chain 'G' and resid 350 through 359 removed outlier: 3.753A pdb=" N ASN G 357 " --> pdb=" O GLU G 353 " (cutoff:3.500A) Processing helix chain 'H' and resid 128 through 151 removed outlier: 4.218A pdb=" N ARG H 151 " --> pdb=" O ALA H 147 " (cutoff:3.500A) Processing helix chain 'H' and resid 166 through 169 Processing helix chain 'J' and resid 136 through 148 Processing helix chain 'J' and resid 182 through 187 Processing helix chain 'J' and resid 305 through 329 removed outlier: 5.638A pdb=" N GLY J 312 " --> pdb=" O GLU J 308 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N ALA J 313 " --> pdb=" O ARG J 309 " (cutoff:3.500A) Processing helix chain 'J' and resid 350 through 359 removed outlier: 3.592A pdb=" N ASN J 357 " --> pdb=" O GLU J 353 " (cutoff:3.500A) Processing helix chain 'K' and resid 127 through 151 removed outlier: 3.965A pdb=" N GLN K 131 " --> pdb=" O TYR K 127 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ARG K 151 " --> pdb=" O ALA K 147 " (cutoff:3.500A) Processing helix chain 'K' and resid 166 through 169 Processing helix chain 'L' and resid 39 through 43 removed outlier: 3.588A pdb=" N ILE L 42 " --> pdb=" O PRO L 39 " (cutoff:3.500A) Processing helix chain 'M' and resid 136 through 148 Processing helix chain 'M' and resid 180 through 187 Processing helix chain 'M' and resid 305 through 329 removed outlier: 5.564A pdb=" N GLY M 312 " --> pdb=" O GLU M 308 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N ALA M 313 " --> pdb=" O ARG M 309 " (cutoff:3.500A) Processing helix chain 'M' and resid 350 through 359 Processing helix chain 'N' and resid 127 through 151 removed outlier: 3.922A pdb=" N GLN N 131 " --> pdb=" O TYR N 127 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ARG N 151 " --> pdb=" O ALA N 147 " (cutoff:3.500A) Processing helix chain 'N' and resid 166 through 169 Processing helix chain 'P' and resid 136 through 148 Processing helix chain 'P' and resid 180 through 187 Processing helix chain 'P' and resid 305 through 329 removed outlier: 5.407A pdb=" N GLY P 312 " --> pdb=" O GLU P 308 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N ALA P 313 " --> pdb=" O ARG P 309 " (cutoff:3.500A) Processing helix chain 'P' and resid 350 through 359 Processing helix chain 'Q' and resid 127 through 151 removed outlier: 3.922A pdb=" N ARG Q 151 " --> pdb=" O ALA Q 147 " (cutoff:3.500A) Processing helix chain 'Q' and resid 166 through 169 Processing helix chain 'S' and resid 136 through 148 Processing helix chain 'S' and resid 180 through 187 Processing helix chain 'S' and resid 305 through 329 removed outlier: 5.564A pdb=" N GLY S 312 " --> pdb=" O GLU S 308 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N ALA S 313 " --> pdb=" O ARG S 309 " (cutoff:3.500A) Processing helix chain 'S' and resid 350 through 359 Processing helix chain 'T' and resid 127 through 151 removed outlier: 3.630A pdb=" N ALA T 138 " --> pdb=" O GLN T 134 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ARG T 151 " --> pdb=" O ALA T 147 " (cutoff:3.500A) Processing helix chain 'V' and resid 136 through 148 Processing helix chain 'V' and resid 182 through 187 Processing helix chain 'V' and resid 305 through 329 removed outlier: 5.355A pdb=" N GLY V 312 " --> pdb=" O GLU V 308 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N ALA V 313 " --> pdb=" O ARG V 309 " (cutoff:3.500A) Processing helix chain 'V' and resid 350 through 359 Processing helix chain 'W' and resid 127 through 150 removed outlier: 3.772A pdb=" N GLU W 137 " --> pdb=" O ARG W 133 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ALA W 138 " --> pdb=" O GLN W 134 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ASN W 139 " --> pdb=" O THR W 135 " (cutoff:3.500A) Processing helix chain 'W' and resid 166 through 169 Processing helix chain 'X' and resid 39 through 43 Processing helix chain 'Y' and resid 136 through 148 Processing helix chain 'Y' and resid 180 through 187 Processing helix chain 'Y' and resid 305 through 329 removed outlier: 5.392A pdb=" N GLY Y 312 " --> pdb=" O GLU Y 308 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N ALA Y 313 " --> pdb=" O ARG Y 309 " (cutoff:3.500A) Processing helix chain 'Y' and resid 350 through 359 Processing helix chain 'Z' and resid 127 through 150 removed outlier: 4.217A pdb=" N GLN Z 131 " --> pdb=" O TYR Z 127 " (cutoff:3.500A) Processing helix chain 'Z' and resid 166 through 169 Processing helix chain 'b' and resid 136 through 148 Processing helix chain 'b' and resid 305 through 329 removed outlier: 5.405A pdb=" N GLY b 312 " --> pdb=" O GLU b 308 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N ALA b 313 " --> pdb=" O ARG b 309 " (cutoff:3.500A) Processing helix chain 'b' and resid 350 through 359 Processing helix chain 'c' and resid 127 through 151 removed outlier: 4.247A pdb=" N ARG c 151 " --> pdb=" O ALA c 147 " (cutoff:3.500A) Processing helix chain 'c' and resid 166 through 169 Processing helix chain 'e' and resid 136 through 148 Processing helix chain 'e' and resid 180 through 187 Processing helix chain 'e' and resid 305 through 329 removed outlier: 5.499A pdb=" N GLY e 312 " --> pdb=" O GLU e 308 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N ALA e 313 " --> pdb=" O ARG e 309 " (cutoff:3.500A) Processing helix chain 'e' and resid 350 through 359 removed outlier: 3.672A pdb=" N ASN e 357 " --> pdb=" O GLU e 353 " (cutoff:3.500A) Processing helix chain 'f' and resid 127 through 151 removed outlier: 3.619A pdb=" N GLN f 131 " --> pdb=" O TYR f 127 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ARG f 151 " --> pdb=" O ALA f 147 " (cutoff:3.500A) Processing helix chain 'f' and resid 166 through 169 Processing helix chain 'g' and resid 39 through 43 removed outlier: 3.536A pdb=" N ILE g 42 " --> pdb=" O PRO g 39 " (cutoff:3.500A) Processing helix chain 'h' and resid 136 through 148 Processing helix chain 'h' and resid 180 through 187 Processing helix chain 'h' and resid 305 through 329 removed outlier: 5.404A pdb=" N GLY h 312 " --> pdb=" O GLU h 308 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N ALA h 313 " --> pdb=" O ARG h 309 " (cutoff:3.500A) Processing helix chain 'h' and resid 350 through 359 Processing helix chain 'i' and resid 127 through 151 removed outlier: 3.556A pdb=" N GLN i 131 " --> pdb=" O TYR i 127 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ARG i 151 " --> pdb=" O ALA i 147 " (cutoff:3.500A) Processing helix chain 'i' and resid 166 through 169 Processing helix chain 'k' and resid 136 through 148 Processing helix chain 'k' and resid 180 through 187 removed outlier: 3.510A pdb=" N GLU k 185 " --> pdb=" O GLY k 181 " (cutoff:3.500A) Processing helix chain 'k' and resid 305 through 329 removed outlier: 5.694A pdb=" N GLY k 312 " --> pdb=" O GLU k 308 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N ALA k 313 " --> pdb=" O ARG k 309 " (cutoff:3.500A) Processing helix chain 'k' and resid 350 through 359 removed outlier: 3.559A pdb=" N ASN k 357 " --> pdb=" O GLU k 353 " (cutoff:3.500A) Processing helix chain 'l' and resid 127 through 151 removed outlier: 3.854A pdb=" N ARG l 151 " --> pdb=" O ALA l 147 " (cutoff:3.500A) Processing helix chain 'l' and resid 166 through 169 Processing helix chain 'm' and resid 39 through 43 removed outlier: 3.530A pdb=" N ILE m 42 " --> pdb=" O PRO m 39 " (cutoff:3.500A) Processing helix chain 'n' and resid 136 through 148 Processing helix chain 'n' and resid 180 through 186 Processing helix chain 'n' and resid 305 through 329 removed outlier: 5.446A pdb=" N GLY n 312 " --> pdb=" O GLU n 308 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N ALA n 313 " --> pdb=" O ARG n 309 " (cutoff:3.500A) Processing helix chain 'n' and resid 350 through 359 Processing helix chain 'o' and resid 127 through 151 removed outlier: 3.952A pdb=" N ARG o 151 " --> pdb=" O ALA o 147 " (cutoff:3.500A) Processing helix chain 'o' and resid 166 through 169 Processing helix chain 'p' and resid 39 through 43 removed outlier: 3.544A pdb=" N ILE p 42 " --> pdb=" O PRO p 39 " (cutoff:3.500A) Processing helix chain 'u' and resid 136 through 148 Processing helix chain 'y' and resid 136 through 148 Processing sheet with id=AA1, first strand: chain 'A' and resid 195 through 196 removed outlier: 6.646A pdb=" N SER A 195 " --> pdb=" O ASP D 382 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 198 through 199 removed outlier: 3.531A pdb=" N VAL D 282 " --> pdb=" O GLY A 198 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N VAL D 270 " --> pdb=" O GLY D 289 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 198 through 199 removed outlier: 3.531A pdb=" N VAL D 282 " --> pdb=" O GLY A 198 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL D 254 " --> pdb=" O SER D 273 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ILE D 275 " --> pdb=" O LYS D 252 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N LYS D 252 " --> pdb=" O ILE D 275 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLY D 227 " --> pdb=" O TYR D 257 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 206 through 207 Processing sheet with id=AA5, first strand: chain 'n' and resid 198 through 199 removed outlier: 3.547A pdb=" N VAL A 282 " --> pdb=" O GLY n 198 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N VAL A 270 " --> pdb=" O GLY A 289 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLY A 255 " --> pdb=" O THR A 229 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N LYS A 252 " --> pdb=" O ILE A 275 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ILE A 275 " --> pdb=" O LYS A 252 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N VAL A 254 " --> pdb=" O SER A 273 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 221 through 222 Processing sheet with id=AA7, first strand: chain 'A' and resid 237 through 238 Processing sheet with id=AA8, first strand: chain 'A' and resid 387 through 391 Processing sheet with id=AA9, first strand: chain 'B' and resid 25 through 26 removed outlier: 6.515A pdb=" N HIS B 55 " --> pdb=" O LEU B 123 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N PHE B 125 " --> pdb=" O HIS B 55 " (cutoff:3.500A) removed outlier: 8.252A pdb=" N MET B 57 " --> pdb=" O PHE B 125 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 44 through 49 removed outlier: 6.990A pdb=" N VAL B 44 " --> pdb=" O ARG B 109 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N GLN B 111 " --> pdb=" O VAL B 44 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N VAL B 46 " --> pdb=" O GLN B 111 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N ARG B 113 " --> pdb=" O VAL B 46 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N THR B 48 " --> pdb=" O ARG B 113 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 64 through 69 Processing sheet with id=AB3, first strand: chain 'B' and resid 202 through 204 removed outlier: 4.619A pdb=" N LYS B 225 " --> pdb=" O VAL B 196 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 172 through 175 Processing sheet with id=AB5, first strand: chain 'B' and resid 258 through 262 Processing sheet with id=AB6, first strand: chain 'D' and resid 195 through 196 removed outlier: 6.793A pdb=" N SER D 195 " --> pdb=" O ASP G 382 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 198 through 199 removed outlier: 4.652A pdb=" N VAL G 270 " --> pdb=" O GLY G 289 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N LYS G 252 " --> pdb=" O ILE G 275 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N ILE G 275 " --> pdb=" O LYS G 252 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N VAL G 254 " --> pdb=" O SER G 273 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 221 through 222 Processing sheet with id=AB9, first strand: chain 'D' and resid 237 through 238 Processing sheet with id=AC1, first strand: chain 'D' and resid 387 through 391 Processing sheet with id=AC2, first strand: chain 'E' and resid 25 through 26 removed outlier: 6.369A pdb=" N HIS E 55 " --> pdb=" O LEU E 123 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N PHE E 125 " --> pdb=" O HIS E 55 " (cutoff:3.500A) removed outlier: 8.301A pdb=" N MET E 57 " --> pdb=" O PHE E 125 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 44 through 48 Processing sheet with id=AC4, first strand: chain 'E' and resid 202 through 204 removed outlier: 4.636A pdb=" N LYS E 225 " --> pdb=" O VAL E 196 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ARG E 233 " --> pdb=" O LEU E 230 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 172 through 175 Processing sheet with id=AC6, first strand: chain 'G' and resid 195 through 196 removed outlier: 6.526A pdb=" N SER G 195 " --> pdb=" O ASP J 382 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 198 through 199 removed outlier: 4.614A pdb=" N VAL J 270 " --> pdb=" O GLY J 289 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY J 255 " --> pdb=" O THR J 229 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N LYS J 252 " --> pdb=" O ILE J 275 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ILE J 275 " --> pdb=" O LYS J 252 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N VAL J 254 " --> pdb=" O SER J 273 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 221 through 222 Processing sheet with id=AC9, first strand: chain 'G' and resid 237 through 238 Processing sheet with id=AD1, first strand: chain 'G' and resid 387 through 391 Processing sheet with id=AD2, first strand: chain 'H' and resid 25 through 26 removed outlier: 6.387A pdb=" N HIS H 55 " --> pdb=" O LEU H 123 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N PHE H 125 " --> pdb=" O HIS H 55 " (cutoff:3.500A) removed outlier: 8.149A pdb=" N MET H 57 " --> pdb=" O PHE H 125 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 44 through 49 removed outlier: 6.553A pdb=" N VAL H 44 " --> pdb=" O ARG H 109 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N GLN H 111 " --> pdb=" O VAL H 44 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N VAL H 46 " --> pdb=" O GLN H 111 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ARG H 113 " --> pdb=" O VAL H 46 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N THR H 48 " --> pdb=" O ARG H 113 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU H 97 " --> pdb=" O PHE H 108 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 64 through 66 removed outlier: 7.177A pdb=" N VAL H 100 " --> pdb=" O LEU H 65 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 202 through 204 removed outlier: 3.589A pdb=" N VAL H 196 " --> pdb=" O LYS H 225 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N LYS H 225 " --> pdb=" O VAL H 196 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 172 through 175 Processing sheet with id=AD7, first strand: chain 'J' and resid 195 through 196 removed outlier: 6.638A pdb=" N SER J 195 " --> pdb=" O ASP M 382 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'J' and resid 198 through 199 removed outlier: 4.589A pdb=" N VAL M 270 " --> pdb=" O GLY M 289 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY M 255 " --> pdb=" O THR M 229 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N LYS M 252 " --> pdb=" O ILE M 275 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ILE M 275 " --> pdb=" O LYS M 252 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N VAL M 254 " --> pdb=" O SER M 273 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 221 through 222 Processing sheet with id=AE1, first strand: chain 'J' and resid 237 through 238 Processing sheet with id=AE2, first strand: chain 'J' and resid 387 through 391 removed outlier: 3.677A pdb=" N GLU J 390 " --> pdb=" O ARG N 259 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'K' and resid 25 through 26 removed outlier: 6.689A pdb=" N HIS K 55 " --> pdb=" O LEU K 123 " (cutoff:3.500A) removed outlier: 8.229A pdb=" N PHE K 125 " --> pdb=" O HIS K 55 " (cutoff:3.500A) removed outlier: 8.558A pdb=" N MET K 57 " --> pdb=" O PHE K 125 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'K' and resid 44 through 48 removed outlier: 6.896A pdb=" N VAL K 44 " --> pdb=" O ARG K 109 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N GLN K 111 " --> pdb=" O VAL K 44 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N VAL K 46 " --> pdb=" O GLN K 111 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'K' and resid 202 through 203 removed outlier: 3.523A pdb=" N VAL K 196 " --> pdb=" O LYS K 225 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N LYS K 225 " --> pdb=" O VAL K 196 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'K' and resid 172 through 175 Processing sheet with id=AE7, first strand: chain 'M' and resid 195 through 196 removed outlier: 6.823A pdb=" N SER M 195 " --> pdb=" O ASP P 382 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'M' and resid 198 through 199 removed outlier: 4.647A pdb=" N VAL P 270 " --> pdb=" O GLY P 289 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY P 255 " --> pdb=" O THR P 229 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N LYS P 252 " --> pdb=" O ILE P 275 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ILE P 275 " --> pdb=" O LYS P 252 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N VAL P 254 " --> pdb=" O SER P 273 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'M' and resid 221 through 222 Processing sheet with id=AF1, first strand: chain 'M' and resid 237 through 238 Processing sheet with id=AF2, first strand: chain 'M' and resid 267 through 268 Processing sheet with id=AF3, first strand: chain 'M' and resid 387 through 391 Processing sheet with id=AF4, first strand: chain 'N' and resid 25 through 26 removed outlier: 7.089A pdb=" N ARG N 34 " --> pdb=" O ALA N 124 " (cutoff:3.500A) removed outlier: 8.188A pdb=" N ARG N 126 " --> pdb=" O ARG N 34 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N VAL N 36 " --> pdb=" O ARG N 126 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N HIS N 55 " --> pdb=" O LEU N 123 " (cutoff:3.500A) removed outlier: 8.462A pdb=" N PHE N 125 " --> pdb=" O HIS N 55 " (cutoff:3.500A) removed outlier: 8.925A pdb=" N MET N 57 " --> pdb=" O PHE N 125 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'N' and resid 44 through 48 removed outlier: 6.479A pdb=" N VAL N 44 " --> pdb=" O ARG N 109 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N GLN N 111 " --> pdb=" O VAL N 44 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N VAL N 46 " --> pdb=" O GLN N 111 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR N 66 " --> pdb=" O VAL N 100 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'N' and resid 202 through 204 removed outlier: 4.472A pdb=" N LYS N 225 " --> pdb=" O VAL N 196 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'N' and resid 172 through 175 Processing sheet with id=AF8, first strand: chain 'P' and resid 195 through 196 removed outlier: 6.706A pdb=" N SER P 195 " --> pdb=" O ASP S 382 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'P' and resid 198 through 199 removed outlier: 3.563A pdb=" N VAL S 282 " --> pdb=" O GLY P 198 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N VAL S 270 " --> pdb=" O GLY S 289 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N LYS S 252 " --> pdb=" O ILE S 275 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N ILE S 275 " --> pdb=" O LYS S 252 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N VAL S 254 " --> pdb=" O SER S 273 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'P' and resid 221 through 222 Processing sheet with id=AG2, first strand: chain 'P' and resid 237 through 238 removed outlier: 6.746A pdb=" N VAL P 237 " --> pdb=" O LEU P 246 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'P' and resid 267 through 268 Processing sheet with id=AG4, first strand: chain 'P' and resid 387 through 391 Processing sheet with id=AG5, first strand: chain 'Q' and resid 25 through 26 removed outlier: 3.630A pdb=" N ARG Q 34 " --> pdb=" O GLU Q 122 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N PHE Q 125 " --> pdb=" O MET Q 57 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'Q' and resid 47 through 48 removed outlier: 6.873A pdb=" N THR Q 48 " --> pdb=" O ARG Q 109 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N GLN Q 111 " --> pdb=" O THR Q 48 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR Q 95 " --> pdb=" O LEU Q 110 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'Q' and resid 64 through 66 Processing sheet with id=AG8, first strand: chain 'Q' and resid 202 through 204 removed outlier: 3.615A pdb=" N VAL Q 196 " --> pdb=" O LYS Q 225 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N LYS Q 225 " --> pdb=" O VAL Q 196 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'Q' and resid 172 through 175 Processing sheet with id=AH1, first strand: chain 'S' and resid 195 through 196 removed outlier: 6.607A pdb=" N SER S 195 " --> pdb=" O ASP V 382 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'S' and resid 221 through 222 Processing sheet with id=AH3, first strand: chain 'S' and resid 237 through 238 Processing sheet with id=AH4, first strand: chain 'S' and resid 267 through 268 Processing sheet with id=AH5, first strand: chain 'S' and resid 388 through 391 Processing sheet with id=AH6, first strand: chain 'T' and resid 25 through 26 removed outlier: 4.113A pdb=" N ARG T 34 " --> pdb=" O GLU T 122 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA T 124 " --> pdb=" O ARG T 34 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N HIS T 55 " --> pdb=" O LEU T 123 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N PHE T 125 " --> pdb=" O HIS T 55 " (cutoff:3.500A) removed outlier: 8.443A pdb=" N MET T 57 " --> pdb=" O PHE T 125 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'T' and resid 44 through 48 removed outlier: 6.499A pdb=" N VAL T 44 " --> pdb=" O ARG T 109 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N GLN T 111 " --> pdb=" O VAL T 44 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N VAL T 46 " --> pdb=" O GLN T 111 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH7 Processing sheet with id=AH8, first strand: chain 'T' and resid 64 through 69 Processing sheet with id=AH9, first strand: chain 'T' and resid 202 through 203 removed outlier: 3.525A pdb=" N VAL T 196 " --> pdb=" O LYS T 225 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N LYS T 225 " --> pdb=" O VAL T 196 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'T' and resid 172 through 175 Processing sheet with id=AI2, first strand: chain 'V' and resid 195 through 196 removed outlier: 6.805A pdb=" N SER V 195 " --> pdb=" O ASP Y 382 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'V' and resid 198 through 199 removed outlier: 3.529A pdb=" N VAL Y 282 " --> pdb=" O GLY V 198 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N VAL Y 270 " --> pdb=" O GLY Y 289 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLY Y 255 " --> pdb=" O THR Y 229 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N LYS Y 252 " --> pdb=" O ILE Y 275 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ILE Y 275 " --> pdb=" O LYS Y 252 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N VAL Y 254 " --> pdb=" O SER Y 273 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'V' and resid 282 through 283 removed outlier: 4.571A pdb=" N VAL V 270 " --> pdb=" O GLY V 289 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N LYS V 252 " --> pdb=" O ILE V 275 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ILE V 275 " --> pdb=" O LYS V 252 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N VAL V 254 " --> pdb=" O SER V 273 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'V' and resid 221 through 222 Processing sheet with id=AI6, first strand: chain 'V' and resid 237 through 238 Processing sheet with id=AI7, first strand: chain 'V' and resid 267 through 268 Processing sheet with id=AI8, first strand: chain 'V' and resid 387 through 391 Processing sheet with id=AI9, first strand: chain 'W' and resid 25 through 26 removed outlier: 6.397A pdb=" N HIS W 55 " --> pdb=" O LEU W 123 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N PHE W 125 " --> pdb=" O HIS W 55 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N MET W 57 " --> pdb=" O PHE W 125 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'W' and resid 44 through 49 removed outlier: 6.653A pdb=" N VAL W 44 " --> pdb=" O ARG W 109 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N GLN W 111 " --> pdb=" O VAL W 44 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N VAL W 46 " --> pdb=" O GLN W 111 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N ARG W 113 " --> pdb=" O VAL W 46 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N THR W 48 " --> pdb=" O ARG W 113 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'W' and resid 202 through 203 removed outlier: 3.603A pdb=" N VAL W 196 " --> pdb=" O LYS W 225 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N LYS W 225 " --> pdb=" O VAL W 196 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'W' and resid 172 through 175 Processing sheet with id=AJ4, first strand: chain 'Y' and resid 195 through 196 removed outlier: 6.786A pdb=" N SER Y 195 " --> pdb=" O ASP b 382 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'Y' and resid 221 through 222 Processing sheet with id=AJ6, first strand: chain 'Y' and resid 237 through 238 Processing sheet with id=AJ7, first strand: chain 'Y' and resid 387 through 391 Processing sheet with id=AJ8, first strand: chain 'Z' and resid 25 through 26 removed outlier: 6.588A pdb=" N HIS Z 55 " --> pdb=" O LEU Z 123 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N PHE Z 125 " --> pdb=" O HIS Z 55 " (cutoff:3.500A) removed outlier: 8.511A pdb=" N MET Z 57 " --> pdb=" O PHE Z 125 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'Z' and resid 44 through 48 removed outlier: 6.495A pdb=" N VAL Z 44 " --> pdb=" O ARG Z 109 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N GLN Z 111 " --> pdb=" O VAL Z 44 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N VAL Z 46 " --> pdb=" O GLN Z 111 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'Z' and resid 202 through 204 removed outlier: 4.671A pdb=" N LYS Z 225 " --> pdb=" O VAL Z 196 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'Z' and resid 172 through 175 Processing sheet with id=AK3, first strand: chain 'b' and resid 195 through 196 removed outlier: 6.912A pdb=" N SER b 195 " --> pdb=" O ASP e 382 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'b' and resid 198 through 199 removed outlier: 3.539A pdb=" N VAL e 282 " --> pdb=" O GLY b 198 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N VAL e 270 " --> pdb=" O GLY e 289 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N LYS e 252 " --> pdb=" O ILE e 275 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ILE e 275 " --> pdb=" O LYS e 252 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N VAL e 254 " --> pdb=" O SER e 273 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'b' and resid 282 through 283 removed outlier: 4.636A pdb=" N VAL b 270 " --> pdb=" O GLY b 289 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLY b 227 " --> pdb=" O TYR b 257 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY b 255 " --> pdb=" O THR b 229 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N LYS b 252 " --> pdb=" O ILE b 275 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ILE b 275 " --> pdb=" O LYS b 252 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N VAL b 254 " --> pdb=" O SER b 273 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'b' and resid 221 through 222 Processing sheet with id=AK7, first strand: chain 'b' and resid 237 through 238 removed outlier: 6.827A pdb=" N VAL b 237 " --> pdb=" O LEU b 246 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'b' and resid 387 through 391 Processing sheet with id=AK9, first strand: chain 'c' and resid 25 through 26 removed outlier: 6.674A pdb=" N HIS c 55 " --> pdb=" O LEU c 123 " (cutoff:3.500A) removed outlier: 8.153A pdb=" N PHE c 125 " --> pdb=" O HIS c 55 " (cutoff:3.500A) removed outlier: 8.614A pdb=" N MET c 57 " --> pdb=" O PHE c 125 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'c' and resid 44 through 48 removed outlier: 6.848A pdb=" N VAL c 44 " --> pdb=" O ARG c 109 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N GLN c 111 " --> pdb=" O VAL c 44 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N VAL c 46 " --> pdb=" O GLN c 111 " (cutoff:3.500A) Processing sheet with id=AL2, first strand: chain 'c' and resid 64 through 66 removed outlier: 3.511A pdb=" N THR c 66 " --> pdb=" O VAL c 100 " (cutoff:3.500A) Processing sheet with id=AL3, first strand: chain 'c' and resid 202 through 204 removed outlier: 4.520A pdb=" N LYS c 225 " --> pdb=" O VAL c 196 " (cutoff:3.500A) Processing sheet with id=AL4, first strand: chain 'c' and resid 172 through 175 Processing sheet with id=AL5, first strand: chain 'e' and resid 195 through 196 removed outlier: 6.711A pdb=" N SER e 195 " --> pdb=" O ASP h 382 " (cutoff:3.500A) Processing sheet with id=AL6, first strand: chain 'e' and resid 198 through 199 removed outlier: 4.572A pdb=" N VAL h 270 " --> pdb=" O GLY h 289 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLY h 255 " --> pdb=" O THR h 229 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N LYS h 252 " --> pdb=" O ILE h 275 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ILE h 275 " --> pdb=" O LYS h 252 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N VAL h 254 " --> pdb=" O SER h 273 " (cutoff:3.500A) Processing sheet with id=AL7, first strand: chain 'e' and resid 221 through 222 Processing sheet with id=AL8, first strand: chain 'e' and resid 237 through 238 Processing sheet with id=AL9, first strand: chain 'e' and resid 387 through 391 Processing sheet with id=AM1, first strand: chain 'f' and resid 25 through 26 removed outlier: 6.755A pdb=" N ARG f 34 " --> pdb=" O ALA f 124 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N ARG f 126 " --> pdb=" O ARG f 34 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N VAL f 36 " --> pdb=" O ARG f 126 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N HIS f 55 " --> pdb=" O LEU f 123 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N PHE f 125 " --> pdb=" O HIS f 55 " (cutoff:3.500A) removed outlier: 8.410A pdb=" N MET f 57 " --> pdb=" O PHE f 125 " (cutoff:3.500A) Processing sheet with id=AM2, first strand: chain 'f' and resid 44 through 49 removed outlier: 7.034A pdb=" N VAL f 44 " --> pdb=" O ARG f 109 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N GLN f 111 " --> pdb=" O VAL f 44 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N VAL f 46 " --> pdb=" O GLN f 111 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N ARG f 113 " --> pdb=" O VAL f 46 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N THR f 48 " --> pdb=" O ARG f 113 " (cutoff:3.500A) Processing sheet with id=AM3, first strand: chain 'f' and resid 202 through 204 removed outlier: 3.516A pdb=" N VAL f 196 " --> pdb=" O LYS f 225 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N LYS f 225 " --> pdb=" O VAL f 196 " (cutoff:3.500A) Processing sheet with id=AM4, first strand: chain 'f' and resid 172 through 175 Processing sheet with id=AM5, first strand: chain 'h' and resid 195 through 196 removed outlier: 6.955A pdb=" N SER h 195 " --> pdb=" O ASP k 382 " (cutoff:3.500A) Processing sheet with id=AM6, first strand: chain 'h' and resid 198 through 199 removed outlier: 4.621A pdb=" N VAL k 270 " --> pdb=" O GLY k 289 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N LYS k 252 " --> pdb=" O ILE k 275 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ILE k 275 " --> pdb=" O LYS k 252 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N VAL k 254 " --> pdb=" O SER k 273 " (cutoff:3.500A) Processing sheet with id=AM7, first strand: chain 'h' and resid 221 through 222 Processing sheet with id=AM8, first strand: chain 'h' and resid 237 through 238 Processing sheet with id=AM9, first strand: chain 'h' and resid 267 through 268 Processing sheet with id=AN1, first strand: chain 'h' and resid 387 through 391 Processing sheet with id=AN2, first strand: chain 'i' and resid 25 through 26 removed outlier: 3.839A pdb=" N ARG i 34 " --> pdb=" O GLU i 122 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA i 124 " --> pdb=" O ARG i 34 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N HIS i 55 " --> pdb=" O LEU i 123 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N PHE i 125 " --> pdb=" O HIS i 55 " (cutoff:3.500A) removed outlier: 8.277A pdb=" N MET i 57 " --> pdb=" O PHE i 125 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE i 86 " --> pdb=" O THR i 54 " (cutoff:3.500A) Processing sheet with id=AN3, first strand: chain 'i' and resid 44 through 48 removed outlier: 3.713A pdb=" N VAL i 46 " --> pdb=" O ARG i 109 " (cutoff:3.500A) Processing sheet with id=AN4, first strand: chain 'i' and resid 202 through 204 removed outlier: 3.556A pdb=" N VAL i 196 " --> pdb=" O LYS i 225 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LYS i 225 " --> pdb=" O VAL i 196 " (cutoff:3.500A) Processing sheet with id=AN5, first strand: chain 'i' and resid 172 through 175 Processing sheet with id=AN6, first strand: chain 'k' and resid 195 through 196 removed outlier: 6.908A pdb=" N SER k 195 " --> pdb=" O ASP n 382 " (cutoff:3.500A) Processing sheet with id=AN7, first strand: chain 'k' and resid 198 through 199 removed outlier: 4.675A pdb=" N VAL n 270 " --> pdb=" O GLY n 289 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLY n 227 " --> pdb=" O TYR n 257 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N LYS n 252 " --> pdb=" O ILE n 275 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ILE n 275 " --> pdb=" O LYS n 252 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL n 254 " --> pdb=" O SER n 273 " (cutoff:3.500A) Processing sheet with id=AN8, first strand: chain 'k' and resid 221 through 222 Processing sheet with id=AN9, first strand: chain 'k' and resid 237 through 238 Processing sheet with id=AO1, first strand: chain 'k' and resid 267 through 268 Processing sheet with id=AO2, first strand: chain 'k' and resid 387 through 391 Processing sheet with id=AO3, first strand: chain 'l' and resid 25 through 26 removed outlier: 6.726A pdb=" N HIS l 55 " --> pdb=" O LEU l 123 " (cutoff:3.500A) removed outlier: 8.542A pdb=" N PHE l 125 " --> pdb=" O HIS l 55 " (cutoff:3.500A) removed outlier: 8.883A pdb=" N MET l 57 " --> pdb=" O PHE l 125 " (cutoff:3.500A) Processing sheet with id=AO4, first strand: chain 'l' and resid 44 through 48 removed outlier: 6.770A pdb=" N VAL l 44 " --> pdb=" O ARG l 109 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N GLN l 111 " --> pdb=" O VAL l 44 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N VAL l 46 " --> pdb=" O GLN l 111 " (cutoff:3.500A) Processing sheet with id=AO5, first strand: chain 'l' and resid 202 through 204 removed outlier: 4.562A pdb=" N LYS l 225 " --> pdb=" O VAL l 196 " (cutoff:3.500A) Processing sheet with id=AO6, first strand: chain 'l' and resid 172 through 175 Processing sheet with id=AO7, first strand: chain 'n' and resid 221 through 222 Processing sheet with id=AO8, first strand: chain 'n' and resid 237 through 238 Processing sheet with id=AO9, first strand: chain 'n' and resid 267 through 268 Processing sheet with id=AP1, first strand: chain 'o' and resid 25 through 26 removed outlier: 3.593A pdb=" N ARG o 34 " --> pdb=" O GLU o 122 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA o 124 " --> pdb=" O ARG o 34 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N HIS o 55 " --> pdb=" O LEU o 123 " (cutoff:3.500A) removed outlier: 8.162A pdb=" N PHE o 125 " --> pdb=" O HIS o 55 " (cutoff:3.500A) removed outlier: 8.810A pdb=" N MET o 57 " --> pdb=" O PHE o 125 " (cutoff:3.500A) Processing sheet with id=AP2, first strand: chain 'o' and resid 44 through 49 removed outlier: 3.509A pdb=" N VAL o 46 " --> pdb=" O ARG o 109 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU o 97 " --> pdb=" O PHE o 108 " (cutoff:3.500A) Processing sheet with id=AP3, first strand: chain 'o' and resid 202 through 203 removed outlier: 4.585A pdb=" N LYS o 225 " --> pdb=" O VAL o 196 " (cutoff:3.500A) Processing sheet with id=AP4, first strand: chain 'o' and resid 172 through 175 Processing sheet with id=AP5, first strand: chain 'v' and resid 25 through 26 removed outlier: 6.422A pdb=" N HIS v 55 " --> pdb=" O LEU v 123 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N PHE v 125 " --> pdb=" O HIS v 55 " (cutoff:3.500A) removed outlier: 8.353A pdb=" N MET v 57 " --> pdb=" O PHE v 125 " (cutoff:3.500A) Processing sheet with id=AP6, first strand: chain 'v' and resid 44 through 48 removed outlier: 6.921A pdb=" N VAL v 44 " --> pdb=" O ARG v 109 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N GLN v 111 " --> pdb=" O VAL v 44 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N VAL v 46 " --> pdb=" O GLN v 111 " (cutoff:3.500A) Processing sheet with id=AP7, first strand: chain 'z' and resid 25 through 26 removed outlier: 6.293A pdb=" N HIS z 55 " --> pdb=" O LEU z 123 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N PHE z 125 " --> pdb=" O HIS z 55 " (cutoff:3.500A) removed outlier: 8.307A pdb=" N MET z 57 " --> pdb=" O PHE z 125 " (cutoff:3.500A) Processing sheet with id=AP8, first strand: chain 'z' and resid 45 through 48 removed outlier: 6.394A pdb=" N VAL z 46 " --> pdb=" O GLN z 111 " (cutoff:3.500A) No H-bonds generated for sheet with id=AP8 Processing sheet with id=AP9, first strand: chain 'z' and resid 64 through 66 2125 hydrogen bonds defined for protein. 5529 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: 24.00 Time building geometry restraints manager: 17.14 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: 18747 1.33 - 1.45: 9203 1.45 - 1.57: 28575 1.57 - 1.69: 3 1.69 - 1.81: 366 Bond restraints: 56894 Sorted by residual: bond pdb=" C GLU M 276 " pdb=" N THR M 277 " ideal model delta sigma weight residual 1.330 1.276 0.054 1.47e-02 4.63e+03 1.33e+01 bond pdb=" C GLU S 276 " pdb=" N THR S 277 " ideal model delta sigma weight residual 1.330 1.283 0.047 1.37e-02 5.33e+03 1.17e+01 bond pdb=" C LYS d 24 " pdb=" N GLN d 25 " ideal model delta sigma weight residual 1.333 1.279 0.054 1.61e-02 3.86e+03 1.13e+01 bond pdb=" C GLU J 276 " pdb=" N THR J 277 " ideal model delta sigma weight residual 1.330 1.281 0.049 1.47e-02 4.63e+03 1.12e+01 bond pdb=" C GLU e 276 " pdb=" N THR e 277 " ideal model delta sigma weight residual 1.330 1.285 0.046 1.37e-02 5.33e+03 1.11e+01 ... (remaining 56889 not shown) Histogram of bond angle deviations from ideal: 95.96 - 103.60: 881 103.60 - 111.23: 22752 111.23 - 118.86: 21515 118.86 - 126.50: 31110 126.50 - 134.13: 778 Bond angle restraints: 77036 Sorted by residual: angle pdb=" O GLN a 43 " pdb=" C GLN a 43 " pdb=" N ARG a 44 " ideal model delta sigma weight residual 122.91 96.21 26.70 1.19e+00 7.06e-01 5.04e+02 angle pdb=" O GLN U 43 " pdb=" C GLN U 43 " pdb=" N ARG U 44 " ideal model delta sigma weight residual 122.67 97.73 24.94 1.13e+00 7.83e-01 4.87e+02 angle pdb=" O GLN I 43 " pdb=" C GLN I 43 " pdb=" N ARG I 44 " ideal model delta sigma weight residual 122.58 98.45 24.13 1.20e+00 6.94e-01 4.04e+02 angle pdb=" O GLN j 43 " pdb=" C GLN j 43 " pdb=" N ARG j 44 " ideal model delta sigma weight residual 122.41 96.63 25.78 1.34e+00 5.57e-01 3.70e+02 angle pdb=" O GLN C 43 " pdb=" C GLN C 43 " pdb=" N ARG C 44 " ideal model delta sigma weight residual 122.91 101.39 21.52 1.19e+00 7.06e-01 3.27e+02 ... (remaining 77031 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 31031 17.97 - 35.94: 2578 35.94 - 53.90: 490 53.90 - 71.87: 74 71.87 - 89.84: 17 Dihedral angle restraints: 34190 sinusoidal: 13744 harmonic: 20446 Sorted by residual: dihedral pdb=" CA MET W 57 " pdb=" C MET W 57 " pdb=" N LEU W 58 " pdb=" CA LEU W 58 " ideal model delta harmonic sigma weight residual 180.00 153.26 26.74 0 5.00e+00 4.00e-02 2.86e+01 dihedral pdb=" CA VAL B 152 " pdb=" C VAL B 152 " pdb=" N GLY B 153 " pdb=" CA GLY B 153 " ideal model delta harmonic sigma weight residual 180.00 154.21 25.79 0 5.00e+00 4.00e-02 2.66e+01 dihedral pdb=" CA PHE B 69 " pdb=" C PHE B 69 " pdb=" N GLY B 70 " pdb=" CA GLY B 70 " ideal model delta harmonic sigma weight residual 180.00 155.75 24.25 0 5.00e+00 4.00e-02 2.35e+01 ... (remaining 34187 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 5935 0.053 - 0.105: 1980 0.105 - 0.158: 446 0.158 - 0.210: 5 0.210 - 0.263: 4 Chirality restraints: 8370 Sorted by residual: chirality pdb=" CB ILE N 98 " pdb=" CA ILE N 98 " pdb=" CG1 ILE N 98 " pdb=" CG2 ILE N 98 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" CB ILE K 98 " pdb=" CA ILE K 98 " pdb=" CG1 ILE K 98 " pdb=" CG2 ILE K 98 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" CB THR E 66 " pdb=" CA THR E 66 " pdb=" OG1 THR E 66 " pdb=" CG2 THR E 66 " both_signs ideal model delta sigma weight residual False 2.55 2.31 0.24 2.00e-01 2.50e+01 1.45e+00 ... (remaining 8367 not shown) Planarity restraints: 10228 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN j 43 " -0.106 2.00e-02 2.50e+03 1.82e-01 3.33e+02 pdb=" C GLN j 43 " 0.316 2.00e-02 2.50e+03 pdb=" O GLN j 43 " -0.114 2.00e-02 2.50e+03 pdb=" N ARG j 44 " -0.096 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN a 43 " 0.106 2.00e-02 2.50e+03 1.82e-01 3.31e+02 pdb=" C GLN a 43 " -0.315 2.00e-02 2.50e+03 pdb=" O GLN a 43 " 0.114 2.00e-02 2.50e+03 pdb=" N ARG a 44 " 0.095 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN U 43 " 0.101 2.00e-02 2.50e+03 1.76e-01 3.08e+02 pdb=" C GLN U 43 " -0.304 2.00e-02 2.50e+03 pdb=" O GLN U 43 " 0.110 2.00e-02 2.50e+03 pdb=" N ARG U 44 " 0.092 2.00e-02 2.50e+03 ... (remaining 10225 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 733 2.63 - 3.20: 47966 3.20 - 3.77: 83619 3.77 - 4.33: 123507 4.33 - 4.90: 211846 Nonbonded interactions: 467671 Sorted by model distance: nonbonded pdb=" OH TYR H 106 " pdb=" OH TYR H 127 " model vdw 2.066 2.440 nonbonded pdb=" OG SER D 148 " pdb=" OD1 ASP E 71 " model vdw 2.113 2.440 nonbonded pdb=" OG1 THR E 253 " pdb=" O VAL E 258 " model vdw 2.131 2.440 nonbonded pdb=" OE1 GLN T 45 " pdb=" NH2 ARG T 109 " model vdw 2.132 2.520 nonbonded pdb=" OE2 GLU c 62 " pdb=" OG1 THR c 101 " model vdw 2.137 2.440 ... (remaining 467666 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 'D' selection = chain 'G' selection = chain 'J' selection = chain 'M' selection = chain 'P' selection = chain 'S' selection = chain 'V' selection = chain 'Y' selection = chain 'b' selection = chain 'e' selection = chain 'h' selection = chain 'k' selection = chain 'n' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'H' selection = chain 'K' selection = chain 'N' selection = chain 'Q' selection = chain 'T' selection = chain 'W' selection = chain 'Z' selection = chain 'c' selection = chain 'f' selection = chain 'i' selection = chain 'l' selection = chain 'o' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'I' selection = chain 'L' selection = chain 'O' selection = chain 'R' selection = chain 'U' selection = chain 'X' selection = chain 'a' selection = chain 'd' selection = chain 'g' selection = chain 'j' selection = chain 'm' selection = chain 'p' } ncs_group { reference = chain 'u' selection = chain 'y' } ncs_group { reference = chain 'v' selection = chain 'z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.030 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: 0.040 Extract box with map and model: 6.470 Check model and map are aligned: 0.320 Set scattering table: 0.410 Process input model: 111.850 Find NCS groups from input model: 3.090 Set up NCS constraints: 0.620 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:2.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 126.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7092 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 : 0.011 0.145 56894 Z= 0.693 Angle : 0.803 26.704 77036 Z= 0.477 Chirality : 0.052 0.263 8370 Planarity : 0.008 0.182 10228 Dihedral : 13.559 89.841 21096 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.03 % Favored : 96.96 % Rotamer: Outliers : 0.07 % Allowed : 0.44 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.09), residues: 7036 helix: 1.12 (0.15), residues: 1125 sheet: -0.62 (0.12), residues: 1936 loop : -0.93 (0.09), residues: 3975 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP h 325 HIS 0.007 0.002 HIS D 305 PHE 0.029 0.002 PHE T 148 TYR 0.037 0.002 TYR K 64 ARG 0.016 0.001 ARG Z 104 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14072 Ramachandran restraints generated. 7036 Oldfield, 0 Emsley, 7036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14072 Ramachandran restraints generated. 7036 Oldfield, 0 Emsley, 7036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 854 residues out of total 5886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 850 time to evaluate : 4.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 140 LEU cc_start: 0.8724 (mt) cc_final: 0.8502 (mt) REVERT: V 140 LEU cc_start: 0.8447 (mt) cc_final: 0.8237 (mt) outliers start: 4 outliers final: 0 residues processed: 854 average time/residue: 0.5789 time to fit residues: 798.5268 Evaluate side-chains 499 residues out of total 5886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 499 time to evaluate : 4.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 694 random chunks: chunk 586 optimal weight: 5.9990 chunk 526 optimal weight: 20.0000 chunk 291 optimal weight: 7.9990 chunk 179 optimal weight: 10.0000 chunk 354 optimal weight: 0.8980 chunk 281 optimal weight: 3.9990 chunk 543 optimal weight: 1.9990 chunk 210 optimal weight: 7.9990 chunk 330 optimal weight: 3.9990 chunk 404 optimal weight: 5.9990 chunk 630 optimal weight: 8.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 271 GLN G 271 GLN J 305 HIS K 31 HIS K 134 GLN K 201 ASN M 209 GLN M 271 GLN M 374 ASN P 271 GLN ** Q 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 271 GLN S 357 ASN ** T 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 201 ASN V 209 GLN W 89 GLN W 201 ASN Y 271 GLN b 209 GLN e 284 ASN f 45 GLN ** f 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 117 ASN h 209 GLN h 212 GLN h 263 GLN ** l 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 374 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7186 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 56894 Z= 0.245 Angle : 0.607 10.074 77036 Z= 0.319 Chirality : 0.044 0.196 8370 Planarity : 0.005 0.083 10228 Dihedral : 4.574 29.425 7996 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.83 % Favored : 98.15 % Rotamer: Outliers : 0.87 % Allowed : 7.84 % Favored : 91.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.10), residues: 7036 helix: 1.95 (0.16), residues: 1128 sheet: -0.39 (0.12), residues: 1878 loop : -0.51 (0.09), residues: 4030 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP h 325 HIS 0.005 0.001 HIS K 31 PHE 0.029 0.001 PHE l 195 TYR 0.022 0.001 TYR V 138 ARG 0.016 0.001 ARG B 82 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14072 Ramachandran restraints generated. 7036 Oldfield, 0 Emsley, 7036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14072 Ramachandran restraints generated. 7036 Oldfield, 0 Emsley, 7036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 633 residues out of total 5886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 582 time to evaluate : 4.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 112 MET cc_start: 0.7855 (tpp) cc_final: 0.7647 (tpp) REVERT: J 140 LEU cc_start: 0.8580 (mt) cc_final: 0.8115 (mm) REVERT: J 145 MET cc_start: 0.7962 (mtt) cc_final: 0.7737 (mmt) REVERT: S 145 MET cc_start: 0.7640 (ttm) cc_final: 0.7278 (ttp) REVERT: v 112 MET cc_start: 0.7355 (tpp) cc_final: 0.7147 (tpt) outliers start: 51 outliers final: 17 residues processed: 611 average time/residue: 0.5499 time to fit residues: 559.4438 Evaluate side-chains 477 residues out of total 5886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 460 time to evaluate : 4.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain J residue 390 GLU Chi-restraints excluded: chain P residue 385 ASP Chi-restraints excluded: chain Z residue 123 LEU Chi-restraints excluded: chain e residue 385 ASP Chi-restraints excluded: chain h residue 263 GLN Chi-restraints excluded: chain h residue 319 ILE Chi-restraints excluded: chain k residue 319 ILE Chi-restraints excluded: chain l residue 134 GLN Chi-restraints excluded: chain u residue 136 THR Chi-restraints excluded: chain v residue 23 VAL Chi-restraints excluded: chain v residue 102 ASP Chi-restraints excluded: chain v residue 107 LYS Chi-restraints excluded: chain z residue 21 LEU Chi-restraints excluded: chain z residue 30 ASP Chi-restraints excluded: chain z residue 102 ASP Chi-restraints excluded: chain z residue 107 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 694 random chunks: chunk 350 optimal weight: 10.0000 chunk 195 optimal weight: 2.9990 chunk 524 optimal weight: 0.8980 chunk 429 optimal weight: 10.0000 chunk 173 optimal weight: 20.0000 chunk 631 optimal weight: 5.9990 chunk 682 optimal weight: 8.9990 chunk 562 optimal weight: 3.9990 chunk 626 optimal weight: 8.9990 chunk 215 optimal weight: 5.9990 chunk 506 optimal weight: 7.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 172 ASN B 201 ASN D 209 GLN D 271 GLN ** E 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 209 GLN J 271 GLN M 271 GLN ** N 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 232 HIS ** T 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 134 GLN V 357 ASN Y 305 HIS ** Z 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 131 GLN f 45 GLN ** f 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 263 GLN h 271 GLN h 357 ASN ** i 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 56894 Z= 0.250 Angle : 0.579 10.157 77036 Z= 0.301 Chirality : 0.043 0.187 8370 Planarity : 0.004 0.064 10228 Dihedral : 4.295 28.518 7996 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.76 % Favored : 98.22 % Rotamer: Outliers : 1.26 % Allowed : 9.12 % Favored : 89.62 % 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: 0.16 (0.10), residues: 7036 helix: 2.20 (0.16), residues: 1132 sheet: -0.20 (0.12), residues: 1902 loop : -0.29 (0.09), residues: 4002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 307 HIS 0.006 0.001 HIS K 31 PHE 0.026 0.001 PHE l 195 TYR 0.019 0.001 TYR D 138 ARG 0.006 0.000 ARG B 82 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14072 Ramachandran restraints generated. 7036 Oldfield, 0 Emsley, 7036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14072 Ramachandran restraints generated. 7036 Oldfield, 0 Emsley, 7036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 564 residues out of total 5886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 490 time to evaluate : 4.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 66 THR cc_start: 0.8515 (OUTLIER) cc_final: 0.8199 (m) REVERT: G 135 LYS cc_start: 0.7883 (mmmt) cc_final: 0.7681 (tptp) REVERT: J 145 MET cc_start: 0.8015 (mtt) cc_final: 0.7762 (mmt) outliers start: 74 outliers final: 25 residues processed: 541 average time/residue: 0.5499 time to fit residues: 500.9090 Evaluate side-chains 464 residues out of total 5886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 438 time to evaluate : 4.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain M residue 136 THR Chi-restraints excluded: chain T residue 22 ASP Chi-restraints excluded: chain Y residue 228 MET Chi-restraints excluded: chain Z residue 123 LEU Chi-restraints excluded: chain c residue 22 ASP Chi-restraints excluded: chain e residue 385 ASP Chi-restraints excluded: chain f residue 152 VAL Chi-restraints excluded: chain h residue 319 ILE Chi-restraints excluded: chain i residue 23 VAL Chi-restraints excluded: chain i residue 99 VAL Chi-restraints excluded: chain k residue 319 ILE Chi-restraints excluded: chain l residue 134 GLN Chi-restraints excluded: chain n residue 376 LEU Chi-restraints excluded: chain o residue 23 VAL Chi-restraints excluded: chain o residue 99 VAL Chi-restraints excluded: chain u residue 136 THR Chi-restraints excluded: chain u residue 151 THR Chi-restraints excluded: chain v residue 23 VAL Chi-restraints excluded: chain v residue 35 TYR Chi-restraints excluded: chain v residue 102 ASP Chi-restraints excluded: chain v residue 107 LYS Chi-restraints excluded: chain z residue 30 ASP Chi-restraints excluded: chain z residue 102 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 694 random chunks: chunk 623 optimal weight: 0.8980 chunk 474 optimal weight: 9.9990 chunk 327 optimal weight: 8.9990 chunk 69 optimal weight: 4.9990 chunk 301 optimal weight: 10.0000 chunk 423 optimal weight: 8.9990 chunk 633 optimal weight: 10.0000 chunk 670 optimal weight: 0.9980 chunk 331 optimal weight: 5.9990 chunk 600 optimal weight: 9.9990 chunk 180 optimal weight: 2.9990 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 271 GLN ** H 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 271 GLN ** N 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 271 GLN ** T 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 262 ASN i 111 GLN ** l 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 131 GLN ** l 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7246 moved from start: 0.2726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 56894 Z= 0.208 Angle : 0.561 10.766 77036 Z= 0.287 Chirality : 0.043 0.255 8370 Planarity : 0.004 0.055 10228 Dihedral : 4.115 28.393 7996 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.75 % Favored : 98.24 % Rotamer: Outliers : 1.33 % Allowed : 10.52 % Favored : 88.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.10), residues: 7036 helix: 2.31 (0.16), residues: 1132 sheet: -0.03 (0.12), residues: 1886 loop : -0.19 (0.09), residues: 4018 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP V 307 HIS 0.008 0.001 HIS v 55 PHE 0.025 0.001 PHE l 195 TYR 0.021 0.001 TYR z 29 ARG 0.007 0.000 ARG y 147 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14072 Ramachandran restraints generated. 7036 Oldfield, 0 Emsley, 7036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14072 Ramachandran restraints generated. 7036 Oldfield, 0 Emsley, 7036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 560 residues out of total 5886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 482 time to evaluate : 4.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 162 MET cc_start: 0.6651 (ppp) cc_final: 0.5855 (ptt) REVERT: W 120 MET cc_start: 0.7183 (tpp) cc_final: 0.6869 (tpp) REVERT: o 112 MET cc_start: 0.7047 (tpp) cc_final: 0.6408 (tpp) REVERT: z 47 ASP cc_start: 0.7879 (t0) cc_final: 0.7595 (t0) REVERT: z 65 LEU cc_start: 0.8647 (mt) cc_final: 0.8023 (mp) outliers start: 78 outliers final: 35 residues processed: 537 average time/residue: 0.5298 time to fit residues: 480.1385 Evaluate side-chains 472 residues out of total 5886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 437 time to evaluate : 4.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain M residue 136 THR Chi-restraints excluded: chain P residue 136 THR Chi-restraints excluded: chain Q residue 23 VAL Chi-restraints excluded: chain Q residue 99 VAL Chi-restraints excluded: chain S residue 319 ILE Chi-restraints excluded: chain T residue 22 ASP Chi-restraints excluded: chain W residue 99 VAL Chi-restraints excluded: chain Y residue 228 MET Chi-restraints excluded: chain c residue 22 ASP Chi-restraints excluded: chain c residue 99 VAL Chi-restraints excluded: chain e residue 385 ASP Chi-restraints excluded: chain f residue 49 VAL Chi-restraints excluded: chain f residue 99 VAL Chi-restraints excluded: chain f residue 152 VAL Chi-restraints excluded: chain h residue 319 ILE Chi-restraints excluded: chain i residue 23 VAL Chi-restraints excluded: chain i residue 99 VAL Chi-restraints excluded: chain k residue 136 THR Chi-restraints excluded: chain l residue 66 THR Chi-restraints excluded: chain l residue 134 GLN Chi-restraints excluded: chain o residue 23 VAL Chi-restraints excluded: chain o residue 99 VAL Chi-restraints excluded: chain u residue 136 THR Chi-restraints excluded: chain v residue 23 VAL Chi-restraints excluded: chain v residue 35 TYR Chi-restraints excluded: chain v residue 48 THR Chi-restraints excluded: chain v residue 59 GLU Chi-restraints excluded: chain v residue 89 GLN Chi-restraints excluded: chain v residue 100 VAL Chi-restraints excluded: chain v residue 107 LYS Chi-restraints excluded: chain z residue 30 ASP Chi-restraints excluded: chain z residue 35 TYR Chi-restraints excluded: chain z residue 102 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 694 random chunks: chunk 558 optimal weight: 9.9990 chunk 380 optimal weight: 8.9990 chunk 9 optimal weight: 10.0000 chunk 499 optimal weight: 5.9990 chunk 276 optimal weight: 0.4980 chunk 572 optimal weight: 5.9990 chunk 463 optimal weight: 30.0000 chunk 0 optimal weight: 20.0000 chunk 342 optimal weight: 8.9990 chunk 602 optimal weight: 10.0000 chunk 169 optimal weight: 7.9990 overall best weight: 5.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 172 ASN D 271 GLN ** E 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 232 HIS M 271 GLN ** N 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 131 GLN ** l 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 220 HIS o 31 HIS ** o 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 0.3154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 56894 Z= 0.324 Angle : 0.599 13.580 77036 Z= 0.305 Chirality : 0.043 0.193 8370 Planarity : 0.004 0.050 10228 Dihedral : 4.112 29.771 7996 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.89 % Favored : 98.10 % Rotamer: Outliers : 1.40 % Allowed : 11.74 % Favored : 86.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.10), residues: 7036 helix: 2.39 (0.16), residues: 1132 sheet: 0.03 (0.12), residues: 1878 loop : -0.06 (0.10), residues: 4026 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP M 307 HIS 0.007 0.001 HIS i 83 PHE 0.021 0.001 PHE l 195 TYR 0.032 0.001 TYR u 138 ARG 0.012 0.000 ARG y 142 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14072 Ramachandran restraints generated. 7036 Oldfield, 0 Emsley, 7036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14072 Ramachandran restraints generated. 7036 Oldfield, 0 Emsley, 7036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 531 residues out of total 5886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 449 time to evaluate : 4.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 120 MET cc_start: 0.7846 (tmm) cc_final: 0.7587 (tpt) REVERT: N 162 MET cc_start: 0.6669 (ppp) cc_final: 0.5997 (ptt) REVERT: Q 57 MET cc_start: 0.8014 (mmm) cc_final: 0.7679 (mmm) REVERT: W 120 MET cc_start: 0.7280 (tpp) cc_final: 0.6900 (tpp) REVERT: c 120 MET cc_start: 0.6839 (ttp) cc_final: 0.6516 (mtm) REVERT: f 120 MET cc_start: 0.6990 (mmp) cc_final: 0.6470 (mmt) REVERT: z 65 LEU cc_start: 0.8779 (mt) cc_final: 0.8523 (mp) REVERT: z 71 ASP cc_start: 0.7131 (t0) cc_final: 0.6883 (t0) outliers start: 82 outliers final: 49 residues processed: 512 average time/residue: 0.5283 time to fit residues: 457.7859 Evaluate side-chains 471 residues out of total 5886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 422 time to evaluate : 6.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain L residue 28 ASP Chi-restraints excluded: chain M residue 136 THR Chi-restraints excluded: chain M residue 376 LEU Chi-restraints excluded: chain M residue 390 GLU Chi-restraints excluded: chain P residue 136 THR Chi-restraints excluded: chain Q residue 23 VAL Chi-restraints excluded: chain Q residue 99 VAL Chi-restraints excluded: chain S residue 319 ILE Chi-restraints excluded: chain T residue 22 ASP Chi-restraints excluded: chain T residue 152 VAL Chi-restraints excluded: chain W residue 99 VAL Chi-restraints excluded: chain Y residue 190 MET Chi-restraints excluded: chain Y residue 228 MET Chi-restraints excluded: chain c residue 22 ASP Chi-restraints excluded: chain c residue 23 VAL Chi-restraints excluded: chain c residue 99 VAL Chi-restraints excluded: chain d residue 28 ASP Chi-restraints excluded: chain e residue 190 MET Chi-restraints excluded: chain e residue 385 ASP Chi-restraints excluded: chain f residue 49 VAL Chi-restraints excluded: chain f residue 57 MET Chi-restraints excluded: chain f residue 99 VAL Chi-restraints excluded: chain f residue 152 VAL Chi-restraints excluded: chain h residue 319 ILE Chi-restraints excluded: chain i residue 23 VAL Chi-restraints excluded: chain i residue 99 VAL Chi-restraints excluded: chain k residue 136 THR Chi-restraints excluded: chain l residue 66 THR Chi-restraints excluded: chain l residue 134 GLN Chi-restraints excluded: chain n residue 136 THR Chi-restraints excluded: chain o residue 23 VAL Chi-restraints excluded: chain o residue 99 VAL Chi-restraints excluded: chain u residue 136 THR Chi-restraints excluded: chain u residue 151 THR Chi-restraints excluded: chain v residue 22 ASP Chi-restraints excluded: chain v residue 23 VAL Chi-restraints excluded: chain v residue 35 TYR Chi-restraints excluded: chain v residue 48 THR Chi-restraints excluded: chain v residue 59 GLU Chi-restraints excluded: chain v residue 89 GLN Chi-restraints excluded: chain v residue 100 VAL Chi-restraints excluded: chain v residue 107 LYS Chi-restraints excluded: chain y residue 136 THR Chi-restraints excluded: chain z residue 30 ASP Chi-restraints excluded: chain z residue 102 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 694 random chunks: chunk 225 optimal weight: 7.9990 chunk 604 optimal weight: 0.7980 chunk 132 optimal weight: 4.9990 chunk 393 optimal weight: 3.9990 chunk 165 optimal weight: 10.0000 chunk 671 optimal weight: 10.0000 chunk 557 optimal weight: 20.0000 chunk 310 optimal weight: 0.7980 chunk 55 optimal weight: 5.9990 chunk 222 optimal weight: 4.9990 chunk 352 optimal weight: 5.9990 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 172 ASN D 271 GLN ** E 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 271 GLN ** N 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 232 HIS c 134 GLN f 55 HIS ** f 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 25 GLN ** l 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7288 moved from start: 0.3346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 56894 Z= 0.204 Angle : 0.575 12.176 77036 Z= 0.291 Chirality : 0.043 0.292 8370 Planarity : 0.004 0.049 10228 Dihedral : 4.010 29.261 7996 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.90 % Favored : 98.08 % Rotamer: Outliers : 1.33 % Allowed : 12.46 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.10), residues: 7036 helix: 2.39 (0.16), residues: 1132 sheet: 0.06 (0.12), residues: 1886 loop : -0.01 (0.10), residues: 4018 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP Y 307 HIS 0.004 0.001 HIS K 31 PHE 0.021 0.001 PHE N 195 TYR 0.023 0.001 TYR y 138 ARG 0.007 0.000 ARG u 147 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14072 Ramachandran restraints generated. 7036 Oldfield, 0 Emsley, 7036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14072 Ramachandran restraints generated. 7036 Oldfield, 0 Emsley, 7036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 5886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 461 time to evaluate : 4.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 162 MET cc_start: 0.6578 (ppp) cc_final: 0.5979 (ptt) REVERT: Q 57 MET cc_start: 0.7956 (mmm) cc_final: 0.7638 (mmm) REVERT: V 139 GLU cc_start: 0.7319 (tm-30) cc_final: 0.6765 (tm-30) REVERT: W 120 MET cc_start: 0.7313 (tpp) cc_final: 0.6939 (tpp) REVERT: c 120 MET cc_start: 0.6772 (ttp) cc_final: 0.6469 (mtm) REVERT: e 205 MET cc_start: 0.6413 (mmm) cc_final: 0.6162 (mmm) outliers start: 78 outliers final: 53 residues processed: 519 average time/residue: 0.5291 time to fit residues: 464.0214 Evaluate side-chains 475 residues out of total 5886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 422 time to evaluate : 4.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain H residue 46 VAL Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain K residue 46 VAL Chi-restraints excluded: chain K residue 66 THR Chi-restraints excluded: chain L residue 28 ASP Chi-restraints excluded: chain M residue 136 THR Chi-restraints excluded: chain M residue 376 LEU Chi-restraints excluded: chain M residue 390 GLU Chi-restraints excluded: chain P residue 136 THR Chi-restraints excluded: chain P residue 385 ASP Chi-restraints excluded: chain Q residue 23 VAL Chi-restraints excluded: chain Q residue 99 VAL Chi-restraints excluded: chain Q residue 152 VAL Chi-restraints excluded: chain S residue 319 ILE Chi-restraints excluded: chain T residue 22 ASP Chi-restraints excluded: chain T residue 99 VAL Chi-restraints excluded: chain T residue 152 VAL Chi-restraints excluded: chain T residue 247 VAL Chi-restraints excluded: chain V residue 315 MET Chi-restraints excluded: chain W residue 99 VAL Chi-restraints excluded: chain Y residue 190 MET Chi-restraints excluded: chain Y residue 228 MET Chi-restraints excluded: chain c residue 22 ASP Chi-restraints excluded: chain c residue 99 VAL Chi-restraints excluded: chain d residue 28 ASP Chi-restraints excluded: chain e residue 190 MET Chi-restraints excluded: chain e residue 385 ASP Chi-restraints excluded: chain f residue 49 VAL Chi-restraints excluded: chain f residue 57 MET Chi-restraints excluded: chain f residue 99 VAL Chi-restraints excluded: chain i residue 99 VAL Chi-restraints excluded: chain k residue 136 THR Chi-restraints excluded: chain l residue 66 THR Chi-restraints excluded: chain l residue 134 GLN Chi-restraints excluded: chain l residue 247 VAL Chi-restraints excluded: chain o residue 23 VAL Chi-restraints excluded: chain o residue 99 VAL Chi-restraints excluded: chain u residue 136 THR Chi-restraints excluded: chain v residue 22 ASP Chi-restraints excluded: chain v residue 23 VAL Chi-restraints excluded: chain v residue 35 TYR Chi-restraints excluded: chain v residue 48 THR Chi-restraints excluded: chain v residue 59 GLU Chi-restraints excluded: chain v residue 107 LYS Chi-restraints excluded: chain z residue 35 TYR Chi-restraints excluded: chain z residue 102 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 694 random chunks: chunk 647 optimal weight: 20.0000 chunk 75 optimal weight: 5.9990 chunk 382 optimal weight: 3.9990 chunk 490 optimal weight: 9.9990 chunk 379 optimal weight: 10.0000 chunk 565 optimal weight: 6.9990 chunk 374 optimal weight: 10.0000 chunk 668 optimal weight: 7.9990 chunk 418 optimal weight: 7.9990 chunk 407 optimal weight: 20.0000 chunk 308 optimal weight: 10.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 172 ASN ** H 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 134 GLN M 271 GLN ** N 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 150 GLN Z 134 GLN a 25 GLN ** c 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 45 GLN ** f 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 188 GLN i 134 GLN ** l 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 271 GLN ** o 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.3617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 56894 Z= 0.353 Angle : 0.626 13.638 77036 Z= 0.316 Chirality : 0.043 0.225 8370 Planarity : 0.004 0.048 10228 Dihedral : 4.081 29.580 7996 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.37 % Allowed : 13.20 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.10), residues: 7036 helix: 2.37 (0.16), residues: 1128 sheet: 0.02 (0.12), residues: 1866 loop : 0.02 (0.10), residues: 4042 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP M 307 HIS 0.005 0.001 HIS K 31 PHE 0.019 0.001 PHE N 195 TYR 0.016 0.001 TYR A 387 ARG 0.009 0.000 ARG E 34 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14072 Ramachandran restraints generated. 7036 Oldfield, 0 Emsley, 7036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14072 Ramachandran restraints generated. 7036 Oldfield, 0 Emsley, 7036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 5886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 418 time to evaluate : 4.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 162 MET cc_start: 0.6611 (ppp) cc_final: 0.6070 (ptt) REVERT: Q 57 MET cc_start: 0.8133 (mmm) cc_final: 0.7812 (mmm) REVERT: Q 162 MET cc_start: 0.6710 (ppp) cc_final: 0.6410 (ptt) REVERT: V 139 GLU cc_start: 0.7027 (tm-30) cc_final: 0.6827 (tm-30) REVERT: Y 145 MET cc_start: 0.7447 (mmp) cc_final: 0.7215 (mmp) REVERT: c 120 MET cc_start: 0.6824 (ttp) cc_final: 0.6539 (mtm) REVERT: e 205 MET cc_start: 0.6324 (mmm) cc_final: 0.6072 (mmm) REVERT: z 57 MET cc_start: 0.7972 (mmm) cc_final: 0.7724 (mmm) outliers start: 80 outliers final: 59 residues processed: 478 average time/residue: 0.5302 time to fit residues: 429.1813 Evaluate side-chains 473 residues out of total 5886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 414 time to evaluate : 4.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain H residue 46 VAL Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain K residue 46 VAL Chi-restraints excluded: chain K residue 66 THR Chi-restraints excluded: chain L residue 28 ASP Chi-restraints excluded: chain M residue 136 THR Chi-restraints excluded: chain M residue 376 LEU Chi-restraints excluded: chain P residue 136 THR Chi-restraints excluded: chain Q residue 23 VAL Chi-restraints excluded: chain Q residue 99 VAL Chi-restraints excluded: chain Q residue 152 VAL Chi-restraints excluded: chain S residue 319 ILE Chi-restraints excluded: chain T residue 22 ASP Chi-restraints excluded: chain T residue 99 VAL Chi-restraints excluded: chain T residue 152 VAL Chi-restraints excluded: chain T residue 247 VAL Chi-restraints excluded: chain W residue 99 VAL Chi-restraints excluded: chain W residue 150 GLN Chi-restraints excluded: chain Y residue 190 MET Chi-restraints excluded: chain Y residue 228 MET Chi-restraints excluded: chain c residue 22 ASP Chi-restraints excluded: chain c residue 89 GLN Chi-restraints excluded: chain c residue 99 VAL Chi-restraints excluded: chain d residue 28 ASP Chi-restraints excluded: chain e residue 190 MET Chi-restraints excluded: chain e residue 385 ASP Chi-restraints excluded: chain f residue 23 VAL Chi-restraints excluded: chain f residue 49 VAL Chi-restraints excluded: chain f residue 57 MET Chi-restraints excluded: chain f residue 99 VAL Chi-restraints excluded: chain f residue 152 VAL Chi-restraints excluded: chain i residue 23 VAL Chi-restraints excluded: chain i residue 99 VAL Chi-restraints excluded: chain k residue 136 THR Chi-restraints excluded: chain l residue 66 THR Chi-restraints excluded: chain l residue 134 GLN Chi-restraints excluded: chain l residue 247 VAL Chi-restraints excluded: chain n residue 136 THR Chi-restraints excluded: chain o residue 23 VAL Chi-restraints excluded: chain o residue 99 VAL Chi-restraints excluded: chain u residue 136 THR Chi-restraints excluded: chain u residue 151 THR Chi-restraints excluded: chain v residue 22 ASP Chi-restraints excluded: chain v residue 23 VAL Chi-restraints excluded: chain v residue 35 TYR Chi-restraints excluded: chain v residue 47 ASP Chi-restraints excluded: chain v residue 48 THR Chi-restraints excluded: chain v residue 59 GLU Chi-restraints excluded: chain v residue 107 LYS Chi-restraints excluded: chain z residue 35 TYR Chi-restraints excluded: chain z residue 99 VAL Chi-restraints excluded: chain z residue 102 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 694 random chunks: chunk 413 optimal weight: 20.0000 chunk 267 optimal weight: 9.9990 chunk 399 optimal weight: 0.9980 chunk 201 optimal weight: 6.9990 chunk 131 optimal weight: 9.9990 chunk 129 optimal weight: 8.9990 chunk 425 optimal weight: 6.9990 chunk 455 optimal weight: 20.0000 chunk 330 optimal weight: 8.9990 chunk 62 optimal weight: 5.9990 chunk 525 optimal weight: 8.9990 overall best weight: 5.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 134 GLN M 271 GLN ** N 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 55 HIS ** T 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 moved from start: 0.3766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 56894 Z= 0.322 Angle : 0.623 16.952 77036 Z= 0.314 Chirality : 0.044 0.233 8370 Planarity : 0.004 0.055 10228 Dihedral : 4.067 29.493 7996 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.23 % Allowed : 13.76 % Favored : 85.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.10), residues: 7036 helix: 2.40 (0.16), residues: 1124 sheet: 0.06 (0.12), residues: 1958 loop : 0.09 (0.10), residues: 3954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP M 307 HIS 0.004 0.001 HIS E 83 PHE 0.019 0.001 PHE N 195 TYR 0.031 0.001 TYR A 387 ARG 0.007 0.000 ARG K 32 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14072 Ramachandran restraints generated. 7036 Oldfield, 0 Emsley, 7036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14072 Ramachandran restraints generated. 7036 Oldfield, 0 Emsley, 7036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 5886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 429 time to evaluate : 4.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 120 MET cc_start: 0.6585 (tpp) cc_final: 0.6279 (tpp) REVERT: M 135 LYS cc_start: 0.7270 (tptp) cc_final: 0.6963 (tppt) REVERT: N 162 MET cc_start: 0.6575 (ppp) cc_final: 0.6060 (ptt) REVERT: Q 57 MET cc_start: 0.8138 (mmm) cc_final: 0.7894 (mmm) REVERT: Q 162 MET cc_start: 0.6699 (ppp) cc_final: 0.6409 (ptt) REVERT: W 131 GLN cc_start: 0.6677 (OUTLIER) cc_final: 0.6436 (mp10) REVERT: c 120 MET cc_start: 0.6777 (ttp) cc_final: 0.6496 (mtm) REVERT: e 205 MET cc_start: 0.6339 (mmm) cc_final: 0.6084 (mmm) REVERT: o 120 MET cc_start: 0.7188 (tpt) cc_final: 0.6877 (tpt) outliers start: 72 outliers final: 61 residues processed: 483 average time/residue: 0.5313 time to fit residues: 435.6031 Evaluate side-chains 468 residues out of total 5886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 406 time to evaluate : 4.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain H residue 46 VAL Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain K residue 46 VAL Chi-restraints excluded: chain K residue 66 THR Chi-restraints excluded: chain L residue 28 ASP Chi-restraints excluded: chain M residue 136 THR Chi-restraints excluded: chain M residue 376 LEU Chi-restraints excluded: chain P residue 136 THR Chi-restraints excluded: chain Q residue 23 VAL Chi-restraints excluded: chain Q residue 99 VAL Chi-restraints excluded: chain Q residue 152 VAL Chi-restraints excluded: chain S residue 319 ILE Chi-restraints excluded: chain T residue 22 ASP Chi-restraints excluded: chain T residue 99 VAL Chi-restraints excluded: chain T residue 152 VAL Chi-restraints excluded: chain T residue 247 VAL Chi-restraints excluded: chain V residue 282 VAL Chi-restraints excluded: chain W residue 99 VAL Chi-restraints excluded: chain W residue 131 GLN Chi-restraints excluded: chain Y residue 190 MET Chi-restraints excluded: chain Y residue 228 MET Chi-restraints excluded: chain c residue 22 ASP Chi-restraints excluded: chain c residue 89 GLN Chi-restraints excluded: chain c residue 99 VAL Chi-restraints excluded: chain d residue 28 ASP Chi-restraints excluded: chain e residue 190 MET Chi-restraints excluded: chain e residue 231 CYS Chi-restraints excluded: chain e residue 385 ASP Chi-restraints excluded: chain f residue 23 VAL Chi-restraints excluded: chain f residue 49 VAL Chi-restraints excluded: chain f residue 57 MET Chi-restraints excluded: chain f residue 99 VAL Chi-restraints excluded: chain f residue 152 VAL Chi-restraints excluded: chain i residue 23 VAL Chi-restraints excluded: chain i residue 99 VAL Chi-restraints excluded: chain k residue 136 THR Chi-restraints excluded: chain l residue 66 THR Chi-restraints excluded: chain l residue 134 GLN Chi-restraints excluded: chain l residue 247 VAL Chi-restraints excluded: chain n residue 275 ILE Chi-restraints excluded: chain o residue 23 VAL Chi-restraints excluded: chain o residue 99 VAL Chi-restraints excluded: chain o residue 195 PHE Chi-restraints excluded: chain u residue 136 THR Chi-restraints excluded: chain u residue 151 THR Chi-restraints excluded: chain v residue 22 ASP Chi-restraints excluded: chain v residue 23 VAL Chi-restraints excluded: chain v residue 47 ASP Chi-restraints excluded: chain v residue 48 THR Chi-restraints excluded: chain v residue 59 GLU Chi-restraints excluded: chain v residue 107 LYS Chi-restraints excluded: chain z residue 35 TYR Chi-restraints excluded: chain z residue 99 VAL Chi-restraints excluded: chain z residue 102 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 694 random chunks: chunk 608 optimal weight: 8.9990 chunk 640 optimal weight: 9.9990 chunk 584 optimal weight: 0.2980 chunk 623 optimal weight: 0.0050 chunk 375 optimal weight: 0.8980 chunk 271 optimal weight: 7.9990 chunk 489 optimal weight: 4.9990 chunk 191 optimal weight: 5.9990 chunk 563 optimal weight: 4.9990 chunk 589 optimal weight: 0.8980 chunk 621 optimal weight: 0.3980 overall best weight: 0.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 172 ASN D 271 GLN ** H 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 134 GLN M 271 GLN ** N 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 63 GLN ** T 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 45 GLN ** f 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 134 GLN ** l 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 moved from start: 0.3882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 56894 Z= 0.151 Angle : 0.605 13.812 77036 Z= 0.302 Chirality : 0.044 0.285 8370 Planarity : 0.004 0.050 10228 Dihedral : 3.921 28.310 7996 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.23 % Allowed : 14.00 % Favored : 84.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.10), residues: 7036 helix: 2.33 (0.16), residues: 1120 sheet: 0.14 (0.12), residues: 1894 loop : 0.05 (0.10), residues: 4022 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP Y 307 HIS 0.004 0.000 HIS f 55 PHE 0.021 0.001 PHE N 195 TYR 0.026 0.001 TYR A 387 ARG 0.007 0.000 ARG u 147 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14072 Ramachandran restraints generated. 7036 Oldfield, 0 Emsley, 7036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14072 Ramachandran restraints generated. 7036 Oldfield, 0 Emsley, 7036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 5886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 443 time to evaluate : 4.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 112 MET cc_start: 0.7710 (tpp) cc_final: 0.7482 (tpp) REVERT: Q 162 MET cc_start: 0.6694 (ppp) cc_final: 0.6427 (ptt) REVERT: S 205 MET cc_start: 0.5453 (mmm) cc_final: 0.5218 (mmm) REVERT: T 120 MET cc_start: 0.6992 (mmp) cc_final: 0.6623 (mmt) REVERT: c 120 MET cc_start: 0.6664 (ttp) cc_final: 0.6395 (mtm) REVERT: o 120 MET cc_start: 0.7027 (tpt) cc_final: 0.6438 (tpt) REVERT: v 120 MET cc_start: 0.7928 (tpt) cc_final: 0.7523 (tpp) outliers start: 72 outliers final: 56 residues processed: 500 average time/residue: 0.5411 time to fit residues: 456.5380 Evaluate side-chains 460 residues out of total 5886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 404 time to evaluate : 4.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain H residue 46 VAL Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain K residue 46 VAL Chi-restraints excluded: chain K residue 66 THR Chi-restraints excluded: chain M residue 136 THR Chi-restraints excluded: chain N residue 152 VAL Chi-restraints excluded: chain P residue 136 THR Chi-restraints excluded: chain Q residue 23 VAL Chi-restraints excluded: chain Q residue 99 VAL Chi-restraints excluded: chain Q residue 152 VAL Chi-restraints excluded: chain S residue 319 ILE Chi-restraints excluded: chain T residue 22 ASP Chi-restraints excluded: chain T residue 99 VAL Chi-restraints excluded: chain T residue 152 VAL Chi-restraints excluded: chain T residue 247 VAL Chi-restraints excluded: chain W residue 99 VAL Chi-restraints excluded: chain Y residue 190 MET Chi-restraints excluded: chain Y residue 228 MET Chi-restraints excluded: chain Z residue 195 PHE Chi-restraints excluded: chain b residue 228 MET Chi-restraints excluded: chain c residue 22 ASP Chi-restraints excluded: chain c residue 89 GLN Chi-restraints excluded: chain c residue 99 VAL Chi-restraints excluded: chain e residue 190 MET Chi-restraints excluded: chain e residue 231 CYS Chi-restraints excluded: chain e residue 385 ASP Chi-restraints excluded: chain f residue 23 VAL Chi-restraints excluded: chain f residue 49 VAL Chi-restraints excluded: chain f residue 99 VAL Chi-restraints excluded: chain f residue 152 VAL Chi-restraints excluded: chain h residue 376 LEU Chi-restraints excluded: chain i residue 23 VAL Chi-restraints excluded: chain i residue 99 VAL Chi-restraints excluded: chain k residue 136 THR Chi-restraints excluded: chain l residue 134 GLN Chi-restraints excluded: chain l residue 247 VAL Chi-restraints excluded: chain n residue 275 ILE Chi-restraints excluded: chain o residue 23 VAL Chi-restraints excluded: chain o residue 99 VAL Chi-restraints excluded: chain u residue 136 THR Chi-restraints excluded: chain v residue 22 ASP Chi-restraints excluded: chain v residue 23 VAL Chi-restraints excluded: chain v residue 47 ASP Chi-restraints excluded: chain v residue 48 THR Chi-restraints excluded: chain v residue 59 GLU Chi-restraints excluded: chain v residue 107 LYS Chi-restraints excluded: chain y residue 143 GLU Chi-restraints excluded: chain z residue 35 TYR Chi-restraints excluded: chain z residue 99 VAL Chi-restraints excluded: chain z residue 102 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 694 random chunks: chunk 409 optimal weight: 3.9990 chunk 659 optimal weight: 4.9990 chunk 402 optimal weight: 0.8980 chunk 312 optimal weight: 7.9990 chunk 458 optimal weight: 20.0000 chunk 691 optimal weight: 20.0000 chunk 636 optimal weight: 0.8980 chunk 550 optimal weight: 7.9990 chunk 57 optimal weight: 9.9990 chunk 425 optimal weight: 10.0000 chunk 337 optimal weight: 30.0000 overall best weight: 3.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 271 GLN ** H 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 134 GLN ** N 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 271 GLN ** W 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.3959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 56894 Z= 0.237 Angle : 0.627 14.797 77036 Z= 0.312 Chirality : 0.044 0.242 8370 Planarity : 0.004 0.050 10228 Dihedral : 3.915 28.909 7996 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.09 % Allowed : 14.24 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.10), residues: 7036 helix: 2.37 (0.16), residues: 1126 sheet: 0.07 (0.12), residues: 1864 loop : 0.08 (0.10), residues: 4046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP e 301 HIS 0.003 0.001 HIS f 55 PHE 0.019 0.001 PHE N 195 TYR 0.020 0.001 TYR A 387 ARG 0.011 0.000 ARG P 147 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14072 Ramachandran restraints generated. 7036 Oldfield, 0 Emsley, 7036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14072 Ramachandran restraints generated. 7036 Oldfield, 0 Emsley, 7036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 5886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 418 time to evaluate : 4.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 112 MET cc_start: 0.7791 (tpp) cc_final: 0.7584 (tpp) REVERT: Q 162 MET cc_start: 0.6657 (ppp) cc_final: 0.6376 (ptt) REVERT: c 120 MET cc_start: 0.6644 (ttp) cc_final: 0.6388 (mtm) outliers start: 64 outliers final: 55 residues processed: 468 average time/residue: 0.5353 time to fit residues: 426.5120 Evaluate side-chains 458 residues out of total 5886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 403 time to evaluate : 4.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain H residue 46 VAL Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain K residue 46 VAL Chi-restraints excluded: chain K residue 66 THR Chi-restraints excluded: chain M residue 136 THR Chi-restraints excluded: chain P residue 136 THR Chi-restraints excluded: chain Q residue 23 VAL Chi-restraints excluded: chain Q residue 99 VAL Chi-restraints excluded: chain Q residue 152 VAL Chi-restraints excluded: chain S residue 319 ILE Chi-restraints excluded: chain T residue 22 ASP Chi-restraints excluded: chain T residue 152 VAL Chi-restraints excluded: chain T residue 247 VAL Chi-restraints excluded: chain Y residue 190 MET Chi-restraints excluded: chain Y residue 228 MET Chi-restraints excluded: chain Z residue 195 PHE Chi-restraints excluded: chain b residue 228 MET Chi-restraints excluded: chain c residue 22 ASP Chi-restraints excluded: chain c residue 89 GLN Chi-restraints excluded: chain c residue 99 VAL Chi-restraints excluded: chain d residue 28 ASP Chi-restraints excluded: chain e residue 190 MET Chi-restraints excluded: chain e residue 231 CYS Chi-restraints excluded: chain e residue 385 ASP Chi-restraints excluded: chain f residue 23 VAL Chi-restraints excluded: chain f residue 49 VAL Chi-restraints excluded: chain f residue 57 MET Chi-restraints excluded: chain f residue 99 VAL Chi-restraints excluded: chain f residue 152 VAL Chi-restraints excluded: chain h residue 376 LEU Chi-restraints excluded: chain i residue 23 VAL Chi-restraints excluded: chain i residue 99 VAL Chi-restraints excluded: chain k residue 136 THR Chi-restraints excluded: chain l residue 134 GLN Chi-restraints excluded: chain l residue 247 VAL Chi-restraints excluded: chain n residue 275 ILE Chi-restraints excluded: chain o residue 23 VAL Chi-restraints excluded: chain o residue 99 VAL Chi-restraints excluded: chain u residue 136 THR Chi-restraints excluded: chain v residue 22 ASP Chi-restraints excluded: chain v residue 23 VAL Chi-restraints excluded: chain v residue 47 ASP Chi-restraints excluded: chain v residue 48 THR Chi-restraints excluded: chain v residue 59 GLU Chi-restraints excluded: chain v residue 107 LYS Chi-restraints excluded: chain y residue 143 GLU Chi-restraints excluded: chain z residue 35 TYR Chi-restraints excluded: chain z residue 99 VAL Chi-restraints excluded: chain z residue 102 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 694 random chunks: chunk 437 optimal weight: 3.9990 chunk 586 optimal weight: 9.9990 chunk 168 optimal weight: 7.9990 chunk 507 optimal weight: 9.9990 chunk 81 optimal weight: 0.3980 chunk 152 optimal weight: 4.9990 chunk 551 optimal weight: 5.9990 chunk 230 optimal weight: 9.9990 chunk 566 optimal weight: 9.9990 chunk 69 optimal weight: 9.9990 chunk 101 optimal weight: 6.9990 overall best weight: 4.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 271 GLN ** H 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 271 GLN ** N 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 271 GLN ** W 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 134 GLN ** l 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 39 ASN ** v 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.041501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2528 r_free = 0.2528 target = 0.029781 restraints weight = 276839.102| |-----------------------------------------------------------------------------| r_work (start): 0.2491 rms_B_bonded: 3.91 r_work: 0.2350 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8788 moved from start: 0.4053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 56894 Z= 0.262 Angle : 0.643 14.704 77036 Z= 0.320 Chirality : 0.044 0.264 8370 Planarity : 0.004 0.050 10228 Dihedral : 3.954 29.113 7996 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.01 % Allowed : 14.51 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.10), residues: 7036 helix: 2.27 (0.16), residues: 1126 sheet: 0.11 (0.12), residues: 1924 loop : 0.13 (0.10), residues: 3986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP M 307 HIS 0.004 0.001 HIS f 55 PHE 0.018 0.001 PHE l 195 TYR 0.023 0.001 TYR h 138 ARG 0.011 0.000 ARG Y 142 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9723.53 seconds wall clock time: 172 minutes 58.76 seconds (10378.76 seconds total)