Starting phenix.real_space_refine on Tue Jun 25 07:56:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rt7_19481/06_2024/8rt7_19481.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rt7_19481/06_2024/8rt7_19481.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rt7_19481/06_2024/8rt7_19481.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rt7_19481/06_2024/8rt7_19481.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rt7_19481/06_2024/8rt7_19481.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rt7_19481/06_2024/8rt7_19481.pdb" } resolution = 2.93 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= 0.022 sd= 0.070 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 GLU 182": "OE1" <-> "OE2" Residue "A ASP 214": "OD1" <-> "OD2" Residue "A ARG 235": "NH1" <-> "NH2" Residue "A ASP 236": "OD1" <-> "OD2" Residue "A ARG 243": "NH1" <-> "NH2" Residue "A ASP 248": "OD1" <-> "OD2" Residue "A ARG 249": "NH1" <-> "NH2" Residue "A ARG 274": "NH1" <-> "NH2" Residue "A ASP 303": "OD1" <-> "OD2" Residue "A ARG 304": "NH1" <-> "NH2" Residue "A GLU 353": "OE1" <-> "OE2" Residue "A ARG 372": "NH1" <-> "NH2" Residue "A ASP 380": "OD1" <-> "OD2" Residue "A ASP 382": "OD1" <-> "OD2" Residue "B ASP 30": "OD1" <-> "OD2" Residue "B TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 62": "OE1" <-> "OE2" Residue "B TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 ARG 141": "NH1" <-> "NH2" Residue "B GLU 145": "OE1" <-> "OE2" 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 GLU 240": "OE1" <-> "OE2" Residue "B ASP 250": "OD1" <-> "OD2" Residue "B ARG 259": "NH1" <-> "NH2" Residue "B ARG 260": "NH1" <-> "NH2" Residue "D GLU 139": "OE1" <-> "OE2" Residue "D GLU 143": "OE1" <-> "OE2" Residue "D ARG 144": "NH1" <-> "NH2" 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 ARG 274": "NH1" <-> "NH2" Residue "D ARG 304": "NH1" <-> "NH2" Residue "D GLU 353": "OE1" <-> "OE2" Residue "D ARG 372": "NH1" <-> "NH2" Residue "D ASP 380": "OD1" <-> "OD2" Residue "E TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 47": "OD1" <-> "OD2" Residue "E GLU 62": "OE1" <-> "OE2" Residue "E GLU 73": "OE1" <-> "OE2" Residue "E TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 91": "OE1" <-> "OE2" Residue "E ASP 102": "OD1" <-> "OD2" Residue "E TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 109": "NH1" <-> "NH2" Residue "E ARG 113": "NH1" <-> "NH2" Residue "E ARG 141": "NH1" <-> "NH2" Residue "E GLU 145": "OE1" <-> "OE2" Residue "E PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 197": "OD1" <-> "OD2" Residue "E GLU 199": "OE1" <-> "OE2" Residue "E ARG 233": "NH1" <-> "NH2" Residue "E GLU 240": "OE1" <-> "OE2" Residue "E ARG 259": "NH1" <-> "NH2" Residue "E ARG 260": "NH1" <-> "NH2" Residue "F GLU 41": "OE1" <-> "OE2" 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 ASP 204": "OD1" <-> "OD2" Residue "G ARG 235": "NH1" <-> "NH2" Residue "G ASP 236": "OD1" <-> "OD2" Residue "G ARG 243": "NH1" <-> "NH2" Residue "G ARG 249": "NH1" <-> "NH2" Residue "G ARG 274": "NH1" <-> "NH2" Residue "G GLU 295": "OE1" <-> "OE2" Residue "G ARG 304": "NH1" <-> "NH2" Residue "G ASP 324": "OD1" <-> "OD2" Residue "G ARG 372": "NH1" <-> "NH2" Residue "G ASP 380": "OD1" <-> "OD2" Residue "G GLU 390": "OE1" <-> "OE2" Residue "H TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 30": "OD1" <-> "OD2" Residue "H GLU 60": "OE1" <-> "OE2" Residue "H TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 91": "OE1" <-> "OE2" Residue "H ASP 102": "OD1" <-> "OD2" Residue "H TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 109": "NH1" <-> "NH2" Residue "H ARG 113": "NH1" <-> "NH2" Residue "H TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 122": "OE1" <-> "OE2" Residue "H PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 141": "NH1" <-> "NH2" Residue "H GLU 149": "OE1" <-> "OE2" Residue "H PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 199": "OE1" <-> "OE2" Residue "H ARG 233": "NH1" <-> "NH2" Residue "H ARG 259": "NH1" <-> "NH2" Residue "H ARG 260": "NH1" <-> "NH2" Residue "I PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 139": "OE1" <-> "OE2" Residue "J GLU 143": "OE1" <-> "OE2" Residue "J ARG 144": "NH1" <-> "NH2" Residue "J GLU 185": "OE1" <-> "OE2" Residue "J ASP 204": "OD1" <-> "OD2" 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 ARG 304": "NH1" <-> "NH2" Residue "J GLU 353": "OE1" <-> "OE2" Residue "J ARG 372": "NH1" <-> "NH2" Residue "J ASP 380": "OD1" <-> "OD2" Residue "K ASP 71": "OD1" <-> "OD2" Residue "K GLU 73": "OE1" <-> "OE2" Residue "K TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 109": "NH1" <-> "NH2" Residue "K ARG 113": "NH1" <-> "NH2" Residue "K ARG 141": "NH1" <-> "NH2" Residue "K GLU 145": "OE1" <-> "OE2" Residue "K ARG 233": "NH1" <-> "NH2" Residue "K ARG 259": "NH1" <-> "NH2" Residue "K ARG 260": "NH1" <-> "NH2" Residue "L GLU 32": "OE1" <-> "OE2" Residue "M GLU 139": "OE1" <-> "OE2" Residue "M GLU 143": "OE1" <-> "OE2" Residue "M ARG 144": "NH1" <-> "NH2" Residue "M GLU 185": "OE1" <-> "OE2" Residue "M ASP 214": "OD1" <-> "OD2" Residue "M ARG 235": "NH1" <-> "NH2" Residue "M ASP 236": "OD1" <-> "OD2" Residue "M ARG 243": "NH1" <-> "NH2" Residue "M ARG 249": "NH1" <-> "NH2" Residue "M ARG 274": "NH1" <-> "NH2" Residue "M ASP 303": "OD1" <-> "OD2" Residue "M ARG 304": "NH1" <-> "NH2" Residue "M ASP 324": "OD1" <-> "OD2" Residue "M ARG 372": "NH1" <-> "NH2" Residue "M ASP 380": "OD1" <-> "OD2" Residue "M GLU 390": "OE1" <-> "OE2" Residue "N GLU 59": "OE1" <-> "OE2" Residue "N GLU 60": "OE1" <-> "OE2" Residue "N GLU 62": "OE1" <-> "OE2" Residue "N ASP 71": "OD1" <-> "OD2" Residue "N TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 102": "OD1" <-> "OD2" Residue "N TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 109": "NH1" <-> "NH2" Residue "N ARG 113": "NH1" <-> "NH2" Residue "N TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 129": "OD1" <-> "OD2" Residue "N ARG 136": "NH1" <-> "NH2" Residue "N ARG 141": "NH1" <-> "NH2" Residue "N TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 197": "OD1" <-> "OD2" Residue "N ARG 233": "NH1" <-> "NH2" Residue "N GLU 240": "OE1" <-> "OE2" 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 ARG 235": "NH1" <-> "NH2" Residue "P ARG 243": "NH1" <-> "NH2" Residue "P ARG 249": "NH1" <-> "NH2" Residue "P ARG 274": "NH1" <-> "NH2" Residue "P GLU 276": "OE1" <-> "OE2" Residue "P ARG 304": "NH1" <-> "NH2" Residue "P GLU 353": "OE1" <-> "OE2" Residue "P ARG 372": "NH1" <-> "NH2" Residue "Q TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 91": "OE1" <-> "OE2" 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 TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 129": "OD1" <-> "OD2" Residue "Q ARG 136": "NH1" <-> "NH2" Residue "Q ARG 141": "NH1" <-> "NH2" Residue "Q GLU 145": "OE1" <-> "OE2" Residue "Q ARG 151": "NH1" <-> "NH2" Residue "Q ASP 167": "OD1" <-> "OD2" Residue "Q ARG 233": "NH1" <-> "NH2" Residue "Q GLU 240": "OE1" <-> "OE2" Residue "Q ARG 259": "NH1" <-> "NH2" Residue "Q ARG 260": "NH1" <-> "NH2" Residue "R ASP 28": "OD1" <-> "OD2" 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 ASP 214": "OD1" <-> "OD2" Residue "S ARG 235": "NH1" <-> "NH2" Residue "S ARG 243": "NH1" <-> "NH2" Residue "S ARG 249": "NH1" <-> "NH2" Residue "S ARG 274": "NH1" <-> "NH2" Residue "S ARG 304": "NH1" <-> "NH2" Residue "S GLU 371": "OE1" <-> "OE2" Residue "S ARG 372": "NH1" <-> "NH2" Residue "S ASP 380": "OD1" <-> "OD2" Residue "S GLU 390": "OE1" <-> "OE2" Residue "T TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 47": "OD1" <-> "OD2" Residue "T ASP 71": "OD1" <-> "OD2" Residue "T TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 91": "OE1" <-> "OE2" Residue "T ARG 109": "NH1" <-> "NH2" Residue "T ARG 113": "NH1" <-> "NH2" Residue "T ARG 141": "NH1" <-> "NH2" Residue "T ARG 233": "NH1" <-> "NH2" Residue "T ARG 259": "NH1" <-> "NH2" Residue "T ARG 260": "NH1" <-> "NH2" Residue "U GLU 32": "OE1" <-> "OE2" Residue "V GLU 139": "OE1" <-> "OE2" Residue "V GLU 143": "OE1" <-> "OE2" Residue "V ARG 144": "NH1" <-> "NH2" Residue "V ARG 235": "NH1" <-> "NH2" Residue "V ARG 243": "NH1" <-> "NH2" Residue "V ARG 249": "NH1" <-> "NH2" Residue "V TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 274": "NH1" <-> "NH2" Residue "V ASP 303": "OD1" <-> "OD2" Residue "V ARG 304": "NH1" <-> "NH2" Residue "V ARG 372": "NH1" <-> "NH2" Residue "V ASP 380": "OD1" <-> "OD2" Residue "V ASP 385": "OD1" <-> "OD2" Residue "W TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 85": "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 TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 129": "OD1" <-> "OD2" Residue "W ARG 136": "NH1" <-> "NH2" Residue "W ARG 141": "NH1" <-> "NH2" Residue "W ASP 167": "OD1" <-> "OD2" Residue "W PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 202": "OE1" <-> "OE2" Residue "W ARG 233": "NH1" <-> "NH2" Residue "W GLU 240": "OE1" <-> "OE2" Residue "W ARG 259": "NH1" <-> "NH2" Residue "W ARG 260": "NH1" <-> "NH2" Residue "X GLU 32": "OE1" <-> "OE2" Residue "X GLU 41": "OE1" <-> "OE2" 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 ASP 236": "OD1" <-> "OD2" Residue "Y ARG 243": "NH1" <-> "NH2" Residue "Y ARG 249": "NH1" <-> "NH2" Residue "Y ARG 274": "NH1" <-> "NH2" Residue "Y ASP 286": "OD1" <-> "OD2" Residue "Y ARG 304": "NH1" <-> "NH2" Residue "Y GLU 353": "OE1" <-> "OE2" Residue "Y ARG 372": "NH1" <-> "NH2" Residue "Y ASP 382": "OD1" <-> "OD2" Residue "Y GLU 390": "OE1" <-> "OE2" Residue "Z TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 42": "OD1" <-> "OD2" Residue "Z GLU 59": "OE1" <-> "OE2" Residue "Z GLU 62": "OE1" <-> "OE2" Residue "Z TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 71": "OD1" <-> "OD2" Residue "Z TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 91": "OE1" <-> "OE2" Residue "Z PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 109": "NH1" <-> "NH2" Residue "Z ARG 113": "NH1" <-> "NH2" Residue "Z ARG 136": "NH1" <-> "NH2" Residue "Z ARG 141": "NH1" <-> "NH2" Residue "Z ASP 165": "OD1" <-> "OD2" Residue "Z ASP 167": "OD1" <-> "OD2" Residue "Z PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 233": "NH1" <-> "NH2" 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 "b GLU 139": "OE1" <-> "OE2" Residue "b GLU 143": "OE1" <-> "OE2" Residue "b ARG 144": "NH1" <-> "NH2" Residue "b ASP 204": "OD1" <-> "OD2" Residue "b ARG 235": "NH1" <-> "NH2" Residue "b ARG 243": "NH1" <-> "NH2" Residue "b ARG 249": "NH1" <-> "NH2" Residue "b ARG 274": "NH1" <-> "NH2" Residue "b GLU 295": "OE1" <-> "OE2" Residue "b ARG 304": "NH1" <-> "NH2" Residue "b GLU 353": "OE1" <-> "OE2" Residue "b ARG 372": "NH1" <-> "NH2" Residue "b ASP 385": "OD1" <-> "OD2" Residue "b GLU 390": "OE1" <-> "OE2" Residue "c GLU 60": "OE1" <-> "OE2" 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 ASP 102": "OD1" <-> "OD2" Residue "c TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 109": "NH1" <-> "NH2" Residue "c ARG 113": "NH1" <-> "NH2" Residue "c PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 141": "NH1" <-> "NH2" Residue "c ASP 167": "OD1" <-> "OD2" Residue "c ARG 233": "NH1" <-> "NH2" Residue "c GLU 240": "OE1" <-> "OE2" 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 ARG 235": "NH1" <-> "NH2" Residue "e ARG 243": "NH1" <-> "NH2" Residue "e ARG 249": "NH1" <-> "NH2" Residue "e ARG 274": "NH1" <-> "NH2" Residue "e ARG 304": "NH1" <-> "NH2" Residue "e GLU 308": "OE1" <-> "OE2" Residue "e ASP 321": "OD1" <-> "OD2" Residue "e ARG 372": "NH1" <-> "NH2" Residue "e ASP 380": "OD1" <-> "OD2" Residue "e ASP 385": "OD1" <-> "OD2" Residue "f TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ASP 102": "OD1" <-> "OD2" Residue "f TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ARG 109": "NH1" <-> "NH2" Residue "f ARG 113": "NH1" <-> "NH2" Residue "f ASP 115": "OD1" <-> "OD2" Residue "f ARG 141": "NH1" <-> "NH2" Residue "f GLU 149": "OE1" <-> "OE2" Residue "f ASP 167": "OD1" <-> "OD2" Residue "f ASP 197": "OD1" <-> "OD2" Residue "f GLU 199": "OE1" <-> "OE2" Residue "f ARG 233": "NH1" <-> "NH2" Residue "f GLU 240": "OE1" <-> "OE2" Residue "f ARG 259": "NH1" <-> "NH2" Residue "f ARG 260": "NH1" <-> "NH2" Residue "g PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 32": "OE1" <-> "OE2" Residue "h GLU 139": "OE1" <-> "OE2" Residue "h GLU 143": "OE1" <-> "OE2" Residue "h ARG 144": "NH1" <-> "NH2" Residue "h GLU 182": "OE1" <-> "OE2" Residue "h GLU 185": "OE1" <-> "OE2" Residue "h ASP 204": "OD1" <-> "OD2" Residue "h ARG 235": "NH1" <-> "NH2" Residue "h ARG 243": "NH1" <-> "NH2" Residue "h ARG 249": "NH1" <-> "NH2" Residue "h PHE 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ARG 274": "NH1" <-> "NH2" Residue "h ARG 304": "NH1" <-> "NH2" Residue "h GLU 308": "OE1" <-> "OE2" Residue "h GLU 353": "OE1" <-> "OE2" Residue "h ARG 372": "NH1" <-> "NH2" Residue "h ASP 380": "OD1" <-> "OD2" Residue "i TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ASP 42": "OD1" <-> "OD2" Residue "i PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i GLU 73": "OE1" <-> "OE2" Residue "i TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 GLU 122": "OE1" <-> "OE2" Residue "i ASP 129": "OD1" <-> "OD2" Residue "i GLU 137": "OE1" <-> "OE2" Residue "i ARG 141": "NH1" <-> "NH2" Residue "i GLU 145": "OE1" <-> "OE2" Residue "i TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ARG 233": "NH1" <-> "NH2" Residue "i GLU 240": "OE1" <-> "OE2" Residue "i ARG 259": "NH1" <-> "NH2" Residue "i ARG 260": "NH1" <-> "NH2" Residue "k GLU 139": "OE1" <-> "OE2" Residue "k GLU 143": "OE1" <-> "OE2" Residue "k ARG 144": "NH1" <-> "NH2" Residue "k GLU 182": "OE1" <-> "OE2" Residue "k GLU 185": "OE1" <-> "OE2" Residue "k ASP 214": "OD1" <-> "OD2" Residue "k ARG 235": "NH1" <-> "NH2" Residue "k ARG 243": "NH1" <-> "NH2" Residue "k ARG 249": "NH1" <-> "NH2" Residue "k ARG 274": "NH1" <-> "NH2" Residue "k ARG 304": "NH1" <-> "NH2" Residue "k ARG 372": "NH1" <-> "NH2" Residue "k ASP 382": "OD1" <-> "OD2" Residue "k ASP 385": "OD1" <-> "OD2" Residue "l TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ASP 102": "OD1" <-> "OD2" Residue "l TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ARG 109": "NH1" <-> "NH2" Residue "l ARG 113": "NH1" <-> "NH2" Residue "l GLU 137": "OE1" <-> "OE2" Residue "l ARG 141": "NH1" <-> "NH2" Residue "l TYR 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l GLU 202": "OE1" <-> "OE2" Residue "l ARG 233": "NH1" <-> "NH2" Residue "l ARG 259": "NH1" <-> "NH2" Residue "l ARG 260": "NH1" <-> "NH2" Residue "m GLU 41": "OE1" <-> "OE2" Residue "n GLU 139": "OE1" <-> "OE2" Residue "n GLU 143": "OE1" <-> "OE2" Residue "n ARG 144": "NH1" <-> "NH2" Residue "n GLU 185": "OE1" <-> "OE2" Residue "n ASP 204": "OD1" <-> "OD2" Residue "n ARG 235": "NH1" <-> "NH2" Residue "n ASP 236": "OD1" <-> "OD2" Residue "n ARG 243": "NH1" <-> "NH2" Residue "n ASP 248": "OD1" <-> "OD2" Residue "n ARG 249": "NH1" <-> "NH2" Residue "n ARG 274": "NH1" <-> "NH2" Residue "n ARG 304": "NH1" <-> "NH2" Residue "n GLU 308": "OE1" <-> "OE2" Residue "n GLU 353": "OE1" <-> "OE2" Residue "n ARG 372": "NH1" <-> "NH2" Residue "n ASP 382": "OD1" <-> "OD2" Residue "n ASP 385": "OD1" <-> "OD2" Residue "o ASP 30": "OD1" <-> "OD2" Residue "o TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o GLU 59": "OE1" <-> "OE2" Residue "o GLU 62": "OE1" <-> "OE2" Residue "o ASP 71": "OD1" <-> "OD2" Residue "o GLU 73": "OE1" <-> "OE2" Residue "o TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o GLU 91": "OE1" <-> "OE2" Residue "o PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ARG 109": "NH1" <-> "NH2" Residue "o ARG 113": "NH1" <-> "NH2" Residue "o PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ASP 129": "OD1" <-> "OD2" Residue "o GLU 137": "OE1" <-> "OE2" Residue "o ARG 141": "NH1" <-> "NH2" Residue "o GLU 149": "OE1" <-> "OE2" Residue "o ARG 233": "NH1" <-> "NH2" Residue "o ARG 259": "NH1" <-> "NH2" Residue "o ARG 260": "NH1" <-> "NH2" Residue "p ASP 28": "OD1" <-> "OD2" Residue "p GLU 32": "OE1" <-> "OE2" Residue "u GLU 139": "OE1" <-> "OE2" Residue "u GLU 143": "OE1" <-> "OE2" Residue "u ARG 144": "NH1" <-> "NH2" Residue "v TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v ASP 47": "OD1" <-> "OD2" Residue "v TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v PHE 69": "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 ARG 109": "NH1" <-> "NH2" Residue "v ARG 113": "NH1" <-> "NH2" Residue "v PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z GLU 73": "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 TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 20.76, per 1000 atoms: 0.37 Number of scatterers: 55802 At special positions: 0 Unit cell: (192.06, 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=2.04 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=2.04 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=2.04 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: 14.91 Conformation dependent library (CDL) restraints added in 7.6 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: 98 helices and 141 sheets defined 17.5% alpha, 27.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.20 Creating SS restraints... Processing helix chain 'A' and resid 136 through 148 Processing helix chain 'A' and resid 180 through 187 Processing helix chain 'A' and resid 305 through 330 removed outlier: 5.704A pdb=" N GLY A 312 " --> pdb=" O GLU A 308 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N ALA A 313 " --> pdb=" O ARG A 309 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLY A 330 " --> pdb=" O ALA A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 359 removed outlier: 3.526A pdb=" N ASN A 357 " --> pdb=" O GLU A 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 149 removed outlier: 4.244A pdb=" N GLN B 131 " --> pdb=" O TYR B 127 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG B 136 " --> pdb=" O ALA B 132 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU B 137 " --> pdb=" O ARG B 133 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA B 138 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 169 Processing helix chain 'C' and resid 39 through 43 Processing helix chain 'D' and resid 136 through 148 Processing helix chain 'D' and resid 180 through 187 Processing helix chain 'D' and resid 305 through 329 removed outlier: 5.521A pdb=" N GLY D 312 " --> pdb=" O GLU D 308 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N ALA D 313 " --> pdb=" O ARG D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 359 removed outlier: 3.580A pdb=" N ASN D 357 " --> pdb=" O GLU D 353 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 150 removed outlier: 3.981A pdb=" N GLN E 131 " --> pdb=" O TYR E 127 " (cutoff:3.500A) Processing helix chain 'E' and resid 166 through 169 removed outlier: 3.537A pdb=" N ALA E 169 " --> pdb=" O LYS E 166 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 166 through 169' 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: 5.429A pdb=" N GLY G 312 " --> pdb=" O GLU G 308 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N ALA G 313 " --> pdb=" O ARG G 309 " (cutoff:3.500A) Processing helix chain 'G' and resid 350 through 359 removed outlier: 3.648A pdb=" N ASN G 357 " --> pdb=" O GLU G 353 " (cutoff:3.500A) Processing helix chain 'H' and resid 127 through 151 removed outlier: 3.507A pdb=" N GLN H 131 " --> pdb=" O TYR H 127 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASN H 139 " --> pdb=" O THR H 135 " (cutoff:3.500A) removed outlier: 4.442A 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 'I' and resid 39 through 43 Processing helix chain 'J' and resid 136 through 148 Processing helix chain 'J' and resid 180 through 187 Processing helix chain 'J' and resid 305 through 329 removed outlier: 5.401A pdb=" N GLY J 312 " --> pdb=" O GLU J 308 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N ALA J 313 " --> pdb=" O ARG J 309 " (cutoff:3.500A) Processing helix chain 'J' and resid 350 through 359 removed outlier: 3.775A pdb=" N ASN J 357 " --> pdb=" O GLU J 353 " (cutoff:3.500A) Processing helix chain 'K' and resid 127 through 151 removed outlier: 3.660A pdb=" N GLN K 131 " --> pdb=" O TYR K 127 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ARG K 151 " --> pdb=" O ALA K 147 " (cutoff:3.500A) Processing helix chain 'K' and resid 166 through 169 removed outlier: 3.614A pdb=" N ALA K 169 " --> pdb=" O LYS K 166 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 166 through 169' Processing helix chain 'L' and resid 39 through 43 Processing helix chain 'M' and resid 136 through 148 Processing helix chain 'M' and resid 180 through 187 Processing helix chain 'M' and resid 202 through 204 No H-bonds generated for 'chain 'M' and resid 202 through 204' Processing helix chain 'M' and resid 305 through 329 removed outlier: 5.451A pdb=" N GLY M 312 " --> pdb=" O GLU M 308 " (cutoff:3.500A) removed outlier: 5.477A 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: 3.528A pdb=" N GLN N 131 " --> pdb=" O TYR N 127 " (cutoff:3.500A) removed outlier: 4.251A 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 'O' and resid 39 through 43 removed outlier: 3.508A pdb=" N ILE O 42 " --> pdb=" O PRO O 39 " (cutoff:3.500A) Processing helix chain 'P' and resid 136 through 148 Processing helix chain 'P' and resid 182 through 187 Processing helix chain 'P' and resid 305 through 329 removed outlier: 5.390A pdb=" N GLY P 312 " --> pdb=" O GLU P 308 " (cutoff:3.500A) removed outlier: 5.408A 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: 4.013A 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 186 Processing helix chain 'S' and resid 202 through 204 No H-bonds generated for 'chain 'S' and resid 202 through 204' Processing helix chain 'S' and resid 305 through 329 removed outlier: 5.616A pdb=" N GLY S 312 " --> pdb=" O GLU S 308 " (cutoff:3.500A) removed outlier: 5.460A 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: 4.127A pdb=" N ARG T 151 " --> pdb=" O ALA T 147 " (cutoff:3.500A) Processing helix chain 'T' and resid 166 through 169 Processing helix chain 'V' and resid 136 through 148 Processing helix chain 'V' and resid 180 through 187 removed outlier: 3.510A pdb=" N GLU V 185 " --> pdb=" O GLY V 181 " (cutoff:3.500A) Processing helix chain 'V' and resid 202 through 204 No H-bonds generated for 'chain 'V' and resid 202 through 204' Processing helix chain 'V' and resid 305 through 329 removed outlier: 5.388A pdb=" N GLY V 312 " --> pdb=" O GLU V 308 " (cutoff:3.500A) removed outlier: 5.404A 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: 4.133A pdb=" N GLU W 137 " --> pdb=" O ARG W 133 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA W 138 " --> pdb=" O GLN W 134 " (cutoff:3.500A) removed outlier: 3.517A 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 '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: 5.462A pdb=" N GLY Y 312 " --> pdb=" O GLU Y 308 " (cutoff:3.500A) removed outlier: 5.453A 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: 3.878A pdb=" N GLN Z 131 " --> pdb=" O TYR Z 127 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLU Z 137 " --> pdb=" O ARG Z 133 " (cutoff:3.500A) Processing helix chain 'Z' and resid 166 through 169 Processing helix chain 'a' and resid 39 through 43 Processing helix chain 'b' and resid 136 through 148 Processing helix chain 'b' and resid 180 through 187 Processing helix chain 'b' and resid 305 through 329 removed outlier: 5.374A pdb=" N GLY b 312 " --> pdb=" O GLU b 308 " (cutoff:3.500A) removed outlier: 5.485A 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: 3.550A pdb=" N GLN c 131 " --> pdb=" O TYR c 127 " (cutoff:3.500A) removed outlier: 4.254A 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 'd' and resid 39 through 43 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: 5.619A pdb=" N GLY e 312 " --> pdb=" O GLU e 308 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N ALA e 313 " --> pdb=" O ARG e 309 " (cutoff:3.500A) Processing helix chain 'e' and resid 350 through 359 Processing helix chain 'f' and resid 127 through 151 removed outlier: 3.992A 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 '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: 5.405A pdb=" N GLY h 312 " --> pdb=" O GLU h 308 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N ALA h 313 " --> pdb=" O ARG h 309 " (cutoff:3.500A) Processing helix chain 'h' and resid 350 through 359 removed outlier: 3.548A pdb=" N ASN h 357 " --> pdb=" O GLU h 353 " (cutoff:3.500A) Processing helix chain 'i' and resid 71 through 73 No H-bonds generated for 'chain 'i' and resid 71 through 73' Processing helix chain 'i' and resid 127 through 151 removed outlier: 3.910A 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 'j' and resid 39 through 43 Processing helix chain 'k' and resid 136 through 148 Processing helix chain 'k' and resid 180 through 187 Processing helix chain 'k' and resid 305 through 329 removed outlier: 5.399A pdb=" N GLY k 312 " --> pdb=" O GLU k 308 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N ALA k 313 " --> pdb=" O ARG k 309 " (cutoff:3.500A) Processing helix chain 'k' and resid 350 through 359 removed outlier: 3.598A pdb=" N ASN k 357 " --> pdb=" O GLU k 353 " (cutoff:3.500A) Processing helix chain 'l' and resid 127 through 151 removed outlier: 3.758A 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 'n' and resid 136 through 148 Processing helix chain 'n' and resid 180 through 187 Processing helix chain 'n' and resid 305 through 329 removed outlier: 5.462A pdb=" N GLY n 312 " --> pdb=" O GLU n 308 " (cutoff:3.500A) removed outlier: 5.400A 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 71 through 73 No H-bonds generated for 'chain 'o' and resid 71 through 73' Processing helix chain 'o' and resid 127 through 151 removed outlier: 3.954A pdb=" N ALA o 138 " --> pdb=" O GLN o 134 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASN o 139 " --> pdb=" O THR o 135 " (cutoff:3.500A) removed outlier: 3.951A 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 '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: 6.703A 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: 4.640A pdb=" N VAL D 270 " --> pdb=" O GLY D 289 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N LYS D 252 " --> pdb=" O ILE D 275 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ILE D 275 " --> pdb=" O LYS D 252 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N VAL D 254 " --> pdb=" O SER D 273 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 206 through 207 Processing sheet with id=AA4, first strand: chain 'n' and resid 198 through 199 removed outlier: 4.616A pdb=" N VAL A 270 " --> pdb=" O GLY A 289 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LYS A 252 " --> pdb=" O ILE A 275 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ILE A 275 " --> pdb=" O LYS A 252 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N VAL A 254 " --> pdb=" O SER A 273 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 221 through 222 Processing sheet with id=AA6, first strand: chain 'A' and resid 237 through 238 Processing sheet with id=AA7, first strand: chain 'A' and resid 387 through 391 Processing sheet with id=AA8, first strand: chain 'B' and resid 25 through 26 removed outlier: 6.514A pdb=" N HIS B 55 " --> pdb=" O LEU B 123 " (cutoff:3.500A) removed outlier: 8.308A pdb=" N PHE B 125 " --> pdb=" O HIS B 55 " (cutoff:3.500A) removed outlier: 8.640A pdb=" N MET B 57 " --> pdb=" O PHE B 125 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ILE B 86 " --> pdb=" O THR B 54 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LYS B 87 " --> pdb=" O ALA B 76 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 44 through 49 removed outlier: 6.537A pdb=" N VAL B 44 " --> pdb=" O ARG B 109 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N GLN B 111 " --> pdb=" O VAL B 44 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N VAL B 46 " --> pdb=" O GLN B 111 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N ARG B 113 " --> pdb=" O VAL B 46 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N THR B 48 " --> pdb=" O ARG B 113 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU B 97 " --> pdb=" O PHE B 108 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 202 through 204 removed outlier: 4.641A pdb=" N LYS B 225 " --> pdb=" O VAL B 196 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 172 through 175 Processing sheet with id=AB3, first strand: chain 'B' and resid 258 through 262 Processing sheet with id=AB4, first strand: chain 'D' and resid 195 through 196 removed outlier: 6.653A pdb=" N SER D 195 " --> pdb=" O ASP G 382 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 198 through 199 removed outlier: 4.605A pdb=" N VAL G 270 " --> pdb=" O GLY G 289 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LYS G 252 " --> pdb=" O ILE G 275 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ILE G 275 " --> pdb=" O LYS G 252 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N VAL G 254 " --> pdb=" O SER G 273 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 221 through 222 Processing sheet with id=AB7, first strand: chain 'D' and resid 237 through 238 Processing sheet with id=AB8, first strand: chain 'D' and resid 387 through 391 Processing sheet with id=AB9, first strand: chain 'E' and resid 25 through 26 removed outlier: 6.353A pdb=" N HIS E 55 " --> pdb=" O LEU E 123 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N PHE E 125 " --> pdb=" O HIS E 55 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N MET E 57 " --> pdb=" O PHE E 125 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N HIS E 83 " --> pdb=" O LYS E 80 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LYS E 80 " --> pdb=" O HIS E 83 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 44 through 48 removed outlier: 6.571A pdb=" N VAL E 44 " --> pdb=" O ARG E 109 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N GLN E 111 " --> pdb=" O VAL E 44 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N VAL E 46 " --> pdb=" O GLN E 111 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 202 through 203 removed outlier: 4.565A pdb=" N LYS E 225 " --> pdb=" O VAL E 196 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 172 through 175 removed outlier: 3.536A pdb=" N ASN E 172 " --> pdb=" O LYS E 183 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 195 through 196 removed outlier: 6.670A pdb=" N SER G 195 " --> pdb=" O ASP J 382 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 198 through 199 removed outlier: 4.772A pdb=" N VAL J 270 " --> pdb=" O GLY J 289 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LYS J 252 " --> pdb=" O ILE J 275 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N ILE J 275 " --> pdb=" O LYS J 252 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N VAL J 254 " --> pdb=" O SER J 273 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 221 through 222 Processing sheet with id=AC7, first strand: chain 'G' and resid 237 through 238 Processing sheet with id=AC8, first strand: chain 'G' and resid 267 through 268 Processing sheet with id=AC9, first strand: chain 'G' and resid 388 through 391 Processing sheet with id=AD1, first strand: chain 'H' and resid 25 through 26 removed outlier: 6.960A pdb=" N HIS H 55 " --> pdb=" O LEU H 123 " (cutoff:3.500A) removed outlier: 8.150A pdb=" N PHE H 125 " --> pdb=" O HIS H 55 " (cutoff:3.500A) removed outlier: 8.604A pdb=" N MET H 57 " --> pdb=" O PHE H 125 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 44 through 48 removed outlier: 6.296A pdb=" N VAL H 44 " --> pdb=" O ARG H 109 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N GLN H 111 " --> pdb=" O VAL H 44 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N VAL H 46 " --> pdb=" O GLN H 111 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 64 through 66 removed outlier: 6.849A pdb=" N VAL H 100 " --> pdb=" O LEU H 65 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 202 through 204 removed outlier: 4.686A pdb=" N LYS H 225 " --> pdb=" O VAL H 196 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 172 through 175 Processing sheet with id=AD6, first strand: chain 'J' and resid 195 through 196 removed outlier: 6.651A pdb=" N SER J 195 " --> pdb=" O ASP M 382 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 198 through 199 removed outlier: 4.516A pdb=" N VAL M 270 " --> pdb=" O GLY M 289 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ASN M 374 " --> pdb=" O THR M 290 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N LYS M 252 " --> pdb=" O ILE M 275 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N ILE M 275 " --> pdb=" O LYS M 252 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N VAL M 254 " --> pdb=" O SER M 273 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'J' and resid 221 through 222 Processing sheet with id=AD9, first strand: chain 'J' and resid 237 through 238 Processing sheet with id=AE1, first strand: chain 'J' and resid 267 through 268 Processing sheet with id=AE2, first strand: chain 'J' and resid 387 through 391 Processing sheet with id=AE3, first strand: chain 'K' and resid 25 through 26 removed outlier: 6.714A pdb=" N HIS K 55 " --> pdb=" O LEU K 123 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N PHE K 125 " --> pdb=" O HIS K 55 " (cutoff:3.500A) removed outlier: 8.188A 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: 6.655A pdb=" N VAL K 44 " --> pdb=" O ARG K 109 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N GLN K 111 " --> pdb=" O VAL K 44 " (cutoff:3.500A) removed outlier: 6.622A 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: 3.552A pdb=" N VAL K 196 " --> pdb=" O LYS K 225 " (cutoff:3.500A) removed outlier: 4.754A 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: 6.764A 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: 4.667A pdb=" N VAL P 270 " --> pdb=" O GLY P 289 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N LYS P 252 " --> pdb=" O ILE P 275 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ILE P 275 " --> pdb=" O LYS P 252 " (cutoff:3.500A) removed outlier: 6.794A 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 388 through 391 Processing sheet with id=AF4, first strand: chain 'N' and resid 25 through 26 removed outlier: 3.570A pdb=" N ALA N 124 " --> pdb=" O ARG N 34 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N HIS N 55 " --> pdb=" O LEU N 123 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N PHE N 125 " --> pdb=" O HIS N 55 " (cutoff:3.500A) removed outlier: 8.338A pdb=" N MET N 57 " --> pdb=" O PHE N 125 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'N' and resid 64 through 69 removed outlier: 7.108A pdb=" N VAL N 100 " --> pdb=" O LEU N 65 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N HIS N 67 " --> pdb=" O ILE N 98 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ILE N 98 " --> pdb=" O HIS N 67 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'N' and resid 202 through 204 removed outlier: 3.504A pdb=" N VAL N 196 " --> pdb=" O LYS N 225 " (cutoff:3.500A) removed outlier: 4.617A 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: 6.714A 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: 6.402A pdb=" N LYS S 252 " --> pdb=" O ILE S 275 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ILE S 275 " --> pdb=" O LYS S 252 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N VAL S 254 " --> pdb=" O SER S 273 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N VAL S 270 " --> pdb=" O GLY S 289 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N ARG S 274 " --> pdb=" O LEU S 285 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N LEU S 285 " --> pdb=" O ARG S 274 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N GLU S 276 " --> pdb=" O ILE S 283 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N ILE S 283 " --> pdb=" O GLU S 276 " (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 Processing sheet with id=AG3, first strand: chain 'P' and resid 387 through 391 Processing sheet with id=AG4, first strand: chain 'Q' and resid 25 through 26 removed outlier: 6.253A pdb=" N HIS Q 55 " --> pdb=" O LEU Q 123 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N PHE Q 125 " --> pdb=" O HIS Q 55 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N MET Q 57 " --> pdb=" O PHE Q 125 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'Q' and resid 44 through 48 removed outlier: 7.029A pdb=" N VAL Q 44 " --> pdb=" O ARG Q 109 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N GLN Q 111 " --> pdb=" O VAL Q 44 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N VAL Q 46 " --> pdb=" O GLN Q 111 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'Q' and resid 202 through 203 removed outlier: 3.685A pdb=" N VAL Q 196 " --> pdb=" O LYS Q 225 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N LYS Q 225 " --> pdb=" O VAL Q 196 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'Q' and resid 172 through 175 Processing sheet with id=AG8, first strand: chain 'S' and resid 195 through 196 removed outlier: 6.548A pdb=" N SER S 195 " --> pdb=" O ASP V 382 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'S' and resid 198 through 199 removed outlier: 4.685A pdb=" N VAL V 270 " --> pdb=" O GLY V 289 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASN V 374 " --> pdb=" O THR V 290 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N LYS V 252 " --> pdb=" O ILE V 275 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ILE V 275 " --> pdb=" O LYS V 252 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N VAL V 254 " --> pdb=" O SER V 273 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'S' and resid 221 through 222 Processing sheet with id=AH2, first strand: chain 'S' and resid 237 through 238 Processing sheet with id=AH3, first strand: chain 'S' and resid 267 through 268 Processing sheet with id=AH4, first strand: chain 'S' and resid 387 through 391 Processing sheet with id=AH5, first strand: chain 'T' and resid 25 through 26 removed outlier: 6.573A pdb=" N ARG T 34 " --> pdb=" O ALA T 124 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N ARG T 126 " --> pdb=" O ARG T 34 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N VAL T 36 " --> pdb=" O ARG T 126 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N HIS T 55 " --> pdb=" O LEU T 123 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N PHE T 125 " --> pdb=" O HIS T 55 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N MET T 57 " --> pdb=" O PHE T 125 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'T' and resid 44 through 48 Processing sheet with id=AH7, first strand: chain 'T' and resid 44 through 48 Processing sheet with id=AH8, first strand: chain 'T' and resid 202 through 203 removed outlier: 4.563A pdb=" N LYS T 225 " --> pdb=" O VAL T 196 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'T' and resid 172 through 175 Processing sheet with id=AI1, first strand: chain 'V' and resid 195 through 196 removed outlier: 6.747A pdb=" N SER V 195 " --> pdb=" O ASP Y 382 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'V' and resid 198 through 199 removed outlier: 4.624A pdb=" N VAL Y 270 " --> pdb=" O GLY Y 289 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N LYS Y 252 " --> pdb=" O ILE Y 275 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ILE Y 275 " --> pdb=" O LYS Y 252 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N VAL Y 254 " --> pdb=" O SER Y 273 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'V' and resid 221 through 222 Processing sheet with id=AI4, first strand: chain 'V' and resid 237 through 238 Processing sheet with id=AI5, first strand: chain 'V' and resid 267 through 268 Processing sheet with id=AI6, first strand: chain 'V' and resid 388 through 391 Processing sheet with id=AI7, first strand: chain 'W' and resid 25 through 26 removed outlier: 6.648A pdb=" N HIS W 55 " --> pdb=" O LEU W 123 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N PHE W 125 " --> pdb=" O HIS W 55 " (cutoff:3.500A) removed outlier: 8.385A pdb=" N MET W 57 " --> pdb=" O PHE W 125 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'W' and resid 44 through 48 removed outlier: 3.762A pdb=" N LEU W 97 " --> pdb=" O PHE W 108 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'W' and resid 44 through 48 Processing sheet with id=AJ1, first strand: chain 'W' and resid 202 through 203 removed outlier: 3.547A pdb=" N VAL W 196 " --> pdb=" O LYS W 225 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N LYS W 225 " --> pdb=" O VAL W 196 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'W' and resid 172 through 175 Processing sheet with id=AJ3, first strand: chain 'Y' and resid 195 through 196 removed outlier: 6.886A pdb=" N SER Y 195 " --> pdb=" O ASP b 382 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'Y' and resid 198 through 199 removed outlier: 4.683A pdb=" N VAL b 270 " --> pdb=" O GLY b 289 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N LYS b 252 " --> pdb=" O ILE b 275 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ILE b 275 " --> pdb=" O LYS b 252 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N VAL b 254 " --> pdb=" O SER b 273 " (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 267 through 268 Processing sheet with id=AJ8, first strand: chain 'Y' and resid 387 through 391 Processing sheet with id=AJ9, first strand: chain 'Z' and resid 25 through 26 removed outlier: 6.957A pdb=" N ARG Z 34 " --> pdb=" O ALA Z 124 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N ARG Z 126 " --> pdb=" O ARG Z 34 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N VAL Z 36 " --> pdb=" O ARG Z 126 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N HIS Z 55 " --> pdb=" O LEU Z 123 " (cutoff:3.500A) removed outlier: 8.220A pdb=" N PHE Z 125 " --> pdb=" O HIS Z 55 " (cutoff:3.500A) removed outlier: 9.051A pdb=" N MET Z 57 " --> pdb=" O PHE Z 125 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N HIS Z 83 " --> pdb=" O LYS Z 80 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'Z' and resid 44 through 49 removed outlier: 6.692A pdb=" N VAL Z 44 " --> pdb=" O ARG Z 109 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N GLN Z 111 " --> pdb=" O VAL Z 44 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N VAL Z 46 " --> pdb=" O GLN Z 111 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N ARG Z 113 " --> pdb=" O VAL Z 46 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N THR Z 48 " --> pdb=" O ARG Z 113 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'Z' and resid 202 through 204 removed outlier: 4.687A pdb=" N LYS Z 225 " --> pdb=" O VAL Z 196 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'Z' and resid 172 through 175 Processing sheet with id=AK4, first strand: chain 'b' and resid 195 through 196 removed outlier: 6.847A pdb=" N SER b 195 " --> pdb=" O ASP e 382 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'b' and resid 198 through 199 removed outlier: 4.643A pdb=" N VAL e 270 " --> pdb=" O GLY e 289 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N LYS e 252 " --> pdb=" O ILE e 275 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N ILE e 275 " --> pdb=" O LYS e 252 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N VAL e 254 " --> pdb=" O SER e 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 Processing sheet with id=AK8, first strand: chain 'b' and resid 387 through 391 removed outlier: 3.533A pdb=" N GLU b 390 " --> pdb=" O ARG f 259 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'c' and resid 25 through 26 removed outlier: 6.591A pdb=" N HIS c 55 " --> pdb=" O LEU c 123 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N PHE c 125 " --> pdb=" O HIS c 55 " (cutoff:3.500A) removed outlier: 8.782A 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 49 removed outlier: 6.658A pdb=" N VAL c 44 " --> pdb=" O ARG c 109 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N GLN c 111 " --> pdb=" O VAL c 44 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N VAL c 46 " --> pdb=" O GLN c 111 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N ARG c 113 " --> pdb=" O VAL c 46 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N THR c 48 " --> pdb=" O ARG c 113 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU c 97 " --> pdb=" O PHE c 108 " (cutoff:3.500A) Processing sheet with id=AL2, first strand: chain 'c' and resid 202 through 204 removed outlier: 4.623A pdb=" N LYS c 225 " --> pdb=" O VAL c 196 " (cutoff:3.500A) Processing sheet with id=AL3, first strand: chain 'c' and resid 172 through 175 Processing sheet with id=AL4, first strand: chain 'e' and resid 195 through 196 removed outlier: 6.695A pdb=" N SER e 195 " --> pdb=" O ASP h 382 " (cutoff:3.500A) Processing sheet with id=AL5, first strand: chain 'e' and resid 198 through 199 removed outlier: 4.566A pdb=" N VAL h 270 " --> pdb=" O GLY h 289 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N LYS h 252 " --> pdb=" O ILE h 275 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ILE h 275 " --> pdb=" O LYS h 252 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N VAL h 254 " --> pdb=" O SER h 273 " (cutoff:3.500A) Processing sheet with id=AL6, first strand: chain 'e' and resid 221 through 222 Processing sheet with id=AL7, first strand: chain 'e' and resid 237 through 238 Processing sheet with id=AL8, first strand: chain 'e' and resid 387 through 391 Processing sheet with id=AL9, first strand: chain 'f' and resid 25 through 26 removed outlier: 6.830A pdb=" N HIS f 55 " --> pdb=" O LEU f 123 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N PHE f 125 " --> pdb=" O HIS f 55 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N MET f 57 " --> pdb=" O PHE f 125 " (cutoff:3.500A) Processing sheet with id=AM1, first strand: chain 'f' and resid 44 through 47 removed outlier: 6.698A pdb=" N VAL f 44 " --> pdb=" O ARG f 109 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N GLN f 111 " --> pdb=" O VAL f 44 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N VAL f 46 " --> pdb=" O GLN f 111 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N ASN f 96 " --> pdb=" O PHE f 69 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N PHE f 69 " --> pdb=" O ASN f 96 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ILE f 98 " --> pdb=" O HIS f 67 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N HIS f 67 " --> pdb=" O ILE f 98 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N VAL f 100 " --> pdb=" O LEU f 65 " (cutoff:3.500A) Processing sheet with id=AM2, first strand: chain 'f' and resid 202 through 203 removed outlier: 3.504A pdb=" N VAL f 196 " --> pdb=" O LYS f 225 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N LYS f 225 " --> pdb=" O VAL f 196 " (cutoff:3.500A) Processing sheet with id=AM3, first strand: chain 'f' and resid 172 through 175 Processing sheet with id=AM4, first strand: chain 'h' and resid 195 through 196 removed outlier: 6.753A pdb=" N SER h 195 " --> pdb=" O ASP k 382 " (cutoff:3.500A) Processing sheet with id=AM5, first strand: chain 'h' and resid 198 through 199 removed outlier: 4.632A pdb=" N VAL k 270 " --> pdb=" O GLY k 289 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N LYS k 252 " --> pdb=" O ILE k 275 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ILE k 275 " --> pdb=" O LYS k 252 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N VAL k 254 " --> pdb=" O SER k 273 " (cutoff:3.500A) Processing sheet with id=AM6, first strand: chain 'h' and resid 221 through 222 Processing sheet with id=AM7, first strand: chain 'h' and resid 237 through 238 Processing sheet with id=AM8, first strand: chain 'h' and resid 267 through 268 Processing sheet with id=AM9, first strand: chain 'h' and resid 387 through 391 Processing sheet with id=AN1, first strand: chain 'i' and resid 25 through 26 removed outlier: 6.504A pdb=" N ARG i 34 " --> pdb=" O ALA i 124 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N ARG i 126 " --> pdb=" O ARG i 34 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N VAL i 36 " --> pdb=" O ARG i 126 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N HIS i 55 " --> pdb=" O LEU i 123 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N PHE i 125 " --> pdb=" O HIS i 55 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N MET i 57 " --> pdb=" O PHE i 125 " (cutoff:3.500A) Processing sheet with id=AN2, first strand: chain 'i' and resid 44 through 48 removed outlier: 6.806A pdb=" N VAL i 44 " --> pdb=" O ARG i 109 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N GLN i 111 " --> pdb=" O VAL i 44 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N VAL i 46 " --> pdb=" O GLN i 111 " (cutoff:3.500A) Processing sheet with id=AN3, first strand: chain 'i' and resid 202 through 203 removed outlier: 3.537A pdb=" N VAL i 196 " --> pdb=" O LYS i 225 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N LYS i 225 " --> pdb=" O VAL i 196 " (cutoff:3.500A) Processing sheet with id=AN4, first strand: chain 'i' and resid 172 through 175 Processing sheet with id=AN5, first strand: chain 'k' and resid 195 through 196 removed outlier: 6.769A pdb=" N SER k 195 " --> pdb=" O ASP n 382 " (cutoff:3.500A) Processing sheet with id=AN6, first strand: chain 'k' and resid 198 through 199 removed outlier: 4.718A pdb=" N VAL n 270 " --> pdb=" O GLY n 289 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LYS n 252 " --> pdb=" O ILE n 275 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ILE n 275 " --> pdb=" O LYS n 252 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N VAL n 254 " --> pdb=" O SER n 273 " (cutoff:3.500A) Processing sheet with id=AN7, first strand: chain 'k' and resid 221 through 222 Processing sheet with id=AN8, first strand: chain 'k' and resid 237 through 238 Processing sheet with id=AN9, first strand: chain 'k' and resid 387 through 391 Processing sheet with id=AO1, first strand: chain 'l' and resid 25 through 26 removed outlier: 6.967A pdb=" N ARG l 34 " --> pdb=" O ALA l 124 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N ARG l 126 " --> pdb=" O ARG l 34 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N VAL l 36 " --> pdb=" O ARG l 126 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N HIS l 55 " --> pdb=" O LEU l 123 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N PHE l 125 " --> pdb=" O HIS l 55 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N MET l 57 " --> pdb=" O PHE l 125 " (cutoff:3.500A) Processing sheet with id=AO2, first strand: chain 'l' and resid 44 through 48 removed outlier: 3.563A pdb=" N VAL l 44 " --> pdb=" O LYS l 107 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR l 66 " --> pdb=" O VAL l 100 " (cutoff:3.500A) Processing sheet with id=AO3, first strand: chain 'l' and resid 202 through 204 removed outlier: 3.584A pdb=" N VAL l 196 " --> pdb=" O LYS l 225 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N LYS l 225 " --> pdb=" O VAL l 196 " (cutoff:3.500A) Processing sheet with id=AO4, first strand: chain 'l' and resid 172 through 175 removed outlier: 3.541A pdb=" N ASN l 172 " --> pdb=" O LYS l 183 " (cutoff:3.500A) Processing sheet with id=AO5, first strand: chain 'n' and resid 221 through 222 Processing sheet with id=AO6, first strand: chain 'n' and resid 237 through 238 Processing sheet with id=AO7, first strand: chain 'n' and resid 267 through 268 Processing sheet with id=AO8, first strand: chain 'o' and resid 25 through 26 removed outlier: 6.861A pdb=" N HIS o 55 " --> pdb=" O LEU o 123 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N PHE o 125 " --> pdb=" O HIS o 55 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N MET o 57 " --> pdb=" O PHE o 125 " (cutoff:3.500A) Processing sheet with id=AO9, first strand: chain 'o' and resid 44 through 48 removed outlier: 3.622A pdb=" N VAL o 46 " --> pdb=" O ARG o 109 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLN o 111 " --> pdb=" O VAL o 46 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR o 66 " --> pdb=" O VAL o 100 " (cutoff:3.500A) Processing sheet with id=AP1, first strand: chain 'o' and resid 202 through 203 removed outlier: 3.536A pdb=" N VAL o 196 " --> pdb=" O LYS o 225 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N LYS o 225 " --> pdb=" O VAL o 196 " (cutoff:3.500A) Processing sheet with id=AP2, first strand: chain 'o' and resid 172 through 175 Processing sheet with id=AP3, first strand: chain 'v' and resid 25 through 26 removed outlier: 6.580A pdb=" N ARG v 34 " --> pdb=" O ALA v 124 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N ARG v 126 " --> pdb=" O ARG v 34 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N VAL v 36 " --> pdb=" O ARG v 126 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N PHE v 125 " --> pdb=" O MET v 57 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE v 84 " --> pdb=" O ILE v 56 " (cutoff:3.500A) Processing sheet with id=AP4, first strand: chain 'v' and resid 44 through 46 removed outlier: 6.894A pdb=" N VAL v 44 " --> pdb=" O ARG v 109 " (cutoff:3.500A) Processing sheet with id=AP5, first strand: chain 'z' and resid 25 through 26 removed outlier: 6.403A pdb=" N HIS z 55 " --> pdb=" O LEU z 123 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N PHE z 125 " --> pdb=" O HIS z 55 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N MET z 57 " --> pdb=" O PHE z 125 " (cutoff:3.500A) Processing sheet with id=AP6, first strand: chain 'z' and resid 44 through 48 removed outlier: 6.914A pdb=" N VAL z 44 " --> pdb=" O ARG z 109 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N GLN z 111 " --> pdb=" O VAL z 44 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N VAL z 46 " --> pdb=" O GLN z 111 " (cutoff:3.500A) 2167 hydrogen bonds defined for protein. 5634 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: 22.73 Time building geometry restraints manager: 16.52 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: 18627 1.33 - 1.45: 8488 1.45 - 1.57: 29412 1.57 - 1.69: 1 1.69 - 1.81: 366 Bond restraints: 56894 Sorted by residual: bond pdb=" C GLU J 276 " pdb=" N THR J 277 " ideal model delta sigma weight residual 1.330 1.286 0.044 1.47e-02 4.63e+03 9.14e+00 bond pdb=" C GLU n 276 " pdb=" N THR n 277 " ideal model delta sigma weight residual 1.330 1.290 0.040 1.47e-02 4.63e+03 7.25e+00 bond pdb=" N GLU e 276 " pdb=" CA GLU e 276 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.22e-02 6.72e+03 6.09e+00 bond pdb=" CB LYS E 221 " pdb=" CG LYS E 221 " ideal model delta sigma weight residual 1.520 1.455 0.065 3.00e-02 1.11e+03 4.73e+00 bond pdb=" CA THR e 277 " pdb=" C THR e 277 " ideal model delta sigma weight residual 1.528 1.553 -0.025 1.18e-02 7.18e+03 4.51e+00 ... (remaining 56889 not shown) Histogram of bond angle deviations from ideal: 90.79 - 99.46: 20 99.46 - 108.14: 2998 108.14 - 116.81: 36949 116.81 - 125.48: 36267 125.48 - 134.16: 802 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 122.67 91.93 30.74 1.13e+00 7.83e-01 7.40e+02 angle pdb=" O GLN L 43 " pdb=" C GLN L 43 " pdb=" N ARG L 44 " ideal model delta sigma weight residual 122.41 90.79 31.62 1.34e+00 5.57e-01 5.57e+02 angle pdb=" O GLN U 43 " pdb=" C GLN U 43 " pdb=" N ARG U 44 " ideal model delta sigma weight residual 122.91 100.63 22.28 1.19e+00 7.06e-01 3.51e+02 angle pdb=" O GLN p 43 " pdb=" C GLN p 43 " pdb=" N ARG p 44 " ideal model delta sigma weight residual 122.58 100.83 21.75 1.20e+00 6.94e-01 3.29e+02 angle pdb=" O GLN m 43 " pdb=" C GLN m 43 " pdb=" N ARG m 44 " ideal model delta sigma weight residual 122.41 102.50 19.91 1.34e+00 5.57e-01 2.21e+02 ... (remaining 77031 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 31021 17.78 - 35.57: 2576 35.57 - 53.35: 471 53.35 - 71.13: 83 71.13 - 88.92: 39 Dihedral angle restraints: 34190 sinusoidal: 13744 harmonic: 20446 Sorted by residual: dihedral pdb=" CA ARG v 113 " pdb=" C ARG v 113 " pdb=" N ASN v 114 " pdb=" CA ASN v 114 " ideal model delta harmonic sigma weight residual -180.00 -151.13 -28.87 0 5.00e+00 4.00e-02 3.33e+01 dihedral pdb=" C THR e 277 " pdb=" N THR e 277 " pdb=" CA THR e 277 " pdb=" CB THR e 277 " ideal model delta harmonic sigma weight residual -122.00 -134.55 12.55 0 2.50e+00 1.60e-01 2.52e+01 dihedral pdb=" CA ARG E 79 " pdb=" C ARG E 79 " pdb=" N LYS E 80 " pdb=" CA LYS E 80 " ideal model delta harmonic sigma weight residual 180.00 155.54 24.46 0 5.00e+00 4.00e-02 2.39e+01 ... (remaining 34187 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 7516 0.086 - 0.172: 845 0.172 - 0.258: 7 0.258 - 0.344: 1 0.344 - 0.430: 1 Chirality restraints: 8370 Sorted by residual: chirality pdb=" CB ILE l 98 " pdb=" CA ILE l 98 " pdb=" CG1 ILE l 98 " pdb=" CG2 ILE l 98 " both_signs ideal model delta sigma weight residual False 2.64 2.21 0.43 2.00e-01 2.50e+01 4.63e+00 chirality pdb=" CA THR e 277 " pdb=" N THR e 277 " pdb=" C THR e 277 " pdb=" CB THR e 277 " both_signs ideal model delta sigma weight residual False 2.53 2.22 0.31 2.00e-01 2.50e+01 2.34e+00 chirality pdb=" CB ILE T 217 " pdb=" CA ILE T 217 " pdb=" CG1 ILE T 217 " pdb=" CG2 ILE T 217 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.21e+00 ... (remaining 8367 not shown) Planarity restraints: 10228 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN L 43 " 0.119 2.00e-02 2.50e+03 1.99e-01 3.96e+02 pdb=" C GLN L 43 " -0.344 2.00e-02 2.50e+03 pdb=" O GLN L 43 " 0.124 2.00e-02 2.50e+03 pdb=" N ARG L 44 " 0.101 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN a 43 " 0.118 2.00e-02 2.50e+03 1.98e-01 3.92e+02 pdb=" C GLN a 43 " -0.343 2.00e-02 2.50e+03 pdb=" O GLN a 43 " 0.124 2.00e-02 2.50e+03 pdb=" N ARG a 44 " 0.101 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN U 43 " 0.096 2.00e-02 2.50e+03 1.70e-01 2.90e+02 pdb=" C GLN U 43 " -0.295 2.00e-02 2.50e+03 pdb=" O GLN U 43 " 0.109 2.00e-02 2.50e+03 pdb=" N ARG U 44 " 0.090 2.00e-02 2.50e+03 ... (remaining 10225 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 693 2.62 - 3.19: 46942 3.19 - 3.76: 84886 3.76 - 4.33: 127728 4.33 - 4.90: 214652 Nonbonded interactions: 474901 Sorted by model distance: nonbonded pdb=" NZ LYS i 87 " pdb=" O MET k 145 " model vdw 2.051 2.520 nonbonded pdb=" NH2 ARG N 116 " pdb=" O ASN Q 94 " model vdw 2.123 2.520 nonbonded pdb=" O HIS z 31 " pdb=" NH1 ARG z 34 " model vdw 2.141 2.520 nonbonded pdb=" NZ LYS S 367 " pdb=" OE1 GLU S 371 " model vdw 2.151 2.520 nonbonded pdb=" OH TYR W 106 " pdb=" OH TYR W 127 " model vdw 2.154 2.440 ... (remaining 474896 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: 1.020 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: 6.270 Check model and map are aligned: 0.300 Set scattering table: 0.380 Process input model: 111.680 Find NCS groups from input model: 3.350 Set up NCS constraints: 0.630 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:10.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 134.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 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 : 0.009 0.095 56894 Z= 0.605 Angle : 0.749 31.619 77036 Z= 0.435 Chirality : 0.051 0.430 8370 Planarity : 0.007 0.199 10228 Dihedral : 13.722 88.917 21096 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.07 % Allowed : 0.82 % Favored : 99.11 % Cbeta Deviations : 0.02 % 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: -0.67 (0.09), residues: 7036 helix: 1.13 (0.15), residues: 1130 sheet: -0.55 (0.12), residues: 1911 loop : -0.82 (0.09), residues: 3995 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP h 325 HIS 0.008 0.001 HIS l 55 PHE 0.053 0.002 PHE o 148 TYR 0.034 0.002 TYR Z 127 ARG 0.014 0.001 ARG N 113 *********************** 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 846 residues out of total 5886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 842 time to evaluate : 4.774 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: X 28 ASP cc_start: 0.6756 (t0) cc_final: 0.6541 (t0) REVERT: e 140 LEU cc_start: 0.9027 (mt) cc_final: 0.8759 (mm) REVERT: i 131 GLN cc_start: 0.8216 (pp30) cc_final: 0.7614 (pp30) REVERT: l 129 ASP cc_start: 0.7669 (p0) cc_final: 0.7434 (p0) REVERT: y 144 ARG cc_start: 0.8399 (tmm-80) cc_final: 0.8136 (tmm-80) REVERT: z 48 THR cc_start: 0.8663 (p) cc_final: 0.8273 (t) REVERT: z 50 LEU cc_start: 0.8609 (tp) cc_final: 0.8247 (tp) REVERT: z 115 ASP cc_start: 0.8208 (p0) cc_final: 0.7480 (p0) outliers start: 4 outliers final: 4 residues processed: 845 average time/residue: 1.8266 time to fit residues: 1849.2697 Evaluate side-chains 507 residues out of total 5886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 503 time to evaluate : 4.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 111 GLN Chi-restraints excluded: chain c residue 111 GLN Chi-restraints excluded: chain o residue 84 ILE Chi-restraints excluded: chain v residue 114 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 694 random chunks: chunk 586 optimal weight: 4.9990 chunk 526 optimal weight: 20.0000 chunk 291 optimal weight: 10.0000 chunk 179 optimal weight: 20.0000 chunk 354 optimal weight: 10.0000 chunk 281 optimal weight: 3.9990 chunk 543 optimal weight: 5.9990 chunk 210 optimal weight: 10.0000 chunk 330 optimal weight: 0.9980 chunk 404 optimal weight: 2.9990 chunk 630 optimal weight: 2.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 GLN B 89 GLN D 271 GLN E 201 ASN ** H 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 271 GLN ** M 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 188 GLN P 271 GLN S 374 ASN V 271 GLN V 357 ASN Y 263 GLN Y 271 GLN ** Z 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 139 ASN b 360 ASN ** c 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 271 GLN e 357 ASN ** f 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 232 HIS h 271 GLN h 374 ASN ** i 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 271 GLN k 374 ASN ** l 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 188 GLN n 357 ASN o 89 GLN ** z 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 56894 Z= 0.253 Angle : 0.640 10.906 77036 Z= 0.332 Chirality : 0.045 0.264 8370 Planarity : 0.005 0.072 10228 Dihedral : 4.744 40.496 8006 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.08 % Allowed : 11.08 % Favored : 87.85 % 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: 1.84 (0.16), residues: 1134 sheet: -0.37 (0.12), residues: 1843 loop : -0.49 (0.09), residues: 4059 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP n 325 HIS 0.006 0.001 HIS Z 55 PHE 0.029 0.001 PHE c 195 TYR 0.019 0.001 TYR A 138 ARG 0.011 0.001 ARG N 151 *********************** 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 645 residues out of total 5886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 582 time to evaluate : 4.775 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: W 57 MET cc_start: 0.7763 (mmm) cc_final: 0.7159 (mmm) REVERT: X 28 ASP cc_start: 0.6763 (t0) cc_final: 0.6545 (t0) REVERT: Y 138 TYR cc_start: 0.7686 (t80) cc_final: 0.7355 (t80) REVERT: Y 142 ARG cc_start: 0.7925 (mtm180) cc_final: 0.7709 (mmm160) REVERT: b 138 TYR cc_start: 0.7796 (t80) cc_final: 0.7548 (t80) REVERT: l 129 ASP cc_start: 0.7791 (p0) cc_final: 0.7577 (p0) REVERT: n 138 TYR cc_start: 0.7498 (t80) cc_final: 0.7221 (t80) REVERT: n 142 ARG cc_start: 0.8422 (OUTLIER) cc_final: 0.7946 (ttp80) REVERT: n 146 LEU cc_start: 0.8374 (mm) cc_final: 0.7983 (mm) REVERT: u 140 LEU cc_start: 0.9088 (mt) cc_final: 0.8834 (pp) REVERT: z 36 VAL cc_start: 0.8196 (p) cc_final: 0.7926 (p) REVERT: z 115 ASP cc_start: 0.8140 (p0) cc_final: 0.7447 (p0) outliers start: 63 outliers final: 17 residues processed: 607 average time/residue: 1.8114 time to fit residues: 1320.8855 Evaluate side-chains 499 residues out of total 5886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 481 time to evaluate : 4.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 66 THR Chi-restraints excluded: chain M residue 228 MET Chi-restraints excluded: chain Q residue 89 GLN Chi-restraints excluded: chain U residue 28 ASP Chi-restraints excluded: chain V residue 145 MET Chi-restraints excluded: chain W residue 134 GLN Chi-restraints excluded: chain e residue 143 GLU Chi-restraints excluded: chain h residue 228 MET Chi-restraints excluded: chain n residue 142 ARG Chi-restraints excluded: chain u residue 151 THR Chi-restraints excluded: chain v residue 48 THR Chi-restraints excluded: chain v residue 49 VAL Chi-restraints excluded: chain v residue 56 ILE Chi-restraints excluded: chain v residue 110 LEU Chi-restraints excluded: chain v residue 114 ASN Chi-restraints excluded: chain y residue 136 THR Chi-restraints excluded: chain y residue 151 THR Chi-restraints excluded: chain z residue 110 LEU 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: 10.0000 chunk 524 optimal weight: 5.9990 chunk 429 optimal weight: 0.0000 chunk 173 optimal weight: 10.0000 chunk 631 optimal weight: 9.9990 chunk 682 optimal weight: 40.0000 chunk 562 optimal weight: 3.9990 chunk 626 optimal weight: 9.9990 chunk 215 optimal weight: 0.9990 chunk 506 optimal weight: 20.0000 overall best weight: 4.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 284 ASN B 89 GLN ** H 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 271 GLN Q 201 ASN S 374 ASN V 188 GLN V 374 ASN W 89 GLN Y 271 GLN ** Z 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 25 GLN c 45 GLN ** c 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 131 GLN ** f 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 188 GLN k 271 GLN k 360 ASN l 89 GLN n 357 ASN ** z 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 56894 Z= 0.282 Angle : 0.617 14.149 77036 Z= 0.316 Chirality : 0.044 0.245 8370 Planarity : 0.004 0.055 10228 Dihedral : 4.391 27.918 7998 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.60 % Allowed : 12.58 % Favored : 85.81 % 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: 0.08 (0.10), residues: 7036 helix: 1.98 (0.16), residues: 1134 sheet: -0.24 (0.12), residues: 1841 loop : -0.31 (0.09), residues: 4061 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP n 325 HIS 0.005 0.001 HIS c 55 PHE 0.025 0.001 PHE Z 195 TYR 0.026 0.001 TYR D 138 ARG 0.011 0.000 ARG J 147 *********************** 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 634 residues out of total 5886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 540 time to evaluate : 4.841 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: G 146 LEU cc_start: 0.8705 (mm) cc_final: 0.8358 (mm) REVERT: W 57 MET cc_start: 0.7965 (OUTLIER) cc_final: 0.7208 (mmm) REVERT: X 28 ASP cc_start: 0.6806 (t0) cc_final: 0.6581 (t0) REVERT: Y 138 TYR cc_start: 0.7784 (t80) cc_final: 0.7345 (t80) REVERT: Y 142 ARG cc_start: 0.8153 (mtm180) cc_final: 0.7911 (mmm160) REVERT: y 146 LEU cc_start: 0.8331 (mm) cc_final: 0.7939 (mm) REVERT: z 115 ASP cc_start: 0.8015 (p0) cc_final: 0.7401 (p0) outliers start: 94 outliers final: 30 residues processed: 592 average time/residue: 1.7494 time to fit residues: 1254.8347 Evaluate side-chains 493 residues out of total 5886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 462 time to evaluate : 4.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain K residue 99 VAL Chi-restraints excluded: chain M residue 228 MET Chi-restraints excluded: chain O residue 28 ASP Chi-restraints excluded: chain P residue 138 TYR Chi-restraints excluded: chain S residue 136 THR Chi-restraints excluded: chain U residue 28 ASP Chi-restraints excluded: chain W residue 57 MET Chi-restraints excluded: chain W residue 66 THR Chi-restraints excluded: chain W residue 134 GLN Chi-restraints excluded: chain Y residue 136 THR Chi-restraints excluded: chain b residue 319 ILE Chi-restraints excluded: chain c residue 57 MET Chi-restraints excluded: chain e residue 143 GLU Chi-restraints excluded: chain h residue 228 MET Chi-restraints excluded: chain l residue 23 VAL Chi-restraints excluded: chain u residue 151 THR Chi-restraints excluded: chain v residue 48 THR Chi-restraints excluded: chain v residue 49 VAL Chi-restraints excluded: chain v residue 86 ILE Chi-restraints excluded: chain v residue 92 LEU Chi-restraints excluded: chain v residue 98 ILE Chi-restraints excluded: chain v residue 110 LEU Chi-restraints excluded: chain v residue 114 ASN Chi-restraints excluded: chain y residue 136 THR Chi-restraints excluded: chain y residue 151 THR Chi-restraints excluded: chain z residue 21 LEU Chi-restraints excluded: chain z residue 44 VAL Chi-restraints excluded: chain z residue 48 THR Chi-restraints excluded: chain z residue 110 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 694 random chunks: chunk 623 optimal weight: 10.0000 chunk 474 optimal weight: 0.8980 chunk 327 optimal weight: 5.9990 chunk 69 optimal weight: 7.9990 chunk 301 optimal weight: 3.9990 chunk 423 optimal weight: 4.9990 chunk 633 optimal weight: 9.9990 chunk 670 optimal weight: 0.2980 chunk 331 optimal weight: 10.0000 chunk 600 optimal weight: 5.9990 chunk 180 optimal weight: 6.9990 overall best weight: 3.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 89 GLN ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 172 ASN ** H 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 271 GLN S 374 ASN ** T 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 271 GLN ** Z 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 131 GLN ** Z 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 374 ASN ** f 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 271 GLN k 360 ASN n 188 GLN n 305 HIS n 357 ASN v 67 HIS z 63 GLN ** z 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.2485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 56894 Z= 0.240 Angle : 0.611 12.624 77036 Z= 0.311 Chirality : 0.044 0.283 8370 Planarity : 0.004 0.049 10228 Dihedral : 4.235 26.204 7998 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.59 % Allowed : 14.32 % Favored : 84.09 % 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: 0.18 (0.10), residues: 7036 helix: 2.00 (0.16), residues: 1131 sheet: -0.16 (0.12), residues: 1835 loop : -0.23 (0.09), residues: 4070 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP V 307 HIS 0.009 0.001 HIS Z 55 PHE 0.024 0.001 PHE Z 195 TYR 0.040 0.001 TYR P 138 ARG 0.012 0.000 ARG D 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 618 residues out of total 5886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 525 time to evaluate : 4.868 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: B 120 MET cc_start: 0.6698 (tpt) cc_final: 0.6495 (tpp) REVERT: G 146 LEU cc_start: 0.8716 (mm) cc_final: 0.8463 (mm) REVERT: M 146 LEU cc_start: 0.8426 (mm) cc_final: 0.8176 (mm) REVERT: W 57 MET cc_start: 0.8012 (OUTLIER) cc_final: 0.7265 (mmm) REVERT: X 28 ASP cc_start: 0.6686 (t0) cc_final: 0.6447 (t0) REVERT: Y 142 ARG cc_start: 0.8244 (mtm180) cc_final: 0.8041 (mmm160) REVERT: k 205 MET cc_start: 0.6064 (OUTLIER) cc_final: 0.5774 (mmp) REVERT: n 146 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.7948 (mm) REVERT: u 140 LEU cc_start: 0.9126 (mt) cc_final: 0.8837 (mm) REVERT: v 123 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8393 (tm) REVERT: y 146 LEU cc_start: 0.8351 (mm) cc_final: 0.7994 (mm) REVERT: z 115 ASP cc_start: 0.7959 (p0) cc_final: 0.7377 (p0) outliers start: 93 outliers final: 35 residues processed: 581 average time/residue: 1.6925 time to fit residues: 1196.3336 Evaluate side-chains 497 residues out of total 5886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 458 time to evaluate : 4.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain G residue 376 LEU Chi-restraints excluded: chain M residue 136 THR Chi-restraints excluded: chain M residue 228 MET Chi-restraints excluded: chain O residue 28 ASP Chi-restraints excluded: chain P residue 143 GLU Chi-restraints excluded: chain S residue 136 THR Chi-restraints excluded: chain U residue 28 ASP Chi-restraints excluded: chain W residue 57 MET Chi-restraints excluded: chain W residue 66 THR Chi-restraints excluded: chain W residue 134 GLN Chi-restraints excluded: chain Y residue 136 THR Chi-restraints excluded: chain Z residue 99 VAL Chi-restraints excluded: chain c residue 23 VAL Chi-restraints excluded: chain e residue 143 GLU Chi-restraints excluded: chain f residue 23 VAL Chi-restraints excluded: chain h residue 228 MET Chi-restraints excluded: chain i residue 23 VAL Chi-restraints excluded: chain k residue 205 MET Chi-restraints excluded: chain l residue 23 VAL Chi-restraints excluded: chain l residue 49 VAL Chi-restraints excluded: chain n residue 146 LEU 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 48 THR Chi-restraints excluded: chain v residue 49 VAL Chi-restraints excluded: chain v residue 56 ILE Chi-restraints excluded: chain v residue 86 ILE Chi-restraints excluded: chain v residue 92 LEU Chi-restraints excluded: chain v residue 110 LEU Chi-restraints excluded: chain v residue 114 ASN Chi-restraints excluded: chain v residue 123 LEU Chi-restraints excluded: chain y residue 136 THR Chi-restraints excluded: chain z residue 44 VAL Chi-restraints excluded: chain z residue 48 THR Chi-restraints excluded: chain z residue 49 VAL Chi-restraints excluded: chain z residue 110 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 694 random chunks: chunk 558 optimal weight: 2.9990 chunk 380 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 chunk 499 optimal weight: 2.9990 chunk 276 optimal weight: 6.9990 chunk 572 optimal weight: 0.0040 chunk 463 optimal weight: 7.9990 chunk 0 optimal weight: 30.0000 chunk 342 optimal weight: 2.9990 chunk 602 optimal weight: 30.0000 chunk 169 optimal weight: 9.9990 overall best weight: 2.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 GLN B 89 GLN ** H 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 271 GLN ** Q 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 271 GLN Y 374 ASN ** Z 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 55 HIS i 83 HIS k 271 GLN n 357 ASN ** o 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 63 GLN ** z 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.2721 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= 0.212 Angle : 0.610 12.666 77036 Z= 0.307 Chirality : 0.044 0.288 8370 Planarity : 0.004 0.046 10228 Dihedral : 4.102 24.370 7998 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.64 % Allowed : 15.07 % Favored : 83.29 % 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: 0.26 (0.10), residues: 7036 helix: 1.99 (0.16), residues: 1131 sheet: -0.08 (0.12), residues: 1835 loop : -0.16 (0.09), residues: 4070 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP n 301 HIS 0.007 0.001 HIS c 55 PHE 0.023 0.001 PHE c 195 TYR 0.025 0.001 TYR D 138 ARG 0.016 0.000 ARG y 147 *********************** 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 617 residues out of total 5886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 521 time to evaluate : 4.818 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: B 120 MET cc_start: 0.6714 (tpt) cc_final: 0.6506 (tpp) REVERT: G 205 MET cc_start: 0.6395 (mmm) cc_final: 0.5645 (mmm) REVERT: K 131 GLN cc_start: 0.7544 (tp40) cc_final: 0.7283 (tp40) REVERT: M 140 LEU cc_start: 0.8696 (mm) cc_final: 0.8322 (OUTLIER) REVERT: M 146 LEU cc_start: 0.8450 (mm) cc_final: 0.8170 (mm) REVERT: W 57 MET cc_start: 0.8020 (OUTLIER) cc_final: 0.7316 (mmm) REVERT: W 120 MET cc_start: 0.7272 (tpp) cc_final: 0.6834 (tpp) REVERT: X 28 ASP cc_start: 0.6725 (t0) cc_final: 0.6462 (t0) REVERT: Y 138 TYR cc_start: 0.7730 (t80) cc_final: 0.7376 (t80) REVERT: n 146 LEU cc_start: 0.8318 (OUTLIER) cc_final: 0.7962 (mm) REVERT: v 57 MET cc_start: 0.5885 (mmm) cc_final: 0.5338 (mmm) REVERT: v 123 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8414 (tm) REVERT: y 146 LEU cc_start: 0.8315 (mm) cc_final: 0.8013 (mm) REVERT: z 115 ASP cc_start: 0.7944 (p0) cc_final: 0.7412 (p0) outliers start: 96 outliers final: 41 residues processed: 584 average time/residue: 1.6459 time to fit residues: 1175.5348 Evaluate side-chains 497 residues out of total 5886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 454 time to evaluate : 4.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain E residue 195 PHE Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain K residue 99 VAL Chi-restraints excluded: chain M residue 136 THR Chi-restraints excluded: chain M residue 228 MET Chi-restraints excluded: chain O residue 28 ASP Chi-restraints excluded: chain P residue 143 GLU Chi-restraints excluded: chain S residue 136 THR Chi-restraints excluded: chain U residue 28 ASP Chi-restraints excluded: chain W residue 57 MET Chi-restraints excluded: chain W residue 66 THR Chi-restraints excluded: chain W residue 107 LYS Chi-restraints excluded: chain W residue 134 GLN Chi-restraints excluded: chain Y residue 136 THR Chi-restraints excluded: chain c residue 23 VAL Chi-restraints excluded: chain c residue 99 VAL Chi-restraints excluded: chain c residue 107 LYS Chi-restraints excluded: chain e residue 143 GLU Chi-restraints excluded: chain f residue 23 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 23 VAL Chi-restraints excluded: chain l residue 49 VAL Chi-restraints excluded: chain n residue 146 LEU 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 48 THR Chi-restraints excluded: chain v residue 49 VAL Chi-restraints excluded: chain v residue 56 ILE Chi-restraints excluded: chain v residue 86 ILE Chi-restraints excluded: chain v residue 92 LEU Chi-restraints excluded: chain v residue 110 LEU Chi-restraints excluded: chain v residue 114 ASN Chi-restraints excluded: chain v residue 123 LEU Chi-restraints excluded: chain y residue 136 THR Chi-restraints excluded: chain z residue 23 VAL Chi-restraints excluded: chain z residue 44 VAL Chi-restraints excluded: chain z residue 48 THR Chi-restraints excluded: chain z residue 110 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 694 random chunks: chunk 225 optimal weight: 9.9990 chunk 604 optimal weight: 30.0000 chunk 132 optimal weight: 5.9990 chunk 393 optimal weight: 10.0000 chunk 165 optimal weight: 6.9990 chunk 671 optimal weight: 0.0060 chunk 557 optimal weight: 20.0000 chunk 310 optimal weight: 30.0000 chunk 55 optimal weight: 7.9990 chunk 222 optimal weight: 10.0000 chunk 352 optimal weight: 10.0000 overall best weight: 6.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 GLN ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 172 ASN ** K 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 25 GLN P 271 GLN ** Q 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 271 GLN Y 374 ASN ** Z 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 271 GLN ** n 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 357 ASN ** o 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 63 GLN z 83 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.2878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 56894 Z= 0.370 Angle : 0.659 12.109 77036 Z= 0.331 Chirality : 0.044 0.271 8370 Planarity : 0.004 0.049 10228 Dihedral : 4.136 22.956 7998 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.60 % Allowed : 16.70 % Favored : 81.70 % 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: 0.33 (0.10), residues: 7036 helix: 2.04 (0.17), residues: 1123 sheet: 0.01 (0.12), residues: 1923 loop : -0.13 (0.10), residues: 3990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP n 301 HIS 0.007 0.001 HIS v 67 PHE 0.022 0.001 PHE Z 195 TYR 0.024 0.001 TYR S 138 ARG 0.010 0.000 ARG P 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 583 residues out of total 5886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 489 time to evaluate : 4.881 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: A 146 LEU cc_start: 0.8360 (mm) cc_final: 0.8116 (mm) REVERT: E 89 GLN cc_start: 0.8698 (OUTLIER) cc_final: 0.8410 (mp10) REVERT: W 57 MET cc_start: 0.8198 (OUTLIER) cc_final: 0.7351 (mmm) REVERT: X 28 ASP cc_start: 0.6711 (t0) cc_final: 0.6449 (t0) REVERT: Y 138 TYR cc_start: 0.7752 (t80) cc_final: 0.7189 (t80) REVERT: Y 142 ARG cc_start: 0.8266 (mmm160) cc_final: 0.7993 (ttm110) REVERT: n 146 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.8087 (mm) REVERT: u 140 LEU cc_start: 0.9165 (mt) cc_final: 0.8941 (mm) REVERT: v 47 ASP cc_start: 0.7279 (t70) cc_final: 0.7037 (t70) REVERT: y 146 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8078 (mm) REVERT: z 115 ASP cc_start: 0.7983 (p0) cc_final: 0.7353 (p0) outliers start: 94 outliers final: 44 residues processed: 545 average time/residue: 1.6456 time to fit residues: 1097.4545 Evaluate side-chains 500 residues out of total 5886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 452 time to evaluate : 4.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain E residue 89 GLN Chi-restraints excluded: chain E residue 195 PHE Chi-restraints excluded: chain G residue 231 CYS Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain K residue 99 VAL Chi-restraints excluded: chain M residue 136 THR Chi-restraints excluded: chain M residue 228 MET Chi-restraints excluded: chain O residue 28 ASP Chi-restraints excluded: chain P residue 143 GLU Chi-restraints excluded: chain S residue 136 THR Chi-restraints excluded: chain T residue 131 GLN Chi-restraints excluded: chain U residue 28 ASP Chi-restraints excluded: chain W residue 57 MET Chi-restraints excluded: chain W residue 66 THR Chi-restraints excluded: chain W residue 107 LYS Chi-restraints excluded: chain W residue 134 GLN Chi-restraints excluded: chain Y residue 136 THR Chi-restraints excluded: chain Z residue 99 VAL Chi-restraints excluded: chain b residue 136 THR Chi-restraints excluded: chain c residue 23 VAL Chi-restraints excluded: chain c residue 99 VAL Chi-restraints excluded: chain f residue 23 VAL Chi-restraints excluded: chain f residue 65 LEU Chi-restraints excluded: chain f residue 99 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 23 VAL Chi-restraints excluded: chain l residue 49 VAL Chi-restraints excluded: chain n residue 146 LEU 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 48 THR Chi-restraints excluded: chain v residue 49 VAL Chi-restraints excluded: chain v residue 56 ILE Chi-restraints excluded: chain v residue 86 ILE Chi-restraints excluded: chain v residue 92 LEU Chi-restraints excluded: chain v residue 110 LEU Chi-restraints excluded: chain y residue 136 THR Chi-restraints excluded: chain y residue 146 LEU Chi-restraints excluded: chain y residue 151 THR Chi-restraints excluded: chain z residue 21 LEU Chi-restraints excluded: chain z residue 44 VAL Chi-restraints excluded: chain z residue 48 THR Chi-restraints excluded: chain z residue 110 LEU 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: 10.0000 chunk 382 optimal weight: 10.0000 chunk 490 optimal weight: 10.0000 chunk 379 optimal weight: 5.9990 chunk 565 optimal weight: 6.9990 chunk 374 optimal weight: 6.9990 chunk 668 optimal weight: 4.9990 chunk 418 optimal weight: 3.9990 chunk 407 optimal weight: 7.9990 chunk 308 optimal weight: 6.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 89 GLN ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 188 GLN G 374 ASN ** H 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 271 GLN ** Q 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 271 GLN ** Y 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 271 GLN k 360 ASN ** k 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 188 GLN n 357 ASN ** o 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 63 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.3021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 56894 Z= 0.351 Angle : 0.683 14.454 77036 Z= 0.339 Chirality : 0.044 0.279 8370 Planarity : 0.004 0.052 10228 Dihedral : 4.114 22.988 7996 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.54 % Allowed : 17.46 % Favored : 81.00 % 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: 2.01 (0.17), residues: 1123 sheet: -0.01 (0.12), residues: 1907 loop : -0.09 (0.10), residues: 4006 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP P 307 HIS 0.009 0.001 HIS E 55 PHE 0.022 0.001 PHE c 195 TYR 0.022 0.001 TYR D 138 ARG 0.014 0.000 ARG A 147 *********************** 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 572 residues out of total 5886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 482 time to evaluate : 4.820 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: A 146 LEU cc_start: 0.8459 (mm) cc_final: 0.8076 (mm) REVERT: B 120 MET cc_start: 0.7040 (tpp) cc_final: 0.6830 (tpt) REVERT: G 146 LEU cc_start: 0.8751 (mm) cc_final: 0.8433 (mm) REVERT: W 57 MET cc_start: 0.8247 (OUTLIER) cc_final: 0.7429 (mmm) REVERT: W 120 MET cc_start: 0.7273 (tpp) cc_final: 0.6708 (tpp) REVERT: W 133 ARG cc_start: 0.7679 (mmm160) cc_final: 0.7446 (mmp80) REVERT: X 28 ASP cc_start: 0.6703 (t0) cc_final: 0.6405 (t0) REVERT: Y 138 TYR cc_start: 0.7805 (t80) cc_final: 0.7141 (t80) REVERT: Y 142 ARG cc_start: 0.8262 (mmm160) cc_final: 0.8000 (ttm110) REVERT: e 143 GLU cc_start: 0.7815 (pm20) cc_final: 0.7422 (pm20) REVERT: f 120 MET cc_start: 0.7442 (mmm) cc_final: 0.7069 (mmp) REVERT: k 205 MET cc_start: 0.6081 (OUTLIER) cc_final: 0.5806 (mmp) REVERT: n 146 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.8141 (mm) REVERT: v 57 MET cc_start: 0.5943 (mmm) cc_final: 0.5102 (mmm) REVERT: z 73 GLU cc_start: 0.8420 (pm20) cc_final: 0.8179 (pm20) REVERT: z 115 ASP cc_start: 0.7956 (p0) cc_final: 0.7351 (p0) outliers start: 90 outliers final: 44 residues processed: 544 average time/residue: 1.6708 time to fit residues: 1109.2631 Evaluate side-chains 502 residues out of total 5886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 455 time to evaluate : 4.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 89 GLN Chi-restraints excluded: chain E residue 195 PHE Chi-restraints excluded: chain F residue 28 ASP Chi-restraints excluded: chain G residue 231 CYS Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain K residue 99 VAL Chi-restraints excluded: chain M residue 136 THR Chi-restraints excluded: chain M residue 228 MET Chi-restraints excluded: chain M residue 376 LEU Chi-restraints excluded: chain O residue 28 ASP Chi-restraints excluded: chain P residue 143 GLU Chi-restraints excluded: chain S residue 136 THR Chi-restraints excluded: chain T residue 131 GLN Chi-restraints excluded: chain U residue 28 ASP Chi-restraints excluded: chain W residue 57 MET Chi-restraints excluded: chain W residue 66 THR Chi-restraints excluded: chain W residue 107 LYS Chi-restraints excluded: chain W residue 134 GLN Chi-restraints excluded: chain Y residue 136 THR Chi-restraints excluded: chain Z residue 99 VAL Chi-restraints excluded: chain b residue 136 THR Chi-restraints excluded: chain c residue 23 VAL Chi-restraints excluded: chain c residue 99 VAL Chi-restraints excluded: chain f residue 23 VAL Chi-restraints excluded: chain f residue 99 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 k residue 205 MET Chi-restraints excluded: chain l residue 23 VAL Chi-restraints excluded: chain l residue 49 VAL Chi-restraints excluded: chain n residue 146 LEU Chi-restraints excluded: chain u residue 151 THR Chi-restraints excluded: chain v residue 23 VAL Chi-restraints excluded: chain v residue 48 THR Chi-restraints excluded: chain v residue 49 VAL Chi-restraints excluded: chain v residue 99 VAL Chi-restraints excluded: chain v residue 110 LEU Chi-restraints excluded: chain y residue 136 THR Chi-restraints excluded: chain z residue 21 LEU Chi-restraints excluded: chain z residue 23 VAL Chi-restraints excluded: chain z residue 44 VAL Chi-restraints excluded: chain z residue 49 VAL Chi-restraints excluded: chain z residue 110 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 694 random chunks: chunk 413 optimal weight: 30.0000 chunk 267 optimal weight: 30.0000 chunk 399 optimal weight: 6.9990 chunk 201 optimal weight: 0.9990 chunk 131 optimal weight: 5.9990 chunk 129 optimal weight: 0.7980 chunk 425 optimal weight: 4.9990 chunk 455 optimal weight: 5.9990 chunk 330 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 chunk 525 optimal weight: 7.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 GLN ** B 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 89 GLN G 374 ASN ** H 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 271 GLN ** Q 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 271 GLN ** Z 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 134 GLN ** Z 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 271 GLN k 360 ASN ** k 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 357 ASN ** o 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.3156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 56894 Z= 0.239 Angle : 0.683 14.570 77036 Z= 0.337 Chirality : 0.044 0.267 8370 Planarity : 0.004 0.048 10228 Dihedral : 4.062 22.544 7996 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.42 % Allowed : 18.44 % Favored : 80.15 % 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: 0.36 (0.10), residues: 7036 helix: 1.97 (0.17), residues: 1123 sheet: -0.03 (0.12), residues: 1891 loop : -0.05 (0.10), residues: 4022 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP k 301 HIS 0.006 0.001 HIS v 67 PHE 0.022 0.001 PHE c 195 TYR 0.030 0.001 TYR M 138 ARG 0.016 0.000 ARG Y 147 *********************** 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 577 residues out of total 5886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 494 time to evaluate : 5.773 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: A 146 LEU cc_start: 0.8484 (mm) cc_final: 0.8120 (mm) REVERT: G 146 LEU cc_start: 0.8679 (mm) cc_final: 0.8376 (mm) REVERT: J 205 MET cc_start: 0.6281 (mmm) cc_final: 0.5534 (mmm) REVERT: W 57 MET cc_start: 0.8151 (OUTLIER) cc_final: 0.7573 (mmm) REVERT: W 120 MET cc_start: 0.7174 (tpp) cc_final: 0.6626 (tpp) REVERT: Y 138 TYR cc_start: 0.7761 (t80) cc_final: 0.7110 (t80) REVERT: Y 142 ARG cc_start: 0.8370 (mmm160) cc_final: 0.8051 (ttm110) REVERT: Y 182 GLU cc_start: 0.5246 (tt0) cc_final: 0.4918 (tt0) REVERT: e 146 LEU cc_start: 0.8142 (mm) cc_final: 0.7742 (mm) REVERT: f 120 MET cc_start: 0.7458 (mmm) cc_final: 0.7152 (mmp) REVERT: k 205 MET cc_start: 0.6103 (OUTLIER) cc_final: 0.5829 (mmp) REVERT: l 120 MET cc_start: 0.7401 (mmm) cc_final: 0.6943 (tpt) REVERT: n 146 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.8112 (mm) REVERT: u 144 ARG cc_start: 0.8266 (ttp80) cc_final: 0.7951 (ptm160) REVERT: u 145 MET cc_start: 0.8338 (OUTLIER) cc_final: 0.8106 (ppp) REVERT: v 57 MET cc_start: 0.5873 (mmm) cc_final: 0.5281 (mmm) REVERT: v 71 ASP cc_start: 0.7584 (t0) cc_final: 0.6931 (t0) REVERT: v 123 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8404 (tm) REVERT: y 146 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.8037 (mm) REVERT: z 115 ASP cc_start: 0.8007 (p0) cc_final: 0.7409 (p0) outliers start: 83 outliers final: 49 residues processed: 546 average time/residue: 1.6849 time to fit residues: 1120.9116 Evaluate side-chains 507 residues out of total 5886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 452 time to evaluate : 4.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain B residue 150 GLN Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 89 GLN Chi-restraints excluded: chain E residue 195 PHE Chi-restraints excluded: chain F residue 28 ASP Chi-restraints excluded: chain G residue 231 CYS Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain K residue 99 VAL Chi-restraints excluded: chain M residue 136 THR Chi-restraints excluded: chain M residue 228 MET Chi-restraints excluded: chain M residue 376 LEU Chi-restraints excluded: chain O residue 28 ASP Chi-restraints excluded: chain P residue 143 GLU Chi-restraints excluded: chain S residue 136 THR Chi-restraints excluded: chain T residue 131 GLN Chi-restraints excluded: chain U residue 28 ASP Chi-restraints excluded: chain W residue 57 MET Chi-restraints excluded: chain W residue 66 THR Chi-restraints excluded: chain W residue 107 LYS Chi-restraints excluded: chain W residue 134 GLN Chi-restraints excluded: chain Y residue 136 THR Chi-restraints excluded: chain Z residue 99 VAL Chi-restraints excluded: chain b residue 136 THR Chi-restraints excluded: chain c residue 23 VAL Chi-restraints excluded: chain c residue 99 VAL Chi-restraints excluded: chain e residue 319 ILE Chi-restraints excluded: chain f residue 23 VAL Chi-restraints excluded: chain f residue 99 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 k residue 205 MET Chi-restraints excluded: chain k residue 275 ILE Chi-restraints excluded: chain l residue 23 VAL Chi-restraints excluded: chain l residue 49 VAL Chi-restraints excluded: chain m residue 42 ILE Chi-restraints excluded: chain n residue 136 THR Chi-restraints excluded: chain n residue 146 LEU Chi-restraints excluded: chain o residue 262 ASN Chi-restraints excluded: chain u residue 145 MET Chi-restraints excluded: chain u residue 151 THR Chi-restraints excluded: chain v residue 23 VAL Chi-restraints excluded: chain v residue 48 THR Chi-restraints excluded: chain v residue 49 VAL Chi-restraints excluded: chain v residue 99 VAL Chi-restraints excluded: chain v residue 110 LEU Chi-restraints excluded: chain v residue 114 ASN Chi-restraints excluded: chain v residue 123 LEU Chi-restraints excluded: chain y residue 136 THR Chi-restraints excluded: chain y residue 146 LEU Chi-restraints excluded: chain z residue 21 LEU Chi-restraints excluded: chain z residue 44 VAL Chi-restraints excluded: chain z residue 110 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 694 random chunks: chunk 608 optimal weight: 30.0000 chunk 640 optimal weight: 0.9990 chunk 584 optimal weight: 5.9990 chunk 623 optimal weight: 0.9990 chunk 375 optimal weight: 5.9990 chunk 271 optimal weight: 6.9990 chunk 489 optimal weight: 10.0000 chunk 191 optimal weight: 6.9990 chunk 563 optimal weight: 4.9990 chunk 589 optimal weight: 9.9990 chunk 621 optimal weight: 8.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 GLN ** B 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 89 GLN ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 188 GLN ** H 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 271 GLN ** Q 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 271 GLN ** Z 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 271 GLN ** k 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.3260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 56894 Z= 0.274 Angle : 0.717 18.274 77036 Z= 0.354 Chirality : 0.044 0.287 8370 Planarity : 0.004 0.054 10228 Dihedral : 4.055 23.276 7996 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.37 % Allowed : 18.78 % Favored : 79.86 % 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: 0.34 (0.10), residues: 7036 helix: 1.85 (0.17), residues: 1131 sheet: -0.03 (0.12), residues: 1897 loop : -0.04 (0.10), residues: 4008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP Y 301 HIS 0.005 0.001 HIS f 83 PHE 0.021 0.001 PHE c 195 TYR 0.028 0.001 TYR M 138 ARG 0.016 0.000 ARG A 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 560 residues out of total 5886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 480 time to evaluate : 4.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 LEU cc_start: 0.8481 (mm) cc_final: 0.8060 (mm) REVERT: G 146 LEU cc_start: 0.8685 (mm) cc_final: 0.8404 (mm) REVERT: J 205 MET cc_start: 0.6312 (mmm) cc_final: 0.5573 (mmm) REVERT: S 205 MET cc_start: 0.6116 (mmm) cc_final: 0.5641 (mmm) REVERT: W 57 MET cc_start: 0.8253 (OUTLIER) cc_final: 0.7631 (mmm) REVERT: W 120 MET cc_start: 0.7205 (tpp) cc_final: 0.6673 (tpp) REVERT: Y 143 GLU cc_start: 0.7356 (pp20) cc_final: 0.6739 (pp20) REVERT: k 205 MET cc_start: 0.6122 (OUTLIER) cc_final: 0.5835 (mmp) REVERT: l 120 MET cc_start: 0.7463 (mmm) cc_final: 0.7187 (tpt) REVERT: n 146 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.8228 (mm) REVERT: u 144 ARG cc_start: 0.8329 (ttp80) cc_final: 0.8086 (ptm160) REVERT: u 145 MET cc_start: 0.8347 (OUTLIER) cc_final: 0.8069 (ppp) REVERT: v 57 MET cc_start: 0.6190 (mmm) cc_final: 0.5654 (mmm) REVERT: v 110 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8488 (mm) REVERT: v 123 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8413 (tm) REVERT: y 146 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.8050 (mm) REVERT: z 73 GLU cc_start: 0.8422 (pm20) cc_final: 0.8205 (pm20) REVERT: z 115 ASP cc_start: 0.8047 (p0) cc_final: 0.7453 (p0) outliers start: 80 outliers final: 50 residues processed: 531 average time/residue: 1.6635 time to fit residues: 1077.6527 Evaluate side-chains 499 residues out of total 5886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 442 time to evaluate : 4.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 89 GLN Chi-restraints excluded: chain E residue 195 PHE Chi-restraints excluded: chain F residue 28 ASP Chi-restraints excluded: chain G residue 231 CYS Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain K residue 99 VAL Chi-restraints excluded: chain M residue 136 THR Chi-restraints excluded: chain M residue 228 MET Chi-restraints excluded: chain M residue 376 LEU Chi-restraints excluded: chain N residue 46 VAL Chi-restraints excluded: chain O residue 28 ASP Chi-restraints excluded: chain P residue 143 GLU Chi-restraints excluded: chain S residue 136 THR Chi-restraints excluded: chain T residue 131 GLN Chi-restraints excluded: chain U residue 28 ASP Chi-restraints excluded: chain W residue 57 MET Chi-restraints excluded: chain W residue 66 THR Chi-restraints excluded: chain W residue 107 LYS Chi-restraints excluded: chain W residue 134 GLN Chi-restraints excluded: chain Y residue 136 THR Chi-restraints excluded: chain Z residue 99 VAL Chi-restraints excluded: chain b residue 136 THR Chi-restraints excluded: chain c residue 23 VAL Chi-restraints excluded: chain c residue 99 VAL Chi-restraints excluded: chain e residue 319 ILE Chi-restraints excluded: chain f residue 23 VAL Chi-restraints excluded: chain f residue 99 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 k residue 205 MET Chi-restraints excluded: chain k residue 275 ILE Chi-restraints excluded: chain l residue 23 VAL Chi-restraints excluded: chain l residue 49 VAL Chi-restraints excluded: chain m residue 42 ILE Chi-restraints excluded: chain n residue 136 THR Chi-restraints excluded: chain n residue 146 LEU Chi-restraints excluded: chain o residue 66 THR Chi-restraints excluded: chain o residue 262 ASN Chi-restraints excluded: chain u residue 136 THR Chi-restraints excluded: chain u residue 145 MET Chi-restraints excluded: chain u residue 151 THR Chi-restraints excluded: chain v residue 23 VAL Chi-restraints excluded: chain v residue 49 VAL Chi-restraints excluded: chain v residue 99 VAL Chi-restraints excluded: chain v residue 110 LEU Chi-restraints excluded: chain v residue 114 ASN Chi-restraints excluded: chain v residue 123 LEU Chi-restraints excluded: chain y residue 136 THR Chi-restraints excluded: chain y residue 146 LEU Chi-restraints excluded: chain z residue 21 LEU Chi-restraints excluded: chain z residue 44 VAL Chi-restraints excluded: chain z residue 49 VAL Chi-restraints excluded: chain z residue 110 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 694 random chunks: chunk 409 optimal weight: 0.0870 chunk 659 optimal weight: 5.9990 chunk 402 optimal weight: 0.0470 chunk 312 optimal weight: 7.9990 chunk 458 optimal weight: 6.9990 chunk 691 optimal weight: 8.9990 chunk 636 optimal weight: 2.9990 chunk 550 optimal weight: 20.0000 chunk 57 optimal weight: 10.0000 chunk 425 optimal weight: 3.9990 chunk 337 optimal weight: 9.9990 overall best weight: 2.6262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 GLN G 271 GLN G 374 ASN M 271 GLN P 271 GLN ** Q 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 271 GLN ** Z 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 111 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 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 271 GLN k 374 ASN ** l 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.3352 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= 0.233 Angle : 0.742 17.935 77036 Z= 0.364 Chirality : 0.045 0.298 8370 Planarity : 0.004 0.059 10228 Dihedral : 4.049 28.911 7996 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.13 % Allowed : 19.20 % Favored : 79.67 % 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: 0.32 (0.10), residues: 7036 helix: 1.81 (0.17), residues: 1131 sheet: -0.10 (0.11), residues: 2025 loop : 0.01 (0.10), residues: 3880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP Y 301 HIS 0.006 0.001 HIS f 83 PHE 0.021 0.001 PHE c 195 TYR 0.034 0.001 TYR Y 138 ARG 0.018 0.000 ARG A 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 531 residues out of total 5886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 465 time to evaluate : 5.082 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: A 146 LEU cc_start: 0.8451 (mm) cc_final: 0.8021 (mm) REVERT: B 120 MET cc_start: 0.6885 (tpp) cc_final: 0.6595 (tpt) REVERT: B 134 GLN cc_start: 0.8347 (pp30) cc_final: 0.8061 (pp30) REVERT: G 146 LEU cc_start: 0.8685 (mm) cc_final: 0.8397 (mm) REVERT: J 205 MET cc_start: 0.6284 (mmm) cc_final: 0.5591 (mmm) REVERT: K 134 GLN cc_start: 0.6828 (pp30) cc_final: 0.6607 (pm20) REVERT: S 205 MET cc_start: 0.6016 (mmm) cc_final: 0.5569 (mmm) REVERT: T 120 MET cc_start: 0.7678 (tmm) cc_final: 0.7450 (tmt) REVERT: V 205 MET cc_start: 0.6072 (mmm) cc_final: 0.5787 (mmm) REVERT: W 57 MET cc_start: 0.8126 (OUTLIER) cc_final: 0.7556 (mmm) REVERT: W 120 MET cc_start: 0.7206 (tpp) cc_final: 0.6705 (tpp) REVERT: Y 138 TYR cc_start: 0.7705 (t80) cc_final: 0.7476 (t80) REVERT: e 146 LEU cc_start: 0.8124 (mm) cc_final: 0.7743 (mm) REVERT: f 120 MET cc_start: 0.7171 (mmm) cc_final: 0.6567 (mmp) REVERT: k 205 MET cc_start: 0.6094 (OUTLIER) cc_final: 0.5819 (mmp) REVERT: l 120 MET cc_start: 0.7503 (mmm) cc_final: 0.7069 (tpt) REVERT: u 145 MET cc_start: 0.8348 (OUTLIER) cc_final: 0.8008 (ppp) REVERT: v 57 MET cc_start: 0.6106 (mmm) cc_final: 0.5608 (mmm) REVERT: v 71 ASP cc_start: 0.7663 (t0) cc_final: 0.7415 (OUTLIER) REVERT: v 73 GLU cc_start: 0.8366 (pm20) cc_final: 0.8151 (pm20) REVERT: v 120 MET cc_start: 0.7482 (OUTLIER) cc_final: 0.7138 (ptt) REVERT: v 123 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8352 (tm) REVERT: y 146 LEU cc_start: 0.8401 (OUTLIER) cc_final: 0.7784 (mm) REVERT: z 115 ASP cc_start: 0.8076 (p0) cc_final: 0.7478 (p0) outliers start: 66 outliers final: 49 residues processed: 506 average time/residue: 1.6332 time to fit residues: 1012.9480 Evaluate side-chains 480 residues out of total 5886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 426 time to evaluate : 4.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain B residue 150 GLN Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 89 GLN Chi-restraints excluded: chain E residue 195 PHE Chi-restraints excluded: chain G residue 231 CYS Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain K residue 99 VAL Chi-restraints excluded: chain M residue 136 THR Chi-restraints excluded: chain M residue 228 MET Chi-restraints excluded: chain M residue 231 CYS Chi-restraints excluded: chain M residue 376 LEU Chi-restraints excluded: chain N residue 46 VAL Chi-restraints excluded: chain O residue 28 ASP Chi-restraints excluded: chain P residue 143 GLU Chi-restraints excluded: chain S residue 136 THR Chi-restraints excluded: chain T residue 131 GLN Chi-restraints excluded: chain U residue 28 ASP Chi-restraints excluded: chain W residue 57 MET Chi-restraints excluded: chain W residue 66 THR Chi-restraints excluded: chain W residue 107 LYS Chi-restraints excluded: chain W residue 134 GLN Chi-restraints excluded: chain Y residue 136 THR Chi-restraints excluded: chain Z residue 99 VAL Chi-restraints excluded: chain b residue 136 THR Chi-restraints excluded: chain b residue 145 MET Chi-restraints excluded: chain b residue 275 ILE Chi-restraints excluded: chain c residue 23 VAL Chi-restraints excluded: chain c residue 99 VAL Chi-restraints excluded: chain c residue 150 GLN Chi-restraints excluded: chain f residue 23 VAL Chi-restraints excluded: chain f residue 99 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 k residue 205 MET Chi-restraints excluded: chain k residue 275 ILE Chi-restraints excluded: chain l residue 23 VAL Chi-restraints excluded: chain l residue 49 VAL Chi-restraints excluded: chain m residue 42 ILE Chi-restraints excluded: chain o residue 66 THR Chi-restraints excluded: chain o residue 262 ASN Chi-restraints excluded: chain u residue 136 THR Chi-restraints excluded: chain u residue 145 MET Chi-restraints excluded: chain u residue 151 THR Chi-restraints excluded: chain v residue 23 VAL Chi-restraints excluded: chain v residue 49 VAL Chi-restraints excluded: chain v residue 114 ASN Chi-restraints excluded: chain v residue 120 MET Chi-restraints excluded: chain v residue 123 LEU Chi-restraints excluded: chain y residue 146 LEU Chi-restraints excluded: chain z residue 44 VAL Chi-restraints excluded: chain z residue 49 VAL Chi-restraints excluded: chain z residue 110 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 694 random chunks: chunk 437 optimal weight: 8.9990 chunk 586 optimal weight: 2.9990 chunk 168 optimal weight: 9.9990 chunk 507 optimal weight: 0.9990 chunk 81 optimal weight: 8.9990 chunk 152 optimal weight: 5.9990 chunk 551 optimal weight: 20.0000 chunk 230 optimal weight: 6.9990 chunk 566 optimal weight: 9.9990 chunk 69 optimal weight: 9.9990 chunk 101 optimal weight: 5.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 GLN G 271 GLN M 271 GLN P 271 GLN ** Q 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 271 GLN Y 271 GLN ** Z 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 271 GLN ** f 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 271 GLN ** k 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.050726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2601 r_free = 0.2601 target = 0.033011 restraints weight = 232355.418| |-----------------------------------------------------------------------------| r_work (start): 0.2535 rms_B_bonded: 3.60 r_work: 0.2393 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.3396 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= 0.308 Angle : 0.762 19.855 77036 Z= 0.374 Chirality : 0.045 0.379 8370 Planarity : 0.004 0.063 10228 Dihedral : 4.095 34.431 7996 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.11 % Allowed : 19.31 % Favored : 79.58 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: 0.35 (0.10), residues: 7036 helix: 1.81 (0.17), residues: 1131 sheet: -0.01 (0.12), residues: 1919 loop : -0.01 (0.10), residues: 3986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP Y 301 HIS 0.007 0.001 HIS f 83 PHE 0.021 0.001 PHE c 195 TYR 0.038 0.001 TYR Y 138 ARG 0.018 0.000 ARG Y 147 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17400.03 seconds wall clock time: 302 minutes 27.81 seconds (18147.81 seconds total)