Starting phenix.real_space_refine on Tue Jun 25 07:58:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rt8_19482/06_2024/8rt8_19482.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rt8_19482/06_2024/8rt8_19482.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rt8_19482/06_2024/8rt8_19482.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rt8_19482/06_2024/8rt8_19482.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rt8_19482/06_2024/8rt8_19482.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rt8_19482/06_2024/8rt8_19482.pdb" } resolution = 3.05 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= 0.024 sd= 0.071 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 ARG 144": "NH1" <-> "NH2" Residue "A ASP 214": "OD1" <-> "OD2" Residue "A GLU 218": "OE1" <-> "OE2" Residue "A ARG 235": "NH1" <-> "NH2" Residue "A ARG 243": "NH1" <-> "NH2" Residue "A ARG 249": "NH1" <-> "NH2" Residue "A TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 274": "NH1" <-> "NH2" Residue "A GLU 295": "OE1" <-> "OE2" Residue "A ARG 304": "NH1" <-> "NH2" Residue "A GLU 308": "OE1" <-> "OE2" Residue "A GLU 353": "OE1" <-> "OE2" Residue "A ARG 372": "NH1" <-> "NH2" Residue "A ASP 380": "OD1" <-> "OD2" Residue "A PHE 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 22": "OD1" <-> "OD2" Residue "B GLU 62": "OE1" <-> "OE2" Residue "B TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 109": "NH1" <-> "NH2" Residue "B ARG 113": "NH1" <-> "NH2" Residue "B ARG 136": "NH1" <-> "NH2" Residue "B PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 199": "OE1" <-> "OE2" Residue "B ARG 233": "NH1" <-> "NH2" Residue "B ARG 259": "NH1" <-> "NH2" Residue "B ARG 260": "NH1" <-> "NH2" Residue "D GLU 143": "OE1" <-> "OE2" Residue "D ARG 144": "NH1" <-> "NH2" Residue "D ARG 235": "NH1" <-> "NH2" Residue "D ARG 243": "NH1" <-> "NH2" Residue "D ASP 248": "OD1" <-> "OD2" Residue "D ARG 249": "NH1" <-> "NH2" Residue "D PHE 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 274": "NH1" <-> "NH2" Residue "D ARG 304": "NH1" <-> "NH2" Residue "D ARG 372": "NH1" <-> "NH2" Residue "E TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 60": "OE1" <-> "OE2" Residue "E TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 109": "NH1" <-> "NH2" Residue "E ARG 113": "NH1" <-> "NH2" Residue "E GLU 122": "OE1" <-> "OE2" Residue "E TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 141": "NH1" <-> "NH2" Residue "E GLU 149": "OE1" <-> "OE2" Residue "E PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 139": "OE1" <-> "OE2" Residue "G ARG 144": "NH1" <-> "NH2" Residue "G ASP 204": "OD1" <-> "OD2" Residue "G GLU 218": "OE1" <-> "OE2" Residue "G ARG 235": "NH1" <-> "NH2" Residue "G ARG 243": "NH1" <-> "NH2" Residue "G ARG 249": "NH1" <-> "NH2" Residue "G PHE 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 274": "NH1" <-> "NH2" Residue "G ARG 304": "NH1" <-> "NH2" Residue "G GLU 308": "OE1" <-> "OE2" Residue "G ARG 372": "NH1" <-> "NH2" Residue "H TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 136": "NH1" <-> "NH2" Residue "H ARG 141": "NH1" <-> "NH2" Residue "H GLU 149": "OE1" <-> "OE2" Residue "H TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 189": "OD1" <-> "OD2" 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 "J TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 139": "OE1" <-> "OE2" Residue "J ARG 144": "NH1" <-> "NH2" Residue "J GLU 182": "OE1" <-> "OE2" Residue "J ASP 214": "OD1" <-> "OD2" Residue "J ARG 235": "NH1" <-> "NH2" Residue "J ASP 236": "OD1" <-> "OD2" Residue "J ARG 243": "NH1" <-> "NH2" Residue "J ARG 249": "NH1" <-> "NH2" Residue "J TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 274": "NH1" <-> "NH2" Residue "J GLU 295": "OE1" <-> "OE2" Residue "J ARG 304": "NH1" <-> "NH2" Residue "J GLU 308": "OE1" <-> "OE2" Residue "J ARG 372": "NH1" <-> "NH2" Residue "J ASP 380": "OD1" <-> "OD2" Residue "J PHE 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 22": "OD1" <-> "OD2" Residue "K TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 109": "NH1" <-> "NH2" Residue "K ARG 113": "NH1" <-> "NH2" Residue "K TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 141": "NH1" <-> "NH2" Residue "K GLU 145": "OE1" <-> "OE2" Residue "K GLU 149": "OE1" <-> "OE2" Residue "K ARG 233": "NH1" <-> "NH2" Residue "K ASP 250": "OD1" <-> "OD2" Residue "K ARG 259": "NH1" <-> "NH2" Residue "K ARG 260": "NH1" <-> "NH2" Residue "L GLU 41": "OE1" <-> "OE2" Residue "M GLU 143": "OE1" <-> "OE2" Residue "M ARG 144": "NH1" <-> "NH2" Residue "M GLU 185": "OE1" <-> "OE2" Residue "M ASP 204": "OD1" <-> "OD2" Residue "M ARG 235": "NH1" <-> "NH2" Residue "M ARG 243": "NH1" <-> "NH2" Residue "M ARG 249": "NH1" <-> "NH2" Residue "M PHE 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 274": "NH1" <-> "NH2" Residue "M ARG 304": "NH1" <-> "NH2" Residue "M ASP 324": "OD1" <-> "OD2" Residue "M ARG 372": "NH1" <-> "NH2" Residue "M TYR 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 109": "NH1" <-> "NH2" Residue "N ARG 113": "NH1" <-> "NH2" Residue "N GLU 122": "OE1" <-> "OE2" Residue "N TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 141": "NH1" <-> "NH2" Residue "N GLU 145": "OE1" <-> "OE2" Residue "N PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 199": "OE1" <-> "OE2" Residue "N ARG 233": "NH1" <-> "NH2" Residue "N ARG 259": "NH1" <-> "NH2" Residue "N ARG 260": "NH1" <-> "NH2" Residue "P GLU 143": "OE1" <-> "OE2" Residue "P ARG 144": "NH1" <-> "NH2" Residue "P GLU 182": "OE1" <-> "OE2" Residue "P ASP 214": "OD1" <-> "OD2" Residue "P ARG 235": "NH1" <-> "NH2" Residue "P ARG 243": "NH1" <-> "NH2" Residue "P ARG 249": "NH1" <-> "NH2" Residue "P TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 274": "NH1" <-> "NH2" Residue "P ARG 304": "NH1" <-> "NH2" Residue "P GLU 371": "OE1" <-> "OE2" Residue "P ARG 372": "NH1" <-> "NH2" Residue "Q GLU 60": "OE1" <-> "OE2" Residue "Q TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 109": "NH1" <-> "NH2" Residue "Q ARG 113": "NH1" <-> "NH2" Residue "Q PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 141": "NH1" <-> "NH2" Residue "Q TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 202": "OE1" <-> "OE2" Residue "Q ARG 233": "NH1" <-> "NH2" Residue "Q PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 240": "OE1" <-> "OE2" Residue "Q ARG 259": "NH1" <-> "NH2" Residue "Q ARG 260": "NH1" <-> "NH2" Residue "R PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 144": "NH1" <-> "NH2" Residue "S ARG 235": "NH1" <-> "NH2" Residue "S ARG 243": "NH1" <-> "NH2" Residue "S ARG 249": "NH1" <-> "NH2" Residue "S TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 274": "NH1" <-> "NH2" Residue "S GLU 276": "OE1" <-> "OE2" Residue "S ARG 304": "NH1" <-> "NH2" Residue "S ASP 324": "OD1" <-> "OD2" Residue "S GLU 371": "OE1" <-> "OE2" Residue "S ARG 372": "NH1" <-> "NH2" Residue "S ASP 380": "OD1" <-> "OD2" Residue "S PHE 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 73": "OE1" <-> "OE2" Residue "T PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 109": "NH1" <-> "NH2" Residue "T ARG 113": "NH1" <-> "NH2" Residue "T ARG 141": "NH1" <-> "NH2" Residue "T GLU 145": "OE1" <-> "OE2" Residue "T TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 233": "NH1" <-> "NH2" Residue "T PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 259": "NH1" <-> "NH2" Residue "T ARG 260": "NH1" <-> "NH2" Residue "U PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 PHE 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 274": "NH1" <-> "NH2" Residue "V ARG 304": "NH1" <-> "NH2" Residue "V GLU 308": "OE1" <-> "OE2" Residue "V GLU 353": "OE1" <-> "OE2" Residue "V ARG 372": "NH1" <-> "NH2" Residue "V ASP 382": "OD1" <-> "OD2" Residue "W TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 62": "OE1" <-> "OE2" Residue "W TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 109": "NH1" <-> "NH2" Residue "W ARG 113": "NH1" <-> "NH2" Residue "W ASP 115": "OD1" <-> "OD2" Residue "W GLU 122": "OE1" <-> "OE2" Residue "W TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 136": "NH1" <-> "NH2" Residue "W GLU 137": "OE1" <-> "OE2" Residue "W ARG 141": "NH1" <-> "NH2" Residue "W PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 149": "OE1" <-> "OE2" Residue "W PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 199": "OE1" <-> "OE2" Residue "W ARG 233": "NH1" <-> "NH2" Residue "W ARG 259": "NH1" <-> "NH2" Residue "W ARG 260": "NH1" <-> "NH2" Residue "Y TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 139": "OE1" <-> "OE2" Residue "Y ARG 144": "NH1" <-> "NH2" Residue "Y ARG 235": "NH1" <-> "NH2" Residue "Y ARG 243": "NH1" <-> "NH2" Residue "Y ASP 248": "OD1" <-> "OD2" Residue "Y ARG 249": "NH1" <-> "NH2" Residue "Y PHE 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 274": "NH1" <-> "NH2" Residue "Y ARG 304": "NH1" <-> "NH2" Residue "Y ARG 372": "NH1" <-> "NH2" Residue "Y ASP 380": "OD1" <-> "OD2" Residue "Y ASP 382": "OD1" <-> "OD2" Residue "Y GLU 390": "OE1" <-> "OE2" Residue "Z ASP 30": "OD1" <-> "OD2" Residue "Z PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 109": "NH1" <-> "NH2" Residue "Z ARG 113": "NH1" <-> "NH2" Residue "Z GLU 137": "OE1" <-> "OE2" Residue "Z ARG 141": "NH1" <-> "NH2" Residue "Z PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 233": "NH1" <-> "NH2" Residue "Z ARG 259": "NH1" <-> "NH2" Residue "Z ARG 260": "NH1" <-> "NH2" Residue "a ASP 28": "OD1" <-> "OD2" Residue "a PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 41": "OE1" <-> "OE2" Residue "b GLU 139": "OE1" <-> "OE2" Residue "b ARG 144": "NH1" <-> "NH2" Residue "b ARG 235": "NH1" <-> "NH2" Residue "b ARG 243": "NH1" <-> "NH2" Residue "b ARG 249": "NH1" <-> "NH2" Residue "b PHE 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 274": "NH1" <-> "NH2" Residue "b GLU 276": "OE1" <-> "OE2" Residue "b ARG 304": "NH1" <-> "NH2" Residue "b ARG 372": "NH1" <-> "NH2" Residue "c PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 91": "OE1" <-> "OE2" Residue "c PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 109": "NH1" <-> "NH2" Residue "c ARG 113": "NH1" <-> "NH2" Residue "c GLU 122": "OE1" <-> "OE2" Residue "c TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 136": "NH1" <-> "NH2" Residue "c ARG 141": "NH1" <-> "NH2" Residue "c GLU 149": "OE1" <-> "OE2" Residue "c ARG 151": "NH1" <-> "NH2" Residue "c PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 199": "OE1" <-> "OE2" Residue "c ARG 233": "NH1" <-> "NH2" Residue "c GLU 240": "OE1" <-> "OE2" Residue "c ASP 250": "OD1" <-> "OD2" Residue "c ARG 259": "NH1" <-> "NH2" Residue "c ARG 260": "NH1" <-> "NH2" Residue "d ASP 28": "OD1" <-> "OD2" Residue "d PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ARG 144": "NH1" <-> "NH2" Residue "e GLU 182": "OE1" <-> "OE2" Residue "e ASP 204": "OD1" <-> "OD2" Residue "e ARG 235": "NH1" <-> "NH2" Residue "e ARG 243": "NH1" <-> "NH2" Residue "e ARG 249": "NH1" <-> "NH2" Residue "e PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ARG 274": "NH1" <-> "NH2" Residue "e GLU 276": "OE1" <-> "OE2" Residue "e GLU 295": "OE1" <-> "OE2" Residue "e ARG 304": "NH1" <-> "NH2" Residue "e GLU 308": "OE1" <-> "OE2" Residue "e ASP 324": "OD1" <-> "OD2" Residue "e ARG 372": "NH1" <-> "NH2" Residue "e ASP 385": "OD1" <-> "OD2" Residue "f GLU 73": "OE1" <-> "OE2" Residue "f TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 91": "OE1" <-> "OE2" 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 TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ARG 141": "NH1" <-> "NH2" Residue "f GLU 149": "OE1" <-> "OE2" Residue "f GLU 202": "OE1" <-> "OE2" Residue "f ARG 233": "NH1" <-> "NH2" Residue "f ARG 259": "NH1" <-> "NH2" Residue "f ARG 260": "NH1" <-> "NH2" Residue "h TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ARG 144": "NH1" <-> "NH2" Residue "h ARG 235": "NH1" <-> "NH2" Residue "h ARG 243": "NH1" <-> "NH2" Residue "h ARG 249": "NH1" <-> "NH2" Residue "h ARG 274": "NH1" <-> "NH2" Residue "h GLU 276": "OE1" <-> "OE2" Residue "h ARG 304": "NH1" <-> "NH2" Residue "h ASP 324": "OD1" <-> "OD2" Residue "h ARG 372": "NH1" <-> "NH2" Residue "h TYR 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ARG 109": "NH1" <-> "NH2" Residue "i ARG 113": "NH1" <-> "NH2" Residue "i PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ARG 141": "NH1" <-> "NH2" Residue "i GLU 145": "OE1" <-> "OE2" Residue "i GLU 149": "OE1" <-> "OE2" Residue "i TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ARG 233": "NH1" <-> "NH2" Residue "i ASP 250": "OD1" <-> "OD2" Residue "i ARG 259": "NH1" <-> "NH2" Residue "i ARG 260": "NH1" <-> "NH2" Residue "k ARG 144": "NH1" <-> "NH2" Residue "k GLU 218": "OE1" <-> "OE2" Residue "k ARG 235": "NH1" <-> "NH2" Residue "k TYR 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ARG 243": "NH1" <-> "NH2" Residue "k ARG 249": "NH1" <-> "NH2" Residue "k TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k PHE 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ARG 274": "NH1" <-> "NH2" Residue "k ARG 304": "NH1" <-> "NH2" Residue "k GLU 308": "OE1" <-> "OE2" Residue "k GLU 371": "OE1" <-> "OE2" Residue "k ARG 372": "NH1" <-> "NH2" Residue "k ASP 380": "OD1" <-> "OD2" Residue "k ASP 382": "OD1" <-> "OD2" Residue "k PHE 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k TYR 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ARG 109": "NH1" <-> "NH2" Residue "l ARG 113": "NH1" <-> "NH2" Residue "l TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ARG 136": "NH1" <-> "NH2" Residue "l GLU 137": "OE1" <-> "OE2" Residue "l ARG 141": "NH1" <-> "NH2" Residue "l TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ARG 233": "NH1" <-> "NH2" Residue "l PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ARG 259": "NH1" <-> "NH2" Residue "l ARG 260": "NH1" <-> "NH2" Residue "m PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n GLU 143": "OE1" <-> "OE2" Residue "n ARG 144": "NH1" <-> "NH2" Residue "n GLU 218": "OE1" <-> "OE2" Residue "n ARG 235": "NH1" <-> "NH2" Residue "n TYR 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ARG 243": "NH1" <-> "NH2" Residue "n ARG 249": "NH1" <-> "NH2" Residue "n PHE 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ARG 274": "NH1" <-> "NH2" Residue "n ASP 286": "OD1" <-> "OD2" Residue "n ARG 304": "NH1" <-> "NH2" Residue "n GLU 353": "OE1" <-> "OE2" Residue "n ARG 372": "NH1" <-> "NH2" Residue "o PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ARG 109": "NH1" <-> "NH2" Residue "o ARG 113": "NH1" <-> "NH2" Residue "o TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ARG 136": "NH1" <-> "NH2" Residue "o ARG 141": "NH1" <-> "NH2" Residue "o GLU 145": "OE1" <-> "OE2" Residue "o ARG 151": "NH1" <-> "NH2" Residue "o TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o TYR 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ARG 233": "NH1" <-> "NH2" Residue "o ARG 259": "NH1" <-> "NH2" Residue "o ARG 260": "NH1" <-> "NH2" Residue "p PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v ASP 47": "OD1" <-> "OD2" Residue "v TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v GLU 91": "OE1" <-> "OE2" Residue "v ARG 109": "NH1" <-> "NH2" Residue "v ARG 113": "NH1" <-> "NH2" Residue "v GLU 122": "OE1" <-> "OE2" Residue "y TYR 138": "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 64": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z ARG 109": "NH1" <-> "NH2" Residue "z ARG 113": "NH1" <-> "NH2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 55802 Number of models: 1 Model: "" Number of chains: 46 Chain: "A" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1670 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 211} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 1955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1955 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 11, 'TRANS': 234} Chain: "C" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 213 Classifications: {'peptide': 28} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 22} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1670 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 211} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 1955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1955 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 11, 'TRANS': 234} Chain: "F" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 213 Classifications: {'peptide': 28} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 22} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1670 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 211} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "H" Number of atoms: 1955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1955 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 11, 'TRANS': 234} Chain: "I" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 213 Classifications: {'peptide': 28} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 22} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "J" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1670 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 211} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "K" Number of atoms: 1955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1955 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 11, 'TRANS': 234} Chain: "L" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 213 Classifications: {'peptide': 28} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 22} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "M" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1670 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 211} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "N" Number of atoms: 1955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1955 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 11, 'TRANS': 234} Chain: "O" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 213 Classifications: {'peptide': 28} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 22} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "P" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1670 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 211} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "Q" Number of atoms: 1955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1955 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 11, 'TRANS': 234} Chain: "R" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 213 Classifications: {'peptide': 28} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 22} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "S" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1670 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 211} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "T" Number of atoms: 1955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1955 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 11, 'TRANS': 234} Chain: "U" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 213 Classifications: {'peptide': 28} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 22} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "V" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1670 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 211} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "W" Number of atoms: 1955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1955 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 11, 'TRANS': 234} Chain: "X" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 213 Classifications: {'peptide': 28} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 22} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "Y" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1670 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 211} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "Z" Number of atoms: 1955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1955 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 11, 'TRANS': 234} Chain: "a" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 213 Classifications: {'peptide': 28} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 22} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "b" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1670 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 211} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "c" Number of atoms: 1955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1955 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 11, 'TRANS': 234} Chain: "d" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 213 Classifications: {'peptide': 28} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 22} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "e" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1670 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 211} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "f" Number of atoms: 1955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1955 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 11, 'TRANS': 234} Chain: "g" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 213 Classifications: {'peptide': 28} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 22} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "h" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1670 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 211} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "i" Number of atoms: 1955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1955 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 11, 'TRANS': 234} Chain: "j" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 213 Classifications: {'peptide': 28} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 22} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "k" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1670 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 211} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "l" Number of atoms: 1955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1955 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 11, 'TRANS': 234} Chain: "m" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 213 Classifications: {'peptide': 28} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 22} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "n" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1670 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 211} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "o" Number of atoms: 1955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1955 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 11, 'TRANS': 234} Chain: "p" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 213 Classifications: {'peptide': 28} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 22} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "u" Number of atoms: 149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 149 Classifications: {'peptide': 19} Link IDs: {'PTRANS': 1, 'TRANS': 17} Chain: "v" Number of atoms: 886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 886 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 4, 'TRANS': 103} Chain: "y" Number of atoms: 149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 149 Classifications: {'peptide': 19} Link IDs: {'PTRANS': 1, 'TRANS': 17} Chain: "z" Number of atoms: 886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 886 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 4, 'TRANS': 103} Time building chain proxies: 21.83, per 1000 atoms: 0.39 Number of scatterers: 55802 At special positions: 0 Unit cell: (192.06, 195.261, 156.849, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 204 16.00 O 10556 8.00 N 10180 7.00 C 34862 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 215 " - pdb=" SG CYS A 231 " distance=2.03 Simple disulfide: pdb=" SG CYS D 215 " - pdb=" SG CYS D 231 " distance=2.03 Simple disulfide: pdb=" SG CYS G 215 " - pdb=" SG CYS G 231 " distance=2.03 Simple disulfide: pdb=" SG CYS J 215 " - pdb=" SG CYS J 231 " distance=2.03 Simple disulfide: pdb=" SG CYS M 215 " - pdb=" SG CYS M 231 " distance=2.03 Simple disulfide: pdb=" SG CYS P 215 " - pdb=" SG CYS P 231 " distance=2.03 Simple disulfide: pdb=" SG CYS S 215 " - pdb=" SG CYS S 231 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS h 215 " - pdb=" SG CYS h 231 " distance=2.05 Simple disulfide: pdb=" SG CYS k 215 " - pdb=" SG CYS k 231 " distance=2.03 Simple disulfide: pdb=" SG CYS n 215 " - pdb=" SG CYS n 231 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 17.08 Conformation dependent library (CDL) restraints added in 8.1 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: 104 helices and 144 sheets defined 17.7% alpha, 26.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.02 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 202 through 204 No H-bonds generated for 'chain 'A' and resid 202 through 204' Processing helix chain 'A' and resid 305 through 329 removed outlier: 6.043A pdb=" N GLY A 312 " --> pdb=" O GLU A 308 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N ALA A 313 " --> pdb=" O ARG A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 359 removed outlier: 3.685A pdb=" N ASN A 357 " --> pdb=" O GLU A 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 151 removed outlier: 3.675A pdb=" N ALA B 138 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ARG B 151 " --> pdb=" O ALA B 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 148 Processing helix chain 'D' and resid 180 through 186 Processing helix chain 'D' and resid 306 through 329 removed outlier: 5.873A pdb=" N GLY D 312 " --> pdb=" O GLU D 308 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N ALA D 313 " --> pdb=" O ARG D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 359 removed outlier: 3.593A pdb=" N ASN D 357 " --> pdb=" O GLU D 353 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 151 removed outlier: 3.980A pdb=" N ALA E 138 " --> pdb=" O GLN E 134 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASN E 139 " --> pdb=" O THR E 135 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA E 146 " --> pdb=" O ALA E 142 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N GLU E 149 " --> pdb=" O GLU E 145 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ARG E 151 " --> pdb=" O ALA E 147 " (cutoff:3.500A) Processing helix chain 'E' and resid 166 through 169 Processing helix chain 'F' and resid 39 through 43 removed outlier: 3.540A pdb=" N ILE F 42 " --> pdb=" O PRO F 39 " (cutoff:3.500A) 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: 5.829A pdb=" N GLY G 312 " --> pdb=" O GLU G 308 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N ALA G 313 " --> pdb=" O ARG G 309 " (cutoff:3.500A) Processing helix chain 'G' and resid 350 through 359 removed outlier: 3.814A pdb=" N ASN G 357 " --> pdb=" O GLU G 353 " (cutoff:3.500A) Processing helix chain 'H' and resid 128 through 150 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 182 through 187 Processing helix chain 'J' and resid 306 through 329 removed outlier: 6.298A pdb=" N GLY J 312 " --> pdb=" O GLU J 308 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N ALA J 313 " --> pdb=" O ARG J 309 " (cutoff:3.500A) Processing helix chain 'J' and resid 350 through 358 Processing helix chain 'K' and resid 127 through 151 removed outlier: 4.380A pdb=" N GLN K 131 " --> pdb=" O TYR K 127 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ARG K 151 " --> pdb=" O ALA K 147 " (cutoff:3.500A) Processing helix chain 'K' and resid 166 through 169 Processing helix chain 'L' and resid 39 through 43 removed outlier: 3.633A pdb=" N ILE L 42 " --> pdb=" O PRO L 39 " (cutoff:3.500A) Processing helix chain 'M' and resid 136 through 148 Processing helix chain 'M' and resid 182 through 187 Processing helix chain 'M' and resid 305 through 329 removed outlier: 6.165A pdb=" N GLY M 312 " --> pdb=" O GLU M 308 " (cutoff:3.500A) removed outlier: 5.582A 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: 3.830A 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 Processing helix chain 'P' and resid 136 through 148 Processing helix chain 'P' and resid 180 through 187 Processing helix chain 'P' and resid 305 through 330 removed outlier: 5.425A pdb=" N GLY P 312 " --> pdb=" O GLU P 308 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N ALA P 313 " --> pdb=" O ARG P 309 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLY P 330 " --> pdb=" O ALA P 326 " (cutoff:3.500A) Processing helix chain 'P' and resid 350 through 358 Processing helix chain 'Q' and resid 127 through 151 removed outlier: 3.790A 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 'R' and resid 39 through 43 Processing helix chain 'S' and resid 136 through 148 removed outlier: 3.694A pdb=" N LEU S 140 " --> pdb=" O THR S 136 " (cutoff:3.500A) Processing helix chain 'S' and resid 180 through 186 Processing helix chain 'S' and resid 305 through 329 removed outlier: 6.266A pdb=" N GLY S 312 " --> pdb=" O GLU S 308 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N ALA S 313 " --> pdb=" O ARG S 309 " (cutoff:3.500A) Processing helix chain 'S' and resid 350 through 359 removed outlier: 3.554A pdb=" N ASN S 357 " --> pdb=" O GLU S 353 " (cutoff:3.500A) Processing helix chain 'T' and resid 127 through 151 removed outlier: 3.508A pdb=" N GLU T 137 " --> pdb=" O ARG T 133 " (cutoff:3.500A) removed outlier: 3.724A 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 'U' and resid 39 through 43 Processing helix chain 'V' and resid 136 through 148 Processing helix chain 'V' and resid 180 through 186 removed outlier: 3.688A pdb=" N ALA V 184 " --> pdb=" O GLY V 180 " (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: 5.692A pdb=" N GLY V 312 " --> pdb=" O GLU V 308 " (cutoff:3.500A) removed outlier: 5.123A 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 71 through 75 removed outlier: 3.811A pdb=" N TYR W 75 " --> pdb=" O SER W 72 " (cutoff:3.500A) Processing helix chain 'W' and resid 128 through 150 removed outlier: 3.502A pdb=" N ARG W 136 " --> pdb=" O ALA W 132 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU W 137 " --> pdb=" O ARG W 133 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA W 138 " --> pdb=" O GLN W 134 " (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 202 through 204 No H-bonds generated for 'chain 'Y' and resid 202 through 204' Processing helix chain 'Y' and resid 305 through 329 removed outlier: 5.750A pdb=" N GLY Y 312 " --> pdb=" O GLU Y 308 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N ALA Y 313 " --> pdb=" O ARG Y 309 " (cutoff:3.500A) Processing helix chain 'Y' and resid 350 through 359 Processing helix chain 'Z' and resid 127 through 150 removed outlier: 4.198A pdb=" N GLN Z 131 " --> pdb=" O TYR Z 127 " (cutoff:3.500A) Processing helix chain 'Z' and resid 166 through 169 Processing helix chain 'b' and resid 136 through 148 Processing helix chain 'b' and resid 180 through 187 Processing helix chain 'b' and resid 306 through 329 removed outlier: 6.045A pdb=" N GLY b 312 " --> pdb=" O GLU b 308 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N ALA b 313 " --> pdb=" O ARG b 309 " (cutoff:3.500A) Processing helix chain 'b' and resid 350 through 359 removed outlier: 3.771A pdb=" N ASN b 357 " --> pdb=" O GLU b 353 " (cutoff:3.500A) Processing helix chain 'c' and resid 127 through 151 removed outlier: 3.744A pdb=" N GLN c 131 " --> pdb=" O TYR c 127 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU c 137 " --> pdb=" O ARG c 133 " (cutoff:3.500A) removed outlier: 4.162A 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 186 Processing helix chain 'e' and resid 202 through 204 No H-bonds generated for 'chain 'e' and resid 202 through 204' Processing helix chain 'e' and resid 305 through 329 removed outlier: 5.756A pdb=" N GLY e 312 " --> pdb=" O GLU e 308 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N ALA e 313 " --> pdb=" O ARG e 309 " (cutoff:3.500A) Processing helix chain 'e' and resid 350 through 359 removed outlier: 3.646A pdb=" N ASN e 357 " --> pdb=" O GLU e 353 " (cutoff:3.500A) Processing helix chain 'f' and resid 127 through 135 Processing helix chain 'f' and resid 136 through 151 removed outlier: 3.772A pdb=" N ARG f 151 " --> pdb=" O ALA f 147 " (cutoff:3.500A) Processing helix chain 'f' and resid 166 through 169 Processing helix chain 'g' and resid 39 through 43 removed outlier: 3.547A pdb=" N ILE g 42 " --> pdb=" O PRO g 39 " (cutoff:3.500A) Processing helix chain 'h' and resid 136 through 148 removed outlier: 3.653A pdb=" N LEU h 140 " --> pdb=" O THR h 136 " (cutoff:3.500A) Processing helix chain 'h' and resid 182 through 187 Processing helix chain 'h' and resid 305 through 330 removed outlier: 5.609A pdb=" N GLY h 312 " --> pdb=" O GLU h 308 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N ALA h 313 " --> pdb=" O ARG h 309 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY h 330 " --> pdb=" O ALA h 326 " (cutoff:3.500A) Processing helix chain 'h' and resid 350 through 359 Processing helix chain 'i' and resid 127 through 151 removed outlier: 3.575A pdb=" N GLN i 131 " --> pdb=" O TYR i 127 " (cutoff:3.500A) removed outlier: 3.825A 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 202 through 204 No H-bonds generated for 'chain 'k' and resid 202 through 204' Processing helix chain 'k' and resid 305 through 329 removed outlier: 5.941A pdb=" N GLY k 312 " --> pdb=" O GLU k 308 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N ALA k 313 " --> pdb=" O ARG k 309 " (cutoff:3.500A) Processing helix chain 'k' and resid 350 through 359 Processing helix chain 'l' and resid 127 through 151 removed outlier: 3.888A pdb=" N ARG l 151 " --> pdb=" O ALA l 147 " (cutoff:3.500A) Processing helix chain 'l' and resid 166 through 169 Processing helix chain 'm' and resid 39 through 43 Processing helix chain 'n' and resid 136 through 148 Processing helix chain 'n' and resid 180 through 186 Processing helix chain 'n' and resid 305 through 329 removed outlier: 5.201A pdb=" N GLY n 312 " --> pdb=" O GLU n 308 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N ALA n 313 " --> pdb=" O ARG n 309 " (cutoff:3.500A) Processing helix chain 'n' and resid 350 through 359 removed outlier: 3.694A pdb=" N ASN n 357 " --> pdb=" O GLU n 353 " (cutoff:3.500A) Processing helix chain 'o' and resid 127 through 150 removed outlier: 3.588A pdb=" N ASN o 139 " --> pdb=" O THR o 135 " (cutoff:3.500A) Processing helix chain 'o' and resid 166 through 169 Processing helix chain 'u' and resid 136 through 148 Processing helix chain 'v' and resid 71 through 75 removed outlier: 3.589A pdb=" N TYR v 75 " --> pdb=" O SER v 72 " (cutoff:3.500A) Processing helix chain 'y' and resid 136 through 148 Processing helix chain 'z' and resid 71 through 73 No H-bonds generated for 'chain 'z' and resid 71 through 73' Processing sheet with id=AA1, first strand: chain 'A' and resid 195 through 196 removed outlier: 6.866A pdb=" N SER A 195 " --> pdb=" O ASP D 382 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 198 through 199 removed outlier: 3.520A pdb=" N ILE D 283 " --> pdb=" O ILE D 275 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 206 through 207 removed outlier: 7.707A pdb=" N ASP A 382 " --> pdb=" O ALA n 197 " (cutoff:3.500A) removed outlier: 9.237A pdb=" N ARG n 199 " --> pdb=" O ASP A 382 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL A 282 " --> pdb=" O GLY n 198 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 212 through 217 removed outlier: 3.584A pdb=" N GLY A 255 " --> pdb=" O THR A 229 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N PHE A 256 " --> pdb=" O TRP A 272 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N TRP A 272 " --> pdb=" O PHE A 256 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N SER A 287 " --> pdb=" O TRP A 272 " (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 removed outlier: 3.629A pdb=" N LEU A 247 " --> pdb=" O VAL A 237 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 388 through 391 removed outlier: 3.520A pdb=" N SER A 388 " --> pdb=" O VAL E 261 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU A 390 " --> pdb=" O ARG E 259 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 25 through 26 removed outlier: 6.685A pdb=" N HIS B 55 " --> pdb=" O LEU B 123 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N PHE B 125 " --> pdb=" O HIS B 55 " (cutoff:3.500A) removed outlier: 8.309A pdb=" N MET B 57 " --> pdb=" O PHE B 125 " (cutoff:3.500A) removed outlier: 3.504A 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: 6.668A pdb=" N VAL B 44 " --> pdb=" O ARG B 109 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N GLN B 111 " --> pdb=" O VAL B 44 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N VAL B 46 " --> pdb=" O GLN B 111 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ARG B 113 " --> pdb=" O VAL B 46 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N THR B 48 " --> pdb=" O ARG B 113 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 64 through 66 Processing sheet with id=AB2, first strand: chain 'B' and resid 202 through 203 removed outlier: 5.014A pdb=" N LYS B 225 " --> pdb=" O VAL B 196 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 172 through 175 Processing sheet with id=AB4, first strand: chain 'B' and resid 258 through 261 removed outlier: 3.759A pdb=" N GLU n 390 " --> pdb=" O ARG B 259 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 195 through 196 removed outlier: 7.012A pdb=" N SER D 195 " --> pdb=" O ASP G 382 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 198 through 199 removed outlier: 3.610A pdb=" N VAL G 282 " --> pdb=" O GLY D 198 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE G 283 " --> pdb=" O ILE G 275 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N PHE G 256 " --> pdb=" O TRP G 272 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N TRP G 272 " --> pdb=" O PHE G 256 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 221 through 222 Processing sheet with id=AB8, first strand: chain 'D' and resid 237 through 238 removed outlier: 6.933A pdb=" N VAL D 237 " --> pdb=" O LEU D 246 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 388 through 391 Processing sheet with id=AC1, first strand: chain 'E' and resid 25 through 26 removed outlier: 3.936A pdb=" N ALA E 124 " --> pdb=" O ARG E 34 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N VAL E 36 " --> pdb=" O ALA E 124 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N HIS E 55 " --> pdb=" O LEU E 123 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N PHE E 125 " --> pdb=" O HIS E 55 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N MET E 57 " --> pdb=" O PHE E 125 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 44 through 49 Processing sheet with id=AC3, first strand: chain 'E' and resid 202 through 203 removed outlier: 3.559A pdb=" N VAL E 196 " --> pdb=" O LYS E 225 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N LYS E 225 " --> pdb=" O VAL E 196 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 172 through 175 removed outlier: 3.515A pdb=" N ASN E 172 " --> pdb=" O LYS E 183 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 195 through 196 removed outlier: 6.408A pdb=" N SER G 195 " --> pdb=" O ASP J 382 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 198 through 199 removed outlier: 3.817A pdb=" N VAL J 282 " --> pdb=" O GLY G 198 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N SER J 273 " --> pdb=" O LEU J 285 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N SER J 287 " --> pdb=" O GLN J 271 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N GLN J 271 " --> pdb=" O SER J 287 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N VAL J 254 " --> pdb=" O SER J 273 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ILE J 275 " --> pdb=" O LYS J 252 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N LYS J 252 " --> pdb=" O ILE J 275 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR J 257 " --> pdb=" O GLY J 227 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLY J 227 " --> pdb=" O TYR J 257 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 198 through 199 removed outlier: 3.817A pdb=" N VAL J 282 " --> pdb=" O GLY G 198 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N CYS J 231 " --> pdb=" O VAL J 253 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR J 257 " --> pdb=" O GLY J 227 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLY J 227 " --> pdb=" O TYR J 257 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 221 through 222 Processing sheet with id=AC9, first strand: chain 'G' and resid 237 through 238 removed outlier: 6.868A pdb=" N VAL G 237 " --> pdb=" O LEU G 246 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 267 through 268 Processing sheet with id=AD2, first strand: chain 'G' and resid 387 through 391 removed outlier: 3.761A pdb=" N GLU G 390 " --> pdb=" O ARG K 259 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 25 through 26 removed outlier: 6.845A pdb=" N ARG H 34 " --> pdb=" O ALA H 124 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N HIS H 55 " --> pdb=" O LEU H 123 " (cutoff:3.500A) removed outlier: 8.429A pdb=" N PHE H 125 " --> pdb=" O HIS H 55 " (cutoff:3.500A) removed outlier: 8.932A pdb=" N MET H 57 " --> pdb=" O PHE H 125 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 44 through 49 removed outlier: 6.600A pdb=" N VAL H 44 " --> pdb=" O ARG H 109 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N GLN H 111 " --> pdb=" O VAL H 44 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL H 46 " --> pdb=" O GLN H 111 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N ARG H 113 " --> pdb=" O VAL H 46 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N THR H 48 " --> pdb=" O ARG H 113 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N ASN H 96 " --> pdb=" O PHE H 69 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N PHE H 69 " --> pdb=" O ASN H 96 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ILE H 98 " --> pdb=" O HIS H 67 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N HIS H 67 " --> pdb=" O ILE H 98 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N VAL H 100 " --> pdb=" O LEU H 65 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 202 through 203 removed outlier: 3.580A pdb=" N VAL H 196 " --> pdb=" O LYS H 225 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N LYS H 225 " --> pdb=" O VAL H 196 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 172 through 175 removed outlier: 3.539A pdb=" N THR H 180 " --> pdb=" O VAL H 219 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 195 through 196 removed outlier: 6.691A pdb=" N SER J 195 " --> pdb=" O ASP M 382 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'J' and resid 198 through 199 removed outlier: 3.771A pdb=" N LEU M 376 " --> pdb=" O PRO M 288 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLY M 227 " --> pdb=" O TYR M 257 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N PHE M 256 " --> pdb=" O TRP M 272 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N TRP M 272 " --> pdb=" O PHE M 256 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ARG M 274 " --> pdb=" O LEU M 285 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N LEU M 285 " --> pdb=" O ARG M 274 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N GLU M 276 " --> pdb=" O ILE M 283 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N ILE M 283 " --> pdb=" O GLU M 276 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 221 through 222 Processing sheet with id=AE1, first strand: chain 'J' and resid 237 through 238 removed outlier: 7.108A pdb=" N VAL J 237 " --> pdb=" O LEU J 246 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 267 through 268 Processing sheet with id=AE3, first strand: chain 'J' and resid 387 through 391 Processing sheet with id=AE4, first strand: chain 'K' and resid 25 through 26 removed outlier: 4.367A pdb=" N ARG K 34 " --> pdb=" O GLU K 122 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA K 124 " --> pdb=" O ARG K 34 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N PHE K 125 " --> pdb=" O MET K 57 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N HIS K 83 " --> pdb=" O LYS K 80 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS K 80 " --> pdb=" O HIS K 83 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'K' and resid 44 through 49 removed outlier: 7.215A pdb=" N VAL K 44 " --> pdb=" O ARG K 109 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N GLN K 111 " --> pdb=" O VAL K 44 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N VAL K 46 " --> pdb=" O GLN K 111 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N ARG K 113 " --> pdb=" O VAL K 46 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N THR K 48 " --> pdb=" O ARG K 113 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'K' and resid 202 through 203 removed outlier: 3.817A pdb=" N VAL K 196 " --> pdb=" O LYS K 225 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N LYS K 225 " --> pdb=" O VAL K 196 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'K' and resid 172 through 175 Processing sheet with id=AE8, first strand: chain 'M' and resid 195 through 196 removed outlier: 6.561A pdb=" N SER M 195 " --> pdb=" O ASP P 382 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'M' and resid 198 through 199 removed outlier: 3.573A pdb=" N VAL P 282 " --> pdb=" O GLY M 198 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU P 376 " --> pdb=" O PRO P 288 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ASN P 374 " --> pdb=" O THR P 290 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLY P 227 " --> pdb=" O TYR P 257 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N LYS P 252 " --> pdb=" O ILE P 275 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ILE P 275 " --> pdb=" O LYS P 252 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N VAL P 254 " --> pdb=" O SER P 273 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ARG P 274 " --> pdb=" O LEU P 285 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N LEU P 285 " --> pdb=" O ARG P 274 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N GLU P 276 " --> pdb=" O ILE P 283 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N ILE P 283 " --> pdb=" O GLU P 276 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'M' and resid 221 through 222 Processing sheet with id=AF2, first strand: chain 'M' and resid 237 through 238 removed outlier: 7.016A pdb=" N VAL M 237 " --> pdb=" O LEU M 246 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'M' and resid 267 through 268 Processing sheet with id=AF4, first strand: chain 'M' and resid 388 through 391 Processing sheet with id=AF5, first strand: chain 'N' and resid 25 through 26 removed outlier: 6.639A pdb=" N HIS N 55 " --> pdb=" O LEU N 123 " (cutoff:3.500A) removed outlier: 8.374A pdb=" N PHE N 125 " --> pdb=" O HIS N 55 " (cutoff:3.500A) removed outlier: 8.455A pdb=" N MET N 57 " --> pdb=" O PHE N 125 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N HIS N 83 " --> pdb=" O LYS N 80 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'N' and resid 44 through 48 removed outlier: 6.631A pdb=" N VAL N 44 " --> pdb=" O ARG N 109 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N GLN N 111 " --> pdb=" O VAL N 44 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N VAL N 46 " --> pdb=" O GLN N 111 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'N' and resid 160 through 164 removed outlier: 5.103A pdb=" N LYS N 225 " --> pdb=" O VAL N 196 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N VAL N 196 " --> pdb=" O LYS N 225 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'N' and resid 172 through 175 removed outlier: 3.561A pdb=" N ASN N 172 " --> pdb=" O LYS N 183 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'S' and resid 206 through 207 removed outlier: 7.204A pdb=" N SER P 195 " --> pdb=" O ASP S 382 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ILE S 283 " --> pdb=" O ILE S 275 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N VAL S 270 " --> pdb=" O GLY S 289 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N SER S 287 " --> pdb=" O TRP S 272 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU S 376 " --> pdb=" O PRO S 288 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLY S 255 " --> pdb=" O THR S 229 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LYS S 252 " --> pdb=" O ILE S 275 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ILE S 275 " --> pdb=" O LYS S 252 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N VAL S 254 " --> pdb=" O SER S 273 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'P' and resid 221 through 222 Processing sheet with id=AG2, first strand: chain 'P' and resid 237 through 238 removed outlier: 6.898A pdb=" N VAL P 237 " --> pdb=" O LEU P 246 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'P' and resid 267 through 268 Processing sheet with id=AG4, first strand: chain 'P' and resid 387 through 391 Processing sheet with id=AG5, first strand: chain 'Q' and resid 25 through 26 removed outlier: 3.805A pdb=" N ARG Q 34 " --> pdb=" O GLU Q 122 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA Q 124 " --> pdb=" O ARG Q 34 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N HIS Q 55 " --> pdb=" O LEU Q 123 " (cutoff:3.500A) removed outlier: 8.222A pdb=" N PHE Q 125 " --> pdb=" O HIS Q 55 " (cutoff:3.500A) removed outlier: 8.207A pdb=" N MET Q 57 " --> pdb=" O PHE Q 125 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'Q' and resid 44 through 49 removed outlier: 6.504A pdb=" N VAL Q 44 " --> pdb=" O ARG Q 109 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N GLN Q 111 " --> pdb=" O VAL Q 44 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N VAL Q 46 " --> pdb=" O GLN Q 111 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ARG Q 113 " --> pdb=" O VAL Q 46 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N THR Q 48 " --> pdb=" O ARG Q 113 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'Q' and resid 202 through 203 removed outlier: 3.761A pdb=" N ARG Q 229 " --> pdb=" O SER Q 192 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N VAL Q 196 " --> pdb=" O LYS Q 225 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N LYS Q 225 " --> pdb=" O VAL Q 196 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'Q' and resid 172 through 175 removed outlier: 3.566A pdb=" N ASN Q 172 " --> pdb=" O LYS Q 183 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TRP Q 174 " --> pdb=" O TYR Q 181 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'S' and resid 195 through 196 removed outlier: 7.069A pdb=" N SER S 195 " --> pdb=" O ASP V 382 " (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 removed outlier: 6.910A pdb=" N VAL S 237 " --> pdb=" O LEU S 246 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'S' and resid 387 through 391 removed outlier: 3.803A pdb=" N GLU S 390 " --> pdb=" O ARG W 259 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'T' and resid 25 through 26 removed outlier: 6.658A pdb=" N ARG T 34 " --> pdb=" O ALA T 124 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N ARG T 126 " --> pdb=" O ARG T 34 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N VAL T 36 " --> pdb=" O ARG T 126 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N HIS T 55 " --> pdb=" O LEU T 123 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N PHE T 125 " --> pdb=" O HIS T 55 " (cutoff:3.500A) removed outlier: 8.350A pdb=" N MET T 57 " --> pdb=" O PHE T 125 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'T' and resid 44 through 48 removed outlier: 6.436A pdb=" N VAL T 44 " --> pdb=" O ARG T 109 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N GLN T 111 " --> pdb=" O VAL T 44 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N VAL T 46 " --> pdb=" O GLN T 111 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'T' and resid 44 through 48 removed outlier: 6.436A pdb=" N VAL T 44 " --> pdb=" O ARG T 109 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N GLN T 111 " --> pdb=" O VAL T 44 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N VAL T 46 " --> pdb=" O GLN T 111 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'T' and resid 202 through 203 removed outlier: 3.577A pdb=" N ARG T 229 " --> pdb=" O SER T 192 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N VAL T 196 " --> pdb=" O LYS T 225 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N LYS T 225 " --> pdb=" O VAL T 196 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'T' and resid 172 through 175 removed outlier: 3.595A pdb=" N ILE T 216 " --> pdb=" O VAL T 210 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'V' and resid 195 through 196 removed outlier: 6.657A pdb=" N SER V 195 " --> pdb=" O ASP Y 382 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'V' and resid 198 through 199 removed outlier: 3.720A pdb=" N VAL Y 282 " --> pdb=" O GLY V 198 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N VAL Y 254 " --> pdb=" O SER Y 273 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ILE Y 275 " --> pdb=" O LYS Y 252 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LYS Y 252 " --> pdb=" O ILE Y 275 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY Y 255 " --> pdb=" O THR Y 229 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N TYR Y 257 " --> pdb=" O GLY Y 227 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLY Y 227 " --> pdb=" O TYR Y 257 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'V' and resid 212 through 213 removed outlier: 3.633A pdb=" N ASN V 374 " --> pdb=" O THR V 290 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU V 376 " --> pdb=" O PRO V 288 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N SER V 287 " --> pdb=" O TRP V 272 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N VAL V 254 " --> pdb=" O SER V 273 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N ILE V 275 " --> pdb=" O LYS V 252 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N LYS V 252 " --> pdb=" O ILE V 275 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N TYR V 257 " --> pdb=" O GLY V 227 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLY V 227 " --> pdb=" O TYR V 257 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'V' and resid 212 through 213 removed outlier: 3.633A pdb=" N ASN V 374 " --> pdb=" O THR V 290 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU V 376 " --> pdb=" O PRO V 288 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N SER V 287 " --> pdb=" O TRP V 272 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'V' and resid 221 through 222 Processing sheet with id=AI5, first strand: chain 'V' and resid 237 through 238 removed outlier: 6.820A pdb=" N VAL V 237 " --> pdb=" O LEU V 246 " (cutoff:3.500A) 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: 3.749A pdb=" N ARG W 34 " --> pdb=" O GLU W 122 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N HIS W 55 " --> pdb=" O LEU W 123 " (cutoff:3.500A) removed outlier: 8.619A pdb=" N PHE W 125 " --> pdb=" O HIS W 55 " (cutoff:3.500A) removed outlier: 8.517A 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 49 removed outlier: 6.825A pdb=" N VAL W 44 " --> pdb=" O ARG W 109 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N GLN W 111 " --> pdb=" O VAL W 44 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N VAL W 46 " --> pdb=" O GLN W 111 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ARG W 113 " --> pdb=" O VAL W 46 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N THR W 48 " --> pdb=" O ARG W 113 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL W 99 " --> pdb=" O TYR W 106 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'W' and resid 202 through 203 removed outlier: 3.657A pdb=" N VAL W 196 " --> pdb=" O LYS W 225 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N LYS W 225 " --> pdb=" O VAL W 196 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'W' and resid 172 through 175 Processing sheet with id=AJ2, first strand: chain 'Y' and resid 195 through 196 removed outlier: 6.725A pdb=" N SER Y 195 " --> pdb=" O ASP b 382 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'Y' and resid 198 through 199 removed outlier: 3.531A pdb=" N ILE b 283 " --> pdb=" O ILE b 275 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE b 275 " --> pdb=" O ILE b 283 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU b 376 " --> pdb=" O PRO b 288 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N PHE b 256 " --> pdb=" O TRP b 272 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N TRP b 272 " --> pdb=" O PHE b 256 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'Y' and resid 231 through 233 Processing sheet with id=AJ5, first strand: chain 'Y' and resid 221 through 222 removed outlier: 3.521A pdb=" N THR Y 364 " --> pdb=" O ASP Y 303 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASP Y 303 " --> pdb=" O THR Y 364 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'Y' and resid 237 through 238 removed outlier: 7.040A pdb=" N VAL Y 237 " --> pdb=" O LEU Y 246 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'Y' and resid 387 through 391 Processing sheet with id=AJ8, first strand: chain 'Z' and resid 25 through 26 removed outlier: 3.627A pdb=" N ARG Z 34 " --> pdb=" O GLU Z 122 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA Z 124 " --> pdb=" O ARG Z 34 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N HIS Z 55 " --> pdb=" O LEU Z 123 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR Z 54 " --> pdb=" O ILE Z 86 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE Z 86 " --> pdb=" O THR Z 54 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS Z 87 " --> pdb=" O ALA Z 76 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'Z' and resid 44 through 49 removed outlier: 6.620A pdb=" N VAL Z 44 " --> pdb=" O ARG Z 109 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N GLN Z 111 " --> pdb=" O VAL Z 44 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N VAL Z 46 " --> pdb=" O GLN Z 111 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N ARG Z 113 " --> pdb=" O VAL Z 46 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N THR Z 48 " --> pdb=" O ARG Z 113 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'Z' and resid 202 through 203 removed outlier: 4.480A pdb=" N LYS Z 225 " --> pdb=" O VAL Z 196 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'Z' and resid 172 through 175 Processing sheet with id=AK3, first strand: chain 'b' and resid 197 through 199 removed outlier: 7.765A pdb=" N ILE e 283 " --> pdb=" O GLU e 276 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N GLU e 276 " --> pdb=" O ILE e 283 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N LEU e 285 " --> pdb=" O ARG e 274 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ARG e 274 " --> pdb=" O LEU e 285 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N TRP e 272 " --> pdb=" O PHE e 256 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N PHE e 256 " --> pdb=" O TRP e 272 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLY e 227 " --> pdb=" O TYR e 257 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'b' and resid 197 through 199 removed outlier: 3.698A pdb=" N LEU e 376 " --> pdb=" O PRO e 288 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'b' and resid 221 through 222 Processing sheet with id=AK6, first strand: chain 'b' and resid 237 through 238 removed outlier: 6.990A pdb=" N VAL b 237 " --> pdb=" O LEU b 246 " (cutoff:3.500A) Processing sheet with id=AK7, first strand: chain 'b' and resid 387 through 391 Processing sheet with id=AK8, first strand: chain 'c' and resid 25 through 26 removed outlier: 6.999A pdb=" N HIS c 55 " --> pdb=" O LEU c 123 " (cutoff:3.500A) removed outlier: 8.302A pdb=" N PHE c 125 " --> pdb=" O HIS c 55 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N MET c 57 " --> pdb=" O PHE c 125 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'c' and resid 44 through 49 removed outlier: 6.787A pdb=" N VAL c 44 " --> pdb=" O ARG c 109 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N GLN c 111 " --> pdb=" O VAL c 44 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N VAL c 46 " --> pdb=" O GLN c 111 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ARG c 113 " --> pdb=" O VAL c 46 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N THR c 48 " --> pdb=" O ARG c 113 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'c' and resid 202 through 203 removed outlier: 3.664A pdb=" N VAL c 196 " --> pdb=" O LYS c 225 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N LYS c 225 " --> pdb=" O VAL c 196 " (cutoff:3.500A) Processing sheet with id=AL2, first strand: chain 'c' and resid 172 through 175 removed outlier: 3.671A pdb=" N THR c 180 " --> pdb=" O VAL c 219 " (cutoff:3.500A) Processing sheet with id=AL3, first strand: chain 'e' and resid 195 through 196 removed outlier: 6.417A pdb=" N SER e 195 " --> pdb=" O ASP h 382 " (cutoff:3.500A) Processing sheet with id=AL4, first strand: chain 'e' and resid 198 through 199 removed outlier: 3.646A pdb=" N LEU h 376 " --> pdb=" O PRO h 288 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLY h 227 " --> pdb=" O TYR h 257 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N PHE h 256 " --> pdb=" O TRP h 272 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N TRP h 272 " --> pdb=" O PHE h 256 " (cutoff:3.500A) Processing sheet with id=AL5, first strand: chain 'e' and resid 206 through 207 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 removed outlier: 6.991A pdb=" N VAL e 237 " --> pdb=" O LEU e 246 " (cutoff:3.500A) Processing sheet with id=AL8, first strand: chain 'e' and resid 267 through 268 Processing sheet with id=AL9, first strand: chain 'e' and resid 387 through 391 Processing sheet with id=AM1, first strand: chain 'f' and resid 25 through 26 removed outlier: 3.511A pdb=" N ALA f 124 " --> pdb=" O ARG f 34 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N HIS f 55 " --> pdb=" O LEU f 123 " (cutoff:3.500A) removed outlier: 8.675A pdb=" N PHE f 125 " --> pdb=" O HIS f 55 " (cutoff:3.500A) removed outlier: 8.321A pdb=" N MET f 57 " --> pdb=" O PHE f 125 " (cutoff:3.500A) Processing sheet with id=AM2, first strand: chain 'f' and resid 44 through 48 removed outlier: 6.728A pdb=" N VAL f 44 " --> pdb=" O ARG f 109 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N GLN f 111 " --> pdb=" O VAL f 44 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N VAL f 46 " --> pdb=" O GLN f 111 " (cutoff:3.500A) Processing sheet with id=AM3, first strand: chain 'f' and resid 202 through 203 removed outlier: 3.825A pdb=" N VAL f 196 " --> pdb=" O LYS f 225 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N LYS f 225 " --> pdb=" O VAL f 196 " (cutoff:3.500A) Processing sheet with id=AM4, first strand: chain 'f' and resid 172 through 175 Processing sheet with id=AM5, first strand: chain 'h' and resid 195 through 196 removed outlier: 6.474A pdb=" N SER h 195 " --> pdb=" O ASP k 382 " (cutoff:3.500A) Processing sheet with id=AM6, first strand: chain 'h' and resid 198 through 199 removed outlier: 3.656A pdb=" N VAL k 282 " --> pdb=" O GLY h 198 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER k 287 " --> pdb=" O TRP k 272 " (cutoff:3.500A) Processing sheet with id=AM7, first strand: chain 'h' and resid 198 through 199 removed outlier: 3.656A pdb=" N VAL k 282 " --> pdb=" O GLY h 198 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N VAL k 254 " --> pdb=" O SER k 273 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ILE k 275 " --> pdb=" O LYS k 252 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N LYS k 252 " --> pdb=" O ILE k 275 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLY k 227 " --> pdb=" O TYR k 257 " (cutoff:3.500A) Processing sheet with id=AM8, first strand: chain 'h' and resid 221 through 222 Processing sheet with id=AM9, first strand: chain 'h' and resid 237 through 238 removed outlier: 6.726A pdb=" N VAL h 237 " --> pdb=" O LEU h 246 " (cutoff:3.500A) Processing sheet with id=AN1, first strand: chain 'h' and resid 267 through 268 Processing sheet with id=AN2, first strand: chain 'h' and resid 387 through 391 Processing sheet with id=AN3, first strand: chain 'i' and resid 25 through 26 removed outlier: 7.048A pdb=" N ARG i 34 " --> pdb=" O ALA i 124 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N ARG i 126 " --> pdb=" O ARG i 34 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N VAL i 36 " --> pdb=" O ARG i 126 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N HIS i 55 " --> pdb=" O LEU i 123 " (cutoff:3.500A) removed outlier: 8.247A pdb=" N PHE i 125 " --> pdb=" O HIS i 55 " (cutoff:3.500A) removed outlier: 8.797A pdb=" N MET i 57 " --> pdb=" O PHE i 125 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA i 78 " --> pdb=" O PHE i 85 " (cutoff:3.500A) Processing sheet with id=AN4, first strand: chain 'i' and resid 44 through 48 removed outlier: 3.583A pdb=" N GLN i 111 " --> pdb=" O VAL i 46 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N THR i 48 " --> pdb=" O GLN i 111 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ILE i 98 " --> pdb=" O HIS i 67 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N HIS i 67 " --> pdb=" O ILE i 98 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N VAL i 100 " --> pdb=" O LEU i 65 " (cutoff:3.500A) Processing sheet with id=AN5, first strand: chain 'i' and resid 202 through 203 removed outlier: 4.332A pdb=" N VAL i 196 " --> pdb=" O LYS i 225 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N LYS i 225 " --> pdb=" O VAL i 196 " (cutoff:3.500A) Processing sheet with id=AN6, first strand: chain 'i' and resid 172 through 175 Processing sheet with id=AN7, first strand: chain 'k' and resid 195 through 196 removed outlier: 6.779A pdb=" N SER k 195 " --> pdb=" O ASP n 382 " (cutoff:3.500A) Processing sheet with id=AN8, first strand: chain 'k' and resid 198 through 199 removed outlier: 3.707A pdb=" N LEU n 376 " --> pdb=" O PRO n 288 " (cutoff:3.500A) Processing sheet with id=AN9, first strand: chain 'k' and resid 198 through 199 removed outlier: 8.011A pdb=" N ILE n 283 " --> pdb=" O GLU n 276 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N GLU n 276 " --> pdb=" O ILE n 283 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N LEU n 285 " --> pdb=" O ARG n 274 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ARG n 274 " --> pdb=" O LEU n 285 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N SER n 287 " --> pdb=" O TRP n 272 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N VAL n 254 " --> pdb=" O SER n 273 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ILE n 275 " --> pdb=" O LYS n 252 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N LYS n 252 " --> pdb=" O ILE n 275 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLY n 255 " --> pdb=" O THR n 229 " (cutoff:3.500A) Processing sheet with id=AO1, first strand: chain 'k' and resid 221 through 222 Processing sheet with id=AO2, first strand: chain 'k' and resid 237 through 238 removed outlier: 6.759A pdb=" N VAL k 237 " --> pdb=" O LEU k 246 " (cutoff:3.500A) Processing sheet with id=AO3, first strand: chain 'k' and resid 267 through 268 Processing sheet with id=AO4, first strand: chain 'k' and resid 387 through 391 removed outlier: 4.239A pdb=" N GLU k 390 " --> pdb=" O ARG o 259 " (cutoff:3.500A) Processing sheet with id=AO5, first strand: chain 'l' and resid 25 through 27 removed outlier: 6.221A pdb=" N ILE l 33 " --> pdb=" O SER l 27 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N HIS l 55 " --> pdb=" O LEU l 123 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N PHE l 125 " --> pdb=" O HIS l 55 " (cutoff:3.500A) removed outlier: 8.749A pdb=" N MET l 57 " --> pdb=" O PHE l 125 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA l 78 " --> pdb=" O PHE l 85 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS l 87 " --> pdb=" O ALA l 76 " (cutoff:3.500A) Processing sheet with id=AO6, first strand: chain 'l' and resid 44 through 49 removed outlier: 6.537A pdb=" N VAL l 44 " --> pdb=" O ARG l 109 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N GLN l 111 " --> pdb=" O VAL l 44 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N VAL l 46 " --> pdb=" O GLN l 111 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N ARG l 113 " --> pdb=" O VAL l 46 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N THR l 48 " --> pdb=" O ARG l 113 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR l 95 " --> pdb=" O LEU l 110 " (cutoff:3.500A) Processing sheet with id=AO7, first strand: chain 'l' and resid 202 through 203 removed outlier: 3.643A pdb=" N ARG l 229 " --> pdb=" O SER l 192 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N VAL l 196 " --> pdb=" O LYS l 225 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N LYS l 225 " --> pdb=" O VAL l 196 " (cutoff:3.500A) Processing sheet with id=AO8, first strand: chain 'l' and resid 172 through 175 Processing sheet with id=AO9, first strand: chain 'n' and resid 221 through 222 Processing sheet with id=AP1, first strand: chain 'n' and resid 237 through 238 removed outlier: 6.720A pdb=" N VAL n 237 " --> pdb=" O LEU n 246 " (cutoff:3.500A) Processing sheet with id=AP2, first strand: chain 'o' and resid 25 through 26 removed outlier: 3.991A pdb=" N ARG o 34 " --> pdb=" O GLU o 122 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N PHE o 125 " --> pdb=" O MET o 57 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N HIS o 83 " --> pdb=" O LYS o 80 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA o 78 " --> pdb=" O PHE o 85 " (cutoff:3.500A) Processing sheet with id=AP3, first strand: chain 'o' and resid 44 through 49 removed outlier: 3.556A pdb=" N VAL o 99 " --> pdb=" O TYR o 106 " (cutoff:3.500A) Processing sheet with id=AP4, first strand: chain 'o' and resid 202 through 204 removed outlier: 3.759A pdb=" N VAL o 196 " --> pdb=" O LYS o 225 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N LYS o 225 " --> pdb=" O VAL o 196 " (cutoff:3.500A) Processing sheet with id=AP5, first strand: chain 'o' and resid 172 through 175 removed outlier: 3.529A pdb=" N ASN o 172 " --> pdb=" O LYS o 183 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TRP o 174 " --> pdb=" O TYR o 181 " (cutoff:3.500A) Processing sheet with id=AP6, first strand: chain 'v' and resid 25 through 26 removed outlier: 7.005A pdb=" N ARG v 34 " --> pdb=" O ALA v 124 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N ARG v 126 " --> pdb=" O ARG v 34 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N VAL v 36 " --> pdb=" O ARG v 126 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N HIS v 55 " --> pdb=" O LEU v 123 " (cutoff:3.500A) removed outlier: 8.504A pdb=" N PHE v 125 " --> pdb=" O HIS v 55 " (cutoff:3.500A) removed outlier: 8.972A pdb=" N MET v 57 " --> pdb=" O PHE v 125 " (cutoff:3.500A) Processing sheet with id=AP7, first strand: chain 'v' and resid 44 through 49 removed outlier: 6.195A pdb=" N VAL v 44 " --> pdb=" O ARG v 109 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N GLN v 111 " --> pdb=" O VAL v 44 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N VAL v 46 " --> pdb=" O GLN v 111 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N ARG v 113 " --> pdb=" O VAL v 46 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N THR v 48 " --> pdb=" O ARG v 113 " (cutoff:3.500A) Processing sheet with id=AP8, first strand: chain 'z' and resid 25 through 26 removed outlier: 3.503A pdb=" N ARG z 34 " --> pdb=" O GLU z 122 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA z 124 " --> pdb=" O ARG z 34 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N HIS z 55 " --> pdb=" O LEU z 123 " (cutoff:3.500A) removed outlier: 8.769A pdb=" N PHE z 125 " --> pdb=" O HIS z 55 " (cutoff:3.500A) removed outlier: 9.180A pdb=" N MET z 57 " --> pdb=" O PHE z 125 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N HIS z 83 " --> pdb=" O LYS z 80 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS z 87 " --> pdb=" O ALA z 76 " (cutoff:3.500A) Processing sheet with id=AP9, first strand: chain 'z' and resid 44 through 48 removed outlier: 3.564A pdb=" N VAL z 46 " --> pdb=" O ARG z 109 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N VAL z 99 " --> pdb=" O TYR z 106 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR z 66 " --> pdb=" O VAL z 100 " (cutoff:3.500A) 2000 hydrogen bonds defined for protein. 5220 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: 22.45 Time building geometry restraints manager: 18.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 19002 1.33 - 1.45: 9177 1.45 - 1.57: 28349 1.57 - 1.69: 0 1.69 - 1.81: 366 Bond restraints: 56894 Sorted by residual: bond pdb=" CA ASP n 286 " pdb=" CB ASP n 286 " ideal model delta sigma weight residual 1.528 1.489 0.040 1.51e-02 4.39e+03 6.97e+00 bond pdb=" C GLU Y 276 " pdb=" N THR Y 277 " ideal model delta sigma weight residual 1.330 1.295 0.036 1.37e-02 5.33e+03 6.83e+00 bond pdb=" CA GLN M 329 " pdb=" C GLN M 329 " ideal model delta sigma weight residual 1.522 1.555 -0.033 1.38e-02 5.25e+03 5.80e+00 bond pdb=" CA ASP S 286 " pdb=" CB ASP S 286 " ideal model delta sigma weight residual 1.528 1.493 0.035 1.51e-02 4.39e+03 5.42e+00 bond pdb=" CA ASP k 286 " pdb=" CB ASP k 286 " ideal model delta sigma weight residual 1.526 1.487 0.039 1.70e-02 3.46e+03 5.17e+00 ... (remaining 56889 not shown) Histogram of bond angle deviations from ideal: 97.50 - 104.82: 1113 104.82 - 112.15: 27582 112.15 - 119.47: 18178 119.47 - 126.80: 29461 126.80 - 134.12: 702 Bond angle restraints: 77036 Sorted by residual: angle pdb=" O GLN F 43 " pdb=" C GLN F 43 " pdb=" N ARG F 44 " ideal model delta sigma weight residual 122.41 98.64 23.77 1.34e+00 5.57e-01 3.15e+02 angle pdb=" O GLN O 43 " pdb=" C GLN O 43 " pdb=" N ARG O 44 " ideal model delta sigma weight residual 122.41 104.63 17.78 1.34e+00 5.57e-01 1.76e+02 angle pdb=" O GLN a 43 " pdb=" C GLN a 43 " pdb=" N ARG a 44 " ideal model delta sigma weight residual 122.41 106.18 16.23 1.34e+00 5.57e-01 1.47e+02 angle pdb=" O GLN m 43 " pdb=" C GLN m 43 " pdb=" N ARG m 44 " ideal model delta sigma weight residual 122.41 106.51 15.90 1.34e+00 5.57e-01 1.41e+02 angle pdb=" O GLN g 43 " pdb=" C GLN g 43 " pdb=" N ARG g 44 " ideal model delta sigma weight residual 122.41 107.16 15.25 1.34e+00 5.57e-01 1.30e+02 ... (remaining 77031 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.10: 31071 18.10 - 36.20: 2627 36.20 - 54.30: 349 54.30 - 72.40: 90 72.40 - 90.50: 53 Dihedral angle restraints: 34190 sinusoidal: 13744 harmonic: 20446 Sorted by residual: dihedral pdb=" CA MET f 57 " pdb=" C MET f 57 " pdb=" N LEU f 58 " pdb=" CA LEU f 58 " ideal model delta harmonic sigma weight residual 180.00 153.85 26.15 0 5.00e+00 4.00e-02 2.74e+01 dihedral pdb=" CA GLU f 137 " pdb=" C GLU f 137 " pdb=" N ALA f 138 " pdb=" CA ALA f 138 " ideal model delta harmonic sigma weight residual 180.00 156.16 23.84 0 5.00e+00 4.00e-02 2.27e+01 dihedral pdb=" CA GLY V 180 " pdb=" C GLY V 180 " pdb=" N GLY V 181 " pdb=" CA GLY V 181 " ideal model delta harmonic sigma weight residual -180.00 -156.55 -23.45 0 5.00e+00 4.00e-02 2.20e+01 ... (remaining 34187 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 6258 0.049 - 0.097: 1653 0.097 - 0.146: 441 0.146 - 0.195: 16 0.195 - 0.243: 2 Chirality restraints: 8370 Sorted by residual: chirality pdb=" CB VAL J 253 " pdb=" CA VAL J 253 " pdb=" CG1 VAL J 253 " pdb=" CG2 VAL J 253 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" CB ILE W 33 " pdb=" CA ILE W 33 " pdb=" CG1 ILE W 33 " pdb=" CG2 ILE W 33 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.94e-01 chirality pdb=" CG LEU N 50 " pdb=" CB LEU N 50 " pdb=" CD1 LEU N 50 " pdb=" CD2 LEU N 50 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 8.74e-01 ... (remaining 8367 not shown) Planarity restraints: 10228 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN F 43 " -0.098 2.00e-02 2.50e+03 1.71e-01 2.93e+02 pdb=" C GLN F 43 " 0.296 2.00e-02 2.50e+03 pdb=" O GLN F 43 " -0.108 2.00e-02 2.50e+03 pdb=" N ARG F 44 " -0.090 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN p 43 " -0.086 2.00e-02 2.50e+03 1.55e-01 2.41e+02 pdb=" C GLN p 43 " 0.269 2.00e-02 2.50e+03 pdb=" O GLN p 43 " -0.099 2.00e-02 2.50e+03 pdb=" N ARG p 44 " -0.084 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN O 43 " 0.084 2.00e-02 2.50e+03 1.53e-01 2.34e+02 pdb=" C GLN O 43 " -0.265 2.00e-02 2.50e+03 pdb=" O GLN O 43 " 0.098 2.00e-02 2.50e+03 pdb=" N ARG O 44 " 0.082 2.00e-02 2.50e+03 ... (remaining 10225 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 742 2.56 - 3.14: 46585 3.14 - 3.73: 87124 3.73 - 4.31: 119120 4.31 - 4.90: 199609 Nonbonded interactions: 453180 Sorted by model distance: nonbonded pdb=" OE1 GLU N 137 " pdb=" NH1 ARG N 141 " model vdw 1.973 2.520 nonbonded pdb=" O GLU D 218 " pdb=" OH TYR E 194 " model vdw 1.998 2.440 nonbonded pdb=" O GLU A 218 " pdb=" OH TYR B 194 " model vdw 2.021 2.440 nonbonded pdb=" O GLU Y 218 " pdb=" OH TYR Z 194 " model vdw 2.044 2.440 nonbonded pdb=" O ARG h 243 " pdb=" OG1 THR l 253 " model vdw 2.059 2.440 ... (remaining 453175 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: 1.350 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: 6.570 Check model and map are aligned: 0.330 Set scattering table: 0.410 Process input model: 116.660 Find NCS groups from input model: 3.250 Set up NCS constraints: 0.640 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: 0.020 Load rotamer database and sin/cos tables:2.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 131.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 56894 Z= 0.424 Angle : 0.809 23.773 77036 Z= 0.476 Chirality : 0.046 0.243 8370 Planarity : 0.007 0.171 10228 Dihedral : 13.745 90.502 21096 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 17.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 0.07 % Allowed : 0.48 % Favored : 99.45 % 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: -0.89 (0.10), residues: 7036 helix: 0.72 (0.16), residues: 1102 sheet: -0.65 (0.11), residues: 2048 loop : -0.89 (0.09), residues: 3886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP S 307 HIS 0.012 0.002 HIS T 67 PHE 0.025 0.002 PHE o 195 TYR 0.031 0.002 TYR z 127 ARG 0.013 0.001 ARG E 133 *********************** 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 940 residues out of total 5886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 936 time to evaluate : 4.961 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: B 112 MET cc_start: 0.8561 (ttp) cc_final: 0.8298 (tpp) REVERT: D 186 LYS cc_start: 0.9157 (mttm) cc_final: 0.8828 (mttm) REVERT: D 353 GLU cc_start: 0.8792 (tp30) cc_final: 0.8398 (tp30) REVERT: E 120 MET cc_start: 0.7727 (mtm) cc_final: 0.6828 (mmt) REVERT: E 131 GLN cc_start: 0.9466 (tm-30) cc_final: 0.9010 (pt0) REVERT: E 227 MET cc_start: 0.8323 (tpp) cc_final: 0.8042 (tpt) REVERT: H 133 ARG cc_start: 0.9425 (ttp-110) cc_final: 0.9209 (tpm170) REVERT: H 134 GLN cc_start: 0.8718 (pp30) cc_final: 0.8462 (pp30) REVERT: J 353 GLU cc_start: 0.8434 (mm-30) cc_final: 0.8000 (tp30) REVERT: K 84 ILE cc_start: 0.8984 (mt) cc_final: 0.8783 (mm) REVERT: K 107 LYS cc_start: 0.8382 (mtmm) cc_final: 0.8146 (mttm) REVERT: M 138 TYR cc_start: 0.8954 (t80) cc_final: 0.8739 (t80) REVERT: M 353 GLU cc_start: 0.8290 (mm-30) cc_final: 0.8077 (tp30) REVERT: N 63 GLN cc_start: 0.9174 (mm-40) cc_final: 0.8672 (mm-40) REVERT: N 98 ILE cc_start: 0.8246 (mm) cc_final: 0.8021 (tp) REVERT: P 353 GLU cc_start: 0.8440 (tp30) cc_final: 0.7926 (tp30) REVERT: Q 120 MET cc_start: 0.6316 (mtt) cc_final: 0.5815 (mtt) REVERT: Q 129 ASP cc_start: 0.8754 (p0) cc_final: 0.8514 (p0) REVERT: V 145 MET cc_start: 0.9010 (ttt) cc_final: 0.8484 (ttt) REVERT: W 67 HIS cc_start: 0.8874 (p-80) cc_final: 0.8580 (p-80) REVERT: W 183 LYS cc_start: 0.9132 (ttpt) cc_final: 0.8914 (ttmm) REVERT: Y 357 ASN cc_start: 0.8855 (m-40) cc_final: 0.8640 (m110) REVERT: Z 108 PHE cc_start: 0.8789 (m-10) cc_final: 0.8584 (m-10) REVERT: e 353 GLU cc_start: 0.8253 (tp30) cc_final: 0.7732 (tp30) REVERT: k 145 MET cc_start: 0.8694 (ttt) cc_final: 0.8223 (tpp) REVERT: k 186 LYS cc_start: 0.9222 (mttm) cc_final: 0.8990 (mtpt) REVERT: l 111 GLN cc_start: 0.8145 (mm110) cc_final: 0.7914 (mp10) REVERT: l 120 MET cc_start: 0.8182 (ptm) cc_final: 0.7726 (tmm) REVERT: l 129 ASP cc_start: 0.8889 (p0) cc_final: 0.8482 (p0) REVERT: n 308 GLU cc_start: 0.8035 (tp30) cc_final: 0.7802 (mm-30) REVERT: u 142 ARG cc_start: 0.9172 (mpt180) cc_final: 0.8888 (mpt180) REVERT: u 145 MET cc_start: 0.9086 (mtt) cc_final: 0.8780 (mmt) REVERT: v 50 LEU cc_start: 0.8479 (tp) cc_final: 0.7556 (tp) REVERT: v 108 PHE cc_start: 0.8775 (m-10) cc_final: 0.8442 (m-80) REVERT: v 115 ASP cc_start: 0.9207 (p0) cc_final: 0.8947 (p0) REVERT: v 117 ASN cc_start: 0.8996 (m110) cc_final: 0.8674 (m-40) REVERT: z 25 SER cc_start: 0.9466 (m) cc_final: 0.9174 (p) REVERT: z 35 TYR cc_start: 0.8895 (m-80) cc_final: 0.8458 (m-80) REVERT: z 89 GLN cc_start: 0.9397 (mp10) cc_final: 0.8870 (mp10) REVERT: z 94 ASN cc_start: 0.8815 (m-40) cc_final: 0.8248 (m-40) REVERT: z 120 MET cc_start: 0.6709 (mtm) cc_final: 0.5909 (mtm) outliers start: 4 outliers final: 0 residues processed: 939 average time/residue: 0.5987 time to fit residues: 897.3807 Evaluate side-chains 530 residues out of total 5886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 530 time to evaluate : 4.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 694 random chunks: chunk 586 optimal weight: 7.9990 chunk 526 optimal weight: 20.0000 chunk 291 optimal weight: 8.9990 chunk 179 optimal weight: 20.0000 chunk 354 optimal weight: 0.9990 chunk 281 optimal weight: 4.9990 chunk 543 optimal weight: 2.9990 chunk 210 optimal weight: 8.9990 chunk 330 optimal weight: 3.9990 chunk 404 optimal weight: 7.9990 chunk 630 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 374 ASN D 271 GLN E 214 ASN ** H 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 45 GLN ** N 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 225 GLN P 305 HIS P 357 ASN ** P 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 89 GLN ** V 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 357 ASN ** Z 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 172 ASN Z 220 HIS c 89 GLN ** e 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 94 ASN ** h 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 209 GLN ** k 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 357 ASN n 360 ASN ** o 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 56894 Z= 0.258 Angle : 0.620 10.967 77036 Z= 0.323 Chirality : 0.045 0.175 8370 Planarity : 0.004 0.073 10228 Dihedral : 4.541 22.687 7996 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 14.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.13 % Allowed : 8.43 % Favored : 90.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.10), residues: 7036 helix: 1.53 (0.16), residues: 1115 sheet: -0.28 (0.11), residues: 2104 loop : -0.51 (0.10), residues: 3817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP b 272 HIS 0.009 0.001 HIS z 55 PHE 0.028 0.002 PHE o 195 TYR 0.022 0.001 TYR n 238 ARG 0.009 0.001 ARG S 147 *********************** 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 672 residues out of total 5886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 606 time to evaluate : 5.065 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 161 MET cc_start: 0.8548 (mmm) cc_final: 0.8241 (mmm) REVERT: D 145 MET cc_start: 0.9107 (ttt) cc_final: 0.8760 (mtp) REVERT: D 188 GLN cc_start: 0.8140 (tt0) cc_final: 0.7868 (tm-30) REVERT: E 57 MET cc_start: 0.5680 (mpp) cc_final: 0.5046 (mmm) REVERT: E 120 MET cc_start: 0.7640 (mtm) cc_final: 0.6830 (mmt) REVERT: E 131 GLN cc_start: 0.9447 (tm-30) cc_final: 0.9038 (pt0) REVERT: J 147 ARG cc_start: 0.9409 (mtm110) cc_final: 0.9199 (ptp90) REVERT: K 86 ILE cc_start: 0.9418 (pt) cc_final: 0.9077 (mm) REVERT: K 162 MET cc_start: 0.8198 (ptp) cc_final: 0.7653 (ptp) REVERT: M 143 GLU cc_start: 0.9373 (pp20) cc_final: 0.9077 (pp20) REVERT: M 188 GLN cc_start: 0.8126 (tm-30) cc_final: 0.7847 (tm-30) REVERT: M 371 GLU cc_start: 0.8296 (mm-30) cc_final: 0.7942 (mp0) REVERT: N 98 ILE cc_start: 0.8437 (mm) cc_final: 0.8194 (tp) REVERT: N 120 MET cc_start: 0.7910 (ttp) cc_final: 0.7635 (mtm) REVERT: P 353 GLU cc_start: 0.8320 (tp30) cc_final: 0.8012 (tp30) REVERT: Q 54 THR cc_start: 0.8826 (m) cc_final: 0.8497 (t) REVERT: Q 129 ASP cc_start: 0.8803 (p0) cc_final: 0.8559 (p0) REVERT: Q 227 MET cc_start: 0.8795 (tpp) cc_final: 0.8591 (tpp) REVERT: T 120 MET cc_start: 0.8555 (tmm) cc_final: 0.8145 (tpt) REVERT: V 138 TYR cc_start: 0.9043 (t80) cc_final: 0.8057 (t80) REVERT: V 142 ARG cc_start: 0.9401 (mmm-85) cc_final: 0.8704 (ttm110) REVERT: V 182 GLU cc_start: 0.8270 (tt0) cc_final: 0.8052 (tt0) REVERT: W 67 HIS cc_start: 0.9108 (p-80) cc_final: 0.8688 (p-80) REVERT: W 150 GLN cc_start: 0.8972 (tm-30) cc_final: 0.8744 (tm-30) REVERT: X 30 ASN cc_start: 0.8321 (p0) cc_final: 0.7698 (p0) REVERT: Y 252 LYS cc_start: 0.8938 (ttpt) cc_final: 0.8648 (ttpp) REVERT: Y 357 ASN cc_start: 0.8725 (m-40) cc_final: 0.8419 (m110) REVERT: Z 131 GLN cc_start: 0.8860 (tm-30) cc_final: 0.8560 (tm-30) REVERT: e 188 GLN cc_start: 0.8150 (pm20) cc_final: 0.7847 (mp10) REVERT: e 390 GLU cc_start: 0.7749 (pp20) cc_final: 0.7431 (pp20) REVERT: f 120 MET cc_start: 0.7958 (OUTLIER) cc_final: 0.7616 (tpp) REVERT: f 263 LYS cc_start: 0.9041 (ptmm) cc_final: 0.8733 (ptmm) REVERT: k 145 MET cc_start: 0.8676 (ttt) cc_final: 0.8182 (mmt) REVERT: l 120 MET cc_start: 0.8197 (ptm) cc_final: 0.7841 (tmm) REVERT: l 129 ASP cc_start: 0.8821 (p0) cc_final: 0.8458 (p0) REVERT: n 138 TYR cc_start: 0.8554 (t80) cc_final: 0.8341 (t80) REVERT: o 120 MET cc_start: 0.8156 (mtm) cc_final: 0.7864 (mtm) REVERT: o 150 GLN cc_start: 0.8668 (pp30) cc_final: 0.8438 (pp30) REVERT: o 162 MET cc_start: 0.8573 (mtm) cc_final: 0.7671 (ptp) REVERT: u 144 ARG cc_start: 0.9147 (ttp80) cc_final: 0.8819 (ttp-110) REVERT: v 73 GLU cc_start: 0.8883 (mt-10) cc_final: 0.8488 (pt0) REVERT: v 86 ILE cc_start: 0.9205 (OUTLIER) cc_final: 0.8921 (mm) REVERT: v 108 PHE cc_start: 0.8727 (m-10) cc_final: 0.8465 (m-80) REVERT: v 115 ASP cc_start: 0.9228 (p0) cc_final: 0.8765 (p0) REVERT: v 117 ASN cc_start: 0.8988 (m110) cc_final: 0.8499 (m110) REVERT: z 54 THR cc_start: 0.8896 (OUTLIER) cc_final: 0.8675 (p) REVERT: z 67 HIS cc_start: 0.8183 (p-80) cc_final: 0.7452 (p-80) REVERT: z 89 GLN cc_start: 0.9429 (mp10) cc_final: 0.9214 (mp10) outliers start: 66 outliers final: 35 residues processed: 641 average time/residue: 0.5788 time to fit residues: 605.8086 Evaluate side-chains 528 residues out of total 5886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 490 time to evaluate : 4.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 ASP Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain B residue 63 GLN Chi-restraints excluded: chain C residue 28 ASP Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain E residue 162 MET Chi-restraints excluded: chain G residue 196 SER Chi-restraints excluded: chain G residue 263 GLN Chi-restraints excluded: chain J residue 385 ASP Chi-restraints excluded: chain M residue 228 MET Chi-restraints excluded: chain M residue 385 ASP Chi-restraints excluded: chain O residue 28 ASP Chi-restraints excluded: chain S residue 140 LEU Chi-restraints excluded: chain T residue 114 ASN Chi-restraints excluded: chain T residue 129 ASP Chi-restraints excluded: chain V residue 384 SER Chi-restraints excluded: chain W residue 227 MET Chi-restraints excluded: chain Y residue 193 SER Chi-restraints excluded: chain Y residue 360 ASN Chi-restraints excluded: chain b residue 357 ASN Chi-restraints excluded: chain b residue 385 ASP Chi-restraints excluded: chain f residue 120 MET Chi-restraints excluded: chain h residue 228 MET Chi-restraints excluded: chain i residue 131 GLN Chi-restraints excluded: chain k residue 319 ILE Chi-restraints excluded: chain m residue 37 THR Chi-restraints excluded: chain n residue 385 ASP Chi-restraints excluded: chain o residue 139 ASN Chi-restraints excluded: chain p residue 28 ASP Chi-restraints excluded: chain v residue 23 VAL Chi-restraints excluded: chain v residue 48 THR Chi-restraints excluded: chain v residue 86 ILE Chi-restraints excluded: chain v residue 114 ASN Chi-restraints excluded: chain z residue 23 VAL Chi-restraints excluded: chain z residue 54 THR Chi-restraints excluded: chain z residue 86 ILE Chi-restraints excluded: chain z residue 110 LEU Chi-restraints excluded: chain z residue 123 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 694 random chunks: chunk 350 optimal weight: 7.9990 chunk 195 optimal weight: 20.0000 chunk 524 optimal weight: 5.9990 chunk 429 optimal weight: 5.9990 chunk 173 optimal weight: 10.0000 chunk 631 optimal weight: 20.0000 chunk 682 optimal weight: 20.0000 chunk 562 optimal weight: 6.9990 chunk 626 optimal weight: 5.9990 chunk 215 optimal weight: 9.9990 chunk 506 optimal weight: 30.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 ASN ** H 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 131 GLN ** N 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 31 HIS ** T 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 374 ASN ** c 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 209 GLN ** k 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 63 GLN o 172 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.3368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 56894 Z= 0.395 Angle : 0.627 12.323 77036 Z= 0.321 Chirality : 0.044 0.206 8370 Planarity : 0.004 0.063 10228 Dihedral : 4.366 25.767 7996 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 14.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.84 % Allowed : 11.03 % Favored : 87.13 % 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: 0.05 (0.10), residues: 7036 helix: 1.80 (0.16), residues: 1119 sheet: -0.29 (0.11), residues: 2290 loop : -0.22 (0.10), residues: 3627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP G 272 HIS 0.007 0.001 HIS T 67 PHE 0.022 0.002 PHE B 195 TYR 0.026 0.002 TYR T 194 ARG 0.015 0.001 ARG l 136 *********************** 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 618 residues out of total 5886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 510 time to evaluate : 5.068 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: B 161 MET cc_start: 0.8672 (mmm) cc_final: 0.8362 (mmm) REVERT: D 145 MET cc_start: 0.9198 (OUTLIER) cc_final: 0.8731 (mtp) REVERT: E 120 MET cc_start: 0.7854 (mtm) cc_final: 0.7087 (mmt) REVERT: E 131 GLN cc_start: 0.9548 (tm-30) cc_final: 0.9035 (mt0) REVERT: E 134 GLN cc_start: 0.8993 (pt0) cc_final: 0.8791 (pp30) REVERT: H 145 GLU cc_start: 0.9171 (OUTLIER) cc_final: 0.8873 (mp0) REVERT: J 145 MET cc_start: 0.9015 (ttt) cc_final: 0.8518 (ppp) REVERT: K 112 MET cc_start: 0.8519 (tpt) cc_final: 0.8221 (tpp) REVERT: M 147 ARG cc_start: 0.9208 (ppt90) cc_final: 0.8683 (ppt170) REVERT: M 371 GLU cc_start: 0.8280 (mm-30) cc_final: 0.7947 (mp0) REVERT: N 98 ILE cc_start: 0.8684 (mm) cc_final: 0.8464 (tp) REVERT: N 112 MET cc_start: 0.8615 (mmm) cc_final: 0.8298 (tpt) REVERT: N 120 MET cc_start: 0.8024 (ttp) cc_final: 0.7566 (mtp) REVERT: P 142 ARG cc_start: 0.8640 (mmp80) cc_final: 0.8432 (mmp80) REVERT: Q 54 THR cc_start: 0.8833 (m) cc_final: 0.8399 (t) REVERT: Q 63 GLN cc_start: 0.8963 (mm-40) cc_final: 0.8546 (mm110) REVERT: S 188 GLN cc_start: 0.8742 (mm-40) cc_final: 0.8511 (mm-40) REVERT: V 138 TYR cc_start: 0.9103 (t80) cc_final: 0.8896 (t80) REVERT: V 144 ARG cc_start: 0.9244 (mtp-110) cc_final: 0.8781 (ptt180) REVERT: W 120 MET cc_start: 0.6609 (mmt) cc_final: 0.6050 (mmm) REVERT: W 150 GLN cc_start: 0.9014 (tm-30) cc_final: 0.8642 (tm-30) REVERT: Z 112 MET cc_start: 0.8757 (mmm) cc_final: 0.8538 (mmm) REVERT: Z 131 GLN cc_start: 0.8665 (tm-30) cc_final: 0.8412 (tm-30) REVERT: b 190 MET cc_start: 0.8843 (ttp) cc_final: 0.8487 (ttp) REVERT: c 63 GLN cc_start: 0.8191 (tm-30) cc_final: 0.7923 (tm-30) REVERT: c 102 ASP cc_start: 0.8113 (m-30) cc_final: 0.7810 (m-30) REVERT: e 185 GLU cc_start: 0.8476 (tm-30) cc_final: 0.8096 (tm-30) REVERT: e 188 GLN cc_start: 0.8245 (OUTLIER) cc_final: 0.7985 (mp10) REVERT: e 205 MET cc_start: 0.8882 (mmm) cc_final: 0.7713 (mmm) REVERT: e 390 GLU cc_start: 0.8000 (pp20) cc_final: 0.7682 (pp20) REVERT: f 161 MET cc_start: 0.8680 (mmm) cc_final: 0.8206 (mmm) REVERT: f 263 LYS cc_start: 0.9218 (ptmm) cc_final: 0.8879 (ttpp) REVERT: k 145 MET cc_start: 0.8748 (ttt) cc_final: 0.8147 (mmt) REVERT: l 120 MET cc_start: 0.8402 (ptm) cc_final: 0.7977 (tmm) REVERT: l 129 ASP cc_start: 0.8802 (p0) cc_final: 0.8235 (p0) REVERT: l 161 MET cc_start: 0.8768 (mmm) cc_final: 0.8567 (mmm) REVERT: n 138 TYR cc_start: 0.8662 (t80) cc_final: 0.8441 (t80) REVERT: o 120 MET cc_start: 0.8483 (mtm) cc_final: 0.8228 (mtm) REVERT: o 150 GLN cc_start: 0.8762 (pp30) cc_final: 0.8544 (pp30) REVERT: v 63 GLN cc_start: 0.7414 (pm20) cc_final: 0.7042 (pm20) REVERT: v 73 GLU cc_start: 0.8729 (mt-10) cc_final: 0.8510 (pt0) REVERT: v 115 ASP cc_start: 0.9252 (p0) cc_final: 0.8984 (p0) REVERT: v 117 ASN cc_start: 0.9045 (m110) cc_final: 0.8608 (m-40) REVERT: z 29 TYR cc_start: 0.8190 (OUTLIER) cc_final: 0.7391 (t80) REVERT: z 54 THR cc_start: 0.8949 (OUTLIER) cc_final: 0.8727 (p) REVERT: z 58 LEU cc_start: 0.8777 (mp) cc_final: 0.8435 (mp) REVERT: z 65 LEU cc_start: 0.9243 (mt) cc_final: 0.9041 (mp) REVERT: z 67 HIS cc_start: 0.8614 (p-80) cc_final: 0.8035 (p-80) REVERT: z 89 GLN cc_start: 0.9579 (mp10) cc_final: 0.9251 (mp10) REVERT: z 107 LYS cc_start: 0.8688 (OUTLIER) cc_final: 0.8118 (mmtm) REVERT: z 112 MET cc_start: 0.9271 (tpp) cc_final: 0.9046 (tpp) outliers start: 108 outliers final: 53 residues processed: 584 average time/residue: 0.5546 time to fit residues: 535.9139 Evaluate side-chains 516 residues out of total 5886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 457 time to evaluate : 4.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 ASP Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 63 GLN Chi-restraints excluded: chain B residue 137 GLU Chi-restraints excluded: chain C residue 28 ASP Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain D residue 145 MET Chi-restraints excluded: chain D residue 196 SER Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain G residue 196 SER Chi-restraints excluded: chain G residue 263 GLN Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 139 ASN Chi-restraints excluded: chain H residue 145 GLU Chi-restraints excluded: chain J residue 248 ASP Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain K residue 131 GLN Chi-restraints excluded: chain M residue 385 ASP Chi-restraints excluded: chain N residue 23 VAL Chi-restraints excluded: chain N residue 66 THR Chi-restraints excluded: chain O residue 28 ASP Chi-restraints excluded: chain T residue 114 ASN Chi-restraints excluded: chain T residue 123 LEU Chi-restraints excluded: chain T residue 125 PHE Chi-restraints excluded: chain T residue 129 ASP Chi-restraints excluded: chain V residue 228 MET Chi-restraints excluded: chain V residue 384 SER Chi-restraints excluded: chain W residue 23 VAL Chi-restraints excluded: chain W residue 227 MET Chi-restraints excluded: chain Y residue 193 SER Chi-restraints excluded: chain Y residue 360 ASN Chi-restraints excluded: chain a residue 28 ASP Chi-restraints excluded: chain b residue 385 ASP Chi-restraints excluded: chain c residue 23 VAL Chi-restraints excluded: chain e residue 188 GLN Chi-restraints excluded: chain h residue 228 MET Chi-restraints excluded: chain i residue 131 GLN Chi-restraints excluded: chain k residue 283 ILE Chi-restraints excluded: chain k residue 385 ASP Chi-restraints excluded: chain l residue 136 ARG Chi-restraints excluded: chain m residue 37 THR Chi-restraints excluded: chain n residue 384 SER Chi-restraints excluded: chain n residue 385 ASP Chi-restraints excluded: chain o residue 99 VAL Chi-restraints excluded: chain p residue 28 ASP Chi-restraints excluded: chain v residue 23 VAL Chi-restraints excluded: chain v residue 35 TYR Chi-restraints excluded: chain v residue 48 THR Chi-restraints excluded: chain v residue 110 LEU Chi-restraints excluded: chain v residue 114 ASN Chi-restraints excluded: chain z residue 23 VAL Chi-restraints excluded: chain z residue 29 TYR Chi-restraints excluded: chain z residue 54 THR Chi-restraints excluded: chain z residue 59 GLU Chi-restraints excluded: chain z residue 107 LYS Chi-restraints excluded: chain z residue 110 LEU Chi-restraints excluded: chain z residue 123 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: 3.9990 chunk 327 optimal weight: 0.8980 chunk 69 optimal weight: 7.9990 chunk 301 optimal weight: 4.9990 chunk 423 optimal weight: 6.9990 chunk 633 optimal weight: 10.0000 chunk 670 optimal weight: 30.0000 chunk 331 optimal weight: 6.9990 chunk 600 optimal weight: 20.0000 chunk 180 optimal weight: 10.0000 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 HIS D 188 GLN D 271 GLN H 220 HIS ** K 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 209 GLN ** V 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 258 GLN ** i 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 134 GLN k 209 GLN ** k 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.3891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 56894 Z= 0.285 Angle : 0.563 9.764 77036 Z= 0.288 Chirality : 0.043 0.317 8370 Planarity : 0.004 0.048 10228 Dihedral : 4.149 23.036 7996 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.20 % Allowed : 12.55 % Favored : 85.25 % 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: 0.25 (0.10), residues: 7036 helix: 1.94 (0.16), residues: 1123 sheet: -0.07 (0.11), residues: 2167 loop : -0.15 (0.10), residues: 3746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP b 272 HIS 0.006 0.001 HIS Z 67 PHE 0.024 0.001 PHE B 195 TYR 0.023 0.001 TYR T 194 ARG 0.008 0.000 ARG l 133 *********************** 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 637 residues out of total 5886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 508 time to evaluate : 5.056 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: A 142 ARG cc_start: 0.8912 (tpp80) cc_final: 0.8634 (tpp80) REVERT: B 134 GLN cc_start: 0.9030 (mp10) cc_final: 0.8665 (mm110) REVERT: D 145 MET cc_start: 0.9309 (OUTLIER) cc_final: 0.8884 (mtp) REVERT: E 120 MET cc_start: 0.8021 (mtm) cc_final: 0.7289 (mmt) REVERT: E 131 GLN cc_start: 0.9565 (tm-30) cc_final: 0.9123 (pt0) REVERT: H 134 GLN cc_start: 0.9094 (pp30) cc_final: 0.8763 (pp30) REVERT: H 145 GLU cc_start: 0.9160 (OUTLIER) cc_final: 0.8860 (mp0) REVERT: H 150 GLN cc_start: 0.8741 (pp30) cc_final: 0.8508 (pp30) REVERT: H 161 MET cc_start: 0.8919 (mmm) cc_final: 0.8594 (mmm) REVERT: J 138 TYR cc_start: 0.8593 (t80) cc_final: 0.8384 (t80) REVERT: J 145 MET cc_start: 0.9033 (ttt) cc_final: 0.8672 (ppp) REVERT: K 107 LYS cc_start: 0.9199 (mmtp) cc_final: 0.8855 (mmtt) REVERT: M 371 GLU cc_start: 0.8229 (mm-30) cc_final: 0.7937 (mp0) REVERT: N 112 MET cc_start: 0.8663 (mmm) cc_final: 0.8187 (tpt) REVERT: N 120 MET cc_start: 0.8239 (ttp) cc_final: 0.7940 (mtp) REVERT: Q 54 THR cc_start: 0.8915 (m) cc_final: 0.8475 (t) REVERT: Q 112 MET cc_start: 0.9357 (tpp) cc_final: 0.9139 (tpt) REVERT: T 161 MET cc_start: 0.8456 (tpp) cc_final: 0.8228 (mpp) REVERT: V 145 MET cc_start: 0.8756 (ttt) cc_final: 0.8458 (ttt) REVERT: V 185 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.8091 (pm20) REVERT: W 150 GLN cc_start: 0.8944 (tm-30) cc_final: 0.8490 (tm-30) REVERT: Y 371 GLU cc_start: 0.8047 (mm-30) cc_final: 0.7833 (mp0) REVERT: Z 112 MET cc_start: 0.8699 (mmm) cc_final: 0.8387 (mmm) REVERT: Z 131 GLN cc_start: 0.8676 (tm-30) cc_final: 0.8463 (tm-30) REVERT: b 146 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8471 (mm) REVERT: b 190 MET cc_start: 0.8801 (ttp) cc_final: 0.8510 (ttp) REVERT: c 102 ASP cc_start: 0.8124 (m-30) cc_final: 0.7920 (m-30) REVERT: e 185 GLU cc_start: 0.8404 (tm-30) cc_final: 0.8103 (tm-30) REVERT: e 188 GLN cc_start: 0.8180 (OUTLIER) cc_final: 0.7900 (mp10) REVERT: e 205 MET cc_start: 0.8859 (mmm) cc_final: 0.7906 (mmm) REVERT: e 390 GLU cc_start: 0.8032 (pp20) cc_final: 0.7747 (pp20) REVERT: f 263 LYS cc_start: 0.9273 (ptmm) cc_final: 0.8957 (ttpp) REVERT: h 205 MET cc_start: 0.8874 (tpp) cc_final: 0.8558 (mpp) REVERT: i 57 MET cc_start: 0.8102 (tpt) cc_final: 0.7801 (tpt) REVERT: k 145 MET cc_start: 0.8754 (ttt) cc_final: 0.8165 (mmt) REVERT: l 120 MET cc_start: 0.8540 (ptm) cc_final: 0.8107 (tmm) REVERT: l 161 MET cc_start: 0.8875 (mmm) cc_final: 0.8590 (mmm) REVERT: n 138 TYR cc_start: 0.8742 (t80) cc_final: 0.8500 (t80) REVERT: o 120 MET cc_start: 0.8548 (mtm) cc_final: 0.8286 (mtm) REVERT: o 150 GLN cc_start: 0.8796 (pp30) cc_final: 0.8568 (pp30) REVERT: v 29 TYR cc_start: 0.8693 (m-80) cc_final: 0.8481 (m-80) REVERT: v 115 ASP cc_start: 0.9249 (p0) cc_final: 0.8550 (p0) REVERT: v 117 ASN cc_start: 0.9052 (m110) cc_final: 0.8331 (m-40) REVERT: z 47 ASP cc_start: 0.8643 (p0) cc_final: 0.8288 (p0) REVERT: z 54 THR cc_start: 0.9035 (OUTLIER) cc_final: 0.8801 (p) REVERT: z 58 LEU cc_start: 0.9005 (mp) cc_final: 0.8686 (mp) REVERT: z 89 GLN cc_start: 0.9637 (mp10) cc_final: 0.9236 (mp10) REVERT: z 107 LYS cc_start: 0.8863 (OUTLIER) cc_final: 0.8391 (mmtm) REVERT: z 120 MET cc_start: 0.7316 (OUTLIER) cc_final: 0.6786 (ptp) outliers start: 129 outliers final: 70 residues processed: 603 average time/residue: 0.5505 time to fit residues: 553.5343 Evaluate side-chains 515 residues out of total 5886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 437 time to evaluate : 5.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 ASP Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 137 GLU Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain C residue 28 ASP Chi-restraints excluded: chain D residue 145 MET Chi-restraints excluded: chain D residue 196 SER Chi-restraints excluded: chain D residue 236 ASP Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain G residue 136 THR Chi-restraints excluded: chain G residue 196 SER Chi-restraints excluded: chain G residue 263 GLN Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 139 ASN Chi-restraints excluded: chain H residue 145 GLU Chi-restraints excluded: chain H residue 205 VAL Chi-restraints excluded: chain J residue 248 ASP Chi-restraints excluded: chain K residue 120 MET Chi-restraints excluded: chain K residue 131 GLN Chi-restraints excluded: chain M residue 385 ASP Chi-restraints excluded: chain N residue 99 VAL Chi-restraints excluded: chain O residue 28 ASP Chi-restraints excluded: chain P residue 231 CYS Chi-restraints excluded: chain S residue 140 LEU Chi-restraints excluded: chain T residue 114 ASN Chi-restraints excluded: chain T residue 123 LEU Chi-restraints excluded: chain T residue 125 PHE Chi-restraints excluded: chain T residue 262 ASN Chi-restraints excluded: chain V residue 185 GLU Chi-restraints excluded: chain V residue 228 MET Chi-restraints excluded: chain V residue 384 SER Chi-restraints excluded: chain V residue 385 ASP Chi-restraints excluded: chain W residue 23 VAL Chi-restraints excluded: chain W residue 49 VAL Chi-restraints excluded: chain W residue 99 VAL Chi-restraints excluded: chain W residue 227 MET Chi-restraints excluded: chain Y residue 271 GLN Chi-restraints excluded: chain Y residue 284 ASN Chi-restraints excluded: chain Z residue 99 VAL Chi-restraints excluded: chain a residue 28 ASP Chi-restraints excluded: chain b residue 146 LEU Chi-restraints excluded: chain b residue 385 ASP Chi-restraints excluded: chain c residue 99 VAL Chi-restraints excluded: chain e residue 188 GLN Chi-restraints excluded: chain f residue 86 ILE Chi-restraints excluded: chain f residue 135 THR Chi-restraints excluded: chain f residue 152 VAL Chi-restraints excluded: chain h residue 228 MET Chi-restraints excluded: chain k residue 283 ILE Chi-restraints excluded: chain k residue 319 ILE Chi-restraints excluded: chain k residue 385 ASP Chi-restraints excluded: chain l residue 23 VAL Chi-restraints excluded: chain l residue 136 ARG Chi-restraints excluded: chain l residue 148 PHE Chi-restraints excluded: chain m residue 34 VAL Chi-restraints excluded: chain n residue 384 SER Chi-restraints excluded: chain n residue 385 ASP Chi-restraints excluded: chain o residue 99 VAL Chi-restraints excluded: chain o residue 139 ASN Chi-restraints excluded: chain p residue 28 ASP Chi-restraints excluded: chain p residue 37 THR Chi-restraints excluded: chain v residue 23 VAL Chi-restraints excluded: chain v residue 35 TYR Chi-restraints excluded: chain v residue 48 THR Chi-restraints excluded: chain v residue 114 ASN Chi-restraints excluded: chain y residue 136 THR Chi-restraints excluded: chain y residue 150 LEU Chi-restraints excluded: chain z residue 23 VAL Chi-restraints excluded: chain z residue 54 THR Chi-restraints excluded: chain z residue 107 LYS Chi-restraints excluded: chain z residue 120 MET Chi-restraints excluded: chain z residue 123 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 694 random chunks: chunk 558 optimal weight: 30.0000 chunk 380 optimal weight: 20.0000 chunk 9 optimal weight: 2.9990 chunk 499 optimal weight: 1.9990 chunk 276 optimal weight: 10.0000 chunk 572 optimal weight: 6.9990 chunk 463 optimal weight: 6.9990 chunk 0 optimal weight: 40.0000 chunk 342 optimal weight: 10.0000 chunk 602 optimal weight: 30.0000 chunk 169 optimal weight: 0.9980 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 GLN D 271 GLN ** E 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 357 ASN ** K 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 262 ASN N 83 HIS N 89 GLN ** N 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 188 GLN ** Z 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 209 GLN ** k 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.4178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 56894 Z= 0.253 Angle : 0.551 10.692 77036 Z= 0.282 Chirality : 0.043 0.172 8370 Planarity : 0.004 0.048 10228 Dihedral : 4.039 23.344 7996 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.41 % Allowed : 13.42 % Favored : 84.18 % 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: 1.96 (0.16), residues: 1127 sheet: -0.02 (0.11), residues: 2147 loop : -0.09 (0.10), residues: 3762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP b 272 HIS 0.004 0.001 HIS Z 83 PHE 0.022 0.001 PHE B 195 TYR 0.019 0.001 TYR e 138 ARG 0.007 0.000 ARG H 136 *********************** 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: 141 poor density : 476 time to evaluate : 5.120 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: A 142 ARG cc_start: 0.8927 (tpp80) cc_final: 0.8656 (tpp80) REVERT: B 134 GLN cc_start: 0.9082 (mp10) cc_final: 0.8714 (mm110) REVERT: D 142 ARG cc_start: 0.9097 (mmt-90) cc_final: 0.8855 (mmp80) REVERT: D 145 MET cc_start: 0.9247 (OUTLIER) cc_final: 0.8762 (mtp) REVERT: D 188 GLN cc_start: 0.8412 (OUTLIER) cc_final: 0.7943 (tm-30) REVERT: D 214 ASP cc_start: 0.7681 (OUTLIER) cc_final: 0.7452 (p0) REVERT: E 120 MET cc_start: 0.8028 (mtm) cc_final: 0.7329 (mmt) REVERT: G 139 GLU cc_start: 0.9170 (OUTLIER) cc_final: 0.8792 (pp20) REVERT: H 145 GLU cc_start: 0.9141 (OUTLIER) cc_final: 0.8860 (mp0) REVERT: H 161 MET cc_start: 0.8880 (mmm) cc_final: 0.8659 (mmm) REVERT: J 145 MET cc_start: 0.9047 (ttt) cc_final: 0.8744 (ppp) REVERT: M 371 GLU cc_start: 0.8245 (mm-30) cc_final: 0.7968 (mp0) REVERT: N 112 MET cc_start: 0.8668 (mmm) cc_final: 0.8214 (tpt) REVERT: N 120 MET cc_start: 0.8178 (ttp) cc_final: 0.7952 (mtp) REVERT: N 227 MET cc_start: 0.8817 (tpp) cc_final: 0.8595 (tpp) REVERT: Q 54 THR cc_start: 0.8954 (m) cc_final: 0.8702 (p) REVERT: V 140 LEU cc_start: 0.9354 (mt) cc_final: 0.8840 (mt) REVERT: V 185 GLU cc_start: 0.8538 (OUTLIER) cc_final: 0.8045 (pm20) REVERT: W 150 GLN cc_start: 0.8941 (tm-30) cc_final: 0.8473 (tm-30) REVERT: X 30 ASN cc_start: 0.8095 (p0) cc_final: 0.7577 (p0) REVERT: Z 66 THR cc_start: 0.9369 (OUTLIER) cc_final: 0.8862 (m) REVERT: Z 112 MET cc_start: 0.8593 (mmm) cc_final: 0.8375 (mmm) REVERT: b 190 MET cc_start: 0.8792 (ttp) cc_final: 0.8530 (ttp) REVERT: c 57 MET cc_start: 0.8894 (mmm) cc_final: 0.8516 (mmm) REVERT: e 185 GLU cc_start: 0.8376 (tm-30) cc_final: 0.8067 (tm-30) REVERT: e 188 GLN cc_start: 0.8108 (OUTLIER) cc_final: 0.7854 (mp10) REVERT: e 205 MET cc_start: 0.8841 (mmm) cc_final: 0.7896 (mmm) REVERT: e 390 GLU cc_start: 0.8021 (pp20) cc_final: 0.7742 (pp20) REVERT: f 161 MET cc_start: 0.8584 (mmm) cc_final: 0.8367 (mmm) REVERT: f 263 LYS cc_start: 0.9307 (ptmm) cc_final: 0.8999 (ttpp) REVERT: h 205 MET cc_start: 0.8860 (tpp) cc_final: 0.8470 (mpp) REVERT: k 145 MET cc_start: 0.8763 (ttt) cc_final: 0.8150 (mmt) REVERT: l 120 MET cc_start: 0.8583 (ptm) cc_final: 0.8197 (tmm) REVERT: l 161 MET cc_start: 0.8957 (mmm) cc_final: 0.8646 (mmm) REVERT: n 138 TYR cc_start: 0.8777 (t80) cc_final: 0.8538 (t80) REVERT: n 142 ARG cc_start: 0.9335 (mtt-85) cc_final: 0.9076 (tpp80) REVERT: o 120 MET cc_start: 0.8566 (mtm) cc_final: 0.8273 (mtm) REVERT: o 150 GLN cc_start: 0.8829 (pp30) cc_final: 0.8607 (pp30) REVERT: v 29 TYR cc_start: 0.8656 (m-80) cc_final: 0.8437 (m-80) REVERT: v 73 GLU cc_start: 0.8515 (mt-10) cc_final: 0.8093 (pt0) REVERT: v 115 ASP cc_start: 0.9246 (p0) cc_final: 0.8522 (p0) REVERT: v 117 ASN cc_start: 0.9094 (m110) cc_final: 0.8462 (m-40) REVERT: z 29 TYR cc_start: 0.8032 (OUTLIER) cc_final: 0.7218 (t80) REVERT: z 54 THR cc_start: 0.9063 (OUTLIER) cc_final: 0.8833 (p) REVERT: z 58 LEU cc_start: 0.8990 (mp) cc_final: 0.8585 (mp) REVERT: z 77 PHE cc_start: 0.9066 (t80) cc_final: 0.8573 (t80) REVERT: z 89 GLN cc_start: 0.9663 (mp10) cc_final: 0.9054 (mp10) outliers start: 141 outliers final: 84 residues processed: 585 average time/residue: 0.5399 time to fit residues: 529.0467 Evaluate side-chains 531 residues out of total 5886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 437 time to evaluate : 4.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 ASP Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 137 GLU Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain C residue 28 ASP Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain D residue 145 MET Chi-restraints excluded: chain D residue 188 GLN Chi-restraints excluded: chain D residue 214 ASP Chi-restraints excluded: chain D residue 236 ASP Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 129 ASP Chi-restraints excluded: chain G residue 136 THR Chi-restraints excluded: chain G residue 139 GLU Chi-restraints excluded: chain G residue 196 SER Chi-restraints excluded: chain G residue 263 GLN Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 139 ASN Chi-restraints excluded: chain H residue 145 GLU Chi-restraints excluded: chain H residue 205 VAL Chi-restraints excluded: chain J residue 248 ASP Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain K residue 99 VAL Chi-restraints excluded: chain K residue 120 MET Chi-restraints excluded: chain K residue 131 GLN Chi-restraints excluded: chain M residue 385 ASP Chi-restraints excluded: chain N residue 56 ILE Chi-restraints excluded: chain N residue 66 THR Chi-restraints excluded: chain N residue 86 ILE Chi-restraints excluded: chain N residue 99 VAL Chi-restraints excluded: chain O residue 28 ASP Chi-restraints excluded: chain P residue 136 THR Chi-restraints excluded: chain P residue 231 CYS Chi-restraints excluded: chain Q residue 23 VAL Chi-restraints excluded: chain Q residue 262 ASN Chi-restraints excluded: chain S residue 140 LEU Chi-restraints excluded: chain S residue 192 LEU Chi-restraints excluded: chain T residue 114 ASN Chi-restraints excluded: chain T residue 123 LEU Chi-restraints excluded: chain T residue 125 PHE Chi-restraints excluded: chain V residue 185 GLU Chi-restraints excluded: chain V residue 206 LEU Chi-restraints excluded: chain V residue 384 SER Chi-restraints excluded: chain V residue 385 ASP Chi-restraints excluded: chain W residue 23 VAL Chi-restraints excluded: chain W residue 49 VAL Chi-restraints excluded: chain W residue 99 VAL Chi-restraints excluded: chain W residue 227 MET Chi-restraints excluded: chain Y residue 270 VAL Chi-restraints excluded: chain Y residue 271 GLN Chi-restraints excluded: chain Y residue 275 ILE Chi-restraints excluded: chain Y residue 360 ASN Chi-restraints excluded: chain Z residue 66 THR Chi-restraints excluded: chain Z residue 195 PHE Chi-restraints excluded: chain a residue 28 ASP Chi-restraints excluded: chain b residue 385 ASP Chi-restraints excluded: chain c residue 23 VAL Chi-restraints excluded: chain c residue 99 VAL Chi-restraints excluded: chain e residue 188 GLN Chi-restraints excluded: chain f residue 86 ILE Chi-restraints excluded: chain f residue 135 THR Chi-restraints excluded: chain f residue 152 VAL Chi-restraints excluded: chain h residue 228 MET Chi-restraints excluded: chain k residue 283 ILE Chi-restraints excluded: chain k residue 319 ILE Chi-restraints excluded: chain k residue 385 ASP Chi-restraints excluded: chain l residue 23 VAL Chi-restraints excluded: chain l residue 99 VAL Chi-restraints excluded: chain l residue 136 ARG Chi-restraints excluded: chain l residue 148 PHE Chi-restraints excluded: chain m residue 37 THR Chi-restraints excluded: chain n residue 385 ASP Chi-restraints excluded: chain o residue 99 VAL Chi-restraints excluded: chain p residue 28 ASP Chi-restraints excluded: chain p residue 35 ASN Chi-restraints excluded: chain p residue 37 THR Chi-restraints excluded: chain u residue 136 THR Chi-restraints excluded: chain u residue 151 THR Chi-restraints excluded: chain v residue 23 VAL Chi-restraints excluded: chain v residue 35 TYR Chi-restraints excluded: chain v residue 48 THR Chi-restraints excluded: chain v residue 114 ASN Chi-restraints excluded: chain y residue 136 THR Chi-restraints excluded: chain z residue 23 VAL Chi-restraints excluded: chain z residue 29 TYR Chi-restraints excluded: chain z residue 54 THR Chi-restraints excluded: chain z residue 110 LEU Chi-restraints excluded: chain z residue 123 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 694 random chunks: chunk 225 optimal weight: 6.9990 chunk 604 optimal weight: 10.0000 chunk 132 optimal weight: 0.3980 chunk 393 optimal weight: 5.9990 chunk 165 optimal weight: 5.9990 chunk 671 optimal weight: 3.9990 chunk 557 optimal weight: 20.0000 chunk 310 optimal weight: 50.0000 chunk 55 optimal weight: 9.9990 chunk 222 optimal weight: 9.9990 chunk 352 optimal weight: 6.9990 overall best weight: 4.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 31 HIS ** E 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 262 ASN ** N 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 150 GLN k 209 GLN ** k 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.4430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 56894 Z= 0.285 Angle : 0.561 12.092 77036 Z= 0.285 Chirality : 0.043 0.198 8370 Planarity : 0.004 0.048 10228 Dihedral : 4.009 22.637 7996 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.44 % Allowed : 14.32 % Favored : 83.24 % 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: 1.99 (0.16), residues: 1130 sheet: -0.01 (0.12), residues: 2129 loop : -0.06 (0.10), residues: 3777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP b 272 HIS 0.006 0.001 HIS T 55 PHE 0.022 0.001 PHE B 195 TYR 0.026 0.001 TYR e 138 ARG 0.008 0.000 ARG H 133 *********************** 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 607 residues out of total 5886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 464 time to evaluate : 5.130 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: B 57 MET cc_start: 0.7445 (mmm) cc_final: 0.7217 (mmm) REVERT: B 134 GLN cc_start: 0.9123 (mp10) cc_final: 0.8920 (mm110) REVERT: D 145 MET cc_start: 0.9269 (OUTLIER) cc_final: 0.8787 (mtp) REVERT: E 120 MET cc_start: 0.8129 (mtm) cc_final: 0.7449 (mmt) REVERT: G 139 GLU cc_start: 0.9170 (OUTLIER) cc_final: 0.8825 (pp20) REVERT: H 134 GLN cc_start: 0.9080 (pp30) cc_final: 0.8796 (pp30) REVERT: H 145 GLU cc_start: 0.9163 (OUTLIER) cc_final: 0.8879 (mp0) REVERT: J 145 MET cc_start: 0.8991 (ttt) cc_final: 0.8588 (tmm) REVERT: M 371 GLU cc_start: 0.8222 (mm-30) cc_final: 0.7950 (mp0) REVERT: N 112 MET cc_start: 0.8662 (mmm) cc_final: 0.8230 (tpt) REVERT: P 145 MET cc_start: 0.9125 (mtp) cc_final: 0.8749 (ttt) REVERT: Q 54 THR cc_start: 0.9037 (m) cc_final: 0.8776 (p) REVERT: Q 112 MET cc_start: 0.9373 (tpp) cc_final: 0.9135 (tpt) REVERT: Q 120 MET cc_start: 0.7589 (mtt) cc_final: 0.6761 (mpp) REVERT: T 112 MET cc_start: 0.7888 (tpt) cc_final: 0.7516 (mmm) REVERT: V 185 GLU cc_start: 0.8579 (OUTLIER) cc_final: 0.8095 (pm20) REVERT: W 120 MET cc_start: 0.6317 (mmt) cc_final: 0.6006 (mmm) REVERT: W 150 GLN cc_start: 0.8932 (tm-30) cc_final: 0.8430 (tm-30) REVERT: X 30 ASN cc_start: 0.8144 (p0) cc_final: 0.7797 (p0) REVERT: Z 112 MET cc_start: 0.8550 (mmm) cc_final: 0.8341 (mmm) REVERT: b 146 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8480 (mm) REVERT: b 190 MET cc_start: 0.8837 (ttp) cc_final: 0.8561 (ttp) REVERT: b 205 MET cc_start: 0.8807 (mmm) cc_final: 0.8035 (mmm) REVERT: c 57 MET cc_start: 0.8967 (mmm) cc_final: 0.8580 (mmm) REVERT: e 185 GLU cc_start: 0.8368 (tm-30) cc_final: 0.8052 (tm-30) REVERT: e 188 GLN cc_start: 0.8162 (OUTLIER) cc_final: 0.7908 (mp10) REVERT: e 205 MET cc_start: 0.8821 (mmm) cc_final: 0.7838 (mmm) REVERT: e 371 GLU cc_start: 0.7678 (mp0) cc_final: 0.7424 (mp0) REVERT: f 161 MET cc_start: 0.8743 (mmm) cc_final: 0.8437 (mmm) REVERT: f 263 LYS cc_start: 0.9346 (ptmm) cc_final: 0.9048 (ttpp) REVERT: h 205 MET cc_start: 0.8817 (tpp) cc_final: 0.8404 (mpp) REVERT: i 120 MET cc_start: 0.8688 (tpt) cc_final: 0.7930 (tpt) REVERT: k 145 MET cc_start: 0.8774 (ttt) cc_final: 0.8107 (mmp) REVERT: l 120 MET cc_start: 0.8676 (ptm) cc_final: 0.8271 (tmm) REVERT: o 120 MET cc_start: 0.8515 (mtm) cc_final: 0.8234 (mtm) REVERT: o 150 GLN cc_start: 0.8866 (pp30) cc_final: 0.8634 (pp30) REVERT: v 29 TYR cc_start: 0.8737 (m-80) cc_final: 0.8479 (m-80) REVERT: v 73 GLU cc_start: 0.8514 (mt-10) cc_final: 0.8016 (pt0) REVERT: v 115 ASP cc_start: 0.9255 (p0) cc_final: 0.8518 (p0) REVERT: v 117 ASN cc_start: 0.9111 (m110) cc_final: 0.8509 (m-40) REVERT: z 58 LEU cc_start: 0.9039 (mp) cc_final: 0.8697 (mp) REVERT: z 77 PHE cc_start: 0.9179 (t80) cc_final: 0.8711 (t80) REVERT: z 89 GLN cc_start: 0.9580 (mp10) cc_final: 0.9117 (mp10) outliers start: 143 outliers final: 100 residues processed: 572 average time/residue: 0.5435 time to fit residues: 524.3986 Evaluate side-chains 542 residues out of total 5886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 436 time to evaluate : 5.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 ASP Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain C residue 28 ASP Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain D residue 145 MET Chi-restraints excluded: chain D residue 196 SER Chi-restraints excluded: chain D residue 236 ASP Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain G residue 136 THR Chi-restraints excluded: chain G residue 139 GLU Chi-restraints excluded: chain G residue 196 SER Chi-restraints excluded: chain G residue 263 GLN Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 139 ASN Chi-restraints excluded: chain H residue 145 GLU Chi-restraints excluded: chain H residue 205 VAL Chi-restraints excluded: chain J residue 248 ASP Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain K residue 54 THR Chi-restraints excluded: chain K residue 99 VAL Chi-restraints excluded: chain K residue 131 GLN Chi-restraints excluded: chain M residue 231 CYS Chi-restraints excluded: chain M residue 385 ASP Chi-restraints excluded: chain N residue 66 THR Chi-restraints excluded: chain N residue 86 ILE Chi-restraints excluded: chain N residue 99 VAL Chi-restraints excluded: chain N residue 222 VAL Chi-restraints excluded: chain O residue 28 ASP Chi-restraints excluded: chain P residue 136 THR Chi-restraints excluded: chain P residue 231 CYS Chi-restraints excluded: chain Q residue 23 VAL Chi-restraints excluded: chain Q residue 262 ASN Chi-restraints excluded: chain S residue 140 LEU Chi-restraints excluded: chain S residue 192 LEU Chi-restraints excluded: chain T residue 114 ASN Chi-restraints excluded: chain T residue 123 LEU Chi-restraints excluded: chain T residue 125 PHE Chi-restraints excluded: chain V residue 185 GLU Chi-restraints excluded: chain V residue 206 LEU Chi-restraints excluded: chain V residue 385 ASP Chi-restraints excluded: chain W residue 23 VAL Chi-restraints excluded: chain W residue 49 VAL Chi-restraints excluded: chain W residue 99 VAL Chi-restraints excluded: chain W residue 227 MET Chi-restraints excluded: chain Y residue 193 SER Chi-restraints excluded: chain Y residue 214 ASP Chi-restraints excluded: chain Y residue 219 THR Chi-restraints excluded: chain Y residue 270 VAL Chi-restraints excluded: chain Y residue 271 GLN Chi-restraints excluded: chain Y residue 275 ILE Chi-restraints excluded: chain Y residue 360 ASN Chi-restraints excluded: chain Z residue 99 VAL Chi-restraints excluded: chain Z residue 195 PHE Chi-restraints excluded: chain a residue 28 ASP Chi-restraints excluded: chain a residue 38 VAL Chi-restraints excluded: chain b residue 146 LEU Chi-restraints excluded: chain c residue 23 VAL Chi-restraints excluded: chain c residue 99 VAL Chi-restraints excluded: chain e residue 188 GLN Chi-restraints excluded: chain e residue 263 GLN Chi-restraints excluded: chain e residue 376 LEU Chi-restraints excluded: chain f residue 23 VAL Chi-restraints excluded: chain f residue 86 ILE Chi-restraints excluded: chain f residue 135 THR Chi-restraints excluded: chain f residue 152 VAL Chi-restraints excluded: chain h residue 190 MET Chi-restraints excluded: chain h residue 228 MET Chi-restraints excluded: chain i residue 150 GLN Chi-restraints excluded: chain k residue 231 CYS Chi-restraints excluded: chain k residue 283 ILE Chi-restraints excluded: chain k residue 285 LEU Chi-restraints excluded: chain k residue 319 ILE Chi-restraints excluded: chain k residue 385 ASP Chi-restraints excluded: chain l residue 23 VAL Chi-restraints excluded: chain l residue 99 VAL Chi-restraints excluded: chain l residue 148 PHE Chi-restraints excluded: chain l residue 205 VAL Chi-restraints excluded: chain m residue 37 THR Chi-restraints excluded: chain n residue 385 ASP Chi-restraints excluded: chain o residue 99 VAL Chi-restraints excluded: chain o residue 139 ASN Chi-restraints excluded: chain o residue 205 VAL Chi-restraints excluded: chain p residue 28 ASP Chi-restraints excluded: chain p residue 37 THR 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 28 ARG Chi-restraints excluded: chain v residue 35 TYR Chi-restraints excluded: chain v residue 48 THR 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 150 LEU Chi-restraints excluded: chain z residue 23 VAL Chi-restraints excluded: chain z residue 110 LEU Chi-restraints excluded: chain z residue 123 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 694 random chunks: chunk 647 optimal weight: 10.0000 chunk 75 optimal weight: 30.0000 chunk 382 optimal weight: 0.0370 chunk 490 optimal weight: 10.0000 chunk 379 optimal weight: 6.9990 chunk 565 optimal weight: 6.9990 chunk 374 optimal weight: 5.9990 chunk 668 optimal weight: 9.9990 chunk 418 optimal weight: 1.9990 chunk 407 optimal weight: 20.0000 chunk 308 optimal weight: 9.9990 overall best weight: 4.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 262 ASN ** N 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 271 GLN ** e 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.4607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 56894 Z= 0.271 Angle : 0.569 12.112 77036 Z= 0.288 Chirality : 0.043 0.228 8370 Planarity : 0.004 0.047 10228 Dihedral : 3.993 25.936 7996 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.48 % Allowed : 14.73 % Favored : 82.79 % 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: 0.40 (0.10), residues: 7036 helix: 1.99 (0.16), residues: 1130 sheet: 0.08 (0.12), residues: 2079 loop : -0.07 (0.10), residues: 3827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP b 272 HIS 0.004 0.001 HIS o 55 PHE 0.029 0.001 PHE V 383 TYR 0.022 0.001 TYR e 138 ARG 0.009 0.000 ARG B 133 *********************** 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 614 residues out of total 5886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 469 time to evaluate : 5.001 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: B 57 MET cc_start: 0.7577 (mmm) cc_final: 0.7334 (mmm) REVERT: B 134 GLN cc_start: 0.9149 (mp10) cc_final: 0.8869 (mm110) REVERT: D 145 MET cc_start: 0.9304 (OUTLIER) cc_final: 0.8741 (mtp) REVERT: D 214 ASP cc_start: 0.7753 (OUTLIER) cc_final: 0.7458 (p0) REVERT: E 120 MET cc_start: 0.8147 (mtm) cc_final: 0.7485 (mmt) REVERT: G 139 GLU cc_start: 0.9179 (OUTLIER) cc_final: 0.8870 (pp20) REVERT: H 145 GLU cc_start: 0.9162 (OUTLIER) cc_final: 0.8864 (mp0) REVERT: J 145 MET cc_start: 0.8962 (ttt) cc_final: 0.8541 (tmm) REVERT: K 161 MET cc_start: 0.8875 (mmm) cc_final: 0.8579 (mmm) REVERT: M 357 ASN cc_start: 0.8570 (m110) cc_final: 0.8282 (m110) REVERT: N 112 MET cc_start: 0.8654 (mmm) cc_final: 0.8232 (tpt) REVERT: N 120 MET cc_start: 0.8210 (ttp) cc_final: 0.7827 (mtp) REVERT: Q 54 THR cc_start: 0.8914 (m) cc_final: 0.8598 (p) REVERT: Q 89 GLN cc_start: 0.9122 (mt0) cc_final: 0.8580 (tp40) REVERT: Q 112 MET cc_start: 0.9349 (tpp) cc_final: 0.9105 (tpt) REVERT: T 112 MET cc_start: 0.7827 (tpt) cc_final: 0.7445 (mmm) REVERT: V 185 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.8103 (pm20) REVERT: W 120 MET cc_start: 0.6481 (mmt) cc_final: 0.6268 (mmm) REVERT: W 150 GLN cc_start: 0.8915 (tm-30) cc_final: 0.8418 (tm-30) REVERT: X 30 ASN cc_start: 0.8198 (p0) cc_final: 0.7839 (p0) REVERT: b 190 MET cc_start: 0.8800 (ttp) cc_final: 0.8539 (ttp) REVERT: c 57 MET cc_start: 0.8938 (mmm) cc_final: 0.8494 (mmm) REVERT: c 161 MET cc_start: 0.8668 (mmm) cc_final: 0.8309 (mmm) REVERT: e 147 ARG cc_start: 0.8744 (ttp80) cc_final: 0.8278 (ptt90) REVERT: e 185 GLU cc_start: 0.8366 (tm-30) cc_final: 0.8044 (tm-30) REVERT: e 188 GLN cc_start: 0.8190 (OUTLIER) cc_final: 0.7943 (mp10) REVERT: e 205 MET cc_start: 0.8807 (mmm) cc_final: 0.7819 (mmm) REVERT: e 371 GLU cc_start: 0.7701 (mp0) cc_final: 0.7411 (mp0) REVERT: f 263 LYS cc_start: 0.9358 (ptmm) cc_final: 0.9058 (ttpp) REVERT: h 205 MET cc_start: 0.8811 (tpp) cc_final: 0.8400 (mpp) REVERT: i 120 MET cc_start: 0.8715 (tpt) cc_final: 0.7983 (tpt) REVERT: k 145 MET cc_start: 0.8768 (ttt) cc_final: 0.8105 (mmp) REVERT: l 120 MET cc_start: 0.8697 (ptm) cc_final: 0.8317 (tmm) REVERT: l 131 GLN cc_start: 0.8830 (tp40) cc_final: 0.8619 (tp40) REVERT: m 32 GLU cc_start: 0.7235 (mp0) cc_final: 0.7029 (mp0) REVERT: o 120 MET cc_start: 0.8516 (mtm) cc_final: 0.8222 (mtm) REVERT: o 150 GLN cc_start: 0.8883 (pp30) cc_final: 0.8651 (pp30) REVERT: u 147 ARG cc_start: 0.9255 (ptt-90) cc_final: 0.8840 (ptt90) REVERT: v 29 TYR cc_start: 0.8788 (m-80) cc_final: 0.8535 (m-80) REVERT: v 73 GLU cc_start: 0.8520 (mt-10) cc_final: 0.8187 (pt0) REVERT: v 115 ASP cc_start: 0.9248 (p0) cc_final: 0.8511 (p0) REVERT: v 117 ASN cc_start: 0.9125 (m110) cc_final: 0.8516 (m-40) REVERT: z 29 TYR cc_start: 0.8031 (OUTLIER) cc_final: 0.7246 (t80) REVERT: z 47 ASP cc_start: 0.8529 (p0) cc_final: 0.7555 (t0) REVERT: z 58 LEU cc_start: 0.9045 (mp) cc_final: 0.8660 (mp) REVERT: z 73 GLU cc_start: 0.8257 (pm20) cc_final: 0.7747 (pm20) REVERT: z 77 PHE cc_start: 0.9190 (t80) cc_final: 0.8724 (t80) REVERT: z 89 GLN cc_start: 0.9430 (mp10) cc_final: 0.9062 (mp10) outliers start: 145 outliers final: 104 residues processed: 584 average time/residue: 0.5843 time to fit residues: 571.1523 Evaluate side-chains 539 residues out of total 5886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 428 time to evaluate : 5.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 ASP Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain C residue 28 ASP Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain D residue 145 MET Chi-restraints excluded: chain D residue 196 SER Chi-restraints excluded: chain D residue 214 ASP Chi-restraints excluded: chain D residue 236 ASP Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 129 ASP Chi-restraints excluded: chain G residue 136 THR Chi-restraints excluded: chain G residue 139 GLU Chi-restraints excluded: chain G residue 196 SER Chi-restraints excluded: chain G residue 263 GLN Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 80 LYS Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 139 ASN Chi-restraints excluded: chain H residue 145 GLU Chi-restraints excluded: chain H residue 205 VAL Chi-restraints excluded: chain J residue 248 ASP Chi-restraints excluded: chain J residue 275 ILE Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain K residue 54 THR Chi-restraints excluded: chain K residue 99 VAL Chi-restraints excluded: chain K residue 131 GLN Chi-restraints excluded: chain M residue 231 CYS Chi-restraints excluded: chain M residue 385 ASP Chi-restraints excluded: chain N residue 48 THR Chi-restraints excluded: chain N residue 66 THR Chi-restraints excluded: chain N residue 86 ILE Chi-restraints excluded: chain N residue 99 VAL Chi-restraints excluded: chain N residue 222 VAL Chi-restraints excluded: chain O residue 28 ASP Chi-restraints excluded: chain P residue 136 THR Chi-restraints excluded: chain P residue 231 CYS Chi-restraints excluded: chain Q residue 23 VAL Chi-restraints excluded: chain Q residue 262 ASN Chi-restraints excluded: chain S residue 140 LEU Chi-restraints excluded: chain S residue 192 LEU Chi-restraints excluded: chain S residue 228 MET Chi-restraints excluded: chain T residue 114 ASN Chi-restraints excluded: chain T residue 123 LEU Chi-restraints excluded: chain T residue 125 PHE Chi-restraints excluded: chain V residue 185 GLU Chi-restraints excluded: chain V residue 206 LEU Chi-restraints excluded: chain V residue 384 SER Chi-restraints excluded: chain V residue 385 ASP Chi-restraints excluded: chain W residue 23 VAL Chi-restraints excluded: chain W residue 49 VAL Chi-restraints excluded: chain W residue 99 VAL Chi-restraints excluded: chain Y residue 193 SER Chi-restraints excluded: chain Y residue 214 ASP Chi-restraints excluded: chain Y residue 219 THR Chi-restraints excluded: chain Y residue 270 VAL Chi-restraints excluded: chain Y residue 271 GLN Chi-restraints excluded: chain Y residue 275 ILE Chi-restraints excluded: chain Y residue 360 ASN Chi-restraints excluded: chain Z residue 99 VAL Chi-restraints excluded: chain Z residue 195 PHE Chi-restraints excluded: chain a residue 28 ASP Chi-restraints excluded: chain a residue 38 VAL Chi-restraints excluded: chain c residue 23 VAL Chi-restraints excluded: chain c residue 99 VAL Chi-restraints excluded: chain e residue 188 GLN Chi-restraints excluded: chain e residue 376 LEU Chi-restraints excluded: chain f residue 23 VAL Chi-restraints excluded: chain f residue 86 ILE Chi-restraints excluded: chain f residue 135 THR Chi-restraints excluded: chain f residue 152 VAL Chi-restraints excluded: chain h residue 190 MET Chi-restraints excluded: chain h residue 228 MET Chi-restraints excluded: chain i residue 131 GLN Chi-restraints excluded: chain k residue 231 CYS Chi-restraints excluded: chain k residue 285 LEU Chi-restraints excluded: chain k residue 319 ILE Chi-restraints excluded: chain k residue 385 ASP Chi-restraints excluded: chain l residue 23 VAL Chi-restraints excluded: chain l residue 99 VAL Chi-restraints excluded: chain l residue 148 PHE Chi-restraints excluded: chain l residue 205 VAL Chi-restraints excluded: chain m residue 37 THR Chi-restraints excluded: chain n residue 385 ASP Chi-restraints excluded: chain o residue 99 VAL Chi-restraints excluded: chain o residue 139 ASN Chi-restraints excluded: chain o residue 205 VAL Chi-restraints excluded: chain p residue 28 ASP Chi-restraints excluded: chain p residue 35 ASN Chi-restraints excluded: chain p residue 37 THR 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 28 ARG Chi-restraints excluded: chain v residue 48 THR 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 150 LEU Chi-restraints excluded: chain z residue 23 VAL Chi-restraints excluded: chain z residue 29 TYR Chi-restraints excluded: chain z residue 66 THR Chi-restraints excluded: chain z residue 110 LEU Chi-restraints excluded: chain z residue 123 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: 20.0000 chunk 399 optimal weight: 6.9990 chunk 201 optimal weight: 9.9990 chunk 131 optimal weight: 6.9990 chunk 129 optimal weight: 20.0000 chunk 425 optimal weight: 9.9990 chunk 455 optimal weight: 9.9990 chunk 330 optimal weight: 0.0670 chunk 62 optimal weight: 6.9990 chunk 525 optimal weight: 0.7980 overall best weight: 4.3724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 GLN ** E 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 188 GLN ** Y 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 134 GLN ** o 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.4751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 56894 Z= 0.271 Angle : 0.586 14.594 77036 Z= 0.296 Chirality : 0.043 0.269 8370 Planarity : 0.004 0.048 10228 Dihedral : 3.998 29.355 7996 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.25 % Allowed : 15.31 % Favored : 82.43 % 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: 0.41 (0.10), residues: 7036 helix: 1.95 (0.16), residues: 1128 sheet: 0.11 (0.12), residues: 2081 loop : -0.05 (0.10), residues: 3827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP b 272 HIS 0.004 0.001 HIS o 55 PHE 0.027 0.001 PHE V 383 TYR 0.017 0.001 TYR c 64 ARG 0.009 0.000 ARG H 133 *********************** 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 576 residues out of total 5886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 444 time to evaluate : 4.985 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: B 57 MET cc_start: 0.7674 (mmm) cc_final: 0.7408 (mmm) REVERT: B 63 GLN cc_start: 0.9399 (mm-40) cc_final: 0.9076 (tp-100) REVERT: B 134 GLN cc_start: 0.9170 (mp10) cc_final: 0.8888 (mm110) REVERT: D 145 MET cc_start: 0.9266 (OUTLIER) cc_final: 0.8793 (mtp) REVERT: D 214 ASP cc_start: 0.7734 (OUTLIER) cc_final: 0.7439 (p0) REVERT: E 120 MET cc_start: 0.8080 (mtm) cc_final: 0.7493 (mmt) REVERT: G 139 GLU cc_start: 0.9184 (OUTLIER) cc_final: 0.8960 (pp20) REVERT: H 63 GLN cc_start: 0.9550 (mm110) cc_final: 0.9329 (mm110) REVERT: H 80 LYS cc_start: 0.9393 (OUTLIER) cc_final: 0.9081 (tttm) REVERT: H 145 GLU cc_start: 0.9156 (OUTLIER) cc_final: 0.8875 (mp0) REVERT: J 145 MET cc_start: 0.8975 (ttt) cc_final: 0.8475 (tmm) REVERT: M 357 ASN cc_start: 0.8589 (m110) cc_final: 0.8292 (m110) REVERT: N 112 MET cc_start: 0.8652 (mmm) cc_final: 0.8245 (tpt) REVERT: N 120 MET cc_start: 0.8264 (ttp) cc_final: 0.7903 (mtm) REVERT: Q 54 THR cc_start: 0.8934 (m) cc_final: 0.8613 (p) REVERT: Q 89 GLN cc_start: 0.9109 (mt0) cc_final: 0.8572 (tp40) REVERT: Q 120 MET cc_start: 0.7488 (mtt) cc_final: 0.6496 (mpp) REVERT: R 32 GLU cc_start: 0.8653 (pt0) cc_final: 0.8308 (pm20) REVERT: T 112 MET cc_start: 0.7786 (tpt) cc_final: 0.7356 (mmm) REVERT: V 185 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.8105 (pm20) REVERT: W 120 MET cc_start: 0.6622 (mmt) cc_final: 0.6093 (mmm) REVERT: W 150 GLN cc_start: 0.8913 (tm-30) cc_final: 0.8406 (tm-30) REVERT: X 30 ASN cc_start: 0.8228 (p0) cc_final: 0.7858 (p0) REVERT: Z 161 MET cc_start: 0.8787 (mmm) cc_final: 0.8228 (mmm) REVERT: b 146 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8608 (mm) REVERT: b 190 MET cc_start: 0.8794 (ttp) cc_final: 0.8539 (ttp) REVERT: b 205 MET cc_start: 0.8804 (mmm) cc_final: 0.8013 (mmm) REVERT: c 57 MET cc_start: 0.8926 (mmm) cc_final: 0.8724 (mmm) REVERT: e 147 ARG cc_start: 0.8753 (ttp80) cc_final: 0.8339 (ptt90) REVERT: e 185 GLU cc_start: 0.8358 (tm-30) cc_final: 0.8033 (tm-30) REVERT: e 188 GLN cc_start: 0.8163 (OUTLIER) cc_final: 0.7922 (mp10) REVERT: e 205 MET cc_start: 0.8792 (mmm) cc_final: 0.7818 (mmm) REVERT: f 263 LYS cc_start: 0.9372 (ptmm) cc_final: 0.9079 (ttpp) REVERT: h 205 MET cc_start: 0.8813 (tpp) cc_final: 0.8397 (mpp) REVERT: i 120 MET cc_start: 0.8736 (tpt) cc_final: 0.8007 (tpt) REVERT: k 145 MET cc_start: 0.8739 (ttt) cc_final: 0.8067 (mmp) REVERT: l 120 MET cc_start: 0.8735 (ptm) cc_final: 0.8387 (tmm) REVERT: l 131 GLN cc_start: 0.8852 (tp40) cc_final: 0.8617 (tp40) REVERT: m 32 GLU cc_start: 0.7259 (mp0) cc_final: 0.6980 (mp0) REVERT: o 120 MET cc_start: 0.8523 (mtm) cc_final: 0.8131 (mtm) REVERT: o 150 GLN cc_start: 0.8886 (pp30) cc_final: 0.8659 (pp30) REVERT: o 161 MET cc_start: 0.8728 (mmm) cc_final: 0.8486 (mmm) REVERT: u 147 ARG cc_start: 0.9257 (ptt-90) cc_final: 0.8848 (ptt90) REVERT: v 29 TYR cc_start: 0.8786 (m-80) cc_final: 0.8530 (m-80) REVERT: v 73 GLU cc_start: 0.8599 (mt-10) cc_final: 0.8242 (pt0) REVERT: v 115 ASP cc_start: 0.9254 (p0) cc_final: 0.8645 (p0) REVERT: v 117 ASN cc_start: 0.9140 (m110) cc_final: 0.8530 (m-40) REVERT: z 29 TYR cc_start: 0.7954 (OUTLIER) cc_final: 0.7220 (t80) REVERT: z 47 ASP cc_start: 0.8429 (p0) cc_final: 0.7416 (t0) REVERT: z 58 LEU cc_start: 0.9135 (mp) cc_final: 0.8758 (mp) REVERT: z 77 PHE cc_start: 0.9187 (t80) cc_final: 0.8636 (t80) REVERT: z 89 GLN cc_start: 0.9375 (mp10) cc_final: 0.9033 (mp10) outliers start: 132 outliers final: 100 residues processed: 544 average time/residue: 0.5277 time to fit residues: 483.3033 Evaluate side-chains 532 residues out of total 5886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 423 time to evaluate : 4.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain C residue 28 ASP Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain D residue 145 MET Chi-restraints excluded: chain D residue 214 ASP Chi-restraints excluded: chain D residue 236 ASP Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 129 ASP Chi-restraints excluded: chain G residue 136 THR Chi-restraints excluded: chain G residue 139 GLU Chi-restraints excluded: chain G residue 196 SER Chi-restraints excluded: chain G residue 263 GLN Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 80 LYS Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 139 ASN Chi-restraints excluded: chain H residue 145 GLU Chi-restraints excluded: chain H residue 205 VAL Chi-restraints excluded: chain J residue 248 ASP Chi-restraints excluded: chain J residue 275 ILE Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain K residue 54 THR Chi-restraints excluded: chain K residue 99 VAL Chi-restraints excluded: chain K residue 131 GLN Chi-restraints excluded: chain M residue 231 CYS Chi-restraints excluded: chain M residue 385 ASP Chi-restraints excluded: chain N residue 33 ILE Chi-restraints excluded: chain N residue 48 THR Chi-restraints excluded: chain N residue 66 THR Chi-restraints excluded: chain N residue 86 ILE Chi-restraints excluded: chain N residue 99 VAL Chi-restraints excluded: chain N residue 222 VAL Chi-restraints excluded: chain O residue 28 ASP Chi-restraints excluded: chain P residue 136 THR Chi-restraints excluded: chain P residue 231 CYS Chi-restraints excluded: chain Q residue 23 VAL Chi-restraints excluded: chain Q residue 262 ASN Chi-restraints excluded: chain S residue 140 LEU Chi-restraints excluded: chain S residue 192 LEU Chi-restraints excluded: chain S residue 228 MET Chi-restraints excluded: chain T residue 114 ASN Chi-restraints excluded: chain T residue 123 LEU Chi-restraints excluded: chain T residue 125 PHE Chi-restraints excluded: chain T residue 217 ILE Chi-restraints excluded: chain V residue 185 GLU Chi-restraints excluded: chain V residue 206 LEU Chi-restraints excluded: chain V residue 384 SER Chi-restraints excluded: chain V residue 385 ASP Chi-restraints excluded: chain W residue 23 VAL Chi-restraints excluded: chain W residue 49 VAL Chi-restraints excluded: chain W residue 99 VAL Chi-restraints excluded: chain Y residue 193 SER Chi-restraints excluded: chain Y residue 219 THR Chi-restraints excluded: chain Y residue 270 VAL Chi-restraints excluded: chain Y residue 271 GLN Chi-restraints excluded: chain Y residue 275 ILE Chi-restraints excluded: chain Y residue 360 ASN Chi-restraints excluded: chain Z residue 99 VAL Chi-restraints excluded: chain Z residue 195 PHE Chi-restraints excluded: chain a residue 28 ASP Chi-restraints excluded: chain a residue 38 VAL Chi-restraints excluded: chain b residue 146 LEU Chi-restraints excluded: chain c residue 23 VAL Chi-restraints excluded: chain c residue 99 VAL Chi-restraints excluded: chain e residue 188 GLN Chi-restraints excluded: chain e residue 376 LEU Chi-restraints excluded: chain f residue 23 VAL Chi-restraints excluded: chain f residue 86 ILE Chi-restraints excluded: chain f residue 135 THR Chi-restraints excluded: chain f residue 152 VAL Chi-restraints excluded: chain h residue 190 MET Chi-restraints excluded: chain h residue 228 MET Chi-restraints excluded: chain i residue 131 GLN Chi-restraints excluded: chain k residue 231 CYS Chi-restraints excluded: chain k residue 285 LEU Chi-restraints excluded: chain k residue 385 ASP Chi-restraints excluded: chain l residue 23 VAL Chi-restraints excluded: chain l residue 99 VAL Chi-restraints excluded: chain l residue 148 PHE Chi-restraints excluded: chain l residue 205 VAL Chi-restraints excluded: chain m residue 37 THR Chi-restraints excluded: chain n residue 385 ASP Chi-restraints excluded: chain o residue 99 VAL Chi-restraints excluded: chain o residue 139 ASN Chi-restraints excluded: chain o residue 205 VAL Chi-restraints excluded: chain p residue 28 ASP Chi-restraints excluded: chain p residue 35 ASN Chi-restraints excluded: chain p residue 37 THR 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 28 ARG Chi-restraints excluded: chain v residue 35 TYR Chi-restraints excluded: chain v residue 48 THR 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 150 LEU Chi-restraints excluded: chain z residue 23 VAL Chi-restraints excluded: chain z residue 29 TYR Chi-restraints excluded: chain z residue 110 LEU Chi-restraints excluded: chain z residue 123 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 694 random chunks: chunk 608 optimal weight: 20.0000 chunk 640 optimal weight: 10.0000 chunk 584 optimal weight: 0.0000 chunk 623 optimal weight: 0.5980 chunk 375 optimal weight: 0.9980 chunk 271 optimal weight: 40.0000 chunk 489 optimal weight: 0.2980 chunk 191 optimal weight: 5.9990 chunk 563 optimal weight: 20.0000 chunk 589 optimal weight: 9.9990 chunk 621 optimal weight: 6.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 188 GLN ** E 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 134 GLN ** e 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 271 GLN ** o 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.4846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 56894 Z= 0.168 Angle : 0.574 13.745 77036 Z= 0.288 Chirality : 0.043 0.201 8370 Planarity : 0.003 0.048 10228 Dihedral : 3.891 30.632 7996 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.93 % Allowed : 15.72 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.45 (0.10), residues: 7036 helix: 1.97 (0.16), residues: 1124 sheet: 0.10 (0.11), residues: 2184 loop : 0.00 (0.10), residues: 3728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 272 HIS 0.008 0.001 HIS W 55 PHE 0.025 0.001 PHE V 383 TYR 0.041 0.001 TYR c 64 ARG 0.012 0.000 ARG H 133 *********************** 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 566 residues out of total 5886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 453 time to evaluate : 5.028 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: B 57 MET cc_start: 0.7600 (mmm) cc_final: 0.7344 (mmm) REVERT: B 63 GLN cc_start: 0.9429 (mm-40) cc_final: 0.9120 (tp-100) REVERT: B 134 GLN cc_start: 0.9190 (mp10) cc_final: 0.8890 (mm110) REVERT: D 145 MET cc_start: 0.9254 (OUTLIER) cc_final: 0.8790 (mtp) REVERT: D 188 GLN cc_start: 0.8374 (OUTLIER) cc_final: 0.8092 (tm-30) REVERT: D 214 ASP cc_start: 0.7738 (OUTLIER) cc_final: 0.7489 (p0) REVERT: E 120 MET cc_start: 0.8060 (mtm) cc_final: 0.7468 (mmt) REVERT: G 139 GLU cc_start: 0.9311 (OUTLIER) cc_final: 0.8948 (pp20) REVERT: G 188 GLN cc_start: 0.8862 (mm-40) cc_final: 0.8556 (mm-40) REVERT: G 205 MET cc_start: 0.8758 (mmp) cc_final: 0.8510 (mmp) REVERT: H 63 GLN cc_start: 0.9530 (mm110) cc_final: 0.9306 (mm110) REVERT: H 80 LYS cc_start: 0.9433 (tppp) cc_final: 0.9132 (tttm) REVERT: H 134 GLN cc_start: 0.9180 (pp30) cc_final: 0.8844 (pp30) REVERT: H 145 GLU cc_start: 0.9115 (OUTLIER) cc_final: 0.8860 (mp0) REVERT: J 145 MET cc_start: 0.8976 (ttt) cc_final: 0.8617 (tmm) REVERT: M 357 ASN cc_start: 0.8543 (m110) cc_final: 0.8265 (m110) REVERT: N 112 MET cc_start: 0.8647 (mmm) cc_final: 0.8214 (tpt) REVERT: N 120 MET cc_start: 0.8211 (ttp) cc_final: 0.7815 (mtp) REVERT: Q 54 THR cc_start: 0.9070 (m) cc_final: 0.8820 (p) REVERT: Q 89 GLN cc_start: 0.9101 (mt0) cc_final: 0.8569 (tp40) REVERT: Q 120 MET cc_start: 0.7578 (mtt) cc_final: 0.6638 (mpp) REVERT: R 30 ASN cc_start: 0.8086 (p0) cc_final: 0.7248 (p0) REVERT: R 32 GLU cc_start: 0.8563 (pt0) cc_final: 0.8325 (pm20) REVERT: V 145 MET cc_start: 0.8585 (ttt) cc_final: 0.8195 (ttt) REVERT: V 185 GLU cc_start: 0.8508 (OUTLIER) cc_final: 0.8057 (pm20) REVERT: W 150 GLN cc_start: 0.8901 (tm-30) cc_final: 0.8356 (tm-30) REVERT: X 30 ASN cc_start: 0.8226 (p0) cc_final: 0.7730 (p0) REVERT: Z 161 MET cc_start: 0.8761 (mmm) cc_final: 0.8263 (mmm) REVERT: b 146 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8580 (mm) REVERT: b 190 MET cc_start: 0.8754 (ttp) cc_final: 0.8486 (ttp) REVERT: b 205 MET cc_start: 0.8769 (mmm) cc_final: 0.8055 (mmm) REVERT: c 57 MET cc_start: 0.8947 (mmm) cc_final: 0.8695 (mmm) REVERT: c 111 GLN cc_start: 0.8642 (tm-30) cc_final: 0.8291 (tm-30) REVERT: e 147 ARG cc_start: 0.8754 (ttp80) cc_final: 0.8351 (ptt90) REVERT: e 185 GLU cc_start: 0.8312 (tm-30) cc_final: 0.7982 (tm-30) REVERT: e 188 GLN cc_start: 0.8085 (OUTLIER) cc_final: 0.7865 (mp10) REVERT: e 205 MET cc_start: 0.8747 (mmm) cc_final: 0.7618 (mmm) REVERT: e 371 GLU cc_start: 0.8177 (mm-30) cc_final: 0.7967 (mp0) REVERT: f 161 MET cc_start: 0.8551 (mmm) cc_final: 0.8221 (mmm) REVERT: h 205 MET cc_start: 0.8732 (tpp) cc_final: 0.8364 (mpp) REVERT: i 120 MET cc_start: 0.8677 (tpt) cc_final: 0.7954 (tpt) REVERT: k 145 MET cc_start: 0.8728 (ttt) cc_final: 0.8042 (mmp) REVERT: l 120 MET cc_start: 0.8671 (ptm) cc_final: 0.8368 (tmm) REVERT: l 131 GLN cc_start: 0.8833 (tp40) cc_final: 0.8573 (tp40) REVERT: m 32 GLU cc_start: 0.7191 (mp0) cc_final: 0.6930 (mp0) REVERT: o 120 MET cc_start: 0.8521 (mtm) cc_final: 0.8191 (mtm) REVERT: u 147 ARG cc_start: 0.9270 (ptt-90) cc_final: 0.8845 (ptt90) REVERT: v 29 TYR cc_start: 0.8750 (m-80) cc_final: 0.8483 (m-80) REVERT: v 73 GLU cc_start: 0.8656 (mt-10) cc_final: 0.8225 (pt0) REVERT: v 115 ASP cc_start: 0.9231 (p0) cc_final: 0.8648 (p0) REVERT: v 117 ASN cc_start: 0.9125 (m110) cc_final: 0.8649 (m-40) REVERT: z 29 TYR cc_start: 0.7947 (OUTLIER) cc_final: 0.7216 (t80) REVERT: z 47 ASP cc_start: 0.8446 (p0) cc_final: 0.7401 (t0) REVERT: z 58 LEU cc_start: 0.9191 (mp) cc_final: 0.8773 (mp) REVERT: z 77 PHE cc_start: 0.9076 (t80) cc_final: 0.8636 (t80) REVERT: z 89 GLN cc_start: 0.9287 (mp10) cc_final: 0.8984 (mp10) outliers start: 113 outliers final: 93 residues processed: 542 average time/residue: 0.5362 time to fit residues: 487.1207 Evaluate side-chains 531 residues out of total 5886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 429 time to evaluate : 4.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain D residue 145 MET Chi-restraints excluded: chain D residue 188 GLN Chi-restraints excluded: chain D residue 214 ASP Chi-restraints excluded: chain D residue 236 ASP Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 129 ASP Chi-restraints excluded: chain E residue 148 PHE Chi-restraints excluded: chain G residue 136 THR Chi-restraints excluded: chain G residue 139 GLU Chi-restraints excluded: chain G residue 196 SER Chi-restraints excluded: chain G residue 263 GLN Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 139 ASN Chi-restraints excluded: chain H residue 145 GLU Chi-restraints excluded: chain H residue 205 VAL Chi-restraints excluded: chain J residue 275 ILE Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain K residue 67 HIS Chi-restraints excluded: chain K residue 99 VAL Chi-restraints excluded: chain K residue 131 GLN Chi-restraints excluded: chain M residue 231 CYS Chi-restraints excluded: chain M residue 385 ASP Chi-restraints excluded: chain N residue 33 ILE Chi-restraints excluded: chain N residue 48 THR Chi-restraints excluded: chain N residue 66 THR Chi-restraints excluded: chain N residue 86 ILE Chi-restraints excluded: chain N residue 99 VAL Chi-restraints excluded: chain N residue 222 VAL Chi-restraints excluded: chain P residue 136 THR Chi-restraints excluded: chain P residue 231 CYS Chi-restraints excluded: chain Q residue 23 VAL Chi-restraints excluded: chain Q residue 262 ASN Chi-restraints excluded: chain S residue 140 LEU Chi-restraints excluded: chain S residue 192 LEU Chi-restraints excluded: chain S residue 228 MET Chi-restraints excluded: chain T residue 114 ASN Chi-restraints excluded: chain T residue 123 LEU Chi-restraints excluded: chain T residue 125 PHE Chi-restraints excluded: chain T residue 217 ILE Chi-restraints excluded: chain V residue 185 GLU Chi-restraints excluded: chain V residue 206 LEU Chi-restraints excluded: chain V residue 283 ILE Chi-restraints excluded: chain V residue 384 SER Chi-restraints excluded: chain V residue 385 ASP Chi-restraints excluded: chain W residue 23 VAL Chi-restraints excluded: chain W residue 49 VAL Chi-restraints excluded: chain W residue 99 VAL Chi-restraints excluded: chain Y residue 214 ASP Chi-restraints excluded: chain Y residue 270 VAL Chi-restraints excluded: chain Y residue 271 GLN Chi-restraints excluded: chain Y residue 275 ILE Chi-restraints excluded: chain Y residue 360 ASN Chi-restraints excluded: chain Z residue 99 VAL Chi-restraints excluded: chain Z residue 195 PHE Chi-restraints excluded: chain a residue 28 ASP Chi-restraints excluded: chain a residue 38 VAL Chi-restraints excluded: chain b residue 146 LEU Chi-restraints excluded: chain c residue 23 VAL Chi-restraints excluded: chain e residue 188 GLN Chi-restraints excluded: chain e residue 376 LEU Chi-restraints excluded: chain f residue 23 VAL Chi-restraints excluded: chain f residue 86 ILE Chi-restraints excluded: chain f residue 135 THR Chi-restraints excluded: chain f residue 152 VAL Chi-restraints excluded: chain h residue 228 MET Chi-restraints excluded: chain i residue 23 VAL Chi-restraints excluded: chain k residue 231 CYS Chi-restraints excluded: chain k residue 385 ASP Chi-restraints excluded: chain l residue 23 VAL Chi-restraints excluded: chain l residue 99 VAL Chi-restraints excluded: chain l residue 148 PHE Chi-restraints excluded: chain l residue 205 VAL Chi-restraints excluded: chain m residue 37 THR Chi-restraints excluded: chain n residue 385 ASP Chi-restraints excluded: chain o residue 99 VAL Chi-restraints excluded: chain o residue 139 ASN Chi-restraints excluded: chain o residue 205 VAL Chi-restraints excluded: chain p residue 28 ASP Chi-restraints excluded: chain p residue 35 ASN Chi-restraints excluded: chain p residue 37 THR 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 28 ARG Chi-restraints excluded: chain v residue 35 TYR Chi-restraints excluded: chain v residue 48 THR Chi-restraints excluded: chain y residue 136 THR Chi-restraints excluded: chain y residue 150 LEU Chi-restraints excluded: chain z residue 23 VAL Chi-restraints excluded: chain z residue 29 TYR Chi-restraints excluded: chain z residue 66 THR Chi-restraints excluded: chain z residue 110 LEU Chi-restraints excluded: chain z residue 123 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 694 random chunks: chunk 409 optimal weight: 10.0000 chunk 659 optimal weight: 6.9990 chunk 402 optimal weight: 10.0000 chunk 312 optimal weight: 4.9990 chunk 458 optimal weight: 8.9990 chunk 691 optimal weight: 30.0000 chunk 636 optimal weight: 0.8980 chunk 550 optimal weight: 7.9990 chunk 57 optimal weight: 10.0000 chunk 425 optimal weight: 9.9990 chunk 337 optimal weight: 50.0000 overall best weight: 5.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 GLN ** E 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 329 GLN ** c 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 134 GLN ** o 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.4989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 56894 Z= 0.353 Angle : 0.634 17.429 77036 Z= 0.318 Chirality : 0.043 0.192 8370 Planarity : 0.004 0.048 10228 Dihedral : 4.060 30.484 7996 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 14.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.91 % Allowed : 15.88 % Favored : 82.21 % Cbeta Deviations : 0.00 % 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: 0.45 (0.10), residues: 7036 helix: 1.99 (0.16), residues: 1126 sheet: 0.07 (0.11), residues: 2204 loop : 0.01 (0.10), residues: 3706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP b 272 HIS 0.005 0.001 HIS Z 83 PHE 0.023 0.001 PHE V 383 TYR 0.037 0.001 TYR c 64 ARG 0.009 0.000 ARG k 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 546 residues out of total 5886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 434 time to evaluate : 5.163 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: B 57 MET cc_start: 0.8071 (mmm) cc_final: 0.7830 (mmm) REVERT: B 63 GLN cc_start: 0.9461 (mm-40) cc_final: 0.9152 (tp-100) REVERT: B 134 GLN cc_start: 0.9199 (mp10) cc_final: 0.8907 (mm110) REVERT: D 145 MET cc_start: 0.9261 (OUTLIER) cc_final: 0.8838 (mtp) REVERT: D 188 GLN cc_start: 0.8512 (OUTLIER) cc_final: 0.8282 (tm-30) REVERT: D 214 ASP cc_start: 0.7779 (OUTLIER) cc_final: 0.7493 (p0) REVERT: E 112 MET cc_start: 0.9118 (tpp) cc_final: 0.8817 (tpt) REVERT: E 120 MET cc_start: 0.8165 (mtm) cc_final: 0.7665 (mmt) REVERT: E 161 MET cc_start: 0.8239 (mmm) cc_final: 0.7926 (mmm) REVERT: H 80 LYS cc_start: 0.9471 (tppp) cc_final: 0.9210 (tttm) REVERT: J 145 MET cc_start: 0.8977 (ttt) cc_final: 0.8478 (tmm) REVERT: M 138 TYR cc_start: 0.9062 (t80) cc_final: 0.8703 (t80) REVERT: M 357 ASN cc_start: 0.8597 (m110) cc_final: 0.8370 (m-40) REVERT: N 112 MET cc_start: 0.8639 (mmm) cc_final: 0.8216 (tpp) REVERT: N 120 MET cc_start: 0.8178 (ttp) cc_final: 0.7928 (mtm) REVERT: P 139 GLU cc_start: 0.9052 (pt0) cc_final: 0.8790 (pp20) REVERT: Q 54 THR cc_start: 0.9005 (m) cc_final: 0.8605 (t) REVERT: Q 89 GLN cc_start: 0.9136 (mt0) cc_final: 0.8587 (tp40) REVERT: Q 112 MET cc_start: 0.9360 (tpp) cc_final: 0.9035 (tpt) REVERT: Q 120 MET cc_start: 0.7569 (mtt) cc_final: 0.6689 (mpp) REVERT: S 205 MET cc_start: 0.8673 (mmm) cc_final: 0.7559 (mmm) REVERT: T 112 MET cc_start: 0.7714 (tpt) cc_final: 0.7277 (mmm) REVERT: V 143 GLU cc_start: 0.9251 (tp30) cc_final: 0.9023 (tp30) REVERT: V 145 MET cc_start: 0.8706 (ttt) cc_final: 0.8349 (ttt) REVERT: V 185 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.8148 (pm20) REVERT: W 150 GLN cc_start: 0.8937 (tm-30) cc_final: 0.8436 (tm-30) REVERT: X 30 ASN cc_start: 0.8235 (p0) cc_final: 0.7855 (p0) REVERT: Z 161 MET cc_start: 0.8875 (mmm) cc_final: 0.8591 (mmm) REVERT: b 146 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8632 (mm) REVERT: b 190 MET cc_start: 0.8822 (ttp) cc_final: 0.8569 (ttp) REVERT: b 205 MET cc_start: 0.8809 (mmm) cc_final: 0.8045 (mmm) REVERT: c 111 GLN cc_start: 0.8644 (tm-30) cc_final: 0.8289 (tm-30) REVERT: e 185 GLU cc_start: 0.8361 (tm-30) cc_final: 0.8079 (tm-30) REVERT: e 188 GLN cc_start: 0.8212 (OUTLIER) cc_final: 0.8005 (mp10) REVERT: e 205 MET cc_start: 0.8821 (mmm) cc_final: 0.7816 (mmm) REVERT: h 205 MET cc_start: 0.8801 (tpp) cc_final: 0.8355 (mpp) REVERT: i 120 MET cc_start: 0.8754 (tpt) cc_final: 0.8052 (tpt) REVERT: k 145 MET cc_start: 0.8731 (ttt) cc_final: 0.8088 (mmt) REVERT: k 147 ARG cc_start: 0.9343 (ttp80) cc_final: 0.8956 (ptt90) REVERT: l 120 MET cc_start: 0.8750 (ptm) cc_final: 0.8437 (tmm) REVERT: l 131 GLN cc_start: 0.8823 (tp40) cc_final: 0.8562 (tp40) REVERT: o 120 MET cc_start: 0.8456 (mtm) cc_final: 0.8181 (mtm) REVERT: u 147 ARG cc_start: 0.9262 (ptt-90) cc_final: 0.8846 (ptt90) REVERT: v 29 TYR cc_start: 0.8783 (m-80) cc_final: 0.8510 (m-80) REVERT: v 63 GLN cc_start: 0.7760 (pm20) cc_final: 0.7502 (pm20) REVERT: v 73 GLU cc_start: 0.8657 (mt-10) cc_final: 0.8224 (pt0) REVERT: v 115 ASP cc_start: 0.9253 (p0) cc_final: 0.8685 (p0) REVERT: v 117 ASN cc_start: 0.9159 (m110) cc_final: 0.8672 (m-40) REVERT: z 29 TYR cc_start: 0.8094 (OUTLIER) cc_final: 0.7318 (t80) REVERT: z 47 ASP cc_start: 0.8374 (p0) cc_final: 0.7363 (t0) REVERT: z 58 LEU cc_start: 0.9189 (mp) cc_final: 0.8862 (mp) REVERT: z 77 PHE cc_start: 0.9200 (t80) cc_final: 0.8662 (t80) REVERT: z 89 GLN cc_start: 0.9318 (mp10) cc_final: 0.9035 (mp10) outliers start: 112 outliers final: 88 residues processed: 518 average time/residue: 0.5344 time to fit residues: 465.8569 Evaluate side-chains 511 residues out of total 5886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 416 time to evaluate : 5.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain D residue 145 MET Chi-restraints excluded: chain D residue 188 GLN Chi-restraints excluded: chain D residue 214 ASP Chi-restraints excluded: chain D residue 236 ASP Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain G residue 136 THR Chi-restraints excluded: chain G residue 196 SER Chi-restraints excluded: chain G residue 263 GLN Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 139 ASN Chi-restraints excluded: chain H residue 205 VAL Chi-restraints excluded: chain J residue 275 ILE Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain K residue 99 VAL Chi-restraints excluded: chain K residue 131 GLN Chi-restraints excluded: chain M residue 231 CYS Chi-restraints excluded: chain M residue 385 ASP Chi-restraints excluded: chain N residue 33 ILE Chi-restraints excluded: chain N residue 48 THR Chi-restraints excluded: chain N residue 66 THR Chi-restraints excluded: chain N residue 86 ILE Chi-restraints excluded: chain N residue 99 VAL Chi-restraints excluded: chain N residue 222 VAL Chi-restraints excluded: chain O residue 28 ASP Chi-restraints excluded: chain P residue 136 THR Chi-restraints excluded: chain Q residue 23 VAL Chi-restraints excluded: chain Q residue 262 ASN Chi-restraints excluded: chain S residue 140 LEU Chi-restraints excluded: chain S residue 192 LEU Chi-restraints excluded: chain T residue 114 ASN Chi-restraints excluded: chain T residue 123 LEU Chi-restraints excluded: chain T residue 125 PHE Chi-restraints excluded: chain V residue 185 GLU Chi-restraints excluded: chain V residue 206 LEU Chi-restraints excluded: chain V residue 283 ILE Chi-restraints excluded: chain V residue 385 ASP Chi-restraints excluded: chain W residue 23 VAL Chi-restraints excluded: chain W residue 49 VAL Chi-restraints excluded: chain W residue 99 VAL Chi-restraints excluded: chain Y residue 193 SER Chi-restraints excluded: chain Y residue 214 ASP Chi-restraints excluded: chain Y residue 270 VAL Chi-restraints excluded: chain Y residue 271 GLN Chi-restraints excluded: chain Y residue 275 ILE Chi-restraints excluded: chain Y residue 360 ASN Chi-restraints excluded: chain Z residue 99 VAL Chi-restraints excluded: chain Z residue 195 PHE Chi-restraints excluded: chain a residue 28 ASP Chi-restraints excluded: chain a residue 38 VAL Chi-restraints excluded: chain b residue 146 LEU Chi-restraints excluded: chain c residue 23 VAL Chi-restraints excluded: chain e residue 188 GLN Chi-restraints excluded: chain e residue 376 LEU Chi-restraints excluded: chain f residue 23 VAL Chi-restraints excluded: chain f residue 86 ILE Chi-restraints excluded: chain f residue 135 THR Chi-restraints excluded: chain f residue 152 VAL Chi-restraints excluded: chain h residue 228 MET Chi-restraints excluded: chain i residue 23 VAL Chi-restraints excluded: chain i residue 131 GLN Chi-restraints excluded: chain k residue 231 CYS Chi-restraints excluded: chain k residue 385 ASP Chi-restraints excluded: chain l residue 23 VAL Chi-restraints excluded: chain l residue 99 VAL Chi-restraints excluded: chain l residue 148 PHE Chi-restraints excluded: chain m residue 37 THR Chi-restraints excluded: chain n residue 385 ASP Chi-restraints excluded: chain o residue 99 VAL Chi-restraints excluded: chain o residue 139 ASN Chi-restraints excluded: chain o residue 205 VAL Chi-restraints excluded: chain p residue 28 ASP Chi-restraints excluded: chain p residue 35 ASN Chi-restraints excluded: chain p residue 37 THR 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 28 ARG Chi-restraints excluded: chain v residue 35 TYR Chi-restraints excluded: chain v residue 48 THR Chi-restraints excluded: chain v residue 110 LEU Chi-restraints excluded: chain y residue 136 THR Chi-restraints excluded: chain y residue 150 LEU Chi-restraints excluded: chain z residue 23 VAL Chi-restraints excluded: chain z residue 29 TYR Chi-restraints excluded: chain z residue 66 THR 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: 9.9990 chunk 586 optimal weight: 6.9990 chunk 168 optimal weight: 8.9990 chunk 507 optimal weight: 10.0000 chunk 81 optimal weight: 7.9990 chunk 152 optimal weight: 0.7980 chunk 551 optimal weight: 40.0000 chunk 230 optimal weight: 9.9990 chunk 566 optimal weight: 9.9990 chunk 69 optimal weight: 0.8980 chunk 101 optimal weight: 4.9990 overall best weight: 4.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 271 GLN ** K 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 134 GLN ** l 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.054175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2679 r_free = 0.2679 target = 0.033826 restraints weight = 245159.754| |-----------------------------------------------------------------------------| r_work (start): 0.2593 rms_B_bonded: 3.64 r_work: 0.2454 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8807 moved from start: 0.5088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 56894 Z= 0.272 Angle : 0.621 15.010 77036 Z= 0.311 Chirality : 0.043 0.211 8370 Planarity : 0.004 0.048 10228 Dihedral : 4.028 31.452 7996 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 14.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.81 % Allowed : 16.11 % Favored : 82.08 % Cbeta Deviations : 0.00 % 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: 0.44 (0.10), residues: 7036 helix: 1.93 (0.16), residues: 1127 sheet: 0.09 (0.11), residues: 2177 loop : 0.01 (0.10), residues: 3732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP b 272 HIS 0.007 0.001 HIS W 83 PHE 0.024 0.001 PHE V 383 TYR 0.034 0.001 TYR c 64 ARG 0.009 0.000 ARG e 147 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11210.93 seconds wall clock time: 198 minutes 12.59 seconds (11892.59 seconds total)