Starting phenix.real_space_refine (version: dev) on Fri Feb 24 16:16:57 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z1u_11040/02_2023/6z1u_11040_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z1u_11040/02_2023/6z1u_11040.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z1u_11040/02_2023/6z1u_11040.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z1u_11040/02_2023/6z1u_11040.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z1u_11040/02_2023/6z1u_11040_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z1u_11040/02_2023/6z1u_11040_trim_updated.pdb" } resolution = 3.47 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 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 Process input model Symmetric amino acids flipped Residue "A GLU 26": "OE1" <-> "OE2" Residue "A GLU 51": "OE1" <-> "OE2" Residue "A PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 144": "OE1" <-> "OE2" Residue "A ASP 154": "OD1" <-> "OD2" Residue "A ARG 219": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 228": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 238": "OD1" <-> "OD2" Residue "A TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 291": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 357": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 358": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 373": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 433": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 446": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 452": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 484": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 486": "OD1" <-> "OD2" Residue "B ASP 24": "OD1" <-> "OD2" Residue "B ARG 45": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 51": "OE1" <-> "OE2" Residue "B ASP 69": "OD1" <-> "OD2" Residue "B ASP 86": "OD1" <-> "OD2" Residue "B ASP 170": "OD1" <-> "OD2" Residue "B PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 268": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 269": "OD1" <-> "OD2" Residue "B TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 297": "OD1" <-> "OD2" Residue "B PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 307": "OE1" <-> "OE2" Residue "B ARG 373": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 393": "OE1" <-> "OE2" Residue "B GLU 440": "OE1" <-> "OE2" Residue "B TYR 446": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 504": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 508": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 50": "OE1" <-> "OE2" Residue "C PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 79": "OD1" <-> "OD2" Residue "C ARG 143": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 144": "OE1" <-> "OE2" Residue "C TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 268": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 307": "OE1" <-> "OE2" Residue "C TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 351": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 353": "OE1" <-> "OE2" Residue "C TYR 358": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 393": "OE1" <-> "OE2" Residue "C ARG 398": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 403": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 433": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 440": "OE1" <-> "OE2" Residue "C GLU 465": "OE1" <-> "OE2" Residue "D GLU 71": "OE1" <-> "OE2" Residue "D ASP 81": "OD1" <-> "OD2" Residue "D GLU 108": "OE1" <-> "OE2" Residue "D PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 129": "OE1" <-> "OE2" Residue "D GLU 135": "OE1" <-> "OE2" Residue "D PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 192": "OE1" <-> "OE2" Residue "D GLU 196": "OE1" <-> "OE2" Residue "D GLU 203": "OE1" <-> "OE2" Residue "D ASP 214": "OD1" <-> "OD2" Residue "D GLU 228": "OE1" <-> "OE2" Residue "D TYR 246": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 247": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 271": "OE1" <-> "OE2" Residue "D TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 292": "OD1" <-> "OD2" Residue "D GLU 298": "OE1" <-> "OE2" Residue "D ASP 320": "OD1" <-> "OD2" Residue "D PHE 330": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 353": "OD1" <-> "OD2" Residue "D GLU 370": "OE1" <-> "OE2" Residue "D PHE 445": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 461": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 469": "OE1" <-> "OE2" Residue "D GLU 480": "OE1" <-> "OE2" Residue "E GLU 52": "OE1" <-> "OE2" Residue "E GLU 59": "OE1" <-> "OE2" Residue "E PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 135": "OE1" <-> "OE2" Residue "E ASP 145": "OD1" <-> "OD2" Residue "E TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 203": "OE1" <-> "OE2" Residue "E TYR 246": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 247": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 260": "OD1" <-> "OD2" Residue "E TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 334": "OD1" <-> "OD2" Residue "E GLU 370": "OE1" <-> "OE2" Residue "E PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 428": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 440": "OE1" <-> "OE2" Residue "E PHE 445": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 452": "OE1" <-> "OE2" Residue "E TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 454": "OD1" <-> "OD2" Residue "E PHE 461": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 475": "OD1" <-> "OD2" Residue "F PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 31": "OE1" <-> "OE2" Residue "F GLU 46": "OE1" <-> "OE2" Residue "F GLU 59": "OE1" <-> "OE2" Residue "F GLU 108": "OE1" <-> "OE2" Residue "F PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 123": "OE1" <-> "OE2" Residue "F ASP 145": "OD1" <-> "OD2" Residue "F TYR 150": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 199": "OD1" <-> "OD2" Residue "F GLU 245": "OE1" <-> "OE2" Residue "F PHE 247": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 254": "OD1" <-> "OD2" Residue "F PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 260": "OD1" <-> "OD2" Residue "F PHE 265": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 349": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 384": "OD1" <-> "OD2" Residue "F PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 440": "OE1" <-> "OE2" Residue "F PHE 445": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 469": "OE1" <-> "OE2" Residue "F ASP 475": "OD1" <-> "OD2" Residue "G ARG 9": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 61": "OE1" <-> "OE2" Residue "G PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ARG 133": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ASP 140": "OD1" <-> "OD2" Residue "G GLU 154": "OE1" <-> "OE2" Residue "G ASP 156": "OD1" <-> "OD2" Residue "G GLU 157": "OE1" <-> "OE2" Residue "G PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 174": "OE1" <-> "OE2" Residue "G ASP 182": "OD1" <-> "OD2" Residue "G GLU 188": "OE1" <-> "OE2" Residue "G ASP 194": "OD1" <-> "OD2" Residue "G ARG 202": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G GLU 261": "OE1" <-> "OE2" Residue "G GLU 264": "OE1" <-> "OE2" Residue "H PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ASP 37": "OD1" <-> "OD2" Residue "H PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ASP 104": "OD1" <-> "OD2" Residue "I TYR 3": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I ARG 5": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I TYR 11": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I ASP 24": "OD1" <-> "OD2" Residue "I GLU 29": "OE1" <-> "OE2" Residue "I PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J ARG 25": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J GLU 26": "OE1" <-> "OE2" Residue "J GLU 31": "OE1" <-> "OE2" Residue "J TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J GLU 40": "OE1" <-> "OE2" Residue "J GLU 52": "OE1" <-> "OE2" Residue "K TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K ARG 38": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L ARG 38": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M ASP 1": "OD1" <-> "OD2" Residue "M ASP 3": "OD1" <-> "OD2" Residue "M PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M GLU 58": "OE1" <-> "OE2" Residue "N PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N ARG 38": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q ARG 38": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Q GLU 58": "OE1" <-> "OE2" Residue "R PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S TYR 18": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S GLU 76": "OE1" <-> "OE2" Residue "S ARG 94": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "S PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S GLU 133": "OE1" <-> "OE2" Residue "S ARG 165": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "S ASP 172": "OD1" <-> "OD2" Residue "b GLU 192": "OE1" <-> "OE2" Residue "h PHE 11": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "h TYR 18": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O ARG 38": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "O PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O GLU 58": "OE1" <-> "OE2" Residue "O PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 65073 Number of models: 1 Model: "" Number of chains: 32 Chain: "A" Number of atoms: 7742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 501, 7742 Classifications: {'peptide': 501} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 482} Chain: "B" Number of atoms: 7761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 502, 7761 Classifications: {'peptide': 502} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 483} Chain breaks: 1 Chain: "C" Number of atoms: 7489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 7489 Classifications: {'peptide': 483} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 464} Chain breaks: 1 Chain: "D" Number of atoms: 7163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 7163 Classifications: {'peptide': 469} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 444} Chain: "E" Number of atoms: 7132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 7132 Classifications: {'peptide': 467} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 442} Chain: "F" Number of atoms: 7131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 7131 Classifications: {'peptide': 467} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 442} Chain: "G" Number of atoms: 4300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 4300 Classifications: {'peptide': 272} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 266} Chain: "H" Number of atoms: 1940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1940 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 4, 'TRANS': 126} Chain: "I" Number of atoms: 764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 764 Classifications: {'peptide': 47} Modifications used: {'NH3': 1} Link IDs: {'TRANS': 46} Chain: "J" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 731 Classifications: {'peptide': 47} Link IDs: {'TRANS': 46} Chain: "K" Number of atoms: 1060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1060 Classifications: {'peptide': 74} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 72} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 1060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1060 Classifications: {'peptide': 74} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 72} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "M" Number of atoms: 1077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1077 Classifications: {'peptide': 75} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "N" Number of atoms: 1077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1077 Classifications: {'peptide': 75} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "P" Number of atoms: 1060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1060 Classifications: {'peptide': 74} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 72} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "Q" Number of atoms: 1077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1077 Classifications: {'peptide': 75} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 1077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1077 Classifications: {'peptide': 75} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "S" Number of atoms: 2989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 2989 Classifications: {'peptide': 187} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 8, 'TRANS': 178} Chain: "b" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 789 Classifications: {'peptide': 47} Link IDs: {'TRANS': 46} Chain: "h" Number of atoms: 381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 381 Classifications: {'peptide': 22} Link IDs: {'PTRANS': 1, 'TRANS': 20} Chain: "O" Number of atoms: 1077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1077 Classifications: {'peptide': 75} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Time building chain proxies: 22.35, per 1000 atoms: 0.34 Number of scatterers: 65073 At special positions: 0 Unit cell: (142.528, 131, 235.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 123 16.00 P 15 15.00 Mg 5 11.99 O 6157 8.00 N 5525 7.00 C 20445 6.00 H 32803 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 44.41 Conformation dependent library (CDL) restraints added in 4.1 seconds 8338 Ramachandran restraints generated. 4169 Oldfield, 0 Emsley, 4169 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7676 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 148 helices and 26 sheets defined 47.3% alpha, 9.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.66 Creating SS restraints... Processing helix chain 'A' and resid 9 through 17 removed outlier: 4.625A pdb=" N GLU A 14 " --> pdb=" O SER A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 81 No H-bonds generated for 'chain 'A' and resid 79 through 81' Processing helix chain 'A' and resid 151 through 155 Processing helix chain 'A' and resid 175 through 191 removed outlier: 3.661A pdb=" N GLN A 186 " --> pdb=" O THR A 182 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N LYS A 187 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N ARG A 188 " --> pdb=" O ILE A 184 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N PHE A 189 " --> pdb=" O ASN A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 222 Processing helix chain 'A' and resid 240 through 244 Processing helix chain 'A' and resid 246 through 260 removed outlier: 3.973A pdb=" N PHE A 257 " --> pdb=" O MET A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 285 Processing helix chain 'A' and resid 291 through 293 No H-bonds generated for 'chain 'A' and resid 291 through 293' Processing helix chain 'A' and resid 300 through 306 removed outlier: 3.654A pdb=" N LEU A 305 " --> pdb=" O LEU A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 354 through 358 Processing helix chain 'A' and resid 381 through 403 removed outlier: 4.067A pdb=" N THR A 389 " --> pdb=" O GLN A 385 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N VAL A 400 " --> pdb=" O GLN A 396 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N ALA A 402 " --> pdb=" O ARG A 398 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N PHE A 403 " --> pdb=" O GLU A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 428 removed outlier: 4.160A pdb=" N ARG A 423 " --> pdb=" O SER A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 449 Processing helix chain 'A' and resid 458 through 473 removed outlier: 4.765A pdb=" N THR A 462 " --> pdb=" O SER A 459 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ILE A 473 " --> pdb=" O SER A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 485 Processing helix chain 'A' and resid 491 through 507 Processing helix chain 'B' and resid 9 through 16 removed outlier: 4.132A pdb=" N GLU B 14 " --> pdb=" O SER B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 21 No H-bonds generated for 'chain 'B' and resid 19 through 21' Processing helix chain 'B' and resid 79 through 81 No H-bonds generated for 'chain 'B' and resid 79 through 81' Processing helix chain 'B' and resid 151 through 156 Processing helix chain 'B' and resid 175 through 184 Processing helix chain 'B' and resid 210 through 223 removed outlier: 3.572A pdb=" N ALA B 223 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 260 Proline residue: B 247 - end of helix removed outlier: 4.135A pdb=" N PHE B 257 " --> pdb=" O MET B 253 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASN B 260 " --> pdb=" O TYR B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 285 Processing helix chain 'B' and resid 303 through 306 No H-bonds generated for 'chain 'B' and resid 303 through 306' Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 354 through 358 Processing helix chain 'B' and resid 375 through 377 No H-bonds generated for 'chain 'B' and resid 375 through 377' Processing helix chain 'B' and resid 381 through 399 removed outlier: 4.550A pdb=" N THR B 389 " --> pdb=" O GLN B 385 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU B 392 " --> pdb=" O GLY B 388 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU B 399 " --> pdb=" O ALA B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 428 Processing helix chain 'B' and resid 438 through 449 Processing helix chain 'B' and resid 458 through 475 removed outlier: 4.258A pdb=" N THR B 462 " --> pdb=" O PRO B 458 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N LYS B 463 " --> pdb=" O SER B 459 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ASN B 466 " --> pdb=" O THR B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 486 Processing helix chain 'B' and resid 491 through 507 removed outlier: 4.092A pdb=" N GLY B 507 " --> pdb=" O ASN B 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 103 No H-bonds generated for 'chain 'C' and resid 101 through 103' Processing helix chain 'C' and resid 151 through 154 No H-bonds generated for 'chain 'C' and resid 151 through 154' Processing helix chain 'C' and resid 176 through 188 removed outlier: 3.658A pdb=" N GLN C 186 " --> pdb=" O THR C 182 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N LYS C 187 " --> pdb=" O ILE C 183 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N ARG C 188 " --> pdb=" O ILE C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 223 removed outlier: 3.805A pdb=" N ALA C 223 " --> pdb=" O ARG C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 259 Proline residue: C 247 - end of helix removed outlier: 4.069A pdb=" N PHE C 257 " --> pdb=" O MET C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 284 Processing helix chain 'C' and resid 291 through 293 No H-bonds generated for 'chain 'C' and resid 291 through 293' Processing helix chain 'C' and resid 298 through 308 removed outlier: 3.900A pdb=" N HIS C 302 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ARG C 304 " --> pdb=" O TYR C 300 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU C 305 " --> pdb=" O LEU C 301 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ARG C 308 " --> pdb=" O ARG C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 356 through 359 No H-bonds generated for 'chain 'C' and resid 356 through 359' Processing helix chain 'C' and resid 375 through 378 Processing helix chain 'C' and resid 381 through 399 removed outlier: 4.038A pdb=" N VAL C 386 " --> pdb=" O ALA C 382 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N THR C 389 " --> pdb=" O GLN C 385 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU C 392 " --> pdb=" O GLY C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 412 through 428 Processing helix chain 'C' and resid 438 through 449 Processing helix chain 'C' and resid 458 through 475 removed outlier: 3.573A pdb=" N ILE C 461 " --> pdb=" O PRO C 458 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N THR C 462 " --> pdb=" O SER C 459 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLN C 475 " --> pdb=" O VAL C 472 " (cutoff:3.500A) Processing helix chain 'C' and resid 477 through 486 Processing helix chain 'C' and resid 491 through 505 Processing helix chain 'D' and resid 127 through 129 No H-bonds generated for 'chain 'D' and resid 127 through 129' Processing helix chain 'D' and resid 142 through 147 Processing helix chain 'D' and resid 166 through 177 Processing helix chain 'D' and resid 195 through 207 Processing helix chain 'D' and resid 230 through 233 No H-bonds generated for 'chain 'D' and resid 230 through 233' Processing helix chain 'D' and resid 236 through 249 Processing helix chain 'D' and resid 264 through 273 removed outlier: 3.712A pdb=" N VAL D 272 " --> pdb=" O ALA D 268 " (cutoff:3.500A) Processing helix chain 'D' and resid 289 through 297 removed outlier: 3.760A pdb=" N MET D 296 " --> pdb=" O ASP D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 319 No H-bonds generated for 'chain 'D' and resid 317 through 319' Processing helix chain 'D' and resid 324 through 332 removed outlier: 4.745A pdb=" N ALA D 331 " --> pdb=" O ALA D 327 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N HIS D 332 " --> pdb=" O THR D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 341 through 344 No H-bonds generated for 'chain 'D' and resid 341 through 344' Processing helix chain 'D' and resid 364 through 367 No H-bonds generated for 'chain 'D' and resid 364 through 367' Processing helix chain 'D' and resid 369 through 395 removed outlier: 3.756A pdb=" N ASP D 390 " --> pdb=" O LYS D 386 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ILE D 391 " --> pdb=" O SER D 387 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ILE D 394 " --> pdb=" O ASP D 390 " (cutoff:3.500A) Processing helix chain 'D' and resid 397 through 399 No H-bonds generated for 'chain 'D' and resid 397 through 399' Processing helix chain 'D' and resid 404 through 417 Processing helix chain 'D' and resid 438 through 450 Processing helix chain 'D' and resid 458 through 460 No H-bonds generated for 'chain 'D' and resid 458 through 460' Processing helix chain 'D' and resid 467 through 479 Processing helix chain 'E' and resid 142 through 147 Processing helix chain 'E' and resid 167 through 180 Processing helix chain 'E' and resid 194 through 207 Processing helix chain 'E' and resid 230 through 232 No H-bonds generated for 'chain 'E' and resid 230 through 232' Processing helix chain 'E' and resid 237 through 251 removed outlier: 3.785A pdb=" N PHE E 247 " --> pdb=" O VAL E 243 " (cutoff:3.500A) Processing helix chain 'E' and resid 264 through 275 Processing helix chain 'E' and resid 289 through 297 removed outlier: 3.801A pdb=" N MET E 296 " --> pdb=" O ASP E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 317 through 319 No H-bonds generated for 'chain 'E' and resid 317 through 319' Processing helix chain 'E' and resid 324 through 329 Processing helix chain 'E' and resid 342 through 345 No H-bonds generated for 'chain 'E' and resid 342 through 345' Processing helix chain 'E' and resid 369 through 394 removed outlier: 3.703A pdb=" N ASP E 390 " --> pdb=" O LYS E 386 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE E 391 " --> pdb=" O SER E 387 " (cutoff:3.500A) Processing helix chain 'E' and resid 397 through 399 No H-bonds generated for 'chain 'E' and resid 397 through 399' Processing helix chain 'E' and resid 402 through 418 removed outlier: 4.404A pdb=" N THR E 407 " --> pdb=" O GLU E 403 " (cutoff:3.500A) Processing helix chain 'E' and resid 424 through 429 removed outlier: 4.183A pdb=" N VAL E 427 " --> pdb=" O VAL E 424 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N THR E 429 " --> pdb=" O GLU E 426 " (cutoff:3.500A) Processing helix chain 'E' and resid 438 through 449 Processing helix chain 'E' and resid 458 through 460 No H-bonds generated for 'chain 'E' and resid 458 through 460' Processing helix chain 'E' and resid 467 through 477 Processing helix chain 'F' and resid 127 through 129 No H-bonds generated for 'chain 'F' and resid 127 through 129' Processing helix chain 'F' and resid 142 through 147 Processing helix chain 'F' and resid 166 through 178 Processing helix chain 'F' and resid 194 through 207 Processing helix chain 'F' and resid 230 through 233 No H-bonds generated for 'chain 'F' and resid 230 through 233' Processing helix chain 'F' and resid 236 through 249 Processing helix chain 'F' and resid 264 through 271 Processing helix chain 'F' and resid 289 through 297 removed outlier: 3.913A pdb=" N MET F 296 " --> pdb=" O ASP F 292 " (cutoff:3.500A) Processing helix chain 'F' and resid 317 through 319 No H-bonds generated for 'chain 'F' and resid 317 through 319' Processing helix chain 'F' and resid 324 through 332 removed outlier: 4.823A pdb=" N ALA F 331 " --> pdb=" O ALA F 327 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N HIS F 332 " --> pdb=" O THR F 328 " (cutoff:3.500A) Processing helix chain 'F' and resid 341 through 346 removed outlier: 3.724A pdb=" N LEU F 346 " --> pdb=" O ALA F 342 " (cutoff:3.500A) Processing helix chain 'F' and resid 364 through 367 No H-bonds generated for 'chain 'F' and resid 364 through 367' Processing helix chain 'F' and resid 369 through 392 removed outlier: 4.662A pdb=" N ASP F 390 " --> pdb=" O LYS F 386 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N ILE F 391 " --> pdb=" O SER F 387 " (cutoff:3.500A) Processing helix chain 'F' and resid 397 through 399 No H-bonds generated for 'chain 'F' and resid 397 through 399' Processing helix chain 'F' and resid 402 through 418 Processing helix chain 'F' and resid 438 through 449 Processing helix chain 'F' and resid 458 through 460 No H-bonds generated for 'chain 'F' and resid 458 through 460' Processing helix chain 'F' and resid 467 through 478 Processing helix chain 'G' and resid 3 through 54 Proline residue: G 40 - end of helix removed outlier: 4.138A pdb=" N VAL G 43 " --> pdb=" O LYS G 39 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N LEU G 51 " --> pdb=" O GLY G 47 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N TYR G 52 " --> pdb=" O SER G 48 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 98 Processing helix chain 'G' and resid 110 through 120 removed outlier: 3.899A pdb=" N ARG G 118 " --> pdb=" O SER G 114 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N THR G 119 " --> pdb=" O ILE G 115 " (cutoff:3.500A) Processing helix chain 'G' and resid 138 through 149 Processing helix chain 'G' and resid 181 through 184 No H-bonds generated for 'chain 'G' and resid 181 through 184' Processing helix chain 'G' and resid 200 through 270 removed outlier: 3.772A pdb=" N ALA G 210 " --> pdb=" O GLU G 206 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LEU G 248 " --> pdb=" O ASP G 244 " (cutoff:3.500A) Processing helix chain 'H' and resid 100 through 102 No H-bonds generated for 'chain 'H' and resid 100 through 102' Processing helix chain 'H' and resid 105 through 119 Processing helix chain 'H' and resid 125 through 144 Processing helix chain 'I' and resid 3 through 6 No H-bonds generated for 'chain 'I' and resid 3 through 6' Processing helix chain 'I' and resid 11 through 24 Processing helix chain 'I' and resid 31 through 35 Processing helix chain 'J' and resid 22 through 52 removed outlier: 4.017A pdb=" N GLN J 27 " --> pdb=" O GLY J 23 " (cutoff:3.500A) Processing helix chain 'K' and resid 2 through 38 removed outlier: 3.880A pdb=" N VAL K 16 " --> pdb=" O GLY K 12 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N GLY K 17 " --> pdb=" O ALA K 13 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N VAL K 18 " --> pdb=" O ALA K 14 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N ALA K 19 " --> pdb=" O THR K 15 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N GLY K 20 " --> pdb=" O VAL K 16 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N SER K 21 " --> pdb=" O GLY K 17 " (cutoff:3.500A) Processing helix chain 'K' and resid 45 through 72 removed outlier: 4.141A pdb=" N MET K 60 " --> pdb=" O LEU K 56 " (cutoff:3.500A) Processing helix chain 'L' and resid 3 through 14 Processing helix chain 'L' and resid 16 through 38 Processing helix chain 'L' and resid 45 through 73 removed outlier: 4.224A pdb=" N MET L 60 " --> pdb=" O LEU L 56 " (cutoff:3.500A) Processing helix chain 'M' and resid 2 through 38 removed outlier: 4.717A pdb=" N PHE M 8 " --> pdb=" O THR M 4 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N VAL M 16 " --> pdb=" O GLY M 12 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N GLY M 17 " --> pdb=" O ALA M 13 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N VAL M 18 " --> pdb=" O ALA M 14 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N ALA M 19 " --> pdb=" O THR M 15 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N GLY M 20 " --> pdb=" O VAL M 16 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N SER M 21 " --> pdb=" O GLY M 17 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ILE M 33 " --> pdb=" O PHE M 29 " (cutoff:3.500A) Processing helix chain 'M' and resid 45 through 72 removed outlier: 3.998A pdb=" N MET M 60 " --> pdb=" O LEU M 56 " (cutoff:3.500A) Processing helix chain 'N' and resid 2 through 38 removed outlier: 3.823A pdb=" N VAL N 16 " --> pdb=" O GLY N 12 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N GLY N 17 " --> pdb=" O ALA N 13 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N VAL N 18 " --> pdb=" O ALA N 14 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N ALA N 19 " --> pdb=" O THR N 15 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N GLY N 20 " --> pdb=" O VAL N 16 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N SER N 21 " --> pdb=" O GLY N 17 " (cutoff:3.500A) Processing helix chain 'N' and resid 45 through 73 removed outlier: 4.047A pdb=" N MET N 60 " --> pdb=" O LEU N 56 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N CYS N 64 " --> pdb=" O MET N 60 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 38 removed outlier: 3.945A pdb=" N VAL P 16 " --> pdb=" O GLY P 12 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N GLY P 17 " --> pdb=" O ALA P 13 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N VAL P 18 " --> pdb=" O ALA P 14 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N ALA P 19 " --> pdb=" O THR P 15 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N GLY P 20 " --> pdb=" O VAL P 16 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N SER P 21 " --> pdb=" O GLY P 17 " (cutoff:3.500A) Processing helix chain 'P' and resid 45 through 71 Processing helix chain 'Q' and resid 2 through 15 removed outlier: 3.573A pdb=" N PHE Q 8 " --> pdb=" O THR Q 4 " (cutoff:3.500A) Processing helix chain 'Q' and resid 17 through 38 Processing helix chain 'Q' and resid 45 through 73 removed outlier: 3.780A pdb=" N MET Q 60 " --> pdb=" O LEU Q 56 " (cutoff:3.500A) Processing helix chain 'R' and resid 2 through 38 removed outlier: 4.438A pdb=" N VAL R 16 " --> pdb=" O GLY R 12 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N GLY R 17 " --> pdb=" O ALA R 13 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N VAL R 18 " --> pdb=" O ALA R 14 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N ALA R 19 " --> pdb=" O THR R 15 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N GLY R 20 " --> pdb=" O VAL R 16 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER R 21 " --> pdb=" O GLY R 17 " (cutoff:3.500A) Processing helix chain 'R' and resid 45 through 72 removed outlier: 4.523A pdb=" N MET R 60 " --> pdb=" O LEU R 56 " (cutoff:3.500A) Processing helix chain 'S' and resid 14 through 27 Processing helix chain 'S' and resid 32 through 45 removed outlier: 3.539A pdb=" N GLN S 44 " --> pdb=" O LEU S 40 " (cutoff:3.500A) Processing helix chain 'S' and resid 49 through 54 Processing helix chain 'S' and resid 62 through 75 Processing helix chain 'S' and resid 80 through 91 Processing helix chain 'S' and resid 95 through 113 Proline residue: S 99 - end of helix removed outlier: 3.704A pdb=" N ILE S 102 " --> pdb=" O PRO S 99 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER S 103 " --> pdb=" O ALA S 100 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N SER S 110 " --> pdb=" O THR S 107 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N VAL S 111 " --> pdb=" O MET S 108 " (cutoff:3.500A) Processing helix chain 'S' and resid 129 through 140 removed outlier: 4.386A pdb=" N SER S 140 " --> pdb=" O THR S 136 " (cutoff:3.500A) Processing helix chain 'S' and resid 175 through 186 Processing helix chain 'b' and resid 164 through 184 removed outlier: 3.864A pdb=" N ASN b 175 " --> pdb=" O GLU b 171 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLN b 183 " --> pdb=" O LYS b 179 " (cutoff:3.500A) Processing helix chain 'b' and resid 190 through 208 Processing helix chain 'h' and resid 9 through 23 Processing helix chain 'O' and resid 3 through 38 removed outlier: 4.247A pdb=" N VAL O 16 " --> pdb=" O GLY O 12 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N GLY O 17 " --> pdb=" O ALA O 13 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N VAL O 18 " --> pdb=" O ALA O 14 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N ALA O 19 " --> pdb=" O THR O 15 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N GLY O 20 " --> pdb=" O VAL O 16 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N SER O 21 " --> pdb=" O GLY O 17 " (cutoff:3.500A) Processing helix chain 'O' and resid 45 through 74 removed outlier: 4.126A pdb=" N MET O 60 " --> pdb=" O LEU O 56 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N PHE O 63 " --> pdb=" O ALA O 59 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N CYS O 64 " --> pdb=" O MET O 60 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N LEU O 65 " --> pdb=" O GLY O 61 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 29 through 31 removed outlier: 6.903A pdb=" N VAL A 74 " --> pdb=" O SER A 63 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N SER A 63 " --> pdb=" O VAL A 74 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 96 through 98 Processing sheet with id= C, first strand: chain 'A' and resid 326 through 328 removed outlier: 6.290A pdb=" N ILE A 167 " --> pdb=" O ILE A 327 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N ILE A 350 " --> pdb=" O ILE A 168 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 199 through 205 removed outlier: 7.466A pdb=" N HIS A 263 " --> pdb=" O TYR A 200 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N ILE A 202 " --> pdb=" O HIS A 263 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N LEU A 265 " --> pdb=" O ILE A 202 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N VAL A 204 " --> pdb=" O LEU A 265 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N ILE A 267 " --> pdb=" O VAL A 204 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'B' and resid 87 through 89 removed outlier: 6.575A pdb=" N ARG B 40 " --> pdb=" O LEU B 32 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N ILE B 34 " --> pdb=" O ILE B 38 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ILE B 38 " --> pdb=" O ILE B 34 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASN B 65 " --> pdb=" O GLY B 72 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N VAL B 74 " --> pdb=" O SER B 63 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N SER B 63 " --> pdb=" O VAL B 74 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 96 through 99 removed outlier: 4.212A pdb=" N ALA B 125 " --> pdb=" O VAL B 99 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 164 through 168 removed outlier: 8.145A pdb=" N GLU B 165 " --> pdb=" O LEU B 321 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ALA B 323 " --> pdb=" O GLU B 165 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ILE B 167 " --> pdb=" O ALA B 323 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA B 264 " --> pdb=" O SER B 320 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N TYR B 268 " --> pdb=" O LEU B 324 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 87 through 89 removed outlier: 6.623A pdb=" N ARG C 40 " --> pdb=" O LEU C 32 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N ILE C 34 " --> pdb=" O ILE C 38 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ILE C 38 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N VAL C 74 " --> pdb=" O SER C 63 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N SER C 63 " --> pdb=" O VAL C 74 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 96 through 98 Processing sheet with id= J, first strand: chain 'C' and resid 229 through 234 removed outlier: 6.580A pdb=" N CYS C 201 " --> pdb=" O ILE C 230 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N VAL C 232 " --> pdb=" O CYS C 201 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N TYR C 203 " --> pdb=" O VAL C 232 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N ALA C 234 " --> pdb=" O TYR C 203 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N ALA C 205 " --> pdb=" O ALA C 234 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N ILE C 267 " --> pdb=" O VAL C 204 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ILE C 206 " --> pdb=" O ILE C 267 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N ASP C 269 " --> pdb=" O ILE C 206 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'D' and resid 14 through 16 removed outlier: 6.571A pdb=" N ARG D 63 " --> pdb=" O ALA D 54 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N GLN D 28 " --> pdb=" O ILE D 17 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N ILE D 17 " --> pdb=" O GLN D 28 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 87 through 90 removed outlier: 4.499A pdb=" N GLN D 116 " --> pdb=" O VAL D 90 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 156 through 158 removed outlier: 3.799A pdb=" N ASP D 260 " --> pdb=" O ALA D 188 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 14 through 16 removed outlier: 6.566A pdb=" N ARG E 63 " --> pdb=" O ALA E 54 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N GLN E 28 " --> pdb=" O ILE E 17 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N ILE E 17 " --> pdb=" O GLN E 28 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 87 through 89 Processing sheet with id= P, first strand: chain 'E' and resid 155 through 158 removed outlier: 6.215A pdb=" N SER E 310 " --> pdb=" O ILE E 156 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N LEU E 158 " --> pdb=" O SER E 310 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N GLN E 312 " --> pdb=" O LEU E 158 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'E' and resid 187 through 192 Processing sheet with id= R, first strand: chain 'F' and resid 14 through 16 removed outlier: 6.678A pdb=" N ARG F 63 " --> pdb=" O ALA F 54 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N HIS F 56 " --> pdb=" O THR F 61 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N THR F 61 " --> pdb=" O HIS F 56 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N GLN F 28 " --> pdb=" O ILE F 17 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N ILE F 17 " --> pdb=" O GLN F 28 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'F' and resid 87 through 89 Processing sheet with id= T, first strand: chain 'F' and resid 156 through 159 removed outlier: 6.476A pdb=" N ALA F 335 " --> pdb=" O GLY F 157 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N PHE F 159 " --> pdb=" O ALA F 335 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N THR F 337 " --> pdb=" O PHE F 159 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain 'F' and resid 220 through 224 removed outlier: 3.735A pdb=" N LEU F 256 " --> pdb=" O TYR F 184 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'G' and resid 170 through 178 removed outlier: 6.194A pdb=" N LYS G 172 " --> pdb=" O PHE G 165 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N PHE G 165 " --> pdb=" O LYS G 172 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N GLU G 174 " --> pdb=" O ASN G 163 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N ASN G 163 " --> pdb=" O GLU G 174 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N LYS G 176 " --> pdb=" O ILE G 161 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N ILE G 161 " --> pdb=" O LYS G 176 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ILE G 178 " --> pdb=" O SER G 159 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N SER G 159 " --> pdb=" O ILE G 178 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS G 104 " --> pdb=" O HIS G 66 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE G 68 " --> pdb=" O LYS G 104 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N GLY G 107 " --> pdb=" O LEU G 125 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N THR G 127 " --> pdb=" O GLY G 107 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'H' and resid 18 through 22 removed outlier: 6.601A pdb=" N VAL H 90 " --> pdb=" O THR H 19 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N ALA H 21 " --> pdb=" O VAL H 90 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LEU H 92 " --> pdb=" O ALA H 21 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'H' and resid 36 through 38 Processing sheet with id= Y, first strand: chain 'H' and resid 61 through 66 Processing sheet with id= Z, first strand: chain 'S' and resid 147 through 154 removed outlier: 3.587A pdb=" N LYS S 149 " --> pdb=" O VAL S 116 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLU S 151 " --> pdb=" O CYS S 118 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N VAL S 120 " --> pdb=" O GLU S 151 " (cutoff:3.500A) 1491 hydrogen bonds defined for protein. 4209 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: 23.59 Time building geometry restraints manager: 46.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 32785 1.03 - 1.23: 150 1.23 - 1.42: 12870 1.42 - 1.61: 19492 1.61 - 1.81: 228 Bond restraints: 65525 Sorted by residual: bond pdb=" C4 ATP C 600 " pdb=" C5 ATP C 600 " ideal model delta sigma weight residual 1.388 1.459 -0.071 1.00e-02 1.00e+04 5.06e+01 bond pdb=" C4 ATP A 600 " pdb=" C5 ATP A 600 " ideal model delta sigma weight residual 1.388 1.458 -0.070 1.00e-02 1.00e+04 4.95e+01 bond pdb=" C4 ATP B 600 " pdb=" C5 ATP B 600 " ideal model delta sigma weight residual 1.388 1.458 -0.070 1.00e-02 1.00e+04 4.89e+01 bond pdb=" C5 ATP C 600 " pdb=" C6 ATP C 600 " ideal model delta sigma weight residual 1.409 1.467 -0.058 1.00e-02 1.00e+04 3.32e+01 bond pdb=" C5 ATP B 600 " pdb=" C6 ATP B 600 " ideal model delta sigma weight residual 1.409 1.466 -0.057 1.00e-02 1.00e+04 3.28e+01 ... (remaining 65520 not shown) Histogram of bond angle deviations from ideal: 97.78 - 105.49: 569 105.49 - 113.20: 79655 113.20 - 120.90: 25254 120.90 - 128.61: 13216 128.61 - 136.32: 119 Bond angle restraints: 118813 Sorted by residual: angle pdb=" PB ATP B 600 " pdb=" O3B ATP B 600 " pdb=" PG ATP B 600 " ideal model delta sigma weight residual 139.87 115.41 24.46 1.00e+00 1.00e+00 5.98e+02 angle pdb=" PB ATP C 600 " pdb=" O3B ATP C 600 " pdb=" PG ATP C 600 " ideal model delta sigma weight residual 139.87 116.56 23.31 1.00e+00 1.00e+00 5.43e+02 angle pdb=" PB ATP A 600 " pdb=" O3B ATP A 600 " pdb=" PG ATP A 600 " ideal model delta sigma weight residual 139.87 117.41 22.46 1.00e+00 1.00e+00 5.04e+02 angle pdb=" PA ATP B 600 " pdb=" O3A ATP B 600 " pdb=" PB ATP B 600 " ideal model delta sigma weight residual 136.83 118.82 18.01 1.00e+00 1.00e+00 3.24e+02 angle pdb=" PA ATP A 600 " pdb=" O3A ATP A 600 " pdb=" PB ATP A 600 " ideal model delta sigma weight residual 136.83 119.24 17.59 1.00e+00 1.00e+00 3.09e+02 ... (remaining 118808 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.45: 24606 26.45 - 52.91: 1033 52.91 - 79.36: 85 79.36 - 105.81: 17 105.81 - 132.27: 1 Dihedral angle restraints: 25742 sinusoidal: 12263 harmonic: 13479 Sorted by residual: dihedral pdb=" O2A ADP E 600 " pdb=" O3A ADP E 600 " pdb=" PA ADP E 600 " pdb=" PB ADP E 600 " ideal model delta sinusoidal sigma weight residual 300.00 167.74 132.27 1 2.00e+01 2.50e-03 4.01e+01 dihedral pdb=" CA LEU D 395 " pdb=" C LEU D 395 " pdb=" N GLY D 396 " pdb=" CA GLY D 396 " ideal model delta harmonic sigma weight residual -180.00 -152.84 -27.16 0 5.00e+00 4.00e-02 2.95e+01 dihedral pdb=" C5' ADP E 600 " pdb=" O5' ADP E 600 " pdb=" PA ADP E 600 " pdb=" O2A ADP E 600 " ideal model delta sinusoidal sigma weight residual -60.00 -146.04 86.05 1 2.00e+01 2.50e-03 2.23e+01 ... (remaining 25739 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 2960 0.034 - 0.067: 1549 0.067 - 0.101: 434 0.101 - 0.135: 206 0.135 - 0.168: 24 Chirality restraints: 5173 Sorted by residual: chirality pdb=" CA ILE S 163 " pdb=" N ILE S 163 " pdb=" C ILE S 163 " pdb=" CB ILE S 163 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.07e-01 chirality pdb=" CA MET D 226 " pdb=" N MET D 226 " pdb=" C MET D 226 " pdb=" CB MET D 226 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.61e-01 chirality pdb=" CA VAL C 73 " pdb=" N VAL C 73 " pdb=" C VAL C 73 " pdb=" CB VAL C 73 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.27e-01 ... (remaining 5170 not shown) Planarity restraints: 9728 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE Q 63 " 0.026 2.00e-02 2.50e+03 1.47e-02 6.49e+00 pdb=" CG PHE Q 63 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 PHE Q 63 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE Q 63 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE Q 63 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE Q 63 " 0.012 2.00e-02 2.50e+03 pdb=" CZ PHE Q 63 " 0.001 2.00e-02 2.50e+03 pdb=" HD1 PHE Q 63 " -0.001 2.00e-02 2.50e+03 pdb=" HD2 PHE Q 63 " -0.004 2.00e-02 2.50e+03 pdb=" HE1 PHE Q 63 " 0.003 2.00e-02 2.50e+03 pdb=" HE2 PHE Q 63 " 0.003 2.00e-02 2.50e+03 pdb=" HZ PHE Q 63 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE B 338 " -0.037 5.00e-02 4.00e+02 5.62e-02 5.06e+00 pdb=" N PRO B 339 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO B 339 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 339 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MET S 173 " 0.010 2.00e-02 2.50e+03 2.01e-02 4.02e+00 pdb=" C MET S 173 " -0.035 2.00e-02 2.50e+03 pdb=" O MET S 173 " 0.013 2.00e-02 2.50e+03 pdb=" N SER S 174 " 0.011 2.00e-02 2.50e+03 ... (remaining 9725 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.14: 2575 2.14 - 2.76: 129720 2.76 - 3.37: 188212 3.37 - 3.99: 246314 3.99 - 4.60: 393442 Nonbonded interactions: 960263 Sorted by model distance: nonbonded pdb=" H GLY E 96 " pdb=" O VAL E 219 " model vdw 1.530 1.850 nonbonded pdb="HE21 GLN E 420 " pdb=" O LYS E 434 " model vdw 1.537 1.850 nonbonded pdb=" HG1 THR F 288 " pdb=" OD2 ASP F 292 " model vdw 1.541 1.850 nonbonded pdb="HH21 ARG B 291 " pdb=" OD1 ASP F 323 " model vdw 1.552 1.850 nonbonded pdb=" OE1 GLU E 468 " pdb=" H GLU E 468 " model vdw 1.553 1.850 ... (remaining 960258 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' and ((resid 23 and (name N or name CA or name C or name O or name CB \ or name CG1 or name CG2 or name HA or name HB or name HG11 or name HG12 or name \ HG13 or name HG21 or name HG22 or name HG23)) or resid 24 through 403 or (resid \ 410 and (name N or name CA or name C or name O or name CB or name CG or name CD1 \ or name CD2 or name HA or name HB2 or name HB3 or name HG or name HD11 or name \ HD12 or name HD13 or name HD21 or name HD22 or name HD23)) or resid 411 through \ 508 or resid 600 through 601)) selection = (chain 'B' and ((resid 23 and (name N or name CA or name C or name O or name CB \ or name CG1 or name CG2 or name HA or name HB or name HG11 or name HG12 or name \ HG13 or name HG21 or name HG22 or name HG23)) or resid 24 through 508 or resid 6 \ 00 through 601)) selection = (chain 'C' and (resid 23 through 403 or resid 410 through 508 or resid 600 throu \ gh 601)) } ncs_group { reference = (chain 'D' and resid 13 through 479) selection = (chain 'E' and (resid 13 through 166 or (resid 167 and (name N or name CA or nam \ e C or name O or name CB or name OG1 or name CG2 or name H or name HA or name HB \ or name HG21 or name HG22 or name HG23)) or resid 168 through 479)) selection = (chain 'F' and resid 13 through 479) } ncs_group { reference = chain 'K' selection = chain 'L' selection = (chain 'M' and resid 1 through 74) selection = (chain 'N' and resid 1 through 74) selection = (chain 'O' and resid 1 through 74) selection = chain 'P' selection = (chain 'Q' and resid 1 through 74) selection = (chain 'R' and resid 1 through 74) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 15 5.49 5 Mg 5 5.21 5 S 123 5.16 5 C 20445 2.51 5 N 5525 2.21 5 O 6157 1.98 5 H 32803 0.53 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.75 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: 0.010 Normalize map: mean=0, sd=1: 6.460 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: 0.760 Extract box with map and model: 28.020 Check model and map are aligned: 0.710 Process input model: 161.250 Find NCS groups from input model: 2.680 Set up NCS constraints: 0.270 Set refine NCS operators: 0.000 Set scattering table: 0.470 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 203.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 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 : 0.008 0.071 32722 Z= 0.505 Angle : 0.743 24.464 44247 Z= 0.467 Chirality : 0.046 0.168 5173 Planarity : 0.004 0.056 5666 Dihedral : 14.814 132.265 12084 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.90 % Favored : 91.10 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.11 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.13), residues: 4169 helix: 0.04 (0.12), residues: 2034 sheet: -2.61 (0.21), residues: 536 loop : -1.89 (0.15), residues: 1599 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8338 Ramachandran restraints generated. 4169 Oldfield, 0 Emsley, 4169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8338 Ramachandran restraints generated. 4169 Oldfield, 0 Emsley, 4169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 176 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Evaluate side-chains 447 residues out of total 3366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 447 time to evaluate : 3.871 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 outliers start: 0 outliers final: 0 residues processed: 447 average time/residue: 0.9361 time to fit residues: 650.7341 Evaluate side-chains 380 residues out of total 3366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 380 time to evaluate : 3.906 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.8065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 349 optimal weight: 10.0000 chunk 313 optimal weight: 2.9990 chunk 174 optimal weight: 1.9990 chunk 107 optimal weight: 0.3980 chunk 211 optimal weight: 1.9990 chunk 167 optimal weight: 1.9990 chunk 324 optimal weight: 5.9990 chunk 125 optimal weight: 0.5980 chunk 197 optimal weight: 0.7980 chunk 241 optimal weight: 0.9980 chunk 375 optimal weight: 9.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 65 ASN B 415 GLN G 117 HIS ** G 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 211 ASN ** S 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.0812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 32722 Z= 0.211 Angle : 0.543 8.070 44247 Z= 0.284 Chirality : 0.041 0.162 5173 Planarity : 0.004 0.043 5666 Dihedral : 5.982 125.388 4623 Min Nonbonded Distance : 1.711 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer Outliers : 0.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.11 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.13), residues: 4169 helix: 0.36 (0.12), residues: 2046 sheet: -2.28 (0.21), residues: 529 loop : -1.57 (0.16), residues: 1594 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8338 Ramachandran restraints generated. 4169 Oldfield, 0 Emsley, 4169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8338 Ramachandran restraints generated. 4169 Oldfield, 0 Emsley, 4169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 176 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Evaluate side-chains 404 residues out of total 3366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 390 time to evaluate : 3.973 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 outliers start: 14 outliers final: 8 residues processed: 394 average time/residue: 0.9599 time to fit residues: 597.6442 Evaluate side-chains 375 residues out of total 3366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 367 time to evaluate : 3.873 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 8 outliers final: 1 residues processed: 8 average time/residue: 0.6026 time to fit residues: 13.8608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 208 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 312 optimal weight: 1.9990 chunk 256 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 376 optimal weight: 9.9990 chunk 406 optimal weight: 8.9990 chunk 335 optimal weight: 9.9990 chunk 373 optimal weight: 8.9990 chunk 128 optimal weight: 2.9990 chunk 302 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 415 GLN G 163 ASN ** G 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 44 GLN ** S 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.0875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.057 32722 Z= 0.361 Angle : 0.565 8.523 44247 Z= 0.297 Chirality : 0.042 0.155 5173 Planarity : 0.004 0.044 5666 Dihedral : 6.019 122.813 4623 Min Nonbonded Distance : 1.658 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer Outliers : 0.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.11 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.13), residues: 4169 helix: 0.37 (0.12), residues: 2046 sheet: -2.38 (0.21), residues: 533 loop : -1.58 (0.16), residues: 1590 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8338 Ramachandran restraints generated. 4169 Oldfield, 0 Emsley, 4169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8338 Ramachandran restraints generated. 4169 Oldfield, 0 Emsley, 4169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 176 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Evaluate side-chains 405 residues out of total 3366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 387 time to evaluate : 3.911 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 outliers start: 18 outliers final: 13 residues processed: 394 average time/residue: 0.9886 time to fit residues: 617.3956 Evaluate side-chains 377 residues out of total 3366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 364 time to evaluate : 3.940 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 2 residues processed: 13 average time/residue: 0.6807 time to fit residues: 21.1030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 372 optimal weight: 6.9990 chunk 283 optimal weight: 1.9990 chunk 195 optimal weight: 0.9980 chunk 41 optimal weight: 3.9990 chunk 179 optimal weight: 1.9990 chunk 252 optimal weight: 0.0980 chunk 377 optimal weight: 10.0000 chunk 400 optimal weight: 4.9990 chunk 197 optimal weight: 1.9990 chunk 358 optimal weight: 7.9990 chunk 107 optimal weight: 1.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 415 GLN ** C 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.1071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 32722 Z= 0.249 Angle : 0.527 8.505 44247 Z= 0.273 Chirality : 0.041 0.156 5173 Planarity : 0.003 0.041 5666 Dihedral : 5.787 115.952 4623 Min Nonbonded Distance : 1.726 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer Outliers : 0.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.11 % Cis-general : 0.15 % 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 (0.13), residues: 4169 helix: 0.58 (0.12), residues: 2041 sheet: -2.21 (0.21), residues: 522 loop : -1.45 (0.16), residues: 1606 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8338 Ramachandran restraints generated. 4169 Oldfield, 0 Emsley, 4169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8338 Ramachandran restraints generated. 4169 Oldfield, 0 Emsley, 4169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 176 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Evaluate side-chains 405 residues out of total 3366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 388 time to evaluate : 3.953 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 outliers start: 17 outliers final: 10 residues processed: 394 average time/residue: 0.9828 time to fit residues: 615.1602 Evaluate side-chains 374 residues out of total 3366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 364 time to evaluate : 3.935 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 10 outliers final: 1 residues processed: 10 average time/residue: 0.6239 time to fit residues: 16.5204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 333 optimal weight: 4.9990 chunk 227 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 chunk 297 optimal weight: 2.9990 chunk 165 optimal weight: 2.9990 chunk 341 optimal weight: 9.9990 chunk 276 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 204 optimal weight: 1.9990 chunk 359 optimal weight: 10.0000 chunk 100 optimal weight: 2.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 415 GLN ** C 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 211 ASN ** H 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 87 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.1120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.053 32722 Z= 0.349 Angle : 0.554 8.820 44247 Z= 0.289 Chirality : 0.042 0.156 5173 Planarity : 0.004 0.042 5666 Dihedral : 5.811 112.679 4623 Min Nonbonded Distance : 1.676 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer Outliers : 0.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.11 % Cis-general : 0.15 % 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: -0.93 (0.13), residues: 4169 helix: 0.56 (0.12), residues: 2045 sheet: -2.29 (0.21), residues: 528 loop : -1.48 (0.16), residues: 1596 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8338 Ramachandran restraints generated. 4169 Oldfield, 0 Emsley, 4169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8338 Ramachandran restraints generated. 4169 Oldfield, 0 Emsley, 4169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 176 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Evaluate side-chains 399 residues out of total 3366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 383 time to evaluate : 4.008 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 outliers start: 16 outliers final: 11 residues processed: 390 average time/residue: 0.9711 time to fit residues: 599.7603 Evaluate side-chains 375 residues out of total 3366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 364 time to evaluate : 3.906 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 11 outliers final: 1 residues processed: 11 average time/residue: 0.6336 time to fit residues: 17.7389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 134 optimal weight: 0.7980 chunk 360 optimal weight: 10.0000 chunk 79 optimal weight: 1.9990 chunk 234 optimal weight: 2.9990 chunk 98 optimal weight: 0.9990 chunk 400 optimal weight: 5.9990 chunk 332 optimal weight: 3.9990 chunk 185 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 132 optimal weight: 0.5980 chunk 210 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 415 GLN ** C 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 45 GLN S 87 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.1311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 32722 Z= 0.210 Angle : 0.514 8.489 44247 Z= 0.264 Chirality : 0.041 0.155 5173 Planarity : 0.003 0.041 5666 Dihedral : 5.558 104.268 4623 Min Nonbonded Distance : 1.734 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer Outliers : 0.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.11 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.13), residues: 4169 helix: 0.78 (0.12), residues: 2042 sheet: -2.08 (0.22), residues: 520 loop : -1.34 (0.16), residues: 1607 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8338 Ramachandran restraints generated. 4169 Oldfield, 0 Emsley, 4169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8338 Ramachandran restraints generated. 4169 Oldfield, 0 Emsley, 4169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 176 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Evaluate side-chains 405 residues out of total 3366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 392 time to evaluate : 3.929 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 outliers start: 13 outliers final: 8 residues processed: 398 average time/residue: 0.9818 time to fit residues: 619.8423 Evaluate side-chains 383 residues out of total 3366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 375 time to evaluate : 3.919 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 8 outliers final: 1 residues processed: 8 average time/residue: 0.6412 time to fit residues: 14.3450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 386 optimal weight: 4.9990 chunk 45 optimal weight: 0.0970 chunk 228 optimal weight: 2.9990 chunk 292 optimal weight: 1.9990 chunk 226 optimal weight: 0.9990 chunk 337 optimal weight: 0.1980 chunk 223 optimal weight: 2.9990 chunk 399 optimal weight: 5.9990 chunk 249 optimal weight: 1.9990 chunk 243 optimal weight: 0.5980 chunk 184 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 415 GLN ** C 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.1496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 32722 Z= 0.170 Angle : 0.497 8.122 44247 Z= 0.252 Chirality : 0.040 0.152 5173 Planarity : 0.003 0.042 5666 Dihedral : 5.326 93.385 4623 Min Nonbonded Distance : 1.771 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer Outliers : 0.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.11 % Cis-general : 0.15 % 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: -0.37 (0.14), residues: 4169 helix: 0.98 (0.12), residues: 2045 sheet: -1.93 (0.22), residues: 522 loop : -1.18 (0.16), residues: 1602 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8338 Ramachandran restraints generated. 4169 Oldfield, 0 Emsley, 4169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8338 Ramachandran restraints generated. 4169 Oldfield, 0 Emsley, 4169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 176 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Evaluate side-chains 416 residues out of total 3366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 408 time to evaluate : 4.005 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 outliers start: 8 outliers final: 5 residues processed: 412 average time/residue: 0.9143 time to fit residues: 595.9305 Evaluate side-chains 381 residues out of total 3366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 376 time to evaluate : 3.933 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 5 average time/residue: 0.5825 time to fit residues: 10.2912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 246 optimal weight: 2.9990 chunk 159 optimal weight: 0.7980 chunk 238 optimal weight: 4.9990 chunk 120 optimal weight: 0.2980 chunk 78 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 253 optimal weight: 0.9990 chunk 271 optimal weight: 1.9990 chunk 197 optimal weight: 0.0970 chunk 37 optimal weight: 2.9990 chunk 313 optimal weight: 2.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 415 GLN ** C 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 45 GLN S 87 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.054 32722 Z= 0.158 Angle : 0.491 7.974 44247 Z= 0.249 Chirality : 0.040 0.149 5173 Planarity : 0.003 0.044 5666 Dihedral : 5.115 81.620 4623 Min Nonbonded Distance : 1.784 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer Outliers : 0.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.11 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.14), residues: 4169 helix: 1.14 (0.12), residues: 2042 sheet: -1.84 (0.22), residues: 536 loop : -1.03 (0.16), residues: 1591 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8338 Ramachandran restraints generated. 4169 Oldfield, 0 Emsley, 4169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8338 Ramachandran restraints generated. 4169 Oldfield, 0 Emsley, 4169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 176 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Evaluate side-chains 409 residues out of total 3366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 403 time to evaluate : 3.966 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 outliers start: 6 outliers final: 3 residues processed: 405 average time/residue: 0.9838 time to fit residues: 638.6104 Evaluate side-chains 392 residues out of total 3366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 389 time to evaluate : 3.887 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 3 average time/residue: 0.6721 time to fit residues: 8.5172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 362 optimal weight: 9.9990 chunk 382 optimal weight: 9.9990 chunk 348 optimal weight: 6.9990 chunk 371 optimal weight: 3.9990 chunk 223 optimal weight: 2.9990 chunk 161 optimal weight: 1.9990 chunk 291 optimal weight: 0.6980 chunk 114 optimal weight: 1.9990 chunk 336 optimal weight: 7.9990 chunk 351 optimal weight: 8.9990 chunk 370 optimal weight: 0.8980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 415 GLN ** C 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 45 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 32722 Z= 0.293 Angle : 0.529 8.499 44247 Z= 0.271 Chirality : 0.041 0.149 5173 Planarity : 0.003 0.041 5666 Dihedral : 5.202 71.751 4623 Min Nonbonded Distance : 1.705 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer Outliers : 0.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.11 % Cis-general : 0.15 % 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: -0.28 (0.14), residues: 4169 helix: 1.06 (0.12), residues: 2033 sheet: -1.92 (0.22), residues: 536 loop : -1.11 (0.16), residues: 1600 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8338 Ramachandran restraints generated. 4169 Oldfield, 0 Emsley, 4169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8338 Ramachandran restraints generated. 4169 Oldfield, 0 Emsley, 4169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 176 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Evaluate side-chains 395 residues out of total 3366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 384 time to evaluate : 4.000 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 9 residues processed: 388 average time/residue: 0.9259 time to fit residues: 570.3133 Evaluate side-chains 384 residues out of total 3366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 375 time to evaluate : 3.963 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 9 outliers final: 1 residues processed: 9 average time/residue: 0.5933 time to fit residues: 15.1056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 244 optimal weight: 2.9990 chunk 393 optimal weight: 2.9990 chunk 239 optimal weight: 1.9990 chunk 186 optimal weight: 1.9990 chunk 273 optimal weight: 1.9990 chunk 412 optimal weight: 0.9980 chunk 379 optimal weight: 5.9990 chunk 328 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 253 optimal weight: 0.0270 chunk 201 optimal weight: 0.5980 overall best weight: 0.9242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 415 GLN ** C 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 45 GLN S 87 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 32722 Z= 0.183 Angle : 0.498 8.197 44247 Z= 0.252 Chirality : 0.040 0.152 5173 Planarity : 0.003 0.072 5666 Dihedral : 5.012 64.599 4623 Min Nonbonded Distance : 1.755 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer Outliers : 0.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.11 % Cis-general : 0.15 % 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: -0.11 (0.14), residues: 4169 helix: 1.18 (0.12), residues: 2037 sheet: -1.84 (0.22), residues: 536 loop : -1.00 (0.16), residues: 1596 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8338 Ramachandran restraints generated. 4169 Oldfield, 0 Emsley, 4169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8338 Ramachandran restraints generated. 4169 Oldfield, 0 Emsley, 4169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 176 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Evaluate side-chains 396 residues out of total 3366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 393 time to evaluate : 3.984 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 outliers start: 3 outliers final: 1 residues processed: 394 average time/residue: 0.9205 time to fit residues: 576.0211 Evaluate side-chains 388 residues out of total 3366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 387 time to evaluate : 3.887 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.5778 time to fit residues: 5.8822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 260 optimal weight: 3.9990 chunk 349 optimal weight: 7.9990 chunk 100 optimal weight: 2.9990 chunk 302 optimal weight: 0.6980 chunk 48 optimal weight: 0.0980 chunk 91 optimal weight: 3.9990 chunk 328 optimal weight: 4.9990 chunk 137 optimal weight: 2.9990 chunk 337 optimal weight: 5.9990 chunk 41 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 415 GLN ** C 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.125800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.090311 restraints weight = 137168.577| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 1.61 r_work: 0.2848 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2729 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3476 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3476 r_free = 0.3476 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3475 r_free = 0.3475 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3475 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.043 32722 Z= 0.297 Angle : 0.529 8.403 44247 Z= 0.272 Chirality : 0.041 0.151 5173 Planarity : 0.003 0.055 5666 Dihedral : 5.091 56.712 4623 Min Nonbonded Distance : 1.700 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer Outliers : 0.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.11 % Cis-general : 0.15 % 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: -0.23 (0.14), residues: 4169 helix: 1.10 (0.12), residues: 2024 sheet: -1.94 (0.22), residues: 529 loop : -1.06 (0.16), residues: 1616 =============================================================================== Job complete usr+sys time: 12186.00 seconds wall clock time: 212 minutes 2.14 seconds (12722.14 seconds total)