Starting phenix.real_space_refine (version: 1.21rc1) on Mon Apr 24 02:57:12 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yj4_10815/04_2023/6yj4_10815_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yj4_10815/04_2023/6yj4_10815.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yj4_10815/04_2023/6yj4_10815_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yj4_10815/04_2023/6yj4_10815_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yj4_10815/04_2023/6yj4_10815_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yj4_10815/04_2023/6yj4_10815.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yj4_10815/04_2023/6yj4_10815.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yj4_10815/04_2023/6yj4_10815_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yj4_10815/04_2023/6yj4_10815_neut_updated.pdb" } resolution = 2.7 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= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Fe 28 7.16 5 Zn 1 6.06 5 P 44 5.49 5 S 315 5.16 5 C 42739 2.51 5 N 10804 2.21 5 O 12380 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 33": "OE1" <-> "OE2" Residue "A ARG 49": "NH1" <-> "NH2" Residue "A ASP 67": "OD1" <-> "OD2" Residue "A GLU 69": "OE1" <-> "OE2" Residue "B ASP 44": "OD1" <-> "OD2" Residue "B PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 99": "OD1" <-> "OD2" Residue "B ARG 102": "NH1" <-> "NH2" Residue "B PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 112": "NH1" <-> "NH2" Residue "B TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 165": "NH1" <-> "NH2" Residue "B ASP 168": "OD1" <-> "OD2" Residue "B ASP 174": "OD1" <-> "OD2" Residue "B TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 199": "NH1" <-> "NH2" Residue "B ARG 209": "NH1" <-> "NH2" Residue "C GLU 37": "OE1" <-> "OE2" Residue "C ASP 45": "OD1" <-> "OD2" Residue "C PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 181": "OE1" <-> "OE2" Residue "C PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 195": "OD1" <-> "OD2" Residue "C ARG 198": "NH1" <-> "NH2" Residue "C PHE 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 221": "OE1" <-> "OE2" Residue "C ARG 230": "NH1" <-> "NH2" Residue "C TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 259": "NH1" <-> "NH2" Residue "C ASP 260": "OD1" <-> "OD2" Residue "C ASP 264": "OD1" <-> "OD2" Residue "C PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 50": "OD1" <-> "OD2" Residue "D PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 54": "NH1" <-> "NH2" Residue "D GLU 60": "OE1" <-> "OE2" Residue "D GLU 63": "OE1" <-> "OE2" Residue "D TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 169": "NH1" <-> "NH2" Residue "D ARG 174": "NH1" <-> "NH2" Residue "D PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 231": "NH1" <-> "NH2" Residue "D ARG 257": "NH1" <-> "NH2" Residue "D ASP 259": "OD1" <-> "OD2" Residue "D ASP 304": "OD1" <-> "OD2" Residue "D ARG 306": "NH1" <-> "NH2" Residue "D TYR 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 362": "OE1" <-> "OE2" Residue "D ASP 363": "OD1" <-> "OD2" Residue "D PHE 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 420": "OE1" <-> "OE2" Residue "D ASP 439": "OD1" <-> "OD2" Residue "D ASP 465": "OD1" <-> "OD2" Residue "D ARG 466": "NH1" <-> "NH2" Residue "E ARG 34": "NH1" <-> "NH2" Residue "E TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 98": "OE1" <-> "OE2" Residue "E GLU 106": "OE1" <-> "OE2" Residue "E PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 142": "OE1" <-> "OE2" Residue "E ASP 158": "OD1" <-> "OD2" Residue "E TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 187": "OD1" <-> "OD2" Residue "E GLU 211": "OE1" <-> "OE2" Residue "E GLU 231": "OE1" <-> "OE2" Residue "F ARG 56": "NH1" <-> "NH2" Residue "F ASP 60": "OD1" <-> "OD2" Residue "F ARG 113": "NH1" <-> "NH2" Residue "F GLU 142": "OE1" <-> "OE2" Residue "F TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 216": "OE1" <-> "OE2" Residue "F ARG 299": "NH1" <-> "NH2" Residue "F ASP 342": "OD1" <-> "OD2" Residue "F ARG 371": "NH1" <-> "NH2" Residue "F GLU 379": "OE1" <-> "OE2" Residue "F ARG 400": "NH1" <-> "NH2" Residue "F ASP 457": "OD1" <-> "OD2" Residue "F ARG 472": "NH1" <-> "NH2" Residue "G ARG 89": "NH1" <-> "NH2" Residue "G GLU 112": "OE1" <-> "OE2" Residue "G ASP 137": "OD1" <-> "OD2" Residue "G GLU 141": "OE1" <-> "OE2" Residue "G ARG 150": "NH1" <-> "NH2" Residue "G ARG 155": "NH1" <-> "NH2" Residue "G ARG 165": "NH1" <-> "NH2" Residue "G ASP 169": "OD1" <-> "OD2" Residue "G ASP 231": "OD1" <-> "OD2" Residue "G ARG 248": "NH1" <-> "NH2" Residue "G ARG 283": "NH1" <-> "NH2" Residue "G ARG 298": "NH1" <-> "NH2" Residue "G ARG 315": "NH1" <-> "NH2" Residue "G ASP 326": "OD1" <-> "OD2" Residue "G ASP 344": "OD1" <-> "OD2" Residue "G PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 377": "OD1" <-> "OD2" Residue "G ARG 392": "NH1" <-> "NH2" Residue "G TYR 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 434": "NH1" <-> "NH2" Residue "G PHE 450": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 451": "OD1" <-> "OD2" Residue "G GLU 463": "OE1" <-> "OE2" Residue "G ASP 490": "OD1" <-> "OD2" Residue "G PHE 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 506": "OE1" <-> "OE2" Residue "G ARG 528": "NH1" <-> "NH2" Residue "G ASP 562": "OD1" <-> "OD2" Residue "G TYR 599": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 631": "OE1" <-> "OE2" Residue "G TYR 639": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 641": "OD1" <-> "OD2" Residue "G ASP 647": "OD1" <-> "OD2" Residue "G ARG 705": "NH1" <-> "NH2" Residue "H PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 27": "NH1" <-> "NH2" Residue "H ARG 35": "NH1" <-> "NH2" Residue "H ARG 36": "NH1" <-> "NH2" Residue "H GLU 61": "OE1" <-> "OE2" Residue "H TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 147": "OE1" <-> "OE2" Residue "H ARG 174": "NH1" <-> "NH2" Residue "H PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 199": "NH1" <-> "NH2" Residue "H PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 203": "OD1" <-> "OD2" Residue "H GLU 210": "OE1" <-> "OE2" Residue "H GLU 218": "OE1" <-> "OE2" Residue "H TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 297": "NH1" <-> "NH2" Residue "H PHE 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 56": "NH1" <-> "NH2" Residue "I ARG 59": "NH1" <-> "NH2" Residue "I ARG 113": "NH1" <-> "NH2" Residue "I GLU 127": "OE1" <-> "OE2" Residue "I GLU 150": "OE1" <-> "OE2" Residue "I TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 225": "OD1" <-> "OD2" Residue "I TYR 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 229": "NH1" <-> "NH2" Residue "J TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 84": "OE1" <-> "OE2" Residue "J ARG 92": "NH1" <-> "NH2" Residue "J ASP 137": "OD1" <-> "OD2" Residue "K PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 49": "OD1" <-> "OD2" Residue "K PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 80": "OE1" <-> "OE2" Residue "L TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 108": "OE1" <-> "OE2" Residue "L PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 241": "OE1" <-> "OE2" Residue "L ARG 265": "NH1" <-> "NH2" Residue "L PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 356": "OE1" <-> "OE2" Residue "L TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 415": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 453": "OE1" <-> "OE2" Residue "L PHE 463": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 486": "OD1" <-> "OD2" Residue "L ASP 501": "OD1" <-> "OD2" Residue "L TYR 585": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 162": "NH1" <-> "NH2" Residue "M PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 268": "OE1" <-> "OE2" Residue "M TYR 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 352": "OD1" <-> "OD2" Residue "M GLU 395": "OE1" <-> "OE2" Residue "M ARG 405": "NH1" <-> "NH2" Residue "M TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 450": "OE1" <-> "OE2" Residue "M PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 20": "OD1" <-> "OD2" Residue "N ARG 22": "NH1" <-> "NH2" Residue "N TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 102": "OE1" <-> "OE2" Residue "N TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 226": "OE1" <-> "OE2" Residue "N TYR 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 283": "NH1" <-> "NH2" Residue "N TYR 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 359": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 412": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 423": "OD1" <-> "OD2" Residue "N PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 61": "OD1" <-> "OD2" Residue "O TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 111": "OD1" <-> "OD2" Residue "O PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 85": "NH1" <-> "NH2" Residue "P GLU 86": "OE1" <-> "OE2" Residue "P ASP 108": "OD1" <-> "OD2" Residue "P ARG 110": "NH1" <-> "NH2" Residue "P TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 142": "OD1" <-> "OD2" Residue "P ASP 251": "OD1" <-> "OD2" Residue "P PHE 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 278": "OE1" <-> "OE2" Residue "P GLU 288": "OE1" <-> "OE2" Residue "P ARG 316": "NH1" <-> "NH2" Residue "P ARG 352": "NH1" <-> "NH2" Residue "Q ARG 56": "NH1" <-> "NH2" Residue "Q ARG 59": "NH1" <-> "NH2" Residue "Q ARG 79": "NH1" <-> "NH2" Residue "Q ASP 81": "OD1" <-> "OD2" Residue "Q ASP 83": "OD1" <-> "OD2" Residue "Q GLU 92": "OE1" <-> "OE2" Residue "Q TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 33": "OE1" <-> "OE2" Residue "R ASP 68": "OD1" <-> "OD2" Residue "R TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 118": "OD1" <-> "OD2" Residue "R TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 45": "NH1" <-> "NH2" Residue "S PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 57": "NH1" <-> "NH2" Residue "S GLU 73": "OE1" <-> "OE2" Residue "T ASP 31": "OD1" <-> "OD2" Residue "T ARG 35": "NH1" <-> "NH2" Residue "T ASP 61": "OD1" <-> "OD2" Residue "T GLU 83": "OE1" <-> "OE2" Residue "T GLU 100": "OE1" <-> "OE2" Residue "T ASP 107": "OD1" <-> "OD2" Residue "U ASP 67": "OD1" <-> "OD2" Residue "U GLU 102": "OE1" <-> "OE2" Residue "U ASP 109": "OD1" <-> "OD2" Residue "V GLU 27": "OE1" <-> "OE2" Residue "V TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 59": "OD1" <-> "OD2" Residue "V GLU 119": "OE1" <-> "OE2" Residue "V GLU 127": "OE1" <-> "OE2" Residue "V TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 61": "OE1" <-> "OE2" Residue "W ARG 62": "NH1" <-> "NH2" Residue "W GLU 82": "OE1" <-> "OE2" Residue "W ASP 117": "OD1" <-> "OD2" Residue "X ARG 3": "NH1" <-> "NH2" Residue "X ASP 67": "OD1" <-> "OD2" Residue "X ARG 74": "NH1" <-> "NH2" Residue "X ASP 85": "OD1" <-> "OD2" Residue "X ASP 92": "OD1" <-> "OD2" Residue "X ARG 136": "NH1" <-> "NH2" Residue "Y PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 111": "NH1" <-> "NH2" Residue "Y ARG 143": "NH1" <-> "NH2" Residue "Y ARG 170": "NH1" <-> "NH2" Residue "Y GLU 181": "OE1" <-> "OE2" Residue "Y GLU 195": "OE1" <-> "OE2" Residue "Z ARG 20": "NH1" <-> "NH2" Residue "Z ARG 21": "NH1" <-> "NH2" Residue "Z ARG 66": "NH1" <-> "NH2" Residue "Z ARG 79": "NH1" <-> "NH2" Residue "a ARG 32": "NH1" <-> "NH2" Residue "a ARG 37": "NH1" <-> "NH2" Residue "a PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 43": "OD1" <-> "OD2" Residue "a ASP 46": "OD1" <-> "OD2" Residue "a ARG 52": "NH1" <-> "NH2" Residue "a ARG 55": "NH1" <-> "NH2" Residue "b ARG 14": "NH1" <-> "NH2" Residue "b ARG 23": "NH1" <-> "NH2" Residue "b ARG 47": "NH1" <-> "NH2" Residue "b ARG 67": "NH1" <-> "NH2" Residue "b ARG 69": "NH1" <-> "NH2" Residue "b GLU 78": "OE1" <-> "OE2" Residue "c PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 25": "NH1" <-> "NH2" Residue "c ARG 45": "NH1" <-> "NH2" Residue "c GLU 54": "OE1" <-> "OE2" Residue "c ASP 78": "OD1" <-> "OD2" Residue "c PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ASP 90": "OD1" <-> "OD2" Residue "c ASP 138": "OD1" <-> "OD2" Residue "c TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 179": "NH1" <-> "NH2" Residue "c PHE 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 62": "OE1" <-> "OE2" Residue "e ARG 12": "NH1" <-> "NH2" Residue "e ASP 30": "OD1" <-> "OD2" Residue "f TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ARG 7": "NH1" <-> "NH2" Residue "f ARG 10": "NH1" <-> "NH2" Residue "f ARG 34": "NH1" <-> "NH2" Residue "f PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 62": "OE1" <-> "OE2" Residue "f GLU 65": "OE1" <-> "OE2" Residue "f TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 53": "OE1" <-> "OE2" Residue "g ARG 62": "NH1" <-> "NH2" Residue "g TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ASP 138": "OD1" <-> "OD2" Residue "g GLU 153": "OE1" <-> "OE2" Residue "g ARG 156": "NH1" <-> "NH2" Residue "g ASP 163": "OD1" <-> "OD2" Residue "g GLU 189": "OE1" <-> "OE2" Residue "g GLU 198": "OE1" <-> "OE2" Residue "g GLU 217": "OE1" <-> "OE2" Residue "g ASP 230": "OD1" <-> "OD2" Residue "h TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ARG 149": "NH1" <-> "NH2" Residue "h GLU 150": "OE1" <-> "OE2" Residue "i ARG 5": "NH1" <-> "NH2" Residue "i TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ASP 11": "OD1" <-> "OD2" Residue "i ARG 53": "NH1" <-> "NH2" Residue "i ARG 55": "NH1" <-> "NH2" Residue "i GLU 56": "OE1" <-> "OE2" Residue "i ARG 75": "NH1" <-> "NH2" Residue "j TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ARG 11": "NH1" <-> "NH2" Residue "k TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ASP 59": "OD1" <-> "OD2" Residue "l ARG 64": "NH1" <-> "NH2" Residue "l PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l GLU 117": "OE1" <-> "OE2" Residue "l GLU 133": "OE1" <-> "OE2" Residue "l PHE 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m ARG 12": "NH1" <-> "NH2" Residue "m PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n PHE 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ARG 33": "NH1" <-> "NH2" Residue "n ARG 44": "NH1" <-> "NH2" Residue "n PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ARG 67": "NH1" <-> "NH2" Residue "n ASP 77": "OD1" <-> "OD2" Residue "o GLU 3": "OE1" <-> "OE2" Residue "o ASP 24": "OD1" <-> "OD2" Residue "o GLU 35": "OE1" <-> "OE2" Residue "o ARG 37": "NH1" <-> "NH2" Residue "o GLU 50": "OE1" <-> "OE2" Residue "o ARG 65": "NH1" <-> "NH2" Residue "o GLU 78": "OE1" <-> "OE2" Residue "p ASP 14": "OD1" <-> "OD2" Residue "p TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p GLU 61": "OE1" <-> "OE2" Residue "p TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p ASP 89": "OD1" <-> "OD2" Time to flip residues: 0.21s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 66311 Number of models: 1 Model: "" Number of chains: 94 Chain: "A" Number of atoms: 1006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1006 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'FME:plan-2': 1, 'PHE:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 16 Chain: "B" Number of atoms: 1395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1395 Classifications: {'peptide': 177} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 162} Chain: "C" Number of atoms: 1999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1999 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 20, 'TRANS': 221} Chain: "D" Number of atoms: 3465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3465 Classifications: {'peptide': 437} Link IDs: {'PTRANS': 25, 'TRANS': 411} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'2MR:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 1688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1688 Classifications: {'peptide': 216} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 197} Chain: "F" Number of atoms: 3559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3559 Classifications: {'peptide': 460} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 437} Chain: "G" Number of atoms: 5274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 694, 5274 Classifications: {'peptide': 694} Link IDs: {'PTRANS': 34, 'TRANS': 659} Chain: "H" Number of atoms: 2709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2709 Classifications: {'peptide': 341} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 326} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'FME:plan-2': 1, 'TYR:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "I" Number of atoms: 1526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1526 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 12, 'TRANS': 178} Chain: "J" Number of atoms: 1462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1462 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 3, 'TRANS': 181} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "K" Number of atoms: 693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 693 Classifications: {'peptide': 89} Link IDs: {'TRANS': 88} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 5207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 655, 5207 Classifications: {'peptide': 655} Link IDs: {'PTRANS': 15, 'TRANS': 639} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "M" Number of atoms: 3857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3857 Classifications: {'peptide': 486} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 471} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "N" Number of atoms: 3776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3776 Classifications: {'peptide': 469} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 461} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "O" Number of atoms: 1305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1305 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 11, 'TRANS': 156} Chain: "P" Number of atoms: 2812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 355, 2812 Classifications: {'peptide': 355} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 15, 'TRANS': 339} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "Q" Number of atoms: 1037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1037 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 4, 'TRANS': 120} Chain: "R" Number of atoms: 922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 922 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 9, 'TRANS': 108} Chain: "S" Number of atoms: 667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 667 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 3, 'TRANS': 82} Chain: "T" Number of atoms: 620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 620 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 5, 'TRANS': 75} Chain: "U" Number of atoms: 667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 667 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 2, 'TRANS': 85} Chain: "V" Number of atoms: 1028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1028 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 7, 'TRANS': 118} Chain: "W" Number of atoms: 1036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1036 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 4, 'TRANS': 118} Chain: "X" Number of atoms: 1345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1345 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 10, 'TRANS': 160} Chain: "Y" Number of atoms: 1327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1327 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 7, 'TRANS': 171} Chain: "Z" Number of atoms: 983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 983 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 9, 'TRANS': 112} Chain: "a" Number of atoms: 681 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 681 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 4, 'TRANS': 81} Chain: "b" Number of atoms: 639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 639 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 10, 'TRANS': 67} Chain: "c" Number of atoms: 1397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1397 Classifications: {'peptide': 182} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 161} Chain: "d" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 510 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "e" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 546 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 1, 'TRANS': 66} Chain: "f" Number of atoms: 1136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1136 Classifications: {'peptide': 137} Link IDs: {'PTRANS': 10, 'TRANS': 126} Chain: "g" Number of atoms: 1585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1585 Classifications: {'peptide': 198} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 10, 'TRANS': 187} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "h" Number of atoms: 909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 909 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 8, 'TRANS': 104} Chain: "i" Number of atoms: 659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 659 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 4, 'TRANS': 81} Chain: "j" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 445 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 6, 'TRANS': 46} Chain: "k" Number of atoms: 373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 373 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 3, 'TRANS': 43} Chain: "l" Number of atoms: 1039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1039 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 10, 'TRANS': 114} Chain: "m" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 735 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "n" Number of atoms: 900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 900 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 11, 'TRANS': 96} Chain: "o" Number of atoms: 681 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 681 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 4, 'TRANS': 78} Chain: "p" Number of atoms: 766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 766 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 4, 'TRANS': 86} Chain: "A" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 78 Unusual residues: {'3PE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 24 Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 43 Unusual residues: {'LMT': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'PLC': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 15 Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'FMN': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 20 Unusual residues: {'FES': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 50 Unusual residues: {'3PE': 1, 'PLC': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 43 Chain: "I" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 62 Unusual residues: {'3PE': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "L" Number of atoms: 291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 291 Unusual residues: {'3PE': 4, 'PLC': 3} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 39 Chain: "M" Number of atoms: 188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 188 Unusual residues: {'3PE': 2, 'CDL': 1, 'LMT': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 49 Chain: "N" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 93 Unusual residues: {'3PE': 1, 'PLC': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "O" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 63 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 37 Chain: "P" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 131 Unusual residues: {'CDL': 1, 'NDP': 1, 'PLC': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 59 Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'EHZ': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Chain: "U" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'EHZ': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Chain: "Y" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 129 Unusual residues: {'3PE': 1, 'LMT': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 27 Chain: "Z" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 132 Unusual residues: {'3PE': 2, 'CDL': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 70 Chain: "a" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 48 Chain: "b" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 117 Unusual residues: {'3PE': 2, 'CDL': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 85 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 85 Chain: "d" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 81 Unusual residues: {'3PE': 2, 'PLC': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 63 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "C" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "D" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "G" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 25 Classifications: {'water': 25} Link IDs: {None: 24} Chain: "H" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "I" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "J" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "K" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "L" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "M" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 25 Classifications: {'water': 25} Link IDs: {None: 24} Chain: "N" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 37 Classifications: {'water': 37} Link IDs: {None: 36} Chain: "O" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "P" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "Q" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "R" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "W" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "X" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "Z" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} 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: "c" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "f" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "h" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "i" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "l" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "m" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "n" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "o" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "p" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1913 SG CYS B 150 94.238 97.657 200.594 1.00 37.69 S ATOM 1409 SG CYS B 86 88.228 100.765 201.867 1.00 39.15 S ATOM 1403 SG CYS B 85 87.667 95.720 200.411 1.00 40.68 S ATOM 2141 SG CYS B 180 91.199 95.810 205.242 1.00 35.97 S ATOM 8682 SG CYS E 127 105.227 50.927 258.414 1.00 64.83 S ATOM 8716 SG CYS E 132 103.542 48.455 260.859 1.00 64.79 S ATOM 8985 SG CYS E 168 107.800 47.046 255.753 1.00 61.96 S ATOM 9008 SG CYS E 172 106.167 44.991 257.047 1.00 65.96 S ATOM 12275 SG CYS F 381 115.370 56.212 239.965 1.00 47.67 S ATOM 12294 SG CYS F 384 111.708 55.520 234.717 1.00 43.90 S ATOM 12645 SG CYS F 427 112.696 50.543 238.782 1.00 48.27 S ATOM 12314 SG CYS F 387 108.816 55.684 239.654 1.00 45.24 S ATOM 13861 SG CYS G 133 104.822 76.545 225.737 1.00 35.83 S ATOM 13921 SG CYS G 142 110.427 73.441 224.119 1.00 37.91 S ATOM 13881 SG CYS G 136 110.800 78.407 227.879 1.00 37.45 S ATOM 14623 SG CYS G 233 117.209 72.567 229.294 1.00 39.67 S ATOM 14251 SG CYS G 183 115.432 69.624 234.900 1.00 39.32 S ATOM 14299 SG CYS G 189 121.636 69.703 233.376 1.00 41.91 S ATOM 14275 SG CYS G 186 118.337 66.962 229.632 1.00 40.79 S ATOM 13367 SG CYS G 69 117.374 60.127 227.263 1.00 40.78 S ATOM 13450 SG CYS G 80 113.762 60.389 226.084 1.00 41.34 S ATOM 13475 SG CYS G 83 114.995 55.648 223.434 1.00 43.18 S ATOM 13577 SG CYS G 97 118.141 55.761 225.144 1.00 44.52 S ATOM 22182 SG CYS I 175 95.620 92.129 216.922 1.00 33.27 S ATOM 22160 SG CYS I 172 93.826 90.305 211.316 1.00 33.95 S ATOM 21907 SG CYS I 140 99.268 92.123 211.871 1.00 32.96 S ATOM 22134 SG CYS I 169 94.743 96.506 211.850 1.00 34.01 S ATOM 21856 SG CYS I 133 103.016 86.495 223.395 1.00 35.20 S ATOM 21879 SG CYS I 136 101.394 90.933 219.415 1.00 33.54 S ATOM 21837 SG CYS I 130 103.158 92.768 225.309 1.00 35.22 S ATOM 22212 SG CYS I 179 97.765 89.105 224.558 1.00 34.33 S ATOM 43399 SG CYS R 97 99.106 85.012 239.722 1.00 43.70 S ATOM 43594 SG CYS R 125 102.251 84.941 237.306 1.00 41.18 S ATOM 43621 SG CYS R 128 100.001 88.063 238.078 1.00 39.47 S Time building chain proxies: 27.64, per 1000 atoms: 0.42 Number of scatterers: 66311 At special positions: 0 Unit cell: (182.515, 192.01, 290.125, 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) Zn 1 29.99 Fe 28 26.01 S 315 16.00 P 44 15.00 O 12380 8.00 N 10804 7.00 C 42739 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS F 127 " - pdb=" SG CYS F 279 " distance=2.05 Simple disulfide: pdb=" SG CYS X 46 " - pdb=" SG CYS X 78 " distance=2.05 Simple disulfide: pdb=" SG CYS e 15 " - pdb=" SG CYS e 47 " distance=2.05 Simple disulfide: pdb=" SG CYS o 36 " - pdb=" SG CYS o 47 " distance=2.05 Simple disulfide: pdb=" SG CYS p 51 " - pdb=" SG CYS p 63 " distance=2.05 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 20.46 Conformation dependent library (CDL) restraints added in 7.0 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E 301 " pdb="FE2 FES E 301 " - pdb=" SG CYS E 172 " pdb="FE1 FES E 301 " - pdb=" SG CYS E 132 " pdb="FE1 FES E 301 " - pdb=" SG CYS E 127 " pdb="FE2 FES E 301 " - pdb=" SG CYS E 168 " pdb=" FES G 803 " pdb="FE1 FES G 803 " - pdb=" SG CYS G 80 " pdb="FE1 FES G 803 " - pdb=" SG CYS G 69 " pdb="FE2 FES G 803 " - pdb=" SG CYS G 83 " pdb="FE2 FES G 803 " - pdb=" SG CYS G 97 " pdb=" SF4 B 301 " pdb="FE4 SF4 B 301 " - pdb=" SG CYS B 180 " pdb="FE1 SF4 B 301 " - pdb=" SG CYS B 150 " pdb="FE2 SF4 B 301 " - pdb=" SG CYS B 86 " pdb="FE3 SF4 B 301 " - pdb=" SG CYS B 85 " pdb=" SF4 F 502 " pdb="FE2 SF4 F 502 " - pdb=" SG CYS F 384 " pdb="FE1 SF4 F 502 " - pdb=" SG CYS F 381 " pdb="FE3 SF4 F 502 " - pdb=" SG CYS F 427 " pdb="FE4 SF4 F 502 " - pdb=" SG CYS F 387 " pdb=" SF4 G 801 " pdb="FE3 SF4 G 801 " - pdb=" NE2 HIS G 129 " pdb="FE1 SF4 G 801 " - pdb=" SG CYS G 133 " pdb="FE2 SF4 G 801 " - pdb=" SG CYS G 142 " pdb="FE4 SF4 G 801 " - pdb=" SG CYS G 136 " pdb=" SF4 G 802 " pdb="FE2 SF4 G 802 " - pdb=" SG CYS G 183 " pdb="FE4 SF4 G 802 " - pdb=" SG CYS G 186 " pdb="FE3 SF4 G 802 " - pdb=" SG CYS G 189 " pdb="FE1 SF4 G 802 " - pdb=" SG CYS G 233 " pdb=" SF4 I6302 " pdb="FE2 SF4 I6302 " - pdb=" SG CYS I 172 " pdb="FE3 SF4 I6302 " - pdb=" SG CYS I 140 " pdb="FE4 SF4 I6302 " - pdb=" SG CYS I 169 " pdb="FE1 SF4 I6302 " - pdb=" SG CYS I 175 " pdb="FE4 SF4 I6302 " - pdb=" NE2 HIS I 118 " pdb=" SF4 I6303 " pdb="FE1 SF4 I6303 " - pdb=" SG CYS I 133 " pdb="FE2 SF4 I6303 " - pdb=" SG CYS I 136 " pdb="FE4 SF4 I6303 " - pdb=" SG CYS I 179 " pdb="FE3 SF4 I6303 " - pdb=" SG CYS I 130 " Number of angles added : 81 Zn2+ tetrahedral coordination pdb=" ZN R 201 " pdb="ZN ZN R 201 " - pdb=" NE2 HIS R 110 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 97 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 128 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 125 " Number of angles added : 3 16064 Ramachandran restraints generated. 8032 Oldfield, 0 Emsley, 8032 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15196 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 330 helices and 32 sheets defined 50.9% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.40 Creating SS restraints... Processing helix chain 'A' and resid 3 through 14 Proline residue: A 12 - end of helix Processing helix chain 'A' and resid 17 through 25 Processing helix chain 'A' and resid 54 through 78 removed outlier: 4.246A pdb=" N ALA A 60 " --> pdb=" O PHE A 56 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU A 64 " --> pdb=" O ALA A 60 " (cutoff:3.500A) Proline residue: A 65 - end of helix removed outlier: 4.035A pdb=" N LEU A 74 " --> pdb=" O ILE A 70 " (cutoff:3.500A) Proline residue: A 75 - end of helix Processing helix chain 'A' and resid 87 through 108 removed outlier: 3.731A pdb=" N GLY A 101 " --> pdb=" O ILE A 97 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE A 102 " --> pdb=" O LEU A 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 50 No H-bonds generated for 'chain 'B' and resid 48 through 50' Processing helix chain 'B' and resid 56 through 74 Processing helix chain 'B' and resid 86 through 93 Processing helix chain 'B' and resid 100 through 103 Processing helix chain 'B' and resid 111 through 113 No H-bonds generated for 'chain 'B' and resid 111 through 113' Processing helix chain 'B' and resid 128 through 136 Processing helix chain 'B' and resid 149 through 153 Processing helix chain 'B' and resid 155 through 157 No H-bonds generated for 'chain 'B' and resid 155 through 157' Processing helix chain 'B' and resid 184 through 199 Processing helix chain 'B' and resid 204 through 209 Processing helix chain 'C' and resid 36 through 38 No H-bonds generated for 'chain 'C' and resid 36 through 38' Processing helix chain 'C' and resid 42 through 44 No H-bonds generated for 'chain 'C' and resid 42 through 44' Processing helix chain 'C' and resid 60 through 81 removed outlier: 3.677A pdb=" N ARG C 63 " --> pdb=" O PRO C 60 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LEU C 65 " --> pdb=" O ASP C 62 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N GLN C 66 " --> pdb=" O ARG C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 114 removed outlier: 4.811A pdb=" N ILE C 106 " --> pdb=" O SER C 103 " (cutoff:3.500A) Proline residue: C 107 - end of helix removed outlier: 3.702A pdb=" N ASP C 114 " --> pdb=" O PHE C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 186 removed outlier: 4.129A pdb=" N TRP C 177 " --> pdb=" O GLY C 174 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N MET C 185 " --> pdb=" O ALA C 182 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N TYR C 186 " --> pdb=" O TYR C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 266 No H-bonds generated for 'chain 'C' and resid 264 through 266' Processing helix chain 'D' and resid 51 through 53 No H-bonds generated for 'chain 'D' and resid 51 through 53' Processing helix chain 'D' and resid 123 through 129 removed outlier: 4.080A pdb=" N GLU D 128 " --> pdb=" O GLU D 124 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N TYR D 129 " --> pdb=" O LYS D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 138 No H-bonds generated for 'chain 'D' and resid 136 through 138' Processing helix chain 'D' and resid 147 through 162 Processing helix chain 'D' and resid 168 through 197 removed outlier: 3.563A pdb=" N CYS D 191 " --> pdb=" O LEU D 187 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N MET D 195 " --> pdb=" O CYS D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 201 through 221 removed outlier: 4.028A pdb=" N GLU D 208 " --> pdb=" O LEU D 204 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLU D 209 " --> pdb=" O TRP D 205 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N PHE D 216 " --> pdb=" O LYS D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 265 removed outlier: 3.983A pdb=" N GLN D 253 " --> pdb=" O MET D 249 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N GLY D 255 " --> pdb=" O ALA D 251 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N ASP D 256 " --> pdb=" O THR D 252 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG D 257 " --> pdb=" O GLN D 253 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU D 264 " --> pdb=" O GLU D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 275 Processing helix chain 'D' and resid 283 through 288 Processing helix chain 'D' and resid 293 through 297 Processing helix chain 'D' and resid 305 through 308 No H-bonds generated for 'chain 'D' and resid 305 through 308' Processing helix chain 'D' and resid 314 through 316 No H-bonds generated for 'chain 'D' and resid 314 through 316' Processing helix chain 'D' and resid 329 through 352 Processing helix chain 'D' and resid 371 through 374 No H-bonds generated for 'chain 'D' and resid 371 through 374' Processing helix chain 'D' and resid 378 through 389 Processing helix chain 'D' and resid 430 through 442 removed outlier: 3.522A pdb=" N HIS D 434 " --> pdb=" O PRO D 430 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N ASP D 439 " --> pdb=" O LEU D 435 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N HIS D 440 " --> pdb=" O GLY D 436 " (cutoff:3.500A) Processing helix chain 'D' and resid 447 through 457 removed outlier: 3.522A pdb=" N VAL D 451 " --> pdb=" O LEU D 447 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA D 452 " --> pdb=" O PRO D 448 " (cutoff:3.500A) Processing helix chain 'D' and resid 461 through 465 Processing helix chain 'E' and resid 49 through 61 removed outlier: 3.689A pdb=" N LYS E 61 " --> pdb=" O GLU E 57 " (cutoff:3.500A) Processing helix chain 'E' and resid 67 through 81 removed outlier: 4.183A pdb=" N MET E 72 " --> pdb=" O ALA E 69 " (cutoff:3.500A) Proline residue: E 73 - end of helix Processing helix chain 'E' and resid 87 through 97 Processing helix chain 'E' and resid 101 through 110 removed outlier: 3.502A pdb=" N VAL E 107 " --> pdb=" O ARG E 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 135 Processing helix chain 'E' and resid 137 through 148 Processing helix chain 'E' and resid 190 through 201 Processing helix chain 'E' and resid 211 through 213 No H-bonds generated for 'chain 'E' and resid 211 through 213' Processing helix chain 'E' and resid 235 through 238 Processing helix chain 'F' and resid 36 through 38 No H-bonds generated for 'chain 'F' and resid 36 through 38' Processing helix chain 'F' and resid 52 through 58 Processing helix chain 'F' and resid 64 through 70 Processing helix chain 'F' and resid 72 through 81 Processing helix chain 'F' and resid 96 through 101 removed outlier: 4.196A pdb=" N MET F 101 " --> pdb=" O LYS F 97 " (cutoff:3.500A) Processing helix chain 'F' and resid 107 through 109 No H-bonds generated for 'chain 'F' and resid 107 through 109' Processing helix chain 'F' and resid 128 through 133 Processing helix chain 'F' and resid 137 through 150 Processing helix chain 'F' and resid 165 through 180 Processing helix chain 'F' and resid 188 through 190 No H-bonds generated for 'chain 'F' and resid 188 through 190' Processing helix chain 'F' and resid 207 through 209 No H-bonds generated for 'chain 'F' and resid 207 through 209' Processing helix chain 'F' and resid 211 through 218 removed outlier: 3.612A pdb=" N ILE F 215 " --> pdb=" O GLU F 211 " (cutoff:3.500A) Processing helix chain 'F' and resid 237 through 239 No H-bonds generated for 'chain 'F' and resid 237 through 239' Processing helix chain 'F' and resid 247 through 259 removed outlier: 3.962A pdb=" N ALA F 253 " --> pdb=" O THR F 249 " (cutoff:3.500A) Proline residue: F 254 - end of helix Processing helix chain 'F' and resid 262 through 266 Processing helix chain 'F' and resid 298 through 304 Processing helix chain 'F' and resid 331 through 334 No H-bonds generated for 'chain 'F' and resid 331 through 334' Processing helix chain 'F' and resid 341 through 346 Processing helix chain 'F' and resid 365 through 379 Processing helix chain 'F' and resid 385 through 403 removed outlier: 4.300A pdb=" N THR F 392 " --> pdb=" O ARG F 388 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG F 400 " --> pdb=" O LYS F 396 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N THR F 403 " --> pdb=" O ASP F 399 " (cutoff:3.500A) Processing helix chain 'F' and resid 409 through 419 Processing helix chain 'F' and resid 429 through 443 Proline residue: F 436 - end of helix Processing helix chain 'F' and resid 445 through 458 Processing helix chain 'G' and resid 54 through 60 Processing helix chain 'G' and resid 112 through 125 Processing helix chain 'G' and resid 143 through 151 Processing helix chain 'G' and resid 188 through 195 Processing helix chain 'G' and resid 208 through 210 No H-bonds generated for 'chain 'G' and resid 208 through 210' Processing helix chain 'G' and resid 226 through 232 Processing helix chain 'G' and resid 249 through 251 No H-bonds generated for 'chain 'G' and resid 249 through 251' Processing helix chain 'G' and resid 295 through 305 removed outlier: 5.104A pdb=" N CYS G 301 " --> pdb=" O SER G 297 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N ASP G 302 " --> pdb=" O ARG G 298 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N GLY G 303 " --> pdb=" O PHE G 299 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LEU G 304 " --> pdb=" O ALA G 300 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N LYS G 305 " --> pdb=" O CYS G 301 " (cutoff:3.500A) Processing helix chain 'G' and resid 325 through 339 Processing helix chain 'G' and resid 343 through 345 No H-bonds generated for 'chain 'G' and resid 343 through 345' Processing helix chain 'G' and resid 356 through 368 Processing helix chain 'G' and resid 392 through 395 Processing helix chain 'G' and resid 401 through 403 No H-bonds generated for 'chain 'G' and resid 401 through 403' Processing helix chain 'G' and resid 422 through 434 removed outlier: 3.672A pdb=" N ARG G 434 " --> pdb=" O LYS G 430 " (cutoff:3.500A) Processing helix chain 'G' and resid 459 through 466 Processing helix chain 'G' and resid 469 through 475 Processing helix chain 'G' and resid 486 through 489 No H-bonds generated for 'chain 'G' and resid 486 through 489' Processing helix chain 'G' and resid 494 through 507 Processing helix chain 'G' and resid 509 through 511 No H-bonds generated for 'chain 'G' and resid 509 through 511' Processing helix chain 'G' and resid 528 through 534 Processing helix chain 'G' and resid 540 through 543 No H-bonds generated for 'chain 'G' and resid 540 through 543' Processing helix chain 'G' and resid 579 through 582 No H-bonds generated for 'chain 'G' and resid 579 through 582' Processing helix chain 'G' and resid 592 through 594 No H-bonds generated for 'chain 'G' and resid 592 through 594' Processing helix chain 'G' and resid 622 through 632 Processing helix chain 'G' and resid 642 through 652 Processing helix chain 'G' and resid 654 through 656 No H-bonds generated for 'chain 'G' and resid 654 through 656' Processing helix chain 'G' and resid 668 through 674 Processing helix chain 'G' and resid 702 through 705 No H-bonds generated for 'chain 'G' and resid 702 through 705' Processing helix chain 'G' and resid 708 through 715 Processing helix chain 'G' and resid 722 through 724 No H-bonds generated for 'chain 'G' and resid 722 through 724' Processing helix chain 'H' and resid 3 through 34 removed outlier: 3.852A pdb=" N VAL H 24 " --> pdb=" O ALA H 20 " (cutoff:3.500A) Processing helix chain 'H' and resid 49 through 59 removed outlier: 3.516A pdb=" N LEU H 59 " --> pdb=" O VAL H 55 " (cutoff:3.500A) Processing helix chain 'H' and resid 70 through 90 Proline residue: H 77 - end of helix removed outlier: 3.733A pdb=" N GLY H 87 " --> pdb=" O THR H 83 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N TRP H 88 " --> pdb=" O ALA H 84 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N VAL H 89 " --> pdb=" O LEU H 85 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N VAL H 90 " --> pdb=" O ILE H 86 " (cutoff:3.500A) Processing helix chain 'H' and resid 105 through 124 removed outlier: 3.623A pdb=" N SER H 114 " --> pdb=" O LEU H 110 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LEU H 115 " --> pdb=" O ALA H 111 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLY H 116 " --> pdb=" O ILE H 112 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N VAL H 117 " --> pdb=" O GLY H 113 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N PHE H 118 " --> pdb=" O SER H 114 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N GLY H 119 " --> pdb=" O LEU H 115 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N SER H 120 " --> pdb=" O GLY H 116 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLY H 124 " --> pdb=" O SER H 120 " (cutoff:3.500A) Processing helix chain 'H' and resid 132 through 158 removed outlier: 3.631A pdb=" N ILE H 137 " --> pdb=" O LEU H 133 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LEU H 148 " --> pdb=" O ILE H 144 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ILE H 149 " --> pdb=" O SER H 145 " (cutoff:3.500A) Processing helix chain 'H' and resid 166 through 174 removed outlier: 3.943A pdb=" N GLN H 173 " --> pdb=" O ILE H 169 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ARG H 174 " --> pdb=" O ILE H 170 " (cutoff:3.500A) Processing helix chain 'H' and resid 178 through 181 No H-bonds generated for 'chain 'H' and resid 178 through 181' Processing helix chain 'H' and resid 183 through 196 removed outlier: 3.523A pdb=" N LEU H 187 " --> pdb=" O LEU H 183 " (cutoff:3.500A) Processing helix chain 'H' and resid 204 through 211 removed outlier: 3.909A pdb=" N LEU H 211 " --> pdb=" O SER H 207 " (cutoff:3.500A) Processing helix chain 'H' and resid 222 through 246 removed outlier: 4.035A pdb=" N ILE H 236 " --> pdb=" O TYR H 232 " (cutoff:3.500A) Processing helix chain 'H' and resid 256 through 262 Processing helix chain 'H' and resid 268 through 299 Processing helix chain 'H' and resid 305 through 333 removed outlier: 5.360A pdb=" N LEU H 317 " --> pdb=" O TRP H 313 " (cutoff:3.500A) Proline residue: H 318 - end of helix removed outlier: 3.864A pdb=" N LEU H 325 " --> pdb=" O PHE H 321 " (cutoff:3.500A) Proline residue: H 328 - end of helix Processing helix chain 'I' and resid 70 through 79 Processing helix chain 'I' and resid 81 through 95 removed outlier: 3.743A pdb=" N GLN I 93 " --> pdb=" O VAL I 89 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE I 94 " --> pdb=" O VAL I 90 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N PHE I 95 " --> pdb=" O LEU I 91 " (cutoff:3.500A) Processing helix chain 'I' and resid 103 through 105 No H-bonds generated for 'chain 'I' and resid 103 through 105' Processing helix chain 'I' and resid 136 through 139 No H-bonds generated for 'chain 'I' and resid 136 through 139' Processing helix chain 'I' and resid 174 through 178 Processing helix chain 'I' and resid 197 through 199 No H-bonds generated for 'chain 'I' and resid 197 through 199' Processing helix chain 'I' and resid 204 through 228 removed outlier: 6.203A pdb=" N LEU I 216 " --> pdb=" O ASP I 212 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N GLU I 217 " --> pdb=" O LYS I 213 " (cutoff:3.500A) Proline residue: I 227 - end of helix Processing helix chain 'J' and resid 3 through 5 No H-bonds generated for 'chain 'J' and resid 3 through 5' Processing helix chain 'J' and resid 8 through 25 removed outlier: 3.616A pdb=" N THR J 12 " --> pdb=" O PHE J 8 " (cutoff:3.500A) Processing helix chain 'J' and resid 29 through 50 Processing helix chain 'J' and resid 53 through 75 removed outlier: 3.761A pdb=" N ILE J 64 " --> pdb=" O ILE J 60 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLY J 65 " --> pdb=" O MET J 61 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ALA J 68 " --> pdb=" O ILE J 64 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N VAL J 69 " --> pdb=" O GLY J 65 " (cutoff:3.500A) Processing helix chain 'J' and resid 87 through 110 removed outlier: 3.661A pdb=" N ILE J 91 " --> pdb=" O VAL J 87 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ARG J 92 " --> pdb=" O LYS J 88 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N ASP J 93 " --> pdb=" O SER J 89 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N LEU J 94 " --> pdb=" O ASN J 90 " (cutoff:3.500A) Proline residue: J 95 - end of helix Processing helix chain 'J' and resid 118 through 125 removed outlier: 3.806A pdb=" N LEU J 122 " --> pdb=" O LEU J 118 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA J 125 " --> pdb=" O LYS J 121 " (cutoff:3.500A) Processing helix chain 'J' and resid 146 through 155 Processing helix chain 'J' and resid 159 through 180 removed outlier: 4.441A pdb=" N ILE J 167 " --> pdb=" O LEU J 163 " (cutoff:3.500A) Proline residue: J 176 - end of helix Processing helix chain 'K' and resid 3 through 16 Processing helix chain 'K' and resid 23 through 47 Processing helix chain 'K' and resid 51 through 81 removed outlier: 3.576A pdb=" N VAL K 75 " --> pdb=" O LEU K 71 " (cutoff:3.500A) Processing helix chain 'L' and resid 4 through 55 Proline residue: L 12 - end of helix Proline residue: L 19 - end of helix removed outlier: 6.365A pdb=" N ARG L 24 " --> pdb=" O LEU L 20 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N GLN L 25 " --> pdb=" O PHE L 21 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N TYR L 28 " --> pdb=" O ARG L 24 " (cutoff:3.500A) removed outlier: 9.246A pdb=" N VAL L 29 " --> pdb=" O GLN L 25 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N PHE L 30 " --> pdb=" O LEU L 26 " (cutoff:3.500A) Processing helix chain 'L' and resid 83 through 106 removed outlier: 3.644A pdb=" N ILE L 104 " --> pdb=" O HIS L 100 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N GLY L 105 " --> pdb=" O ILE L 101 " (cutoff:3.500A) Processing helix chain 'L' and resid 113 through 132 Processing helix chain 'L' and resid 136 through 154 Processing helix chain 'L' and resid 161 through 191 removed outlier: 3.878A pdb=" N GLY L 177 " --> pdb=" O MET L 173 " (cutoff:3.500A) Processing helix chain 'L' and resid 197 through 206 removed outlier: 3.505A pdb=" N ALA L 202 " --> pdb=" O SER L 198 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N TYR L 205 " --> pdb=" O PHE L 201 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N LEU L 206 " --> pdb=" O ALA L 202 " (cutoff:3.500A) Processing helix chain 'L' and resid 209 through 226 Processing helix chain 'L' and resid 230 through 232 No H-bonds generated for 'chain 'L' and resid 230 through 232' Processing helix chain 'L' and resid 234 through 241 removed outlier: 3.979A pdb=" N LEU L 238 " --> pdb=" O ASN L 234 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N MET L 240 " --> pdb=" O LEU L 236 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N GLU L 241 " --> pdb=" O THR L 237 " (cutoff:3.500A) Processing helix chain 'L' and resid 244 through 253 removed outlier: 3.706A pdb=" N HIS L 251 " --> pdb=" O SER L 247 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ALA L 252 " --> pdb=" O SER L 248 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA L 253 " --> pdb=" O LEU L 249 " (cutoff:3.500A) Processing helix chain 'L' and resid 255 through 272 removed outlier: 4.313A pdb=" N GLY L 259 " --> pdb=" O VAL L 256 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ASN L 268 " --> pdb=" O ARG L 265 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N GLU L 271 " --> pdb=" O ASN L 268 " (cutoff:3.500A) Processing helix chain 'L' and resid 274 through 297 removed outlier: 3.563A pdb=" N GLY L 292 " --> pdb=" O THR L 288 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N CYS L 297 " --> pdb=" O LEU L 293 " (cutoff:3.500A) Processing helix chain 'L' and resid 301 through 321 Processing helix chain 'L' and resid 325 through 352 removed outlier: 3.689A pdb=" N PHE L 337 " --> pdb=" O LEU L 333 " (cutoff:3.500A) Processing helix chain 'L' and resid 360 through 362 No H-bonds generated for 'chain 'L' and resid 360 through 362' Processing helix chain 'L' and resid 371 through 382 Processing helix chain 'L' and resid 391 through 405 removed outlier: 4.648A pdb=" N ILE L 398 " --> pdb=" O TYR L 394 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N ILE L 399 " --> pdb=" O THR L 395 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE L 400 " --> pdb=" O LYS L 396 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N TYR L 404 " --> pdb=" O ILE L 400 " (cutoff:3.500A) Processing helix chain 'L' and resid 410 through 437 removed outlier: 3.590A pdb=" N VAL L 413 " --> pdb=" O SER L 410 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N CYS L 426 " --> pdb=" O VAL L 423 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N SER L 429 " --> pdb=" O CYS L 426 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N LYS L 431 " --> pdb=" O TYR L 428 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU L 435 " --> pdb=" O ILE L 432 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THR L 436 " --> pdb=" O LEU L 433 " (cutoff:3.500A) Processing helix chain 'L' and resid 445 through 449 Processing helix chain 'L' and resid 456 through 480 Proline residue: L 461 - end of helix removed outlier: 6.509A pdb=" N GLY L 473 " --> pdb=" O ALA L 469 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N TRP L 474 " --> pdb=" O MET L 470 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N ASP L 478 " --> pdb=" O TRP L 474 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N ILE L 479 " --> pdb=" O ILE L 475 " (cutoff:3.500A) Processing helix chain 'L' and resid 494 through 496 No H-bonds generated for 'chain 'L' and resid 494 through 496' Processing helix chain 'L' and resid 499 through 505 removed outlier: 3.551A pdb=" N PHE L 504 " --> pdb=" O PHE L 500 " (cutoff:3.500A) Processing helix chain 'L' and resid 508 through 531 Proline residue: L 514 - end of helix removed outlier: 3.866A pdb=" N ILE L 523 " --> pdb=" O ILE L 519 " (cutoff:3.500A) Processing helix chain 'L' and resid 533 through 536 Processing helix chain 'L' and resid 541 through 551 removed outlier: 3.694A pdb=" N VAL L 546 " --> pdb=" O TYR L 542 " (cutoff:3.500A) Processing helix chain 'L' and resid 556 through 563 removed outlier: 3.586A pdb=" N ASN L 561 " --> pdb=" O ASP L 557 " (cutoff:3.500A) Processing helix chain 'L' and resid 565 through 578 Processing helix chain 'L' and resid 583 through 586 No H-bonds generated for 'chain 'L' and resid 583 through 586' Processing helix chain 'L' and resid 589 through 604 Processing helix chain 'L' and resid 613 through 637 removed outlier: 3.538A pdb=" N ASN L 617 " --> pdb=" O SER L 613 " (cutoff:3.500A) Processing helix chain 'L' and resid 640 through 654 Proline residue: L 644 - end of helix Processing helix chain 'M' and resid 3 through 20 Processing helix chain 'M' and resid 25 through 44 Processing helix chain 'M' and resid 83 through 103 removed outlier: 3.573A pdb=" N PHE M 88 " --> pdb=" O LEU M 84 " (cutoff:3.500A) Proline residue: M 97 - end of helix removed outlier: 4.034A pdb=" N ASN M 103 " --> pdb=" O THR M 99 " (cutoff:3.500A) Processing helix chain 'M' and resid 111 through 129 Processing helix chain 'M' and resid 134 through 141 Processing helix chain 'M' and resid 144 through 155 Processing helix chain 'M' and resid 160 through 189 removed outlier: 4.083A pdb=" N THR M 171 " --> pdb=" O VAL M 167 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N PHE M 177 " --> pdb=" O SER M 173 " (cutoff:3.500A) Processing helix chain 'M' and resid 204 through 221 removed outlier: 4.042A pdb=" N ILE M 209 " --> pdb=" O ASP M 205 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LEU M 212 " --> pdb=" O THR M 208 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLY M 213 " --> pdb=" O ILE M 209 " (cutoff:3.500A) Processing helix chain 'M' and resid 229 through 237 removed outlier: 4.270A pdb=" N VAL M 233 " --> pdb=" O VAL M 229 " (cutoff:3.500A) Processing helix chain 'M' and resid 240 through 261 removed outlier: 4.916A pdb=" N LEU M 251 " --> pdb=" O ALA M 247 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N LYS M 252 " --> pdb=" O GLY M 248 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ALA M 254 " --> pdb=" O ILE M 250 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LEU M 255 " --> pdb=" O LEU M 251 " (cutoff:3.500A) Processing helix chain 'M' and resid 267 through 294 Proline residue: M 275 - end of helix removed outlier: 3.622A pdb=" N THR M 288 " --> pdb=" O THR M 284 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ARG M 294 " --> pdb=" O LEU M 290 " (cutoff:3.500A) Processing helix chain 'M' and resid 298 through 317 removed outlier: 3.820A pdb=" N ILE M 307 " --> pdb=" O ALA M 303 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N SER M 308 " --> pdb=" O TYR M 304 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N HIS M 309 " --> pdb=" O SER M 305 " (cutoff:3.500A) Processing helix chain 'M' and resid 322 through 347 Proline residue: M 340 - end of helix Processing helix chain 'M' and resid 350 through 354 Processing helix chain 'M' and resid 359 through 361 No H-bonds generated for 'chain 'M' and resid 359 through 361' Processing helix chain 'M' and resid 370 through 383 Processing helix chain 'M' and resid 390 through 405 Processing helix chain 'M' and resid 407 through 432 removed outlier: 4.045A pdb=" N CYS M 414 " --> pdb=" O GLY M 410 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N ILE M 415 " --> pdb=" O GLY M 411 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N SER M 416 " --> pdb=" O ILE M 412 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N VAL M 417 " --> pdb=" O SER M 413 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N LEU M 418 " --> pdb=" O CYS M 414 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ALA M 421 " --> pdb=" O VAL M 417 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N LEU M 427 " --> pdb=" O TYR M 423 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LYS M 430 " --> pdb=" O LYS M 426 " (cutoff:3.500A) Processing helix chain 'M' and resid 448 through 466 removed outlier: 3.594A pdb=" N THR M 461 " --> pdb=" O LEU M 457 " (cutoff:3.500A) Processing helix chain 'M' and resid 468 through 474 removed outlier: 4.396A pdb=" N ASN M 473 " --> pdb=" O ILE M 470 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU M 474 " --> pdb=" O MET M 471 " (cutoff:3.500A) Processing helix chain 'M' and resid 478 through 481 No H-bonds generated for 'chain 'M' and resid 478 through 481' Processing helix chain 'N' and resid 3 through 14 removed outlier: 3.898A pdb=" N THR N 11 " --> pdb=" O ILE N 7 " (cutoff:3.500A) Processing helix chain 'N' and resid 18 through 38 removed outlier: 3.839A pdb=" N ASN N 21 " --> pdb=" O LEU N 18 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N ARG N 22 " --> pdb=" O SER N 19 " (cutoff:3.500A) Processing helix chain 'N' and resid 40 through 49 removed outlier: 3.550A pdb=" N TYR N 43 " --> pdb=" O SER N 40 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU N 47 " --> pdb=" O LEU N 44 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ASN N 48 " --> pdb=" O LEU N 45 " (cutoff:3.500A) Processing helix chain 'N' and resid 63 through 84 removed outlier: 3.568A pdb=" N TYR N 83 " --> pdb=" O ILE N 79 " (cutoff:3.500A) Processing helix chain 'N' and resid 91 through 96 Processing helix chain 'N' and resid 103 through 118 Processing helix chain 'N' and resid 123 through 142 removed outlier: 3.634A pdb=" N SER N 136 " --> pdb=" O LEU N 132 " (cutoff:3.500A) Processing helix chain 'N' and resid 148 through 179 Processing helix chain 'N' and resid 184 through 186 No H-bonds generated for 'chain 'N' and resid 184 through 186' Processing helix chain 'N' and resid 189 through 194 Processing helix chain 'N' and resid 198 through 212 removed outlier: 3.990A pdb=" N LYS N 211 " --> pdb=" O GLY N 207 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ILE N 212 " --> pdb=" O LEU N 208 " (cutoff:3.500A) Processing helix chain 'N' and resid 219 through 227 Processing helix chain 'N' and resid 230 through 236 removed outlier: 4.503A pdb=" N TYR N 235 " --> pdb=" O LEU N 231 " (cutoff:3.500A) Processing helix chain 'N' and resid 239 through 250 Processing helix chain 'N' and resid 258 through 273 Processing helix chain 'N' and resid 281 through 300 removed outlier: 4.050A pdb=" N LEU N 299 " --> pdb=" O TYR N 295 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LEU N 300 " --> pdb=" O MET N 296 " (cutoff:3.500A) Processing helix chain 'N' and resid 306 through 333 removed outlier: 3.913A pdb=" N ILE N 331 " --> pdb=" O ILE N 327 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N TYR N 332 " --> pdb=" O ILE N 328 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N TYR N 333 " --> pdb=" O PHE N 329 " (cutoff:3.500A) Processing helix chain 'N' and resid 347 through 350 Processing helix chain 'N' and resid 353 through 356 No H-bonds generated for 'chain 'N' and resid 353 through 356' Processing helix chain 'N' and resid 358 through 372 Processing helix chain 'N' and resid 378 through 392 Processing helix chain 'N' and resid 397 through 420 removed outlier: 3.549A pdb=" N ALA N 410 " --> pdb=" O SER N 406 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LEU N 411 " --> pdb=" O LEU N 407 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N TYR N 412 " --> pdb=" O ILE N 408 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N LEU N 416 " --> pdb=" O TYR N 412 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU N 417 " --> pdb=" O TYR N 413 " (cutoff:3.500A) Processing helix chain 'N' and resid 437 through 467 removed outlier: 5.580A pdb=" N PHE N 454 " --> pdb=" O ILE N 450 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ILE N 455 " --> pdb=" O THR N 451 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N TYR N 456 " --> pdb=" O PHE N 452 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ASN N 457 " --> pdb=" O GLY N 453 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N SER N 458 " --> pdb=" O PHE N 454 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N LEU N 459 " --> pdb=" O ILE N 455 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL N 466 " --> pdb=" O ASP N 462 " (cutoff:3.500A) Processing helix chain 'O' and resid 28 through 33 Processing helix chain 'O' and resid 37 through 60 Proline residue: O 51 - end of helix Processing helix chain 'O' and resid 72 through 99 Processing helix chain 'O' and resid 105 through 120 Processing helix chain 'O' and resid 133 through 143 Processing helix chain 'O' and resid 146 through 149 Processing helix chain 'P' and resid 64 through 76 removed outlier: 4.039A pdb=" N TYR P 68 " --> pdb=" O PHE P 64 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N HIS P 76 " --> pdb=" O LYS P 72 " (cutoff:3.500A) Processing helix chain 'P' and resid 91 through 96 removed outlier: 3.833A pdb=" N VAL P 95 " --> pdb=" O HIS P 92 " (cutoff:3.500A) Processing helix chain 'P' and resid 112 through 119 Processing helix chain 'P' and resid 140 through 144 Processing helix chain 'P' and resid 146 through 157 Processing helix chain 'P' and resid 178 through 193 removed outlier: 3.795A pdb=" N LYS P 191 " --> pdb=" O GLU P 187 " (cutoff:3.500A) Processing helix chain 'P' and resid 214 through 219 Processing helix chain 'P' and resid 238 through 250 removed outlier: 3.527A pdb=" N PHE P 250 " --> pdb=" O GLU P 246 " (cutoff:3.500A) Processing helix chain 'P' and resid 252 through 254 No H-bonds generated for 'chain 'P' and resid 252 through 254' Processing helix chain 'P' and resid 269 through 280 Processing helix chain 'P' and resid 291 through 301 removed outlier: 3.719A pdb=" N ALA P 296 " --> pdb=" O ALA P 292 " (cutoff:3.500A) Processing helix chain 'P' and resid 311 through 318 removed outlier: 4.430A pdb=" N PHE P 318 " --> pdb=" O VAL P 314 " (cutoff:3.500A) Processing helix chain 'P' and resid 331 through 333 No H-bonds generated for 'chain 'P' and resid 331 through 333' Processing helix chain 'P' and resid 340 through 351 removed outlier: 4.685A pdb=" N PHE P 345 " --> pdb=" O PRO P 341 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N LYS P 346 " --> pdb=" O ASP P 342 " (cutoff:3.500A) Proline residue: P 350 - end of helix Processing helix chain 'P' and resid 364 through 369 removed outlier: 4.064A pdb=" N THR P 369 " --> pdb=" O ASN P 365 " (cutoff:3.500A) Processing helix chain 'Q' and resid 42 through 46 Processing helix chain 'Q' and resid 51 through 54 No H-bonds generated for 'chain 'Q' and resid 51 through 54' Processing helix chain 'Q' and resid 86 through 88 No H-bonds generated for 'chain 'Q' and resid 86 through 88' Processing helix chain 'Q' and resid 115 through 125 Processing helix chain 'Q' and resid 145 through 148 Processing helix chain 'R' and resid 33 through 36 No H-bonds generated for 'chain 'R' and resid 33 through 36' Processing helix chain 'R' and resid 53 through 63 removed outlier: 6.986A pdb=" N VAL R 62 " --> pdb=" O LYS R 58 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N ARG R 63 " --> pdb=" O ASN R 59 " (cutoff:3.500A) Processing helix chain 'R' and resid 78 through 81 No H-bonds generated for 'chain 'R' and resid 78 through 81' Processing helix chain 'S' and resid 17 through 36 removed outlier: 3.779A pdb=" N ALA S 20 " --> pdb=" O SER S 17 " (cutoff:3.500A) Proline residue: S 21 - end of helix removed outlier: 4.393A pdb=" N GLN S 29 " --> pdb=" O VAL S 26 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N ILE S 30 " --> pdb=" O LYS S 27 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N GLY S 31 " --> pdb=" O ASN S 28 " (cutoff:3.500A) Processing helix chain 'S' and resid 73 through 85 Processing helix chain 'T' and resid 33 through 42 removed outlier: 3.657A pdb=" N GLU T 41 " --> pdb=" O ALA T 37 " (cutoff:3.500A) Processing helix chain 'T' and resid 68 through 79 removed outlier: 3.775A pdb=" N VAL T 73 " --> pdb=" O THR T 69 " (cutoff:3.500A) Processing helix chain 'T' and resid 86 through 89 No H-bonds generated for 'chain 'T' and resid 86 through 89' Processing helix chain 'T' and resid 95 through 104 removed outlier: 3.509A pdb=" N VAL T 99 " --> pdb=" O VAL T 95 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ALA T 104 " --> pdb=" O GLU T 100 " (cutoff:3.500A) Processing helix chain 'U' and resid 52 through 64 Processing helix chain 'U' and resid 91 through 103 Processing helix chain 'U' and resid 109 through 112 No H-bonds generated for 'chain 'U' and resid 109 through 112' Processing helix chain 'U' and resid 118 through 127 Processing helix chain 'V' and resid 42 through 60 Processing helix chain 'V' and resid 66 through 84 Processing helix chain 'V' and resid 88 through 94 Processing helix chain 'V' and resid 100 through 119 removed outlier: 3.820A pdb=" N ILE V 105 " --> pdb=" O GLU V 101 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLU V 119 " --> pdb=" O LYS V 115 " (cutoff:3.500A) Processing helix chain 'W' and resid 18 through 42 removed outlier: 3.625A pdb=" N LYS W 23 " --> pdb=" O GLN W 19 " (cutoff:3.500A) Proline residue: W 37 - end of helix Processing helix chain 'W' and resid 49 through 61 Processing helix chain 'W' and resid 69 through 87 Processing helix chain 'W' and resid 93 through 98 removed outlier: 3.840A pdb=" N LYS W 98 " --> pdb=" O ALA W 94 " (cutoff:3.500A) Processing helix chain 'W' and resid 115 through 120 Processing helix chain 'X' and resid 32 through 37 Processing helix chain 'X' and resid 39 through 60 removed outlier: 3.589A pdb=" N LYS X 45 " --> pdb=" O PHE X 41 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LYS X 47 " --> pdb=" O GLY X 43 " (cutoff:3.500A) Proline residue: X 48 - end of helix Processing helix chain 'X' and resid 64 through 67 No H-bonds generated for 'chain 'X' and resid 64 through 67' Processing helix chain 'X' and resid 69 through 89 Processing helix chain 'X' and resid 91 through 103 Processing helix chain 'X' and resid 108 through 110 No H-bonds generated for 'chain 'X' and resid 108 through 110' Processing helix chain 'X' and resid 112 through 125 removed outlier: 3.823A pdb=" N LEU X 117 " --> pdb=" O LYS X 113 " (cutoff:3.500A) Processing helix chain 'X' and resid 142 through 144 No H-bonds generated for 'chain 'X' and resid 142 through 144' Processing helix chain 'X' and resid 157 through 168 Processing helix chain 'Y' and resid 25 through 50 Processing helix chain 'Y' and resid 59 through 62 No H-bonds generated for 'chain 'Y' and resid 59 through 62' Processing helix chain 'Y' and resid 67 through 88 Processing helix chain 'Y' and resid 95 through 111 removed outlier: 3.749A pdb=" N ARG Y 111 " --> pdb=" O VAL Y 107 " (cutoff:3.500A) Processing helix chain 'Y' and resid 115 through 134 Processing helix chain 'Y' and resid 172 through 179 Processing helix chain 'Y' and resid 190 through 193 No H-bonds generated for 'chain 'Y' and resid 190 through 193' Processing helix chain 'Z' and resid 30 through 95 Proline residue: Z 71 - end of helix removed outlier: 3.575A pdb=" N LEU Z 89 " --> pdb=" O SER Z 85 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLU Z 94 " --> pdb=" O GLU Z 90 " (cutoff:3.500A) Processing helix chain 'a' and resid 5 through 33 Proline residue: a 10 - end of helix Processing helix chain 'a' and resid 44 through 56 Processing helix chain 'b' and resid 12 through 22 Processing helix chain 'b' and resid 24 through 42 removed outlier: 4.038A pdb=" N ALA b 29 " --> pdb=" O HIS b 25 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLY b 36 " --> pdb=" O ILE b 32 " (cutoff:3.500A) Proline residue: b 37 - end of helix Processing helix chain 'b' and resid 44 through 50 Processing helix chain 'c' and resid 20 through 25 Processing helix chain 'c' and resid 49 through 51 No H-bonds generated for 'chain 'c' and resid 49 through 51' Processing helix chain 'c' and resid 53 through 57 removed outlier: 3.550A pdb=" N VAL c 57 " --> pdb=" O GLU c 54 " (cutoff:3.500A) Processing helix chain 'c' and resid 64 through 67 No H-bonds generated for 'chain 'c' and resid 64 through 67' Processing helix chain 'c' and resid 74 through 76 No H-bonds generated for 'chain 'c' and resid 74 through 76' Processing helix chain 'c' and resid 91 through 99 Processing helix chain 'c' and resid 112 through 122 removed outlier: 3.660A pdb=" N ILE c 121 " --> pdb=" O ALA c 117 " (cutoff:3.500A) Processing helix chain 'c' and resid 128 through 133 Processing helix chain 'c' and resid 137 through 143 removed outlier: 4.457A pdb=" N GLY c 142 " --> pdb=" O ASP c 138 " (cutoff:3.500A) Processing helix chain 'd' and resid 3 through 24 Processing helix chain 'd' and resid 34 through 67 removed outlier: 3.690A pdb=" N LYS d 65 " --> pdb=" O LEU d 61 " (cutoff:3.500A) Processing helix chain 'e' and resid 16 through 28 Processing helix chain 'e' and resid 34 through 49 Proline residue: e 39 - end of helix removed outlier: 3.507A pdb=" N HIS e 49 " --> pdb=" O GLU e 46 " (cutoff:3.500A) Processing helix chain 'e' and resid 51 through 63 Processing helix chain 'f' and resid 5 through 14 Processing helix chain 'f' and resid 17 through 26 Processing helix chain 'f' and resid 70 through 72 No H-bonds generated for 'chain 'f' and resid 70 through 72' Processing helix chain 'f' and resid 77 through 80 No H-bonds generated for 'chain 'f' and resid 77 through 80' Processing helix chain 'g' and resid 53 through 64 removed outlier: 4.987A pdb=" N GLN g 61 " --> pdb=" O LEU g 57 " (cutoff:3.500A) Processing helix chain 'g' and resid 69 through 72 No H-bonds generated for 'chain 'g' and resid 69 through 72' Processing helix chain 'g' and resid 85 through 95 Processing helix chain 'g' and resid 105 through 108 No H-bonds generated for 'chain 'g' and resid 105 through 108' Processing helix chain 'g' and resid 113 through 136 removed outlier: 3.516A pdb=" N LEU g 118 " --> pdb=" O LYS g 114 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N LEU g 125 " --> pdb=" O ASP g 121 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU g 126 " --> pdb=" O ASN g 122 " (cutoff:3.500A) Processing helix chain 'g' and resid 165 through 171 removed outlier: 3.606A pdb=" N PHE g 170 " --> pdb=" O ASN g 166 " (cutoff:3.500A) Processing helix chain 'g' and resid 173 through 189 removed outlier: 3.972A pdb=" N ARG g 188 " --> pdb=" O VAL g 184 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N GLU g 189 " --> pdb=" O TYR g 185 " (cutoff:3.500A) Processing helix chain 'g' and resid 191 through 206 Processing helix chain 'g' and resid 208 through 210 No H-bonds generated for 'chain 'g' and resid 208 through 210' Processing helix chain 'g' and resid 218 through 228 Processing helix chain 'h' and resid 49 through 74 Processing helix chain 'h' and resid 79 through 83 removed outlier: 4.125A pdb=" N PHE h 83 " --> pdb=" O TRP h 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 79 through 83' Processing helix chain 'h' and resid 89 through 116 Processing helix chain 'h' and resid 123 through 126 No H-bonds generated for 'chain 'h' and resid 123 through 126' Processing helix chain 'i' and resid 26 through 48 Processing helix chain 'i' and resid 61 through 77 Processing helix chain 'j' and resid 21 through 50 Proline residue: j 47 - end of helix Processing helix chain 'k' and resid 10 through 17 removed outlier: 5.280A pdb=" N TRP k 15 " --> pdb=" O ARG k 11 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N ARG k 16 " --> pdb=" O ARG k 12 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N TYR k 17 " --> pdb=" O GLU k 13 " (cutoff:3.500A) Processing helix chain 'k' and resid 34 through 46 Processing helix chain 'l' and resid 28 through 31 No H-bonds generated for 'chain 'l' and resid 28 through 31' Processing helix chain 'l' and resid 34 through 36 No H-bonds generated for 'chain 'l' and resid 34 through 36' Processing helix chain 'l' and resid 90 through 114 removed outlier: 3.720A pdb=" N THR l 112 " --> pdb=" O SER l 108 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N TYR l 113 " --> pdb=" O TYR l 109 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N PHE l 114 " --> pdb=" O VAL l 110 " (cutoff:3.500A) Processing helix chain 'l' and resid 141 through 144 No H-bonds generated for 'chain 'l' and resid 141 through 144' Processing helix chain 'm' and resid 31 through 40 Processing helix chain 'm' and resid 42 through 44 No H-bonds generated for 'chain 'm' and resid 42 through 44' Processing helix chain 'm' and resid 52 through 59 Processing helix chain 'm' and resid 62 through 73 Processing helix chain 'n' and resid 9 through 29 Processing helix chain 'n' and resid 33 through 49 Processing helix chain 'n' and resid 56 through 72 Processing helix chain 'o' and resid 10 through 16 Processing helix chain 'o' and resid 27 through 39 removed outlier: 4.206A pdb=" N VAL o 31 " --> pdb=" O ALA o 28 " (cutoff:3.500A) Proline residue: o 32 - end of helix Processing helix chain 'o' and resid 48 through 83 Processing helix chain 'p' and resid 20 through 62 Proline residue: p 57 - end of helix removed outlier: 4.927A pdb=" N PHE p 60 " --> pdb=" O GLY p 56 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N GLU p 61 " --> pdb=" O PRO p 57 " (cutoff:3.500A) Processing helix chain 'p' and resid 64 through 73 Processing helix chain 'p' and resid 83 through 86 No H-bonds generated for 'chain 'p' and resid 83 through 86' Processing sheet with id= A, first strand: chain 'B' and resid 116 through 120 removed outlier: 6.851A pdb=" N TRP B 143 " --> pdb=" O MET B 117 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N VAL B 119 " --> pdb=" O TRP B 143 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N ILE B 145 " --> pdb=" O VAL B 119 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL B 175 " --> pdb=" O SER B 146 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'C' and resid 122 through 130 removed outlier: 6.700A pdb=" N ASN C 143 " --> pdb=" O ILE C 124 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ILE C 126 " --> pdb=" O VAL C 141 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N VAL C 141 " --> pdb=" O ILE C 126 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ALA C 128 " --> pdb=" O GLU C 139 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N GLU C 139 " --> pdb=" O ALA C 128 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N LEU C 96 " --> pdb=" O ARG C 152 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N TYR C 158 " --> pdb=" O VAL C 100 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 220 through 225 Processing sheet with id= D, first strand: chain 'D' and resid 83 through 86 removed outlier: 3.568A pdb=" N ARG D 111 " --> pdb=" O GLU D 103 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N SER D 105 " --> pdb=" O ILE D 109 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N ILE D 109 " --> pdb=" O SER D 105 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'D' and resid 397 through 405 removed outlier: 3.500A pdb=" N THR D 401 " --> pdb=" O VAL D 412 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS D 424 " --> pdb=" O VAL D 415 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'E' and resid 122 through 127 Processing sheet with id= G, first strand: chain 'E' and resid 178 through 180 Processing sheet with id= H, first strand: chain 'F' and resid 241 through 246 removed outlier: 3.539A pdb=" N THR F 243 " --> pdb=" O TYR F 114 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ALA F 155 " --> pdb=" O LEU F 115 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N VAL F 117 " --> pdb=" O ALA F 155 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N TYR F 157 " --> pdb=" O VAL F 117 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ASP F 196 " --> pdb=" O ALA F 156 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N ILE F 158 " --> pdb=" O ASP F 196 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N TYR F 198 " --> pdb=" O ILE F 158 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N ILE F 160 " --> pdb=" O TYR F 198 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N HIS F 200 " --> pdb=" O ILE F 160 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'F' and resid 288 through 293 removed outlier: 3.548A pdb=" N GLY F 318 " --> pdb=" O ILE F 359 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'G' and resid 39 through 41 Processing sheet with id= K, first strand: chain 'G' and resid 176 through 178 Processing sheet with id= L, first strand: chain 'G' and resid 203 through 205 Processing sheet with id= M, first strand: chain 'G' and resid 253 through 258 removed outlier: 6.571A pdb=" N LYS G 273 " --> pdb=" O VAL G 277 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N VAL G 277 " --> pdb=" O LYS G 273 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'G' and resid 312 through 315 Processing sheet with id= O, first strand: chain 'G' and resid 374 through 376 removed outlier: 7.896A pdb=" N THR G 375 " --> pdb=" O PHE G 346 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N ALA G 348 " --> pdb=" O THR G 375 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N MET G 549 " --> pdb=" O LYS G 347 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N VAL G 349 " --> pdb=" O MET G 549 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N TRP G 551 " --> pdb=" O VAL G 349 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N PHE G 568 " --> pdb=" O VAL G 550 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N LEU G 552 " --> pdb=" O PHE G 568 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N VAL G 570 " --> pdb=" O LEU G 552 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N VAL G 585 " --> pdb=" O TYR G 571 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N GLY G 573 " --> pdb=" O VAL G 585 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N LEU G 587 " --> pdb=" O GLY G 573 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'G' and resid 438 through 442 Processing sheet with id= Q, first strand: chain 'G' and resid 598 through 600 Processing sheet with id= R, first strand: chain 'I' and resid 118 through 120 Processing sheet with id= S, first strand: chain 'I' and resid 145 through 151 removed outlier: 6.294A pdb=" N GLU I 150 " --> pdb=" O THR I 159 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N THR I 159 " --> pdb=" O GLU I 150 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'L' and resid 60 through 63 removed outlier: 4.336A pdb=" N ILE L 60 " --> pdb=" O ILE L 81 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'L' and resid 66 through 69 removed outlier: 6.873A pdb=" N ILE L 75 " --> pdb=" O TYR L 67 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'M' and resid 57 through 59 Processing sheet with id= W, first strand: chain 'N' and resid 52 through 54 Processing sheet with id= X, first strand: chain 'P' and resid 31 through 33 Processing sheet with id= Y, first strand: chain 'P' and resid 258 through 261 removed outlier: 6.618A pdb=" N ILE P 199 " --> pdb=" O PHE P 259 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N LEU P 261 " --> pdb=" O ILE P 199 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ARG P 201 " --> pdb=" O LEU P 261 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N THR P 79 " --> pdb=" O ALA P 56 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N VAL P 58 " --> pdb=" O THR P 79 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N VAL P 81 " --> pdb=" O VAL P 58 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'Q' and resid 128 through 132 removed outlier: 4.414A pdb=" N GLN Q 62 " --> pdb=" O GLN Q 132 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'R' and resid 20 through 22 Processing sheet with id= AB, first strand: chain 'R' and resid 94 through 97 Processing sheet with id= AC, first strand: chain 'S' and resid 42 through 46 removed outlier: 6.677A pdb=" N ILE S 8 " --> pdb=" O LEU S 43 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N ARG S 45 " --> pdb=" O ILE S 8 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N PHE S 10 " --> pdb=" O ARG S 45 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'c' and resid 163 through 165 removed outlier: 3.967A pdb=" N LYS c 163 " --> pdb=" O HIS c 182 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N THR c 180 " --> pdb=" O ILE c 165 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'f' and resid 59 through 62 removed outlier: 6.361A pdb=" N GLU f 47 " --> pdb=" O LEU f 35 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N LEU f 35 " --> pdb=" O GLU f 47 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'g' and resid 140 through 143 removed outlier: 3.696A pdb=" N VAL g 142 " --> pdb=" O THR g 151 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N THR g 151 " --> pdb=" O VAL g 142 " (cutoff:3.500A) 2730 hydrogen bonds defined for protein. 7704 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 22.79 Time building geometry restraints manager: 22.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.40: 27340 1.40 - 1.62: 39595 1.62 - 1.85: 557 1.85 - 2.07: 1 2.07 - 2.30: 80 Bond restraints: 67573 Sorted by residual: bond pdb=" OB3 CDL O 401 " pdb=" PB2 CDL O 401 " ideal model delta sigma weight residual 1.529 1.444 0.085 1.00e-02 1.00e+04 7.31e+01 bond pdb=" C2 FMN F 501 " pdb=" O2 FMN F 501 " ideal model delta sigma weight residual 1.230 1.400 -0.170 2.00e-02 2.50e+03 7.23e+01 bond pdb=" C4 FMN F 501 " pdb=" O4 FMN F 501 " ideal model delta sigma weight residual 1.230 1.395 -0.165 2.00e-02 2.50e+03 6.82e+01 bond pdb=" CB7 CDL M 501 " pdb=" OB8 CDL M 501 " ideal model delta sigma weight residual 1.334 1.423 -0.089 1.10e-02 8.26e+03 6.56e+01 bond pdb=" OA3 CDL M 501 " pdb=" PA1 CDL M 501 " ideal model delta sigma weight residual 1.529 1.451 0.078 1.00e-02 1.00e+04 6.13e+01 ... (remaining 67568 not shown) Histogram of bond angle deviations from ideal: 73.14 - 88.72: 78 88.72 - 104.31: 1190 104.31 - 119.89: 59287 119.89 - 135.47: 30986 135.47 - 151.06: 2 Bond angle restraints: 91543 Sorted by residual: angle pdb=" C5 PLC H 601 " pdb=" N PLC H 601 " pdb=" C6 PLC H 601 " ideal model delta sigma weight residual 111.23 151.06 -39.83 3.00e+00 1.11e-01 1.76e+02 angle pdb=" C7 PLC H 601 " pdb=" N PLC H 601 " pdb=" C8 PLC H 601 " ideal model delta sigma weight residual 108.25 146.20 -37.95 3.00e+00 1.11e-01 1.60e+02 angle pdb=" O12 3PE H 602 " pdb=" P 3PE H 602 " pdb=" O14 3PE H 602 " ideal model delta sigma weight residual 123.79 100.16 23.63 3.00e+00 1.11e-01 6.20e+01 angle pdb=" O12 3PE Y4203 " pdb=" P 3PE Y4203 " pdb=" O14 3PE Y4203 " ideal model delta sigma weight residual 123.79 100.55 23.24 3.00e+00 1.11e-01 6.00e+01 angle pdb=" O12 3PE d4601 " pdb=" P 3PE d4601 " pdb=" O14 3PE d4601 " ideal model delta sigma weight residual 123.79 100.60 23.19 3.00e+00 1.11e-01 5.97e+01 ... (remaining 91538 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.95: 38873 30.95 - 61.89: 1124 61.89 - 92.84: 109 92.84 - 123.79: 7 123.79 - 154.73: 4 Dihedral angle restraints: 40117 sinusoidal: 16453 harmonic: 23664 Sorted by residual: dihedral pdb=" C10 FMN F 501 " pdb=" C1' FMN F 501 " pdb=" N10 FMN F 501 " pdb=" C2' FMN F 501 " ideal model delta sinusoidal sigma weight residual 257.59 102.86 154.73 1 2.00e+01 2.50e-03 4.57e+01 dihedral pdb=" CA LYS U 73 " pdb=" C LYS U 73 " pdb=" N ASN U 74 " pdb=" CA ASN U 74 " ideal model delta harmonic sigma weight residual 180.00 153.43 26.57 0 5.00e+00 4.00e-02 2.82e+01 dihedral pdb=" CA VAL Y 155 " pdb=" C VAL Y 155 " pdb=" N GLN Y 156 " pdb=" CA GLN Y 156 " ideal model delta harmonic sigma weight residual -180.00 -153.83 -26.17 0 5.00e+00 4.00e-02 2.74e+01 ... (remaining 40114 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.245: 10121 4.245 - 8.490: 28 8.490 - 12.735: 0 12.735 - 16.980: 0 16.980 - 21.224: 8 Chirality restraints: 10157 Sorted by residual: chirality pdb="FE4 SF4 F 502 " pdb=" S1 SF4 F 502 " pdb=" S2 SF4 F 502 " pdb=" S3 SF4 F 502 " both_signs ideal model delta sigma weight residual False 10.55 -10.67 21.22 2.00e-01 2.50e+01 1.13e+04 chirality pdb="FE1 SF4 B 301 " pdb=" S2 SF4 B 301 " pdb=" S3 SF4 B 301 " pdb=" S4 SF4 B 301 " both_signs ideal model delta sigma weight residual False -10.55 10.60 -21.16 2.00e-01 2.50e+01 1.12e+04 chirality pdb="FE2 SF4 B 301 " pdb=" S1 SF4 B 301 " pdb=" S3 SF4 B 301 " pdb=" S4 SF4 B 301 " both_signs ideal model delta sigma weight residual False 10.55 -10.59 21.15 2.00e-01 2.50e+01 1.12e+04 ... (remaining 10154 not shown) Planarity restraints: 11470 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' FMN F 501 " -0.107 2.00e-02 2.50e+03 1.06e-01 5.30e+02 pdb=" C10 FMN F 501 " -0.091 2.00e-02 2.50e+03 pdb=" C2 FMN F 501 " 0.087 2.00e-02 2.50e+03 pdb=" C4 FMN F 501 " -0.067 2.00e-02 2.50e+03 pdb=" C4A FMN F 501 " -0.078 2.00e-02 2.50e+03 pdb=" C5A FMN F 501 " -0.009 2.00e-02 2.50e+03 pdb=" C6 FMN F 501 " 0.038 2.00e-02 2.50e+03 pdb=" C7 FMN F 501 " 0.055 2.00e-02 2.50e+03 pdb=" C7M FMN F 501 " 0.110 2.00e-02 2.50e+03 pdb=" C8 FMN F 501 " 0.033 2.00e-02 2.50e+03 pdb=" C8M FMN F 501 " 0.058 2.00e-02 2.50e+03 pdb=" C9 FMN F 501 " -0.011 2.00e-02 2.50e+03 pdb=" C9A FMN F 501 " -0.040 2.00e-02 2.50e+03 pdb=" N1 FMN F 501 " -0.122 2.00e-02 2.50e+03 pdb=" N10 FMN F 501 " -0.070 2.00e-02 2.50e+03 pdb=" N3 FMN F 501 " 0.010 2.00e-02 2.50e+03 pdb=" N5 FMN F 501 " -0.022 2.00e-02 2.50e+03 pdb=" O2 FMN F 501 " 0.342 2.00e-02 2.50e+03 pdb=" O4 FMN F 501 " -0.116 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS D 95 " 0.050 2.00e-02 2.50e+03 4.23e-02 2.68e+01 pdb=" CG HIS D 95 " -0.087 2.00e-02 2.50e+03 pdb=" ND1 HIS D 95 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 HIS D 95 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 HIS D 95 " 0.014 2.00e-02 2.50e+03 pdb=" NE2 HIS D 95 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL L 555 " 0.024 2.00e-02 2.50e+03 4.79e-02 2.30e+01 pdb=" C VAL L 555 " -0.083 2.00e-02 2.50e+03 pdb=" O VAL L 555 " 0.032 2.00e-02 2.50e+03 pdb=" N SER L 556 " 0.028 2.00e-02 2.50e+03 ... (remaining 11467 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 754 2.61 - 3.18: 58034 3.18 - 3.75: 104979 3.75 - 4.33: 157559 4.33 - 4.90: 255517 Nonbonded interactions: 576843 Sorted by model distance: nonbonded pdb=" OG SER c 136 " pdb=" OD1 ASP c 138 " model vdw 2.031 2.440 nonbonded pdb=" OD2 ASP C 125 " pdb=" OG1 THR C 127 " model vdw 2.068 2.440 nonbonded pdb=" O LEU H 276 " pdb=" OG SER H 280 " model vdw 2.071 2.440 nonbonded pdb=" OG1 THR i 16 " pdb=" O2P PLC L1007 " model vdw 2.071 2.440 nonbonded pdb=" OE2 GLU H 274 " pdb=" O HOH H 701 " model vdw 2.071 2.440 ... (remaining 576838 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.870 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: 0.070 Extract box with map and model: 22.780 Check model and map are aligned: 0.750 Set scattering table: 0.430 Process input model: 150.020 Find NCS groups from input model: 2.200 Set up NCS constraints: 0.240 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:11.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 192.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.011 0.170 67573 Z= 0.728 Angle : 1.101 39.827 91543 Z= 0.511 Chirality : 0.648 21.224 10157 Planarity : 0.006 0.106 11470 Dihedral : 14.884 154.734 24906 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.15 % Favored : 95.84 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.17 (0.08), residues: 8032 helix: -1.02 (0.07), residues: 4145 sheet: -1.23 (0.25), residues: 365 loop : -1.90 (0.10), residues: 3522 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16064 Ramachandran restraints generated. 8032 Oldfield, 0 Emsley, 8032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16064 Ramachandran restraints generated. 8032 Oldfield, 0 Emsley, 8032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1518 residues out of total 6944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1516 time to evaluate : 5.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 5 residues processed: 1517 average time/residue: 1.5817 time to fit residues: 3093.6771 Evaluate side-chains 902 residues out of total 6944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 897 time to evaluate : 5.889 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 5 residues processed: 1 average time/residue: 0.6006 time to fit residues: 8.9444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 667 optimal weight: 0.8980 chunk 599 optimal weight: 1.9990 chunk 332 optimal weight: 5.9990 chunk 204 optimal weight: 6.9990 chunk 404 optimal weight: 0.9990 chunk 320 optimal weight: 0.9990 chunk 619 optimal weight: 5.9990 chunk 239 optimal weight: 1.9990 chunk 376 optimal weight: 5.9990 chunk 461 optimal weight: 0.7980 chunk 718 optimal weight: 0.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 ASN A 114 ASN B 100 GLN B 125 ASN B 137 GLN C 66 GLN C 87 GLN D 43 HIS D 86 ASN D 90 GLN D 193 HIS D 434 HIS E 133 GLN E 174 ASN F 332 ASN F 424 HIS F 438 GLN F 456 HIS G 387 HIS G 572 GLN H 242 ASN I 93 GLN J 81 ASN ** K 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 37 ASN L 66 ASN L 234 ASN M 441 HIS M 481 ASN N 21 ASN N 90 ASN N 121 ASN N 185 HIS N 335 ASN ** N 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 355 HIS O 142 ASN O 157 ASN P 29 GLN P 230 GLN P 237 HIS P 265 GLN Q 93 ASN Q 147 ASN S 11 HIS T 48 ASN V 93 ASN V 134 GLN ** W 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 17 ASN Y 149 GLN Y 186 ASN Z 80 GLN a 33 ASN b 3 ASN b 22 ASN b 25 HIS b 60 GLN c 91 GLN e 40 ASN f 23 GLN f 136 GLN g 207 HIS g 238 GLN h 68 ASN j 54 ASN l 90 ASN ** n 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 16 ASN p 34 GLN Total number of N/Q/H flips: 66 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.253 67573 Z= 0.326 Angle : 1.033 50.631 91543 Z= 0.637 Chirality : 0.185 6.533 10157 Planarity : 0.005 0.069 11470 Dihedral : 10.547 179.155 9751 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.15 % Favored : 96.84 % Rotamer Outliers : 2.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.09), residues: 8032 helix: 0.32 (0.08), residues: 4167 sheet: -0.97 (0.24), residues: 410 loop : -1.37 (0.10), residues: 3455 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16064 Ramachandran restraints generated. 8032 Oldfield, 0 Emsley, 8032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16064 Ramachandran restraints generated. 8032 Oldfield, 0 Emsley, 8032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1139 residues out of total 6944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 973 time to evaluate : 5.856 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 166 outliers final: 51 residues processed: 1061 average time/residue: 1.5319 time to fit residues: 2129.7228 Evaluate side-chains 923 residues out of total 6944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 872 time to evaluate : 5.871 Switching outliers to nearest non-outliers outliers start: 51 outliers final: 28 residues processed: 24 average time/residue: 0.7878 time to fit residues: 37.8695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 399 optimal weight: 4.9990 chunk 222 optimal weight: 0.9990 chunk 597 optimal weight: 10.0000 chunk 489 optimal weight: 7.9990 chunk 198 optimal weight: 0.4980 chunk 719 optimal weight: 2.9990 chunk 777 optimal weight: 1.9990 chunk 640 optimal weight: 9.9990 chunk 713 optimal weight: 3.9990 chunk 245 optimal weight: 10.0000 chunk 577 optimal weight: 10.0000 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 ASN A 114 ASN B 100 GLN C 87 GLN C 99 HIS D 43 HIS ** D 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 326 ASN E 174 ASN F 363 GLN G 71 HIS ** G 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 337 GLN G 425 ASN G 513 ASN G 696 ASN I 93 GLN J 136 GLN K 21 ASN L 602 ASN M 481 ASN N 90 ASN N 185 HIS N 227 ASN N 339 ASN O 157 ASN P 62 ASN P 313 GLN Q 147 ASN R 85 GLN R 91 HIS S 34 GLN U 56 GLN V 58 GLN V 77 HIS V 80 GLN ** W 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 31 GLN ** X 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 149 GLN Z 80 GLN b 3 ASN b 60 GLN c 38 ASN c 91 GLN f 23 GLN f 136 GLN Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.2339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.244 67573 Z= 0.357 Angle : 1.025 50.422 91543 Z= 0.637 Chirality : 0.183 6.453 10157 Planarity : 0.005 0.070 11470 Dihedral : 9.959 179.271 9751 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.54 % Favored : 96.45 % Rotamer Outliers : 2.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.09), residues: 8032 helix: 0.79 (0.08), residues: 4188 sheet: -0.50 (0.25), residues: 393 loop : -1.03 (0.10), residues: 3451 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16064 Ramachandran restraints generated. 8032 Oldfield, 0 Emsley, 8032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16064 Ramachandran restraints generated. 8032 Oldfield, 0 Emsley, 8032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1109 residues out of total 6944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 207 poor density : 902 time to evaluate : 6.012 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 207 outliers final: 75 residues processed: 1025 average time/residue: 1.5930 time to fit residues: 2132.9922 Evaluate side-chains 905 residues out of total 6944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 830 time to evaluate : 6.030 Switching outliers to nearest non-outliers outliers start: 75 outliers final: 51 residues processed: 25 average time/residue: 0.9688 time to fit residues: 44.2078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 710 optimal weight: 7.9990 chunk 541 optimal weight: 5.9990 chunk 373 optimal weight: 7.9990 chunk 79 optimal weight: 0.9980 chunk 343 optimal weight: 5.9990 chunk 483 optimal weight: 0.9990 chunk 722 optimal weight: 9.9990 chunk 764 optimal weight: 10.0000 chunk 377 optimal weight: 9.9990 chunk 684 optimal weight: 5.9990 chunk 206 optimal weight: 0.0010 overall best weight: 2.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 ASN A 114 ASN B 100 GLN D 43 HIS D 440 HIS ** E 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 138 HIS ** G 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 337 GLN ** G 513 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 93 GLN ** K 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 21 ASN N 86 ASN N 90 ASN N 227 ASN N 339 ASN O 145 HIS P 62 ASN S 34 GLN U 56 GLN V 58 GLN ** W 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 31 GLN W 110 HIS ** X 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 149 GLN Z 80 GLN b 60 GLN c 91 GLN e 24 HIS f 55 HIS f 136 GLN h 114 HIS o 16 HIS p 16 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.2830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.243 67573 Z= 0.377 Angle : 1.032 50.531 91543 Z= 0.641 Chirality : 0.183 6.455 10157 Planarity : 0.005 0.072 11470 Dihedral : 9.864 179.474 9751 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.40 % Favored : 96.59 % Rotamer Outliers : 3.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.09), residues: 8032 helix: 0.91 (0.08), residues: 4208 sheet: -0.31 (0.26), residues: 384 loop : -0.91 (0.10), residues: 3440 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16064 Ramachandran restraints generated. 8032 Oldfield, 0 Emsley, 8032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16064 Ramachandran restraints generated. 8032 Oldfield, 0 Emsley, 8032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1099 residues out of total 6944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 219 poor density : 880 time to evaluate : 6.126 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 219 outliers final: 95 residues processed: 1009 average time/residue: 1.5339 time to fit residues: 2030.6331 Evaluate side-chains 917 residues out of total 6944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 822 time to evaluate : 5.933 Switching outliers to nearest non-outliers outliers start: 95 outliers final: 61 residues processed: 36 average time/residue: 0.8047 time to fit residues: 53.3205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 636 optimal weight: 3.9990 chunk 434 optimal weight: 0.8980 chunk 11 optimal weight: 5.9990 chunk 569 optimal weight: 4.9990 chunk 315 optimal weight: 0.9990 chunk 652 optimal weight: 0.6980 chunk 528 optimal weight: 0.7980 chunk 0 optimal weight: 9.9990 chunk 390 optimal weight: 0.8980 chunk 686 optimal weight: 10.0000 chunk 192 optimal weight: 5.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 ASN A 114 ASN ** D 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 224 GLN F 47 ASN F 332 ASN ** G 513 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 515 ASN I 93 GLN J 158 ASN ** K 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 351 HIS N 21 ASN N 90 ASN N 227 ASN N 339 ASN Q 143 GLN S 34 GLN U 56 GLN V 58 GLN ** W 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 72 GLN X 169 ASN b 3 ASN b 60 GLN c 91 GLN f 91 ASN f 136 GLN g 238 GLN h 114 HIS ** k 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 50 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.2975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.246 67573 Z= 0.316 Angle : 0.987 50.557 91543 Z= 0.622 Chirality : 0.181 6.390 10157 Planarity : 0.004 0.068 11470 Dihedral : 9.270 176.142 9751 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer Outliers : 2.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.09), residues: 8032 helix: 1.23 (0.08), residues: 4211 sheet: -0.29 (0.26), residues: 395 loop : -0.76 (0.11), residues: 3426 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16064 Ramachandran restraints generated. 8032 Oldfield, 0 Emsley, 8032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16064 Ramachandran restraints generated. 8032 Oldfield, 0 Emsley, 8032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1057 residues out of total 6944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 882 time to evaluate : 6.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 175 outliers final: 73 residues processed: 1003 average time/residue: 1.4975 time to fit residues: 1984.8427 Evaluate side-chains 907 residues out of total 6944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 834 time to evaluate : 5.917 Switching outliers to nearest non-outliers outliers start: 73 outliers final: 57 residues processed: 18 average time/residue: 0.9167 time to fit residues: 32.8191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 257 optimal weight: 9.9990 chunk 688 optimal weight: 5.9990 chunk 151 optimal weight: 0.9990 chunk 448 optimal weight: 7.9990 chunk 188 optimal weight: 9.9990 chunk 765 optimal weight: 1.9990 chunk 635 optimal weight: 0.0870 chunk 354 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 253 optimal weight: 8.9990 chunk 401 optimal weight: 2.9990 overall best weight: 1.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 ASN A 114 ASN ** E 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 47 ASN ** G 513 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 515 ASN H 260 ASN I 93 GLN ** K 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 351 HIS N 21 ASN N 90 ASN N 227 ASN N 335 ASN P 165 HIS ** W 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 31 GLN X 169 ASN Z 22 ASN b 60 GLN c 33 ASN c 91 GLN e 36 GLN f 25 ASN f 91 ASN f 136 GLN g 238 GLN h 114 HIS ** k 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 16 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.3085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.244 67573 Z= 0.334 Angle : 0.997 50.549 91543 Z= 0.626 Chirality : 0.182 6.418 10157 Planarity : 0.004 0.072 11470 Dihedral : 9.138 175.228 9751 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer Outliers : 2.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.09), residues: 8032 helix: 1.31 (0.08), residues: 4198 sheet: -0.21 (0.26), residues: 385 loop : -0.67 (0.11), residues: 3449 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16064 Ramachandran restraints generated. 8032 Oldfield, 0 Emsley, 8032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16064 Ramachandran restraints generated. 8032 Oldfield, 0 Emsley, 8032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1045 residues out of total 6944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 182 poor density : 863 time to evaluate : 5.953 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 182 outliers final: 98 residues processed: 988 average time/residue: 1.5534 time to fit residues: 2027.9555 Evaluate side-chains 927 residues out of total 6944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 829 time to evaluate : 5.932 Switching outliers to nearest non-outliers outliers start: 98 outliers final: 73 residues processed: 28 average time/residue: 0.8654 time to fit residues: 46.3972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 737 optimal weight: 6.9990 chunk 86 optimal weight: 5.9990 chunk 436 optimal weight: 1.9990 chunk 558 optimal weight: 9.9990 chunk 433 optimal weight: 1.9990 chunk 644 optimal weight: 9.9990 chunk 427 optimal weight: 0.8980 chunk 762 optimal weight: 9.9990 chunk 477 optimal weight: 0.9980 chunk 464 optimal weight: 9.9990 chunk 351 optimal weight: 10.0000 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 ASN A 114 ASN D 72 ASN ** E 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 513 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 515 ASN G 725 GLN I 93 GLN ** K 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 90 ASN N 227 ASN N 335 ASN N 339 ASN N 392 ASN Q 42 HIS Q 143 GLN S 34 GLN U 74 ASN ** W 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 169 ASN Z 109 ASN b 60 GLN c 91 GLN e 36 GLN f 91 ASN f 136 GLN g 167 GLN g 238 GLN j 7 ASN ** k 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 16 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.3181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.243 67573 Z= 0.357 Angle : 1.013 50.551 91543 Z= 0.632 Chirality : 0.183 6.440 10157 Planarity : 0.004 0.075 11470 Dihedral : 9.208 174.892 9751 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer Outliers : 2.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.09), residues: 8032 helix: 1.25 (0.08), residues: 4199 sheet: -0.24 (0.26), residues: 374 loop : -0.67 (0.10), residues: 3459 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16064 Ramachandran restraints generated. 8032 Oldfield, 0 Emsley, 8032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16064 Ramachandran restraints generated. 8032 Oldfield, 0 Emsley, 8032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1016 residues out of total 6944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 850 time to evaluate : 6.035 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 166 outliers final: 91 residues processed: 968 average time/residue: 1.5728 time to fit residues: 2003.0362 Evaluate side-chains 919 residues out of total 6944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 828 time to evaluate : 5.880 Switching outliers to nearest non-outliers outliers start: 91 outliers final: 70 residues processed: 22 average time/residue: 0.7488 time to fit residues: 34.9017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 471 optimal weight: 5.9990 chunk 304 optimal weight: 3.9990 chunk 455 optimal weight: 6.9990 chunk 229 optimal weight: 6.9990 chunk 149 optimal weight: 0.3980 chunk 147 optimal weight: 1.9990 chunk 484 optimal weight: 10.0000 chunk 519 optimal weight: 0.1980 chunk 376 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 chunk 599 optimal weight: 7.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 ASN A 114 ASN ** D 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 332 ASN ** G 513 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 93 GLN K 21 ASN L 351 HIS M 400 GLN N 21 ASN N 90 ASN N 227 ASN N 335 ASN N 339 ASN P 103 ASN S 34 GLN ** W 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 31 GLN X 169 ASN b 10 ASN c 91 GLN e 36 GLN f 91 ASN f 136 GLN g 238 GLN j 11 ASN ** k 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 16 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.3266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.245 67573 Z= 0.320 Angle : 0.990 50.569 91543 Z= 0.623 Chirality : 0.181 6.392 10157 Planarity : 0.004 0.074 11470 Dihedral : 8.879 172.595 9751 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer Outliers : 2.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.09), residues: 8032 helix: 1.40 (0.08), residues: 4207 sheet: -0.18 (0.26), residues: 373 loop : -0.60 (0.11), residues: 3452 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16064 Ramachandran restraints generated. 8032 Oldfield, 0 Emsley, 8032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16064 Ramachandran restraints generated. 8032 Oldfield, 0 Emsley, 8032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1002 residues out of total 6944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 860 time to evaluate : 6.039 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 142 outliers final: 81 residues processed: 958 average time/residue: 1.5759 time to fit residues: 1994.9115 Evaluate side-chains 905 residues out of total 6944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 824 time to evaluate : 8.156 Switching outliers to nearest non-outliers outliers start: 81 outliers final: 65 residues processed: 17 average time/residue: 1.0481 time to fit residues: 34.2996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 693 optimal weight: 0.9990 chunk 730 optimal weight: 2.9990 chunk 666 optimal weight: 9.9990 chunk 710 optimal weight: 9.9990 chunk 427 optimal weight: 7.9990 chunk 309 optimal weight: 5.9990 chunk 557 optimal weight: 10.0000 chunk 218 optimal weight: 7.9990 chunk 641 optimal weight: 4.9990 chunk 671 optimal weight: 0.9990 chunk 707 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 ASN A 114 ASN ** E 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 513 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 515 ASN I 93 GLN L 605 ASN N 21 ASN N 90 ASN N 133 GLN N 227 ASN N 304 ASN N 339 ASN ** W 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 31 GLN X 169 ASN c 33 ASN c 91 GLN e 36 GLN f 91 ASN f 136 GLN g 167 GLN g 238 GLN j 11 ASN p 16 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.3322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.241 67573 Z= 0.383 Angle : 1.034 50.575 91543 Z= 0.641 Chirality : 0.183 6.460 10157 Planarity : 0.004 0.076 11470 Dihedral : 9.223 173.664 9751 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer Outliers : 1.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.09), residues: 8032 helix: 1.22 (0.08), residues: 4210 sheet: -0.24 (0.26), residues: 375 loop : -0.65 (0.10), residues: 3447 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16064 Ramachandran restraints generated. 8032 Oldfield, 0 Emsley, 8032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16064 Ramachandran restraints generated. 8032 Oldfield, 0 Emsley, 8032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 969 residues out of total 6944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 839 time to evaluate : 6.408 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 130 outliers final: 90 residues processed: 932 average time/residue: 1.5986 time to fit residues: 1957.6180 Evaluate side-chains 912 residues out of total 6944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 822 time to evaluate : 5.936 Switching outliers to nearest non-outliers outliers start: 90 outliers final: 73 residues processed: 18 average time/residue: 0.8965 time to fit residues: 32.6297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 466 optimal weight: 3.9990 chunk 751 optimal weight: 1.9990 chunk 458 optimal weight: 3.9990 chunk 356 optimal weight: 10.0000 chunk 522 optimal weight: 2.9990 chunk 788 optimal weight: 8.9990 chunk 725 optimal weight: 0.0000 chunk 627 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 484 optimal weight: 8.9990 chunk 384 optimal weight: 2.9990 overall best weight: 1.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 ASN ** E 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 513 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 93 GLN N 90 ASN N 227 ASN N 339 ASN ** W 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 169 ASN c 91 GLN e 36 GLN f 91 ASN f 136 GLN g 238 GLN j 11 ASN ** k 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 16 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.3367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.244 67573 Z= 0.340 Angle : 1.008 50.612 91543 Z= 0.631 Chirality : 0.182 6.424 10157 Planarity : 0.004 0.075 11470 Dihedral : 9.064 172.278 9751 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer Outliers : 1.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.09), residues: 8032 helix: 1.31 (0.08), residues: 4206 sheet: -0.29 (0.26), residues: 379 loop : -0.62 (0.11), residues: 3447 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16064 Ramachandran restraints generated. 8032 Oldfield, 0 Emsley, 8032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16064 Ramachandran restraints generated. 8032 Oldfield, 0 Emsley, 8032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 933 residues out of total 6944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 826 time to evaluate : 6.150 Fit side-chains revert: symmetry clash outliers start: 107 outliers final: 81 residues processed: 912 average time/residue: 1.5597 time to fit residues: 1874.4239 Evaluate side-chains 888 residues out of total 6944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 807 time to evaluate : 5.996 Switching outliers to nearest non-outliers outliers start: 81 outliers final: 71 residues processed: 11 average time/residue: 0.9426 time to fit residues: 23.6117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 498 optimal weight: 2.9990 chunk 668 optimal weight: 1.9990 chunk 192 optimal weight: 1.9990 chunk 578 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 chunk 174 optimal weight: 0.8980 chunk 628 optimal weight: 0.7980 chunk 263 optimal weight: 0.9990 chunk 645 optimal weight: 2.9990 chunk 79 optimal weight: 9.9990 chunk 115 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 ASN ** D 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 332 ASN ** G 513 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 93 GLN K 21 ASN N 21 ASN N 90 ASN N 227 ASN N 339 ASN P 230 GLN ** W 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 169 ASN c 91 GLN e 36 GLN f 91 ASN f 136 GLN g 167 GLN g 238 GLN j 11 ASN p 16 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.119538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.099811 restraints weight = 87095.568| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 1.26 r_work: 0.3105 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.3433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.245 67573 Z= 0.318 Angle : 0.990 50.553 91543 Z= 0.624 Chirality : 0.181 6.390 10157 Planarity : 0.004 0.074 11470 Dihedral : 8.668 170.077 9751 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer Outliers : 1.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.09), residues: 8032 helix: 1.48 (0.08), residues: 4198 sheet: -0.12 (0.26), residues: 373 loop : -0.57 (0.11), residues: 3461 =============================================================================== Job complete usr+sys time: 27978.80 seconds wall clock time: 485 minutes 37.96 seconds (29137.96 seconds total)