Starting phenix.real_space_refine (version: 1.21rc1) on Sun Apr 23 05:24:02 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o6y_12741/04_2023/7o6y_12741_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o6y_12741/04_2023/7o6y_12741.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o6y_12741/04_2023/7o6y_12741_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o6y_12741/04_2023/7o6y_12741_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o6y_12741/04_2023/7o6y_12741_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o6y_12741/04_2023/7o6y_12741.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o6y_12741/04_2023/7o6y_12741.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o6y_12741/04_2023/7o6y_12741_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o6y_12741/04_2023/7o6y_12741_updated.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned 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 46 5.49 5 S 310 5.16 5 C 42107 2.51 5 N 10537 2.21 5 O 11837 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 89": "NH1" <-> "NH2" Residue "A ASP 110": "OD1" <-> "OD2" Residue "A ARG 150": "NH1" <-> "NH2" Residue "A ARG 155": "NH1" <-> "NH2" Residue "A GLU 168": "OE1" <-> "OE2" Residue "A ARG 182": "NH1" <-> "NH2" Residue "A ARG 207": "NH1" <-> "NH2" Residue "A ARG 246": "NH1" <-> "NH2" Residue "A GLU 251": "OE1" <-> "OE2" Residue "A GLU 286": "OE1" <-> "OE2" Residue "A GLU 290": "OE1" <-> "OE2" Residue "A ARG 315": "NH1" <-> "NH2" Residue "A ASP 326": "OD1" <-> "OD2" Residue "A GLU 345": "OE1" <-> "OE2" Residue "A PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 355": "OE1" <-> "OE2" Residue "A GLU 372": "OE1" <-> "OE2" Residue "A ARG 418": "NH1" <-> "NH2" Residue "A GLU 454": "OE1" <-> "OE2" Residue "A PHE 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 498": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 506": "OE1" <-> "OE2" Residue "A GLU 514": "OE1" <-> "OE2" Residue "A ARG 524": "NH1" <-> "NH2" Residue "A ARG 528": "NH1" <-> "NH2" Residue "A ARG 610": "NH1" <-> "NH2" Residue "A GLU 621": "OE1" <-> "OE2" Residue "A TYR 632": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 639": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 646": "NH1" <-> "NH2" Residue "A GLU 651": "OE1" <-> "OE2" Residue "A ASP 720": "OD1" <-> "OD2" Residue "B PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 87": "NH1" <-> "NH2" Residue "B ARG 113": "NH1" <-> "NH2" Residue "B ASP 129": "OD1" <-> "OD2" Residue "B ARG 130": "NH1" <-> "NH2" Residue "B ARG 134": "NH1" <-> "NH2" Residue "B ARG 149": "NH1" <-> "NH2" Residue "B ARG 161": "NH1" <-> "NH2" Residue "B TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 201": "NH1" <-> "NH2" Residue "B GLU 216": "OE1" <-> "OE2" Residue "B ARG 226": "NH1" <-> "NH2" Residue "B ARG 240": "NH1" <-> "NH2" Residue "B ARG 258": "NH1" <-> "NH2" Residue "B PHE 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 269": "NH1" <-> "NH2" Residue "B ARG 271": "NH1" <-> "NH2" Residue "B ARG 299": "NH1" <-> "NH2" Residue "B ASP 314": "OD1" <-> "OD2" Residue "B GLU 335": "OE1" <-> "OE2" Residue "B ARG 367": "NH1" <-> "NH2" Residue "B ARG 388": "NH1" <-> "NH2" Residue "B ARG 402": "NH1" <-> "NH2" Residue "B ARG 409": "NH1" <-> "NH2" Residue "B GLU 410": "OE1" <-> "OE2" Residue "B ASP 420": "OD1" <-> "OD2" Residue "B PHE 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 151": "OE1" <-> "OE2" Residue "C ARG 169": "NH1" <-> "NH2" Residue "C PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 209": "OE1" <-> "OE2" Residue "C GLU 211": "OE1" <-> "OE2" Residue "C GLU 215": "OE1" <-> "OE2" Residue "C ARG 219": "NH1" <-> "NH2" Residue "C ARG 224": "NH1" <-> "NH2" Residue "C ARG 231": "NH1" <-> "NH2" Residue "C ASP 245": "OD1" <-> "OD2" Residue "C ARG 257": "NH1" <-> "NH2" Residue "C GLU 260": "OE1" <-> "OE2" Residue "C GLU 262": "OE1" <-> "OE2" Residue "C ARG 269": "NH1" <-> "NH2" Residue "C ARG 274": "NH1" <-> "NH2" Residue "C ASP 304": "OD1" <-> "OD2" Residue "C ARG 306": "NH1" <-> "NH2" Residue "C TYR 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 363": "OD1" <-> "OD2" Residue "C GLU 404": "OE1" <-> "OE2" Residue "C PHE 461": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 466": "NH1" <-> "NH2" Residue "G ARG 43": "NH1" <-> "NH2" Residue "G ASP 70": "OD1" <-> "OD2" Residue "G TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 113": "NH1" <-> "NH2" Residue "G ARG 134": "NH1" <-> "NH2" Residue "G ARG 148": "NH1" <-> "NH2" Residue "G PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 184": "OD1" <-> "OD2" Residue "G PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 223": "NH1" <-> "NH2" Residue "G GLU 226": "OE1" <-> "OE2" Residue "G ARG 230": "NH1" <-> "NH2" Residue "G ARG 259": "NH1" <-> "NH2" Residue "G ASP 260": "OD1" <-> "OD2" Residue "G ARG 262": "NH1" <-> "NH2" Residue "H PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 50": "OE1" <-> "OE2" Residue "H GLU 56": "OE1" <-> "OE2" Residue "H ARG 103": "NH1" <-> "NH2" Residue "H ARG 116": "NH1" <-> "NH2" Residue "H GLU 165": "OE1" <-> "OE2" Residue "H GLU 167": "OE1" <-> "OE2" Residue "H ASP 183": "OD1" <-> "OD2" Residue "H ARG 215": "NH1" <-> "NH2" Residue "H ASP 217": "OD1" <-> "OD2" Residue "I ARG 59": "NH1" <-> "NH2" Residue "I ARG 115": "NH1" <-> "NH2" Residue "I GLU 127": "OE1" <-> "OE2" Residue "I GLU 128": "OE1" <-> "OE2" Residue "I ARG 129": "NH1" <-> "NH2" Residue "I GLU 137": "OE1" <-> "OE2" Residue "I GLU 150": "OE1" <-> "OE2" Residue "I GLU 205": "OE1" <-> "OE2" Residue "I ASP 212": "OD1" <-> "OD2" Residue "I GLU 217": "OE1" <-> "OE2" Residue "I ASP 223": "OD1" <-> "OD2" Residue "K PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 89": "OE1" <-> "OE2" Residue "K ASP 101": "OD1" <-> "OD2" Residue "K ARG 102": "NH1" <-> "NH2" Residue "K PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 185": "OE1" <-> "OE2" Residue "K ARG 196": "NH1" <-> "NH2" Residue "K ARG 199": "NH1" <-> "NH2" Residue "L PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 19": "NH1" <-> "NH2" Residue "L ARG 20": "NH1" <-> "NH2" Residue "L PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 66": "OE1" <-> "OE2" Residue "L TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 79": "NH1" <-> "NH2" Residue "S ARG 49": "NH1" <-> "NH2" Residue "S ARG 62": "NH1" <-> "NH2" Residue "S GLU 85": "OE1" <-> "OE2" Residue "S TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 120": "NH1" <-> "NH2" Residue "S ARG 156": "NH1" <-> "NH2" Residue "S ARG 188": "NH1" <-> "NH2" Residue "j ARG 39": "NH1" <-> "NH2" Residue "j TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ARG 50": "NH1" <-> "NH2" Residue "j GLU 75": "OE1" <-> "OE2" Residue "1 GLU 26": "OE1" <-> "OE2" Residue "1 GLU 67": "OE1" <-> "OE2" Residue "1 GLU 101": "OE1" <-> "OE2" Residue "1 GLU 147": "OE1" <-> "OE2" Residue "1 ARG 174": "NH1" <-> "NH2" Residue "1 PHE 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 TYR 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 PHE 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 PHE 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ARG 22": "NH1" <-> "NH2" Residue "2 TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ASP 196": "OD1" <-> "OD2" Residue "2 PHE 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 GLU 306": "OE1" <-> "OE2" Residue "2 TYR 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ASP 423": "OD1" <-> "OD2" Residue "2 TYR 467": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 GLU 33": "OE1" <-> "OE2" Residue "3 PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ASP 67": "OD1" <-> "OD2" Residue "3 GLU 69": "OE1" <-> "OE2" Residue "3 PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 58": "OE1" <-> "OE2" Residue "4 ASP 72": "OD1" <-> "OD2" Residue "4 PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 142": "OE1" <-> "OE2" Residue "4 ARG 162": "NH1" <-> "NH2" Residue "4 GLU 268": "OE1" <-> "OE2" Residue "4 TYR 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 PHE 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ARG 353": "NH1" <-> "NH2" Residue "4 PHE 403": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ARG 405": "NH1" <-> "NH2" Residue "4 TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ARG 449": "NH1" <-> "NH2" Residue "4 PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 TYR 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 TYR 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ARG 175": "NH1" <-> "NH2" Residue "5 PHE 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ASP 210": "OD1" <-> "OD2" Residue "5 PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 GLU 241": "OE1" <-> "OE2" Residue "5 ASP 300": "OD1" <-> "OD2" Residue "5 ARG 303": "NH1" <-> "NH2" Residue "5 PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ASP 359": "OD1" <-> "OD2" Residue "5 TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 TYR 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 TYR 394": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ASP 397": "OD1" <-> "OD2" Residue "5 GLU 401": "OE1" <-> "OE2" Residue "5 TYR 407": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 TYR 415": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 TYR 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 GLU 453": "OE1" <-> "OE2" Residue "5 PHE 463": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 PHE 536": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 PHE 550": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 PHE 654": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ASP 137": "OD1" <-> "OD2" Residue "6 GLU 142": "OE1" <-> "OE2" Residue "g ARG 17": "NH1" <-> "NH2" Residue "g PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ARG 47": "NH1" <-> "NH2" Residue "g TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ARG 69": "NH1" <-> "NH2" Residue "g ASP 76": "OD1" <-> "OD2" Residue "D PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 37": "NH1" <-> "NH2" Residue "D ASP 46": "OD1" <-> "OD2" Residue "D GLU 51": "OE1" <-> "OE2" Residue "D ARG 62": "NH1" <-> "NH2" Residue "D GLU 83": "OE1" <-> "OE2" Residue "D ARG 84": "NH1" <-> "NH2" Residue "E GLU 25": "OE1" <-> "OE2" Residue "E ARG 35": "NH1" <-> "NH2" Residue "E ARG 48": "NH1" <-> "NH2" Residue "E ARG 51": "NH1" <-> "NH2" Residue "E TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 85": "NH1" <-> "NH2" Residue "E GLU 86": "OE1" <-> "OE2" Residue "E ARG 91": "NH1" <-> "NH2" Residue "E ARG 110": "NH1" <-> "NH2" Residue "E GLU 113": "OE1" <-> "OE2" Residue "E GLU 117": "OE1" <-> "OE2" Residue "E ARG 120": "NH1" <-> "NH2" Residue "E ARG 131": "NH1" <-> "NH2" Residue "E TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 149": "NH1" <-> "NH2" Residue "E ARG 150": "NH1" <-> "NH2" Residue "E GLU 172": "OE1" <-> "OE2" Residue "E ARG 201": "NH1" <-> "NH2" Residue "E ARG 208": "NH1" <-> "NH2" Residue "E PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 252": "OD1" <-> "OD2" Residue "E TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 281": "NH1" <-> "NH2" Residue "E GLU 283": "OE1" <-> "OE2" Residue "E GLU 288": "OE1" <-> "OE2" Residue "E ASP 334": "OD1" <-> "OD2" Residue "E TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 26": "NH1" <-> "NH2" Residue "F GLU 27": "OE1" <-> "OE2" Residue "F GLU 51": "OE1" <-> "OE2" Residue "F ASP 64": "OD1" <-> "OD2" Residue "F GLU 72": "OE1" <-> "OE2" Residue "F GLU 86": "OE1" <-> "OE2" Residue "F GLU 101": "OE1" <-> "OE2" Residue "F GLU 119": "OE1" <-> "OE2" Residue "F GLU 125": "OE1" <-> "OE2" Residue "J PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 91": "NH1" <-> "NH2" Residue "J ARG 143": "NH1" <-> "NH2" Residue "J GLU 165": "OE1" <-> "OE2" Residue "J ARG 183": "NH1" <-> "NH2" Residue "M ARG 42": "NH1" <-> "NH2" Residue "M ARG 88": "NH1" <-> "NH2" Residue "M ARG 131": "NH1" <-> "NH2" Residue "M GLU 135": "OE1" <-> "OE2" Residue "O GLU 33": "OE1" <-> "OE2" Residue "O ARG 35": "NH1" <-> "NH2" Residue "O ASP 61": "OD1" <-> "OD2" Residue "O GLU 77": "OE1" <-> "OE2" Residue "O GLU 83": "OE1" <-> "OE2" Residue "O GLU 91": "OE1" <-> "OE2" Residue "O GLU 100": "OE1" <-> "OE2" Residue "P ARG 30": "NH1" <-> "NH2" Residue "P ASP 41": "OD1" <-> "OD2" Residue "P ARG 57": "NH1" <-> "NH2" Residue "P GLU 59": "OE1" <-> "OE2" Residue "P ARG 62": "NH1" <-> "NH2" Residue "P GLU 82": "OE1" <-> "OE2" Residue "P GLU 85": "OE1" <-> "OE2" Residue "P PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 103": "OE1" <-> "OE2" Residue "P ARG 109": "NH1" <-> "NH2" Residue "P PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 114": "OE1" <-> "OE2" Residue "R ARG 37": "NH1" <-> "NH2" Residue "R ARG 44": "NH1" <-> "NH2" Residue "R PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 57": "NH1" <-> "NH2" Residue "R ASP 64": "OD1" <-> "OD2" Residue "R TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 92": "NH1" <-> "NH2" Residue "R ARG 97": "NH1" <-> "NH2" Residue "R GLU 99": "OE1" <-> "OE2" Residue "U ASP 24": "OD1" <-> "OD2" Residue "U GLU 27": "OE1" <-> "OE2" Residue "U TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 51": "OD1" <-> "OD2" Residue "U ASP 52": "OD1" <-> "OD2" Residue "U GLU 59": "OE1" <-> "OE2" Residue "U ARG 73": "NH1" <-> "NH2" Residue "U ARG 74": "NH1" <-> "NH2" Residue "U GLU 84": "OE1" <-> "OE2" Residue "U ARG 112": "NH1" <-> "NH2" Residue "U GLU 115": "OE1" <-> "OE2" Residue "U PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 129": "OE1" <-> "OE2" Residue "U ASP 147": "OD1" <-> "OD2" Residue "U ASP 156": "OD1" <-> "OD2" Residue "U ARG 161": "NH1" <-> "NH2" Residue "U TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 165": "OE1" <-> "OE2" Residue "W GLU 15": "OE1" <-> "OE2" Residue "W ARG 20": "NH1" <-> "NH2" Residue "W ARG 21": "NH1" <-> "NH2" Residue "W ARG 26": "NH1" <-> "NH2" Residue "W ARG 29": "NH1" <-> "NH2" Residue "W ARG 47": "NH1" <-> "NH2" Residue "W ARG 60": "NH1" <-> "NH2" Residue "W ARG 66": "NH1" <-> "NH2" Residue "W GLU 76": "OE1" <-> "OE2" Residue "W ASP 78": "OD1" <-> "OD2" Residue "W ARG 83": "NH1" <-> "NH2" Residue "W ARG 84": "NH1" <-> "NH2" Residue "W GLU 90": "OE1" <-> "OE2" Residue "W ARG 91": "NH1" <-> "NH2" Residue "X TYR 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 25": "OD1" <-> "OD2" Residue "X TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 69": "NH1" <-> "NH2" Residue "X PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 76": "NH1" <-> "NH2" Residue "X GLU 112": "OE1" <-> "OE2" Residue "X ARG 118": "NH1" <-> "NH2" Residue "X GLU 124": "OE1" <-> "OE2" Residue "X GLU 167": "OE1" <-> "OE2" Residue "Y PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 79": "NH1" <-> "NH2" Residue "Y ASP 86": "OD1" <-> "OD2" Residue "Y PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 140": "NH1" <-> "NH2" Residue "Y TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 159": "NH1" <-> "NH2" Residue "Z GLU 22": "OE1" <-> "OE2" Residue "Z ASP 68": "OD1" <-> "OD2" Residue "Z ARG 77": "NH1" <-> "NH2" Residue "Z ASP 78": "OD1" <-> "OD2" Residue "Z ARG 80": "NH1" <-> "NH2" Residue "Z ARG 81": "NH1" <-> "NH2" Residue "Z GLU 112": "OE1" <-> "OE2" Residue "Z ARG 179": "NH1" <-> "NH2" Residue "a ASP 39": "OD1" <-> "OD2" Residue "a TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 75": "OD1" <-> "OD2" Residue "a PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ARG 123": "NH1" <-> "NH2" Residue "a PHE 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ARG 147": "NH1" <-> "NH2" Residue "b PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 25": "NH1" <-> "NH2" Residue "b TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 11": "NH1" <-> "NH2" Residue "c ARG 16": "NH1" <-> "NH2" Residue "c ARG 23": "NH1" <-> "NH2" Residue "c ARG 26": "NH1" <-> "NH2" Residue "c PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 6": "NH1" <-> "NH2" Residue "d GLU 25": "OE1" <-> "OE2" Residue "d ARG 32": "NH1" <-> "NH2" Residue "d PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 37": "NH1" <-> "NH2" Residue "d GLU 39": "OE1" <-> "OE2" Residue "d ARG 45": "NH1" <-> "NH2" Residue "d GLU 54": "OE1" <-> "OE2" Residue "d GLU 68": "OE1" <-> "OE2" Residue "d TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ARG 41": "NH1" <-> "NH2" Residue "e TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ARG 6": "NH1" <-> "NH2" Residue "f GLU 7": "OE1" <-> "OE2" Residue "f ARG 9": "NH1" <-> "NH2" Residue "f ARG 23": "NH1" <-> "NH2" Residue "f PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ARG 45": "NH1" <-> "NH2" Residue "f ARG 57": "NH1" <-> "NH2" Residue "f PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ARG 79": "NH1" <-> "NH2" Residue "h ARG 10": "NH1" <-> "NH2" Residue "h ARG 18": "NH1" <-> "NH2" Residue "h ASP 39": "OD1" <-> "OD2" Residue "h GLU 47": "OE1" <-> "OE2" Residue "h ASP 49": "OD1" <-> "OD2" Residue "h GLU 53": "OE1" <-> "OE2" Residue "h ARG 57": "NH1" <-> "NH2" Residue "h GLU 62": "OE1" <-> "OE2" Residue "h TYR 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 65": "OE1" <-> "OE2" Residue "h ASP 69": "OD1" <-> "OD2" Residue "h TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 95": "OE1" <-> "OE2" Residue "h TYR 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ARG 137": "NH1" <-> "NH2" Residue "i TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ARG 53": "NH1" <-> "NH2" Residue "i ARG 55": "NH1" <-> "NH2" Residue "i ARG 75": "NH1" <-> "NH2" Residue "i ARG 77": "NH1" <-> "NH2" Residue "i GLU 85": "OE1" <-> "OE2" Residue "n TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n GLU 89": "OE1" <-> "OE2" Residue "n GLU 90": "OE1" <-> "OE2" Residue "n TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ASP 103": "OD1" <-> "OD2" Residue "8 GLU 11": "OE1" <-> "OE2" Residue "8 ARG 37": "NH1" <-> "NH2" Residue "8 TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 ARG 51": "NH1" <-> "NH2" Residue "8 ARG 65": "NH1" <-> "NH2" Residue "9 ARG 14": "NH1" <-> "NH2" Residue "9 GLU 46": "OE1" <-> "OE2" Residue "9 GLU 53": "OE1" <-> "OE2" Residue "9 ARG 58": "NH1" <-> "NH2" Time to flip residues: 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 64866 Number of models: 1 Model: "" Number of chains: 67 Chain: "A" Number of atoms: 5269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 693, 5269 Classifications: {'peptide': 693} Link IDs: {'PTRANS': 34, 'TRANS': 658} Chain: "B" Number of atoms: 3528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 457, 3528 Classifications: {'peptide': 457} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 434} Chain: "C" Number of atoms: 3247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 410, 3247 Classifications: {'peptide': 410} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 386} Chain breaks: 2 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: "G" Number of atoms: 1978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1978 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 18, 'TRANS': 220} Chain: "H" Number of atoms: 1688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1688 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 18, 'TRANS': 197} Chain: "I" Number of atoms: 1519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1519 Classifications: {'peptide': 190} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 177} Chain: "K" 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: "L" Number of atoms: 669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 669 Classifications: {'peptide': 86} Link IDs: {'TRANS': 85} 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: "S" Number of atoms: 1492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1492 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 7, 'TRANS': 174} Chain breaks: 2 Chain: "j" Number of atoms: 724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 724 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 4, 'TRANS': 85} Chain: "1" Number of atoms: 2716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2716 Classifications: {'peptide': 340} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 325} 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: "2" 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: "3" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 930 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 4, 'TRANS': 112} Chain breaks: 2 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: "4" Number of atoms: 3815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 3815 Classifications: {'peptide': 481} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 466} Chain: "5" Number of atoms: 5151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 648, 5151 Classifications: {'peptide': 648} Link IDs: {'PTRANS': 15, 'TRANS': 632} Chain breaks: 1 Chain: "6" Number of atoms: 1078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1078 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 2, 'TRANS': 132} Chain breaks: 2 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: "g" Number of atoms: 622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 622 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 10, 'TRANS': 65} Chain: "D" 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: "E" Number of atoms: 2673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2673 Classifications: {'peptide': 334} Link IDs: {'PTRANS': 15, 'TRANS': 318} Chain: "F" Number of atoms: 981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 981 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 7, 'TRANS': 112} Chain: "J" Number of atoms: 1274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1274 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 6, 'TRANS': 165} Chain breaks: 1 Chain: "M" Number of atoms: 912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 912 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 9, 'TRANS': 107} Chain: "O" Number of atoms: 543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 543 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Chain: "P" 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: "Q" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 648 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 2, 'TRANS': 82} Chain: "R" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 884 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 10, 'TRANS': 95} Chain: "U" 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: "W" Number of atoms: 974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 974 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 9, 'TRANS': 111} Chain: "X" Number of atoms: 1275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1275 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 11, 'TRANS': 152} Chain: "Y" 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: "Z" Number of atoms: 1389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1389 Classifications: {'peptide': 181} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 160} Chain: "a" Number of atoms: 1030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1030 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 10, 'TRANS': 113} Chain: "b" Number of atoms: 490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 490 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "c" Number of atoms: 353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 353 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 2, 'TRANS': 41} Chain: "d" Number of atoms: 751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 751 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 4, 'TRANS': 84} Chain: "e" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 436 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 6, 'TRANS': 45} Chain: "f" Number of atoms: 642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 642 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 3, 'TRANS': 78} Chain: "h" Number of atoms: 1130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1130 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 10, 'TRANS': 125} Chain: "i" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 646 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 4, 'TRANS': 78} Chain: "n" Number of atoms: 913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 913 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 9, 'TRANS': 104} Chain breaks: 1 Chain: "8" Number of atoms: 594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 594 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 2, 'TRANS': 68} Chain: "9" Number of atoms: 672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 672 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 4, 'TRANS': 81} Chain: "A" 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: "B" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 83 Unusual residues: {'FMN': 1, 'NAI': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'UQ9': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'UQ9:plan-9': 1, 'UQ9:plan-8': 1, 'UQ9:plan-3': 1, 'UQ9:plan-2': 1, 'UQ9:plan-7': 1, 'UQ9:plan-6': 1, 'UQ9:plan-5': 1, 'UQ9:plan-4': 1, 'UQ9:plan-10': 1} Unresolved non-hydrogen planarities: 44 Chain: "H" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Unusual residues: {'3PE': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "K" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'PLC': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Chain: "1" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 154 Unusual residues: {'3PE': 2, 'PLC': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 32 Chain: "2" Number of atoms: 146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 146 Unusual residues: {'3PE': 1, 'CPL': 1, 'T7X': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 18 Chain: "3" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'T7X': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'T7X:plan-5': 1, 'T7X:plan-4': 1} Unresolved non-hydrogen planarities: 7 Chain: "4" Number of atoms: 171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 171 Unusual residues: {'3PE': 3, 'PLC': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 24 Chain: "5" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 127 Unusual residues: {'3PE': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 26 Chain: "6" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 84 Unusual residues: {'3PE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 19 Chain: "g" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 123 Unusual residues: {'3PE': 1, 'CDL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 28 Chain: "E" Number of atoms: 156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 156 Unusual residues: {'3PE': 1, 'CDL': 1, 'NDP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 43 Chain: "J" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 110 Unusual residues: {'3PE': 1, 'LMN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 33 Unusual residues: {'ZMP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Chain: "R" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 33 Unusual residues: {'ZMP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Chain: "W" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 95 Unusual residues: {'CDL': 1, 'PLC': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 47 Chain: "X" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 86 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 14 Chain: "Z" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 76 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 24 Chain: "a" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 65 Unusual residues: {'LMN': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "b" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 90 Unusual residues: {'3PE': 1, 'T7X': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 22 Chain: "i" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'PLC': 1} Classifications: {'undetermined': 1} Chain: "n" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 92 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 749 SG CYS A 133 62.247 146.282 146.125 1.00 33.06 S ATOM 769 SG CYS A 136 66.118 149.773 150.301 1.00 31.18 S ATOM 809 SG CYS A 142 64.614 143.971 151.825 1.00 28.76 S ATOM 1511 SG CYS A 233 65.725 149.249 159.055 1.00 28.83 S ATOM 1139 SG CYS A 183 59.500 151.068 160.779 1.00 31.27 S ATOM 1187 SG CYS A 189 64.113 151.207 165.227 1.00 31.17 S ATOM 1163 SG CYS A 186 62.906 145.745 162.917 1.00 30.21 S ATOM 255 SG CYS A 69 59.636 139.783 165.830 1.00 28.80 S ATOM 338 SG CYS A 80 58.277 138.515 162.683 1.00 28.82 S ATOM 363 SG CYS A 83 58.137 133.468 165.249 1.00 31.60 S ATOM 465 SG CYS A 97 59.550 135.679 168.119 1.00 31.65 S ATOM 7999 SG CYS B 384 49.159 141.927 165.583 1.00 36.27 S ATOM 8019 SG CYS B 387 45.129 144.794 164.786 1.00 34.85 S ATOM 7980 SG CYS B 381 49.054 147.099 169.790 1.00 46.04 S ATOM 8350 SG CYS B 427 45.363 142.114 170.948 1.00 38.85 S ATOM 14839 SG CYS H 127 29.476 156.848 170.187 1.00 75.27 S ATOM 14873 SG CYS H 132 26.208 157.240 169.644 1.00 81.82 S ATOM 15142 SG CYS H 168 29.982 152.807 172.857 1.00 78.60 S ATOM 15165 SG CYS H 172 27.006 151.889 173.342 1.00 90.95 S ATOM 16767 SG CYS I 172 71.603 141.152 126.155 1.00 40.23 S ATOM 16789 SG CYS I 175 70.623 147.122 127.591 1.00 55.82 S ATOM 16741 SG CYS I 169 75.479 145.325 123.595 1.00 40.54 S ATOM 16514 SG CYS I 140 76.151 143.558 129.517 1.00 43.54 S ATOM 16463 SG CYS I 133 68.002 149.965 138.363 1.00 33.83 S ATOM 16444 SG CYS I 130 70.818 155.388 135.281 1.00 55.82 S ATOM 16819 SG CYS I 179 65.826 151.621 133.431 1.00 35.03 S ATOM 16486 SG CYS I 136 72.224 149.385 133.783 1.00 55.82 S ATOM 17632 SG CYS K 86 79.696 139.232 113.389 1.00 34.38 S ATOM 17626 SG CYS K 85 77.669 133.748 115.881 1.00 37.75 S ATOM 18364 SG CYS K 180 76.771 138.988 119.021 1.00 31.48 S ATOM 18136 SG CYS K 150 82.209 137.123 119.233 1.00 27.08 S ATOM 45835 SG CYS M 97 55.437 161.408 140.109 1.00 33.96 S ATOM 46030 SG CYS M 125 58.674 160.624 142.016 1.00 31.76 S ATOM 46057 SG CYS M 128 58.753 162.408 139.048 1.00 28.54 S Time building chain proxies: 25.72, per 1000 atoms: 0.40 Number of scatterers: 64866 At special positions: 0 Unit cell: (232.668, 191.268, 218.592, 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 310 16.00 P 46 15.00 O 11837 8.00 N 10537 7.00 C 42107 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS U 46 " - pdb=" SG CYS U 78 " distance=2.04 Simple disulfide: pdb=" SG CYS U 56 " - pdb=" SG CYS U 68 " distance=2.05 Simple disulfide: pdb=" SG CYS U 90 " - pdb=" SG CYS U 121 " distance=2.04 Simple disulfide: pdb=" SG CYS U 100 " - pdb=" SG CYS U 111 " distance=2.04 Simple disulfide: pdb=" SG CYS d 51 " - pdb=" SG CYS d 63 " distance=2.04 Simple disulfide: pdb=" SG CYS 8 26 " - pdb=" SG CYS 8 57 " distance=2.04 Simple disulfide: pdb=" SG CYS 8 36 " - pdb=" SG CYS 8 47 " distance=2.04 Simple disulfide: pdb=" SG CYS 9 15 " - pdb=" SG CYS 9 47 " distance=2.04 Simple disulfide: pdb=" SG CYS 9 25 " - pdb=" SG CYS 9 37 " distance=2.02 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: 22.17 Conformation dependent library (CDL) restraints added in 7.2 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES A 803 " pdb="FE1 FES A 803 " - pdb=" SG CYS A 80 " pdb="FE1 FES A 803 " - pdb=" SG CYS A 69 " pdb="FE2 FES A 803 " - pdb=" SG CYS A 83 " pdb="FE2 FES A 803 " - pdb=" SG CYS A 97 " pdb=" FES H 301 " pdb="FE1 FES H 301 " - pdb=" SG CYS H 132 " pdb="FE1 FES H 301 " - pdb=" SG CYS H 127 " pdb="FE2 FES H 301 " - pdb=" SG CYS H 172 " pdb="FE2 FES H 301 " - pdb=" SG CYS H 168 " pdb=" SF4 A 801 " pdb="FE2 SF4 A 801 " - pdb=" NE2 HIS A 129 " pdb="FE3 SF4 A 801 " - pdb=" SG CYS A 136 " pdb="FE4 SF4 A 801 " - pdb=" SG CYS A 142 " pdb="FE1 SF4 A 801 " - pdb=" SG CYS A 133 " pdb=" SF4 A 802 " pdb="FE1 SF4 A 802 " - pdb=" SG CYS A 233 " pdb="FE2 SF4 A 802 " - pdb=" SG CYS A 183 " pdb="FE4 SF4 A 802 " - pdb=" SG CYS A 186 " pdb="FE3 SF4 A 802 " - pdb=" SG CYS A 189 " pdb=" SF4 B 501 " pdb="FE4 SF4 B 501 " - pdb=" SG CYS B 427 " pdb="FE1 SF4 B 501 " - pdb=" SG CYS B 384 " pdb="FE3 SF4 B 501 " - pdb=" SG CYS B 381 " pdb="FE2 SF4 B 501 " - pdb=" SG CYS B 387 " pdb=" SF4 I 502 " pdb="FE2 SF4 I 502 " - pdb=" SG CYS I 175 " pdb="FE4 SF4 I 502 " - pdb=" SG CYS I 140 " pdb="FE3 SF4 I 502 " - pdb=" SG CYS I 169 " pdb="FE1 SF4 I 502 " - pdb=" SG CYS I 172 " pdb=" SF4 I 503 " pdb="FE4 SF4 I 503 " - pdb=" SG CYS I 136 " pdb="FE3 SF4 I 503 " - pdb=" SG CYS I 179 " pdb="FE2 SF4 I 503 " - pdb=" SG CYS I 130 " pdb="FE1 SF4 I 503 " - pdb=" SG CYS I 133 " pdb=" SF4 K 301 " pdb="FE3 SF4 K 301 " - pdb=" SG CYS K 180 " pdb="FE1 SF4 K 301 " - pdb=" SG CYS K 86 " pdb="FE2 SF4 K 301 " - pdb=" SG CYS K 85 " pdb="FE4 SF4 K 301 " - pdb=" SG CYS K 150 " Number of angles added : 81 Zn2+ tetrahedral coordination pdb=" ZN M 201 " pdb="ZN ZN M 201 " - pdb=" NE2 HIS M 110 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 128 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 125 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 97 " Number of angles added : 3 15628 Ramachandran restraints generated. 7814 Oldfield, 0 Emsley, 7814 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14812 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 328 helices and 33 sheets defined 53.0% alpha, 4.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.74 Creating SS restraints... Processing helix chain 'A' and resid 54 through 60 Processing helix chain 'A' and resid 112 through 126 Processing helix chain 'A' and resid 143 through 151 Processing helix chain 'A' and resid 180 through 182 No H-bonds generated for 'chain 'A' and resid 180 through 182' Processing helix chain 'A' and resid 188 through 195 Processing helix chain 'A' and resid 208 through 210 No H-bonds generated for 'chain 'A' and resid 208 through 210' Processing helix chain 'A' and resid 226 through 232 Processing helix chain 'A' and resid 249 through 251 No H-bonds generated for 'chain 'A' and resid 249 through 251' Processing helix chain 'A' and resid 295 through 304 removed outlier: 5.060A pdb=" N CYS A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ASP A 302 " --> pdb=" O ARG A 298 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N GLY A 303 " --> pdb=" O PHE A 299 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LEU A 304 " --> pdb=" O ALA A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 339 Processing helix chain 'A' and resid 343 through 345 No H-bonds generated for 'chain 'A' and resid 343 through 345' Processing helix chain 'A' and resid 356 through 368 Processing helix chain 'A' and resid 392 through 394 No H-bonds generated for 'chain 'A' and resid 392 through 394' Processing helix chain 'A' and resid 401 through 406 Processing helix chain 'A' and resid 417 through 420 No H-bonds generated for 'chain 'A' and resid 417 through 420' Processing helix chain 'A' and resid 422 through 434 Processing helix chain 'A' and resid 459 through 466 Processing helix chain 'A' and resid 469 through 476 Processing helix chain 'A' and resid 486 through 489 No H-bonds generated for 'chain 'A' and resid 486 through 489' Processing helix chain 'A' and resid 492 through 507 removed outlier: 4.505A pdb=" N GLY A 495 " --> pdb=" O GLU A 492 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE A 501 " --> pdb=" O PHE A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 528 through 534 Processing helix chain 'A' and resid 541 through 544 Processing helix chain 'A' and resid 578 through 581 No H-bonds generated for 'chain 'A' and resid 578 through 581' Processing helix chain 'A' and resid 592 through 594 No H-bonds generated for 'chain 'A' and resid 592 through 594' Processing helix chain 'A' and resid 622 through 633 Processing helix chain 'A' and resid 642 through 652 Processing helix chain 'A' and resid 668 through 675 Processing helix chain 'A' and resid 702 through 706 Processing helix chain 'A' and resid 708 through 716 Processing helix chain 'A' and resid 722 through 724 No H-bonds generated for 'chain 'A' and resid 722 through 724' Processing helix chain 'B' and resid 42 through 45 removed outlier: 4.141A pdb=" N TYR B 45 " --> pdb=" O GLN B 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 42 through 45' Processing helix chain 'B' and resid 52 through 58 Processing helix chain 'B' and resid 64 through 69 Processing helix chain 'B' and resid 72 through 82 Processing helix chain 'B' and resid 94 through 100 Processing helix chain 'B' and resid 128 through 135 Processing helix chain 'B' and resid 137 through 151 removed outlier: 3.531A pdb=" N VAL B 141 " --> pdb=" O PRO B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 181 Processing helix chain 'B' and resid 206 through 209 Processing helix chain 'B' and resid 211 through 219 Processing helix chain 'B' and resid 237 through 239 No H-bonds generated for 'chain 'B' and resid 237 through 239' Processing helix chain 'B' and resid 247 through 259 removed outlier: 3.728A pdb=" N ALA B 253 " --> pdb=" O THR B 249 " (cutoff:3.500A) Proline residue: B 254 - end of helix Processing helix chain 'B' and resid 261 through 266 Processing helix chain 'B' and resid 298 through 305 Processing helix chain 'B' and resid 313 through 315 No H-bonds generated for 'chain 'B' and resid 313 through 315' Processing helix chain 'B' and resid 333 through 335 No H-bonds generated for 'chain 'B' and resid 333 through 335' Processing helix chain 'B' and resid 341 through 346 Processing helix chain 'B' and resid 365 through 379 Processing helix chain 'B' and resid 385 through 403 removed outlier: 4.572A pdb=" N THR B 392 " --> pdb=" O ARG B 388 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N TRP B 393 " --> pdb=" O GLU B 389 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ARG B 400 " --> pdb=" O LYS B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 424 removed outlier: 3.667A pdb=" N GLU B 422 " --> pdb=" O LYS B 419 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N GLY B 423 " --> pdb=" O ASP B 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 458 Proline residue: B 436 - end of helix removed outlier: 3.726A pdb=" N ARG B 445 " --> pdb=" O ILE B 441 " (cutoff:3.500A) Proline residue: B 446 - end of helix Processing helix chain 'C' and resid 123 through 129 removed outlier: 3.900A pdb=" N GLU C 128 " --> pdb=" O GLU C 124 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N TYR C 129 " --> pdb=" O LYS C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 140 Proline residue: C 137 - end of helix removed outlier: 3.949A pdb=" N ASP C 140 " --> pdb=" O LEU C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 162 Processing helix chain 'C' and resid 168 through 197 Processing helix chain 'C' and resid 201 through 221 removed outlier: 3.599A pdb=" N GLU C 209 " --> pdb=" O TRP C 205 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N PHE C 216 " --> pdb=" O LYS C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 265 removed outlier: 4.096A pdb=" N GLN C 253 " --> pdb=" O MET C 249 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N GLY C 255 " --> pdb=" O ALA C 251 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N ASP C 256 " --> pdb=" O THR C 252 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE C 261 " --> pdb=" O ARG C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 275 Processing helix chain 'C' and resid 283 through 289 Processing helix chain 'C' and resid 293 through 299 removed outlier: 4.602A pdb=" N GLY C 298 " --> pdb=" O MET C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 308 No H-bonds generated for 'chain 'C' and resid 305 through 308' Processing helix chain 'C' and resid 329 through 353 removed outlier: 3.766A pdb=" N ARG C 341 " --> pdb=" O MET C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 371 through 374 No H-bonds generated for 'chain 'C' and resid 371 through 374' Processing helix chain 'C' and resid 378 through 389 Processing helix chain 'C' and resid 430 through 441 removed outlier: 4.535A pdb=" N ASP C 439 " --> pdb=" O LEU C 435 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N HIS C 440 " --> pdb=" O GLY C 436 " (cutoff:3.500A) Processing helix chain 'C' and resid 447 through 457 Processing helix chain 'G' and resid 36 through 38 No H-bonds generated for 'chain 'G' and resid 36 through 38' Processing helix chain 'G' and resid 42 through 44 No H-bonds generated for 'chain 'G' and resid 42 through 44' Processing helix chain 'G' and resid 60 through 81 removed outlier: 3.759A pdb=" N ARG G 63 " --> pdb=" O PRO G 60 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N GLN G 66 " --> pdb=" O ARG G 63 " (cutoff:3.500A) Processing helix chain 'G' and resid 102 through 114 removed outlier: 4.578A pdb=" N ILE G 106 " --> pdb=" O SER G 103 " (cutoff:3.500A) Proline residue: G 107 - end of helix Processing helix chain 'G' and resid 173 through 186 removed outlier: 3.793A pdb=" N TRP G 177 " --> pdb=" O GLY G 174 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N MET G 185 " --> pdb=" O ALA G 182 " (cutoff:3.500A) Processing helix chain 'G' and resid 245 through 248 Processing helix chain 'G' and resid 264 through 266 No H-bonds generated for 'chain 'G' and resid 264 through 266' Processing helix chain 'H' and resid 49 through 61 removed outlier: 3.983A pdb=" N LYS H 61 " --> pdb=" O GLU H 57 " (cutoff:3.500A) Processing helix chain 'H' and resid 67 through 81 removed outlier: 4.474A pdb=" N MET H 72 " --> pdb=" O ALA H 69 " (cutoff:3.500A) Proline residue: H 73 - end of helix Processing helix chain 'H' and resid 87 through 96 Processing helix chain 'H' and resid 101 through 110 Processing helix chain 'H' and resid 130 through 135 removed outlier: 3.671A pdb=" N CYS H 135 " --> pdb=" O PRO H 131 " (cutoff:3.500A) Processing helix chain 'H' and resid 137 through 147 Processing helix chain 'H' and resid 190 through 202 removed outlier: 3.845A pdb=" N LYS H 195 " --> pdb=" O GLU H 191 " (cutoff:3.500A) Processing helix chain 'H' and resid 235 through 237 No H-bonds generated for 'chain 'H' and resid 235 through 237' Processing helix chain 'I' and resid 70 through 79 Processing helix chain 'I' and resid 81 through 95 removed outlier: 3.504A pdb=" N GLN I 93 " --> pdb=" O VAL I 89 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N PHE I 94 " --> pdb=" O VAL I 90 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N PHE I 95 " --> pdb=" O LEU I 91 " (cutoff:3.500A) Processing helix chain 'I' and resid 135 through 139 Processing helix chain 'I' and resid 174 through 178 Processing helix chain 'I' and resid 197 through 200 Processing helix chain 'I' and resid 204 through 228 removed outlier: 5.675A pdb=" N LEU I 216 " --> pdb=" O ASP I 212 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N GLU I 217 " --> pdb=" O LYS I 213 " (cutoff:3.500A) Proline residue: I 227 - end of helix Processing helix chain 'K' and resid 48 through 50 No H-bonds generated for 'chain 'K' and resid 48 through 50' Processing helix chain 'K' and resid 56 through 74 Processing helix chain 'K' and resid 85 through 94 removed outlier: 3.527A pdb=" N VAL K 93 " --> pdb=" O MET K 90 " (cutoff:3.500A) Processing helix chain 'K' and resid 100 through 103 Processing helix chain 'K' and resid 128 through 136 Processing helix chain 'K' and resid 149 through 153 Processing helix chain 'K' and resid 155 through 157 No H-bonds generated for 'chain 'K' and resid 155 through 157' Processing helix chain 'K' and resid 167 through 169 No H-bonds generated for 'chain 'K' and resid 167 through 169' Processing helix chain 'K' and resid 184 through 199 Processing helix chain 'K' and resid 204 through 209 Processing helix chain 'L' and resid 3 through 16 Processing helix chain 'L' and resid 23 through 47 Processing helix chain 'L' and resid 50 through 81 removed outlier: 3.982A pdb=" N LEU L 80 " --> pdb=" O SER L 76 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ARG L 81 " --> pdb=" O TYR L 77 " (cutoff:3.500A) Processing helix chain 'S' and resid 53 through 64 removed outlier: 4.505A pdb=" N GLN S 61 " --> pdb=" O LEU S 57 " (cutoff:3.500A) Processing helix chain 'S' and resid 85 through 98 removed outlier: 3.959A pdb=" N TYR S 98 " --> pdb=" O ILE S 94 " (cutoff:3.500A) Processing helix chain 'S' and resid 105 through 108 No H-bonds generated for 'chain 'S' and resid 105 through 108' Processing helix chain 'S' and resid 113 through 137 Processing helix chain 'S' and resid 164 through 188 removed outlier: 4.294A pdb=" N ALA S 173 " --> pdb=" O TYR S 169 " (cutoff:3.500A) Proline residue: S 174 - end of helix removed outlier: 4.076A pdb=" N ARG S 188 " --> pdb=" O VAL S 184 " (cutoff:3.500A) Processing helix chain 'S' and resid 191 through 206 Processing helix chain 'S' and resid 208 through 211 Processing helix chain 'S' and resid 215 through 228 removed outlier: 3.935A pdb=" N ASP S 219 " --> pdb=" O GLU S 215 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ALA S 220 " --> pdb=" O ASN S 216 " (cutoff:3.500A) Processing helix chain 'S' and resid 234 through 237 No H-bonds generated for 'chain 'S' and resid 234 through 237' Processing helix chain 'S' and resid 239 through 241 No H-bonds generated for 'chain 'S' and resid 239 through 241' Processing helix chain 'j' and resid 30 through 40 Processing helix chain 'j' and resid 42 through 44 No H-bonds generated for 'chain 'j' and resid 42 through 44' Processing helix chain 'j' and resid 50 through 59 Processing helix chain 'j' and resid 62 through 73 Processing helix chain '1' and resid 3 through 33 removed outlier: 3.569A pdb=" N THR 1 23 " --> pdb=" O VAL 1 19 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N VAL 1 24 " --> pdb=" O ALA 1 20 " (cutoff:3.500A) Processing helix chain '1' and resid 44 through 46 No H-bonds generated for 'chain '1' and resid 44 through 46' Processing helix chain '1' and resid 49 through 59 Processing helix chain '1' and resid 70 through 90 Proline residue: 1 77 - end of helix removed outlier: 4.475A pdb=" N TRP 1 88 " --> pdb=" O ALA 1 84 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N VAL 1 89 " --> pdb=" O LEU 1 85 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N VAL 1 90 " --> pdb=" O ILE 1 86 " (cutoff:3.500A) Processing helix chain '1' and resid 105 through 116 removed outlier: 3.875A pdb=" N GLY 1 116 " --> pdb=" O ILE 1 112 " (cutoff:3.500A) Processing helix chain '1' and resid 118 through 127 removed outlier: 3.913A pdb=" N GLY 1 124 " --> pdb=" O SER 1 120 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N TRP 1 125 " --> pdb=" O LEU 1 121 " (cutoff:3.500A) Processing helix chain '1' and resid 131 through 160 removed outlier: 3.822A pdb=" N ILE 1 149 " --> pdb=" O SER 1 145 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N PHE 1 160 " --> pdb=" O ILE 1 156 " (cutoff:3.500A) Processing helix chain '1' and resid 166 through 174 removed outlier: 3.889A pdb=" N GLN 1 173 " --> pdb=" O ILE 1 169 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ARG 1 174 " --> pdb=" O ILE 1 170 " (cutoff:3.500A) Processing helix chain '1' and resid 178 through 181 No H-bonds generated for 'chain '1' and resid 178 through 181' Processing helix chain '1' and resid 183 through 196 Processing helix chain '1' and resid 204 through 206 No H-bonds generated for 'chain '1' and resid 204 through 206' Processing helix chain '1' and resid 215 through 218 removed outlier: 4.551A pdb=" N GLU 1 218 " --> pdb=" O TYR 1 215 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 215 through 218' Processing helix chain '1' and resid 221 through 246 removed outlier: 3.522A pdb=" N SER 1 233 " --> pdb=" O ALA 1 230 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU 1 246 " --> pdb=" O GLY 1 243 " (cutoff:3.500A) Processing helix chain '1' and resid 256 through 262 Processing helix chain '1' and resid 268 through 299 Processing helix chain '1' and resid 305 through 314 Processing helix chain '1' and resid 316 through 334 Proline residue: 1 328 - end of helix Processing helix chain '2' and resid 3 through 15 Processing helix chain '2' and resid 18 through 38 removed outlier: 3.779A pdb=" N ASN 2 21 " --> pdb=" O LEU 2 18 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N ARG 2 22 " --> pdb=" O SER 2 19 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU 2 38 " --> pdb=" O VAL 2 35 " (cutoff:3.500A) Processing helix chain '2' and resid 40 through 49 removed outlier: 6.279A pdb=" N ASN 2 48 " --> pdb=" O LEU 2 45 " (cutoff:3.500A) Processing helix chain '2' and resid 63 through 84 removed outlier: 3.781A pdb=" N TYR 2 83 " --> pdb=" O ILE 2 79 " (cutoff:3.500A) Processing helix chain '2' and resid 91 through 96 Processing helix chain '2' and resid 103 through 118 Processing helix chain '2' and resid 123 through 142 Processing helix chain '2' and resid 148 through 179 Processing helix chain '2' and resid 189 through 194 Processing helix chain '2' and resid 198 through 212 removed outlier: 3.894A pdb=" N LYS 2 211 " --> pdb=" O GLY 2 207 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ILE 2 212 " --> pdb=" O LEU 2 208 " (cutoff:3.500A) Processing helix chain '2' and resid 219 through 227 Processing helix chain '2' and resid 230 through 236 removed outlier: 4.180A pdb=" N TYR 2 235 " --> pdb=" O LEU 2 231 " (cutoff:3.500A) Processing helix chain '2' and resid 239 through 251 Processing helix chain '2' and resid 258 through 274 Processing helix chain '2' and resid 281 through 301 removed outlier: 4.068A pdb=" N LEU 2 299 " --> pdb=" O TYR 2 295 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LEU 2 300 " --> pdb=" O MET 2 296 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N LEU 2 301 " --> pdb=" O MET 2 297 " (cutoff:3.500A) Processing helix chain '2' and resid 306 through 331 removed outlier: 3.733A pdb=" N ILE 2 331 " --> pdb=" O ILE 2 327 " (cutoff:3.500A) Processing helix chain '2' and resid 347 through 350 Processing helix chain '2' and resid 353 through 356 No H-bonds generated for 'chain '2' and resid 353 through 356' Processing helix chain '2' and resid 358 through 372 Processing helix chain '2' and resid 378 through 392 Processing helix chain '2' and resid 396 through 421 removed outlier: 3.914A pdb=" N LEU 2 411 " --> pdb=" O LEU 2 407 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N TYR 2 412 " --> pdb=" O ILE 2 408 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N LEU 2 416 " --> pdb=" O TYR 2 412 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LEU 2 417 " --> pdb=" O TYR 2 413 " (cutoff:3.500A) Processing helix chain '2' and resid 437 through 452 Processing helix chain '2' and resid 454 through 467 removed outlier: 4.993A pdb=" N SER 2 458 " --> pdb=" O ILE 2 455 " (cutoff:3.500A) Processing helix chain '3' and resid 3 through 25 Proline residue: 3 12 - end of helix Processing helix chain '3' and resid 32 through 35 No H-bonds generated for 'chain '3' and resid 32 through 35' Processing helix chain '3' and resid 54 through 77 removed outlier: 3.710A pdb=" N ALA 3 60 " --> pdb=" O PHE 3 56 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU 3 64 " --> pdb=" O ALA 3 60 " (cutoff:3.500A) Proline residue: 3 65 - end of helix removed outlier: 3.732A pdb=" N LEU 3 73 " --> pdb=" O GLU 3 69 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N LEU 3 74 " --> pdb=" O ILE 3 70 " (cutoff:3.500A) Proline residue: 3 75 - end of helix Processing helix chain '3' and resid 80 through 107 removed outlier: 6.083A pdb=" N ASN 3 85 " --> pdb=" O TYR 3 81 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N TYR 3 86 " --> pdb=" O LEU 3 82 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLY 3 101 " --> pdb=" O ILE 3 97 " (cutoff:3.500A) Processing helix chain '4' and resid 7 through 21 Processing helix chain '4' and resid 24 through 44 Processing helix chain '4' and resid 83 through 103 removed outlier: 3.672A pdb=" N PHE 4 88 " --> pdb=" O LEU 4 84 " (cutoff:3.500A) Proline residue: 4 97 - end of helix removed outlier: 4.138A pdb=" N ASN 4 103 " --> pdb=" O THR 4 99 " (cutoff:3.500A) Processing helix chain '4' and resid 111 through 130 removed outlier: 3.610A pdb=" N TRP 4 130 " --> pdb=" O LEU 4 126 " (cutoff:3.500A) Processing helix chain '4' and resid 134 through 155 removed outlier: 4.282A pdb=" N THR 4 144 " --> pdb=" O LEU 4 140 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N LEU 4 145 " --> pdb=" O PHE 4 141 " (cutoff:3.500A) Proline residue: 4 146 - end of helix Processing helix chain '4' and resid 160 through 189 removed outlier: 3.946A pdb=" N THR 4 171 " --> pdb=" O VAL 4 167 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N PHE 4 177 " --> pdb=" O SER 4 173 " (cutoff:3.500A) Processing helix chain '4' and resid 197 through 199 No H-bonds generated for 'chain '4' and resid 197 through 199' Processing helix chain '4' and resid 204 through 221 removed outlier: 3.756A pdb=" N LEU 4 212 " --> pdb=" O THR 4 208 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLY 4 213 " --> pdb=" O ILE 4 209 " (cutoff:3.500A) Processing helix chain '4' and resid 229 through 237 removed outlier: 4.317A pdb=" N VAL 4 233 " --> pdb=" O VAL 4 229 " (cutoff:3.500A) Processing helix chain '4' and resid 240 through 248 Processing helix chain '4' and resid 250 through 261 removed outlier: 3.820A pdb=" N ALA 4 254 " --> pdb=" O ILE 4 250 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU 4 255 " --> pdb=" O LEU 4 251 " (cutoff:3.500A) Processing helix chain '4' and resid 267 through 294 Proline residue: 4 275 - end of helix removed outlier: 3.959A pdb=" N LEU 4 293 " --> pdb=" O SER 4 289 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ARG 4 294 " --> pdb=" O LEU 4 290 " (cutoff:3.500A) Processing helix chain '4' and resid 298 through 317 removed outlier: 3.557A pdb=" N SER 4 306 " --> pdb=" O ILE 4 302 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE 4 307 " --> pdb=" O ALA 4 303 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER 4 308 " --> pdb=" O TYR 4 304 " (cutoff:3.500A) Processing helix chain '4' and resid 322 through 348 Proline residue: 4 340 - end of helix Processing helix chain '4' and resid 350 through 354 Processing helix chain '4' and resid 370 through 383 Processing helix chain '4' and resid 390 through 405 Processing helix chain '4' and resid 407 through 432 removed outlier: 4.438A pdb=" N ILE 4 415 " --> pdb=" O GLY 4 411 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N SER 4 416 " --> pdb=" O ILE 4 412 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N VAL 4 417 " --> pdb=" O SER 4 413 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N LEU 4 418 " --> pdb=" O CYS 4 414 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS 4 430 " --> pdb=" O LYS 4 426 " (cutoff:3.500A) Processing helix chain '4' and resid 448 through 466 Processing helix chain '4' and resid 468 through 475 removed outlier: 4.597A pdb=" N ASN 4 473 " --> pdb=" O ILE 4 470 " (cutoff:3.500A) Processing helix chain '4' and resid 478 through 481 No H-bonds generated for 'chain '4' and resid 478 through 481' Processing helix chain '5' and resid 4 through 55 Proline residue: 5 12 - end of helix Proline residue: 5 19 - end of helix removed outlier: 6.182A pdb=" N ARG 5 24 " --> pdb=" O LEU 5 20 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N GLN 5 25 " --> pdb=" O PHE 5 21 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N TYR 5 28 " --> pdb=" O ARG 5 24 " (cutoff:3.500A) removed outlier: 9.386A pdb=" N VAL 5 29 " --> pdb=" O GLN 5 25 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N PHE 5 30 " --> pdb=" O LEU 5 26 " (cutoff:3.500A) Processing helix chain '5' and resid 83 through 106 removed outlier: 3.567A pdb=" N ILE 5 104 " --> pdb=" O HIS 5 100 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLY 5 105 " --> pdb=" O ILE 5 101 " (cutoff:3.500A) Processing helix chain '5' and resid 114 through 132 Processing helix chain '5' and resid 136 through 154 removed outlier: 3.726A pdb=" N GLY 5 147 " --> pdb=" O TRP 5 143 " (cutoff:3.500A) Processing helix chain '5' and resid 161 through 192 Processing helix chain '5' and resid 197 through 206 removed outlier: 5.257A pdb=" N TYR 5 205 " --> pdb=" O PHE 5 201 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N LEU 5 206 " --> pdb=" O ALA 5 202 " (cutoff:3.500A) Processing helix chain '5' and resid 209 through 226 Processing helix chain '5' and resid 234 through 241 removed outlier: 4.295A pdb=" N MET 5 240 " --> pdb=" O LEU 5 236 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N GLU 5 241 " --> pdb=" O THR 5 237 " (cutoff:3.500A) Processing helix chain '5' and resid 244 through 252 removed outlier: 3.541A pdb=" N ALA 5 252 " --> pdb=" O SER 5 248 " (cutoff:3.500A) Processing helix chain '5' and resid 257 through 272 removed outlier: 5.253A pdb=" N ASN 5 268 " --> pdb=" O LEU 5 264 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N ILE 5 269 " --> pdb=" O ARG 5 265 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N TYR 5 272 " --> pdb=" O ASN 5 268 " (cutoff:3.500A) Processing helix chain '5' and resid 274 through 296 Processing helix chain '5' and resid 301 through 321 Processing helix chain '5' and resid 325 through 351 removed outlier: 3.824A pdb=" N PHE 5 337 " --> pdb=" O LEU 5 333 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N PHE 5 338 " --> pdb=" O GLY 5 334 " (cutoff:3.500A) Processing helix chain '5' and resid 360 through 362 No H-bonds generated for 'chain '5' and resid 360 through 362' Processing helix chain '5' and resid 371 through 384 Processing helix chain '5' and resid 391 through 405 removed outlier: 3.630A pdb=" N THR 5 395 " --> pdb=" O THR 5 391 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N ILE 5 398 " --> pdb=" O TYR 5 394 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N THR 5 403 " --> pdb=" O ILE 5 399 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N TYR 5 404 " --> pdb=" O ILE 5 400 " (cutoff:3.500A) Processing helix chain '5' and resid 409 through 437 removed outlier: 3.525A pdb=" N TYR 5 412 " --> pdb=" O ILE 5 409 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TYR 5 434 " --> pdb=" O LYS 5 431 " (cutoff:3.500A) Processing helix chain '5' and resid 445 through 450 Processing helix chain '5' and resid 456 through 480 Proline residue: 5 461 - end of helix removed outlier: 6.088A pdb=" N GLY 5 473 " --> pdb=" O ALA 5 469 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N TRP 5 474 " --> pdb=" O MET 5 470 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N ASP 5 478 " --> pdb=" O TRP 5 474 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N ILE 5 479 " --> pdb=" O ILE 5 475 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TYR 5 480 " --> pdb=" O LEU 5 476 " (cutoff:3.500A) Processing helix chain '5' and resid 499 through 504 removed outlier: 3.710A pdb=" N GLU 5 503 " --> pdb=" O TYR 5 499 " (cutoff:3.500A) Processing helix chain '5' and resid 508 through 531 Proline residue: 5 514 - end of helix Processing helix chain '5' and resid 533 through 536 No H-bonds generated for 'chain '5' and resid 533 through 536' Processing helix chain '5' and resid 541 through 551 Processing helix chain '5' and resid 553 through 563 removed outlier: 5.383A pdb=" N ASP 5 557 " --> pdb=" O LEU 5 554 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLN 5 558 " --> pdb=" O VAL 5 555 " (cutoff:3.500A) Processing helix chain '5' and resid 565 through 578 Processing helix chain '5' and resid 583 through 586 No H-bonds generated for 'chain '5' and resid 583 through 586' Processing helix chain '5' and resid 589 through 604 Processing helix chain '5' and resid 615 through 637 Processing helix chain '5' and resid 639 through 654 removed outlier: 3.700A pdb=" N ILE 5 643 " --> pdb=" O PHE 5 639 " (cutoff:3.500A) Proline residue: 5 644 - end of helix Processing helix chain '6' and resid 3 through 23 removed outlier: 4.669A pdb=" N ILE 6 9 " --> pdb=" O THR 6 5 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N GLU 6 10 " --> pdb=" O TYR 6 6 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N PHE 6 22 " --> pdb=" O ILE 6 17 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N ILE 6 23 " --> pdb=" O LEU 6 18 " (cutoff:3.500A) Processing helix chain '6' and resid 29 through 49 Processing helix chain '6' and resid 53 through 62 Processing helix chain '6' and resid 67 through 77 Processing helix chain '6' and resid 146 through 155 Processing helix chain '6' and resid 159 through 180 Proline residue: 6 176 - end of helix Processing helix chain 'g' and resid 12 through 22 Processing helix chain 'g' and resid 24 through 50 removed outlier: 3.823A pdb=" N GLY g 36 " --> pdb=" O ILE g 32 " (cutoff:3.500A) Proline residue: g 37 - end of helix Proline residue: g 45 - end of helix Processing helix chain 'D' and resid 5 through 33 Proline residue: D 10 - end of helix Processing helix chain 'D' and resid 44 through 57 Processing helix chain 'D' and resid 72 through 75 Processing helix chain 'E' and resid 64 through 76 removed outlier: 4.191A pdb=" N TYR E 68 " --> pdb=" O PHE E 64 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N HIS E 76 " --> pdb=" O LYS E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 96 removed outlier: 3.551A pdb=" N LYS E 90 " --> pdb=" O GLU E 87 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ARG E 91 " --> pdb=" O MET E 88 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N HIS E 92 " --> pdb=" O ALA E 89 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL E 95 " --> pdb=" O HIS E 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 119 Processing helix chain 'E' and resid 140 through 144 Processing helix chain 'E' and resid 146 through 158 Processing helix chain 'E' and resid 178 through 193 Processing helix chain 'E' and resid 214 through 218 Processing helix chain 'E' and resid 238 through 250 Processing helix chain 'E' and resid 252 through 254 No H-bonds generated for 'chain 'E' and resid 252 through 254' Processing helix chain 'E' and resid 269 through 280 Processing helix chain 'E' and resid 291 through 303 removed outlier: 4.475A pdb=" N ALA E 303 " --> pdb=" O LYS E 299 " (cutoff:3.500A) Processing helix chain 'E' and resid 311 through 318 removed outlier: 4.027A pdb=" N PHE E 318 " --> pdb=" O VAL E 314 " (cutoff:3.500A) Processing helix chain 'E' and resid 330 through 333 Processing helix chain 'E' and resid 340 through 351 removed outlier: 5.039A pdb=" N PHE E 345 " --> pdb=" O PRO E 341 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N LYS E 346 " --> pdb=" O ASP E 342 " (cutoff:3.500A) Proline residue: E 350 - end of helix Processing helix chain 'F' and resid 42 through 60 Processing helix chain 'F' and resid 66 through 84 Processing helix chain 'F' and resid 88 through 95 Processing helix chain 'F' and resid 100 through 120 removed outlier: 3.841A pdb=" N GLU F 119 " --> pdb=" O LYS F 115 " (cutoff:3.500A) Processing helix chain 'J' and resid 25 through 50 Processing helix chain 'J' and resid 59 through 62 No H-bonds generated for 'chain 'J' and resid 59 through 62' Processing helix chain 'J' and resid 67 through 89 Processing helix chain 'J' and resid 94 through 112 removed outlier: 3.983A pdb=" N ARG J 111 " --> pdb=" O VAL J 107 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N THR J 112 " --> pdb=" O LEU J 108 " (cutoff:3.500A) Processing helix chain 'J' and resid 115 through 135 Processing helix chain 'J' and resid 147 through 149 No H-bonds generated for 'chain 'J' and resid 147 through 149' Processing helix chain 'J' and resid 172 through 179 Processing helix chain 'J' and resid 190 through 193 No H-bonds generated for 'chain 'J' and resid 190 through 193' Processing helix chain 'M' and resid 33 through 35 No H-bonds generated for 'chain 'M' and resid 33 through 35' Processing helix chain 'M' and resid 53 through 60 Processing helix chain 'M' and resid 69 through 71 No H-bonds generated for 'chain 'M' and resid 69 through 71' Processing helix chain 'M' and resid 78 through 84 Processing helix chain 'O' and resid 33 through 41 Processing helix chain 'O' and resid 49 through 51 No H-bonds generated for 'chain 'O' and resid 49 through 51' Processing helix chain 'O' and resid 66 through 80 Processing helix chain 'O' and resid 86 through 90 Processing helix chain 'O' and resid 95 through 101 Processing helix chain 'P' and resid 18 through 42 removed outlier: 3.584A pdb=" N ARG P 24 " --> pdb=" O GLU P 20 " (cutoff:3.500A) Proline residue: P 37 - end of helix Processing helix chain 'P' and resid 49 through 63 removed outlier: 4.362A pdb=" N HIS P 63 " --> pdb=" O GLU P 59 " (cutoff:3.500A) Processing helix chain 'P' and resid 69 through 87 Processing helix chain 'P' and resid 93 through 99 removed outlier: 3.592A pdb=" N LYS P 98 " --> pdb=" O ALA P 94 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N TYR P 99 " --> pdb=" O GLN P 95 " (cutoff:3.500A) Processing helix chain 'P' and resid 115 through 121 Processing helix chain 'Q' and resid 52 through 65 Processing helix chain 'Q' and resid 89 through 103 removed outlier: 3.893A pdb=" N VAL Q 93 " --> pdb=" O SER Q 89 " (cutoff:3.500A) Processing helix chain 'Q' and resid 109 through 114 removed outlier: 3.548A pdb=" N ASP Q 113 " --> pdb=" O ASP Q 109 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLU Q 114 " --> pdb=" O HIS Q 110 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 109 through 114' Processing helix chain 'Q' and resid 118 through 127 Processing helix chain 'R' and resid 9 through 29 Processing helix chain 'R' and resid 33 through 52 removed outlier: 3.661A pdb=" N ASN R 50 " --> pdb=" O LYS R 46 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N GLN R 52 " --> pdb=" O ASP R 48 " (cutoff:3.500A) Processing helix chain 'R' and resid 56 through 72 Processing helix chain 'U' and resid 32 through 60 removed outlier: 5.077A pdb=" N TYR U 40 " --> pdb=" O LEU U 36 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N PHE U 41 " --> pdb=" O SER U 37 " (cutoff:3.500A) Proline residue: U 48 - end of helix Processing helix chain 'U' and resid 64 through 67 No H-bonds generated for 'chain 'U' and resid 64 through 67' Processing helix chain 'U' and resid 69 through 89 Processing helix chain 'U' and resid 91 through 104 Processing helix chain 'U' and resid 108 through 110 No H-bonds generated for 'chain 'U' and resid 108 through 110' Processing helix chain 'U' and resid 112 through 126 removed outlier: 3.524A pdb=" N LEU U 117 " --> pdb=" O LYS U 113 " (cutoff:3.500A) Processing helix chain 'U' and resid 142 through 144 No H-bonds generated for 'chain 'U' and resid 142 through 144' Processing helix chain 'U' and resid 157 through 169 Processing helix chain 'W' and resid 30 through 95 Proline residue: W 71 - end of helix Processing helix chain 'X' and resid 28 through 33 Processing helix chain 'X' and resid 37 through 60 Proline residue: X 51 - end of helix Processing helix chain 'X' and resid 72 through 99 Processing helix chain 'X' and resid 105 through 120 Processing helix chain 'X' and resid 133 through 143 Processing helix chain 'X' and resid 146 through 149 Processing helix chain 'Y' and resid 50 through 54 Processing helix chain 'Y' and resid 115 through 125 Processing helix chain 'Y' and resid 144 through 148 Processing helix chain 'Z' and resid 9 through 11 No H-bonds generated for 'chain 'Z' and resid 9 through 11' Processing helix chain 'Z' and resid 19 through 28 Processing helix chain 'Z' and resid 49 through 51 No H-bonds generated for 'chain 'Z' and resid 49 through 51' Processing helix chain 'Z' and resid 53 through 56 Processing helix chain 'Z' and resid 74 through 76 No H-bonds generated for 'chain 'Z' and resid 74 through 76' Processing helix chain 'Z' and resid 91 through 100 Processing helix chain 'Z' and resid 111 through 123 removed outlier: 3.616A pdb=" N THR Z 115 " --> pdb=" O GLY Z 111 " (cutoff:3.500A) Processing helix chain 'Z' and resid 128 through 134 Processing helix chain 'Z' and resid 137 through 143 Processing helix chain 'Z' and resid 167 through 169 No H-bonds generated for 'chain 'Z' and resid 167 through 169' Processing helix chain 'a' and resid 28 through 36 removed outlier: 3.565A pdb=" N GLU a 33 " --> pdb=" O PHE a 29 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLU a 34 " --> pdb=" O ASP a 30 " (cutoff:3.500A) Proline residue: a 35 - end of helix Processing helix chain 'a' and resid 74 through 76 No H-bonds generated for 'chain 'a' and resid 74 through 76' Processing helix chain 'a' and resid 90 through 113 removed outlier: 3.984A pdb=" N TYR a 113 " --> pdb=" O TYR a 109 " (cutoff:3.500A) Processing helix chain 'a' and resid 126 through 130 Processing helix chain 'b' and resid 3 through 24 Processing helix chain 'b' and resid 33 through 63 removed outlier: 3.761A pdb=" N VAL b 37 " --> pdb=" O PRO b 33 " (cutoff:3.500A) Processing helix chain 'c' and resid 14 through 17 Processing helix chain 'c' and resid 19 through 21 No H-bonds generated for 'chain 'c' and resid 19 through 21' Processing helix chain 'c' and resid 23 through 26 No H-bonds generated for 'chain 'c' and resid 23 through 26' Processing helix chain 'c' and resid 34 through 48 Processing helix chain 'd' and resid 20 through 74 Proline residue: d 57 - end of helix removed outlier: 5.053A pdb=" N PHE d 60 " --> pdb=" O GLY d 56 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N GLU d 61 " --> pdb=" O PRO d 57 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N ASN d 65 " --> pdb=" O GLU d 61 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N LEU d 66 " --> pdb=" O ASP d 62 " (cutoff:3.500A) Processing helix chain 'd' and resid 83 through 86 No H-bonds generated for 'chain 'd' and resid 83 through 86' Processing helix chain 'e' and resid 21 through 50 Proline residue: e 47 - end of helix Processing helix chain 'f' and resid 20 through 36 removed outlier: 6.395A pdb=" N GLY f 31 " --> pdb=" O LYS f 27 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N ALA f 32 " --> pdb=" O ASN f 28 " (cutoff:3.500A) Processing helix chain 'f' and resid 73 through 84 Processing helix chain 'h' and resid 5 through 15 Processing helix chain 'h' and resid 17 through 26 Processing helix chain 'h' and resid 70 through 72 No H-bonds generated for 'chain 'h' and resid 70 through 72' Processing helix chain 'h' and resid 77 through 81 Processing helix chain 'h' and resid 89 through 91 No H-bonds generated for 'chain 'h' and resid 89 through 91' Processing helix chain 'i' and resid 26 through 51 removed outlier: 3.548A pdb=" N LEU i 49 " --> pdb=" O SER i 45 " (cutoff:3.500A) Proline residue: i 50 - end of helix Processing helix chain 'i' and resid 61 through 77 Processing helix chain 'n' and resid 19 through 45 Processing helix chain 'n' and resid 51 through 53 No H-bonds generated for 'chain 'n' and resid 51 through 53' Processing helix chain 'n' and resid 59 through 88 removed outlier: 3.660A pdb=" N ARG n 88 " --> pdb=" O HIS n 84 " (cutoff:3.500A) Processing helix chain 'n' and resid 93 through 96 No H-bonds generated for 'chain 'n' and resid 93 through 96' Processing helix chain '8' and resid 10 through 15 Processing helix chain '8' and resid 20 through 22 No H-bonds generated for 'chain '8' and resid 20 through 22' Processing helix chain '8' and resid 27 through 39 Proline residue: 8 32 - end of helix Processing helix chain '8' and resid 48 through 75 Processing helix chain '9' and resid 16 through 28 Processing helix chain '9' and resid 34 through 49 Proline residue: 9 39 - end of helix Processing helix chain '9' and resid 51 through 65 Processing helix chain '9' and resid 81 through 83 No H-bonds generated for 'chain '9' and resid 81 through 83' Processing sheet with id= A, first strand: chain 'A' and resid 36 through 41 Processing sheet with id= B, first strand: chain 'A' and resid 176 through 178 Processing sheet with id= C, first strand: chain 'A' and resid 203 through 205 Processing sheet with id= D, first strand: chain 'A' and resid 253 through 258 removed outlier: 6.599A pdb=" N LYS A 273 " --> pdb=" O VAL A 277 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N VAL A 277 " --> pdb=" O LYS A 273 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 312 through 316 removed outlier: 3.623A pdb=" N LYS A 319 " --> pdb=" O VAL A 316 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 374 through 376 removed outlier: 7.548A pdb=" N THR A 375 " --> pdb=" O PHE A 346 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N ALA A 348 " --> pdb=" O THR A 375 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N MET A 549 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N VAL A 349 " --> pdb=" O MET A 549 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N TRP A 551 " --> pdb=" O VAL A 349 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N PHE A 568 " --> pdb=" O VAL A 550 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N LEU A 552 " --> pdb=" O PHE A 568 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N VAL A 570 " --> pdb=" O LEU A 552 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N VAL A 585 " --> pdb=" O TYR A 571 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N GLY A 573 " --> pdb=" O VAL A 585 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N LEU A 587 " --> pdb=" O GLY A 573 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'A' and resid 438 through 442 Processing sheet with id= H, first strand: chain 'A' and resid 598 through 600 Processing sheet with id= I, first strand: chain 'B' and resid 244 through 246 removed outlier: 9.074A pdb=" N THR B 245 " --> pdb=" O TYR B 114 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N VAL B 116 " --> pdb=" O THR B 245 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ALA B 155 " --> pdb=" O LEU B 115 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N VAL B 117 " --> pdb=" O ALA B 155 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N TYR B 157 " --> pdb=" O VAL B 117 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ASP B 196 " --> pdb=" O ALA B 156 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N ILE B 158 " --> pdb=" O ASP B 196 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N TYR B 198 " --> pdb=" O ILE B 158 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N ILE B 160 " --> pdb=" O TYR B 198 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N HIS B 200 " --> pdb=" O ILE B 160 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'B' and resid 288 through 293 removed outlier: 6.262A pdb=" N VAL B 356 " --> pdb=" O SER B 281 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 472 through 474 Processing sheet with id= L, first strand: chain 'C' and resid 83 through 87 removed outlier: 3.637A pdb=" N ARG C 111 " --> pdb=" O GLU C 103 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N SER C 105 " --> pdb=" O ILE C 109 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N ILE C 109 " --> pdb=" O SER C 105 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 397 through 405 Processing sheet with id= N, first strand: chain 'G' and resid 122 through 130 removed outlier: 6.697A pdb=" N ASN G 143 " --> pdb=" O ILE G 124 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ILE G 126 " --> pdb=" O VAL G 141 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N VAL G 141 " --> pdb=" O ILE G 126 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ALA G 128 " --> pdb=" O GLU G 139 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N GLU G 139 " --> pdb=" O ALA G 128 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N LEU G 96 " --> pdb=" O ARG G 152 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N TYR G 158 " --> pdb=" O VAL G 100 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY G 88 " --> pdb=" O HIS G 99 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'G' and resid 220 through 225 Processing sheet with id= P, first strand: chain 'H' and resid 122 through 127 Processing sheet with id= Q, first strand: chain 'H' and resid 177 through 179 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: 6.164A pdb=" N GLU I 150 " --> pdb=" O THR I 159 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N THR I 159 " --> pdb=" O GLU I 150 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'K' and resid 116 through 120 removed outlier: 6.613A pdb=" N TRP K 143 " --> pdb=" O MET K 117 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N VAL K 119 " --> pdb=" O TRP K 143 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ILE K 145 " --> pdb=" O VAL K 119 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N VAL K 175 " --> pdb=" O SER K 146 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain '2' and resid 52 through 54 Processing sheet with id= V, first strand: chain '4' and resid 57 through 59 Processing sheet with id= W, first strand: chain '5' and resid 60 through 63 removed outlier: 3.920A pdb=" N ILE 5 60 " --> pdb=" O ILE 5 81 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain '5' and resid 66 through 70 removed outlier: 6.465A pdb=" N ILE 5 75 " --> pdb=" O TYR 5 67 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ASN 5 69 " --> pdb=" O LEU 5 73 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N LEU 5 73 " --> pdb=" O ASN 5 69 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'E' and resid 31 through 33 Processing sheet with id= Z, first strand: chain 'E' and resid 258 through 261 removed outlier: 6.659A pdb=" N ILE E 199 " --> pdb=" O PHE E 259 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N LEU E 261 " --> pdb=" O ILE E 199 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N ARG E 201 " --> pdb=" O LEU E 261 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N THR E 79 " --> pdb=" O ALA E 56 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N VAL E 58 " --> pdb=" O THR E 79 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N VAL E 81 " --> pdb=" O VAL E 58 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'E' and resid 223 through 225 Processing sheet with id= AB, first strand: chain 'M' and resid 20 through 22 Processing sheet with id= AC, first strand: chain 'M' and resid 88 through 90 Processing sheet with id= AD, first strand: chain 'M' and resid 94 through 97 Processing sheet with id= AE, first strand: chain 'Y' and resid 128 through 132 removed outlier: 4.539A pdb=" N GLN Y 62 " --> pdb=" O GLN Y 132 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'f' and resid 41 through 46 Processing sheet with id= AG, first strand: chain 'h' and resid 59 through 62 removed outlier: 3.624A pdb=" N GLY h 37 " --> pdb=" O PHE h 45 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N GLU h 47 " --> pdb=" O LEU h 35 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N LEU h 35 " --> pdb=" O GLU h 47 " (cutoff:3.500A) 2864 hydrogen bonds defined for protein. 7857 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: 19.14 Time building geometry restraints manager: 24.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.11 - 1.35: 20166 1.35 - 1.58: 45567 1.58 - 1.81: 549 1.81 - 2.04: 15 2.04 - 2.28: 80 Bond restraints: 66377 Sorted by residual: bond pdb=" C ARG H 215 " pdb=" N ARG H 216 " ideal model delta sigma weight residual 1.331 1.531 -0.200 1.33e-02 5.65e+03 2.25e+02 bond pdb=" C MET 6 30 " pdb=" N VAL 6 31 " ideal model delta sigma weight residual 1.335 1.214 0.121 1.26e-02 6.30e+03 9.20e+01 bond pdb=" C FME L 1 " pdb=" N PHE L 2 " ideal model delta sigma weight residual 1.329 1.462 -0.133 1.40e-02 5.10e+03 9.01e+01 bond pdb=" C TYR 2 52 " pdb=" N THR 2 53 " ideal model delta sigma weight residual 1.330 1.451 -0.122 1.39e-02 5.18e+03 7.65e+01 bond pdb=" C THR 6 76 " pdb=" N LEU 6 77 " ideal model delta sigma weight residual 1.332 1.213 0.119 1.36e-02 5.41e+03 7.63e+01 ... (remaining 66372 not shown) Histogram of bond angle deviations from ideal: 73.40 - 85.89: 77 85.89 - 98.38: 23 98.38 - 110.87: 24300 110.87 - 123.36: 63177 123.36 - 135.85: 2267 Bond angle restraints: 89844 Sorted by residual: angle pdb=" O ARG H 215 " pdb=" C ARG H 215 " pdb=" N ARG H 216 " ideal model delta sigma weight residual 123.42 135.85 -12.43 1.07e+00 8.73e-01 1.35e+02 angle pdb=" C ARG H 215 " pdb=" N ARG H 216 " pdb=" CA ARG H 216 " ideal model delta sigma weight residual 122.06 106.06 16.00 1.39e+00 5.18e-01 1.32e+02 angle pdb=" O ASN L 18 " pdb=" C ASN L 18 " pdb=" N ARG L 19 " ideal model delta sigma weight residual 122.96 135.45 -12.49 1.26e+00 6.30e-01 9.83e+01 angle pdb=" CA ASN L 18 " pdb=" C ASN L 18 " pdb=" N ARG L 19 " ideal model delta sigma weight residual 116.43 102.95 13.48 1.37e+00 5.33e-01 9.68e+01 angle pdb=" CA MET 6 30 " pdb=" C MET 6 30 " pdb=" N VAL 6 31 " ideal model delta sigma weight residual 116.92 106.17 10.75 1.16e+00 7.43e-01 8.59e+01 ... (remaining 89839 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.91: 38211 33.91 - 67.82: 1105 67.82 - 101.73: 101 101.73 - 135.64: 8 135.64 - 169.55: 2 Dihedral angle restraints: 39427 sinusoidal: 16358 harmonic: 23069 Sorted by residual: dihedral pdb=" C ASN 2 48 " pdb=" N ASN 2 48 " pdb=" CA ASN 2 48 " pdb=" CB ASN 2 48 " ideal model delta harmonic sigma weight residual -122.60 -144.42 21.82 0 2.50e+00 1.60e-01 7.61e+01 dihedral pdb=" N ASN 2 48 " pdb=" C ASN 2 48 " pdb=" CA ASN 2 48 " pdb=" CB ASN 2 48 " ideal model delta harmonic sigma weight residual 122.80 140.99 -18.19 0 2.50e+00 1.60e-01 5.29e+01 dihedral pdb=" C10 FMN B 502 " pdb=" C1' FMN B 502 " pdb=" N10 FMN B 502 " pdb=" C2' FMN B 502 " ideal model delta sinusoidal sigma weight residual -102.41 67.14 -169.55 1 2.00e+01 2.50e-03 4.76e+01 ... (remaining 39424 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.976: 9936 0.976 - 1.952: 0 1.952 - 2.928: 0 2.928 - 3.904: 0 3.904 - 4.880: 3 Chirality restraints: 9939 Sorted by residual: chirality pdb=" C1 T7X b 501 " pdb=" C2 T7X b 501 " pdb=" C6 T7X b 501 " pdb=" O1 T7X b 501 " both_signs ideal model delta sigma weight residual False -2.42 2.46 -4.88 2.00e-01 2.50e+01 5.95e+02 chirality pdb=" C1 T7X 3 201 " pdb=" C2 T7X 3 201 " pdb=" C6 T7X 3 201 " pdb=" O1 T7X 3 201 " both_signs ideal model delta sigma weight residual False -2.42 2.28 -4.70 2.00e-01 2.50e+01 5.52e+02 chirality pdb=" C1 T7X 2 502 " pdb=" C2 T7X 2 502 " pdb=" C6 T7X 2 502 " pdb=" O1 T7X 2 502 " both_signs ideal model delta sigma weight residual False -2.42 2.17 -4.59 2.00e-01 2.50e+01 5.26e+02 ... (remaining 9936 not shown) Planarity restraints: 11205 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 UQ9 C 601 " -0.001 2.00e-02 2.50e+03 1.31e-01 5.16e+02 pdb=" C1M UQ9 C 601 " 0.046 2.00e-02 2.50e+03 pdb=" C2 UQ9 C 601 " -0.191 2.00e-02 2.50e+03 pdb=" C3 UQ9 C 601 " -0.237 2.00e-02 2.50e+03 pdb=" C4 UQ9 C 601 " -0.075 2.00e-02 2.50e+03 pdb=" C5 UQ9 C 601 " 0.122 2.00e-02 2.50e+03 pdb=" C6 UQ9 C 601 " 0.158 2.00e-02 2.50e+03 pdb=" C7 UQ9 C 601 " -0.062 2.00e-02 2.50e+03 pdb=" O2 UQ9 C 601 " 0.128 2.00e-02 2.50e+03 pdb=" O3 UQ9 C 601 " 0.064 2.00e-02 2.50e+03 pdb=" O4 UQ9 C 601 " 0.168 2.00e-02 2.50e+03 pdb=" O5 UQ9 C 601 " -0.118 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" N FME 6 1 " 0.231 2.00e-02 2.50e+03 1.90e-01 3.61e+02 pdb=" CA FME 6 1 " -0.081 2.00e-02 2.50e+03 pdb=" CN FME 6 1 " -0.267 2.00e-02 2.50e+03 pdb=" O1 FME 6 1 " 0.117 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA FME L 1 " -0.059 2.00e-02 2.50e+03 1.05e-01 1.10e+02 pdb=" C FME L 1 " 0.181 2.00e-02 2.50e+03 pdb=" O FME L 1 " -0.068 2.00e-02 2.50e+03 pdb=" N PHE L 2 " -0.054 2.00e-02 2.50e+03 ... (remaining 11202 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 349 2.49 - 3.10: 50393 3.10 - 3.70: 102267 3.70 - 4.30: 155874 4.30 - 4.90: 252103 Nonbonded interactions: 560986 Sorted by model distance: nonbonded pdb=" CE1 TYR j 48 " pdb=" NH1 ARG 5 586 " model vdw 1.892 3.420 nonbonded pdb=" CZ2 TRP G 36 " pdb=" OE2 GLU G 37 " model vdw 1.906 3.340 nonbonded pdb=" O ALA f 4 " pdb=" CG2 THR f 40 " model vdw 1.940 3.460 nonbonded pdb=" O LYS B 57 " pdb=" ND2 ASN H 234 " model vdw 2.003 2.520 nonbonded pdb=" CB GLN f 24 " pdb=" OE2 GLU f 73 " model vdw 2.014 3.440 ... (remaining 560981 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=0.70 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: 3.130 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: 0.050 Extract box with map and model: 17.500 Check model and map are aligned: 0.700 Set scattering table: 0.430 Process input model: 141.970 Find NCS groups from input model: 1.830 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 168.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.200 66377 Z= 0.595 Angle : 1.087 26.512 89844 Z= 0.572 Chirality : 0.099 4.880 9939 Planarity : 0.006 0.190 11205 Dihedral : 15.473 169.551 24588 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 15.31 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.48 % Favored : 96.43 % Rotamer Outliers : 0.65 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 3.35 % 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: -0.16 (0.09), residues: 7814 helix: 0.55 (0.08), residues: 4160 sheet: -0.39 (0.25), residues: 412 loop : -0.84 (0.10), residues: 3242 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15628 Ramachandran restraints generated. 7814 Oldfield, 0 Emsley, 7814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15628 Ramachandran restraints generated. 7814 Oldfield, 0 Emsley, 7814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1426 residues out of total 6770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 1382 time to evaluate : 5.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 44 outliers final: 9 residues processed: 1409 average time/residue: 0.6569 time to fit residues: 1550.0036 Evaluate side-chains 962 residues out of total 6770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 953 time to evaluate : 5.617 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.5749 time to fit residues: 16.6667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 776 random chunks: chunk 655 optimal weight: 5.9990 chunk 588 optimal weight: 2.9990 chunk 326 optimal weight: 0.9990 chunk 200 optimal weight: 10.0000 chunk 396 optimal weight: 9.9990 chunk 314 optimal weight: 0.8980 chunk 608 optimal weight: 10.0000 chunk 235 optimal weight: 0.7980 chunk 369 optimal weight: 0.9980 chunk 452 optimal weight: 7.9990 chunk 704 optimal weight: 20.0000 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 GLN A 220 ASN A 267 ASN ** A 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 380 ASN A 607 GLN ** B 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 363 GLN ** C 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 150 ASN C 186 HIS H 145 GLN H 146 ASN H 224 GLN ** L 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 132 ASN ** S 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 238 GLN 1 307 ASN 2 29 ASN 2 48 ASN 2 50 GLN 2 119 HIS ** 3 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 235 HIS 5 299 ASN 5 312 GLN 5 452 HIS 5 617 ASN 6 140 ASN ** g 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 22 ASN g 71 GLN D 26 GLN D 76 HIS E 127 ASN J 31 GLN ** M 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 92 GLN Q 128 GLN U 8 HIS Y 93 ASN Y 123 ASN Z 148 ASN a 90 ASN ** a 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 58 ASN d 69 GLN ** f 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 22 ASN n 18 GLN 8 16 HIS Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.062 66377 Z= 0.201 Angle : 0.605 9.678 89844 Z= 0.309 Chirality : 0.042 0.210 9939 Planarity : 0.005 0.069 11205 Dihedral : 12.062 168.059 9760 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.60 % Favored : 97.36 % Rotamer Outliers : 1.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.35 % 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: 0.43 (0.09), residues: 7814 helix: 1.07 (0.08), residues: 4169 sheet: -0.22 (0.25), residues: 430 loop : -0.61 (0.11), residues: 3215 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15628 Ramachandran restraints generated. 7814 Oldfield, 0 Emsley, 7814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15628 Ramachandran restraints generated. 7814 Oldfield, 0 Emsley, 7814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1232 residues out of total 6770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 1116 time to evaluate : 5.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 116 outliers final: 67 residues processed: 1180 average time/residue: 0.6308 time to fit residues: 1253.1986 Evaluate side-chains 1024 residues out of total 6770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 957 time to evaluate : 5.671 Switching outliers to nearest non-outliers outliers start: 67 outliers final: 0 residues processed: 67 average time/residue: 0.4537 time to fit residues: 65.9638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 776 random chunks: chunk 391 optimal weight: 5.9990 chunk 218 optimal weight: 10.0000 chunk 586 optimal weight: 20.0000 chunk 479 optimal weight: 8.9990 chunk 194 optimal weight: 6.9990 chunk 705 optimal weight: 0.9990 chunk 762 optimal weight: 6.9990 chunk 628 optimal weight: 10.0000 chunk 700 optimal weight: 9.9990 chunk 240 optimal weight: 1.9990 chunk 566 optimal weight: 7.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 GLN ** A 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 380 ASN A 425 ASN ** A 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 443 ASN C 91 HIS C 284 GLN G 67 HIS H 146 ASN S 115 HIS S 167 GLN S 211 ASN 2 48 ASN 2 49 ASN 2 50 GLN 2 198 ASN ** 3 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 85 ASN ** 4 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 444 ASN 5 52 GLN 5 112 HIS 5 452 HIS ** 5 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 605 ASN ** 5 617 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 61 HIS J 149 GLN ** M 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 63 HIS P 72 GLN P 84 GLN Y 93 ASN Z 120 ASN a 146 GLN b 51 HIS d 4 HIS d 69 GLN ** f 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 22 ASN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.100 66377 Z= 0.377 Angle : 0.660 11.676 89844 Z= 0.334 Chirality : 0.046 0.273 9939 Planarity : 0.005 0.060 11205 Dihedral : 11.455 165.538 9760 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.54 % Favored : 96.43 % Rotamer Outliers : 1.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.35 % 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: 0.20 (0.09), residues: 7814 helix: 0.90 (0.08), residues: 4175 sheet: -0.38 (0.25), residues: 414 loop : -0.75 (0.11), residues: 3225 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15628 Ramachandran restraints generated. 7814 Oldfield, 0 Emsley, 7814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15628 Ramachandran restraints generated. 7814 Oldfield, 0 Emsley, 7814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1158 residues out of total 6770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 1023 time to evaluate : 5.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 135 outliers final: 75 residues processed: 1109 average time/residue: 0.6421 time to fit residues: 1204.1755 Evaluate side-chains 988 residues out of total 6770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 913 time to evaluate : 5.664 Switching outliers to nearest non-outliers outliers start: 75 outliers final: 0 residues processed: 75 average time/residue: 0.4863 time to fit residues: 76.8140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 776 random chunks: chunk 697 optimal weight: 8.9990 chunk 530 optimal weight: 6.9990 chunk 366 optimal weight: 6.9990 chunk 78 optimal weight: 4.9990 chunk 336 optimal weight: 5.9990 chunk 474 optimal weight: 9.9990 chunk 708 optimal weight: 30.0000 chunk 750 optimal weight: 0.3980 chunk 370 optimal weight: 5.9990 chunk 671 optimal weight: 6.9990 chunk 202 optimal weight: 10.0000 overall best weight: 4.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 367 ASN A 380 ASN ** B 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 372 ASN I 93 GLN ** S 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 11 GLN ** 3 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 15 ASN ** 4 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 452 HIS ** 5 617 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 158 ASN 6 183 HIS J 87 ASN J 149 GLN ** M 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 63 HIS ** Q 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 93 ASN ** f 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 25 ASN i 22 ASN i 78 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.2956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.061 66377 Z= 0.377 Angle : 0.642 10.185 89844 Z= 0.324 Chirality : 0.045 0.286 9939 Planarity : 0.005 0.061 11205 Dihedral : 11.127 166.567 9760 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.46 % Favored : 96.52 % Rotamer Outliers : 1.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.35 % 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: 7814 helix: 0.85 (0.08), residues: 4168 sheet: -0.62 (0.25), residues: 411 loop : -0.81 (0.11), residues: 3235 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15628 Ramachandran restraints generated. 7814 Oldfield, 0 Emsley, 7814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15628 Ramachandran restraints generated. 7814 Oldfield, 0 Emsley, 7814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1110 residues out of total 6770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 983 time to evaluate : 5.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 127 outliers final: 75 residues processed: 1061 average time/residue: 0.6398 time to fit residues: 1140.7444 Evaluate side-chains 971 residues out of total 6770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 896 time to evaluate : 5.669 Switching outliers to nearest non-outliers outliers start: 75 outliers final: 0 residues processed: 75 average time/residue: 0.4737 time to fit residues: 74.9618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 776 random chunks: chunk 624 optimal weight: 10.0000 chunk 425 optimal weight: 9.9990 chunk 10 optimal weight: 2.9990 chunk 558 optimal weight: 8.9990 chunk 309 optimal weight: 7.9990 chunk 640 optimal weight: 1.9990 chunk 518 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 383 optimal weight: 3.9990 chunk 673 optimal weight: 7.9990 chunk 189 optimal weight: 5.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 380 ASN ** B 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 284 GLN ** S 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 469 GLN 4 481 ASN 5 452 HIS ** 5 617 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 140 ASN 6 152 ASN D 76 HIS E 165 HIS J 149 GLN ** M 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 63 HIS ** Q 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 93 ASN c 18 GLN ** f 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 18 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.3150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.052 66377 Z= 0.273 Angle : 0.589 10.961 89844 Z= 0.298 Chirality : 0.043 0.278 9939 Planarity : 0.005 0.059 11205 Dihedral : 10.817 166.535 9760 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.52 % Favored : 96.46 % Rotamer Outliers : 1.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.35 % 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: 0.23 (0.09), residues: 7814 helix: 0.97 (0.08), residues: 4161 sheet: -0.62 (0.25), residues: 431 loop : -0.75 (0.11), residues: 3222 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15628 Ramachandran restraints generated. 7814 Oldfield, 0 Emsley, 7814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15628 Ramachandran restraints generated. 7814 Oldfield, 0 Emsley, 7814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1056 residues out of total 6770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 971 time to evaluate : 6.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 85 outliers final: 43 residues processed: 1021 average time/residue: 0.6606 time to fit residues: 1132.9264 Evaluate side-chains 949 residues out of total 6770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 906 time to evaluate : 5.683 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 0 residues processed: 43 average time/residue: 0.4926 time to fit residues: 47.6106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 776 random chunks: chunk 252 optimal weight: 9.9990 chunk 675 optimal weight: 0.3980 chunk 148 optimal weight: 2.9990 chunk 440 optimal weight: 5.9990 chunk 185 optimal weight: 0.9990 chunk 750 optimal weight: 3.9990 chunk 623 optimal weight: 9.9990 chunk 347 optimal weight: 6.9990 chunk 62 optimal weight: 8.9990 chunk 248 optimal weight: 20.0000 chunk 394 optimal weight: 0.8980 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 380 ASN ** A 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 93 GLN L 37 ASN S 52 ASN ** S 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 85 ASN ** 4 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 235 HIS 4 469 GLN 5 251 HIS 5 452 HIS ** 5 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 562 HIS ** 5 617 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 140 ASN E 127 ASN E 165 HIS J 87 ASN J 149 GLN ** M 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 128 GLN Y 157 HIS c 18 GLN e 11 ASN ** f 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.3360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.068 66377 Z= 0.201 Angle : 0.555 12.954 89844 Z= 0.280 Chirality : 0.041 0.207 9939 Planarity : 0.004 0.058 11205 Dihedral : 10.318 166.822 9760 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.98 % Favored : 96.99 % Rotamer Outliers : 1.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.09), residues: 7814 helix: 1.11 (0.08), residues: 4160 sheet: -0.54 (0.25), residues: 431 loop : -0.66 (0.11), residues: 3223 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15628 Ramachandran restraints generated. 7814 Oldfield, 0 Emsley, 7814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15628 Ramachandran restraints generated. 7814 Oldfield, 0 Emsley, 7814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1080 residues out of total 6770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 999 time to evaluate : 5.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 81 outliers final: 43 residues processed: 1037 average time/residue: 0.6582 time to fit residues: 1143.0813 Evaluate side-chains 950 residues out of total 6770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 907 time to evaluate : 5.639 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 0 residues processed: 43 average time/residue: 0.4871 time to fit residues: 47.1664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 776 random chunks: chunk 723 optimal weight: 5.9990 chunk 84 optimal weight: 20.0000 chunk 427 optimal weight: 5.9990 chunk 548 optimal weight: 40.0000 chunk 424 optimal weight: 10.0000 chunk 632 optimal weight: 0.7980 chunk 419 optimal weight: 4.9990 chunk 747 optimal weight: 40.0000 chunk 468 optimal weight: 5.9990 chunk 455 optimal weight: 3.9990 chunk 345 optimal weight: 1.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 93 GLN S 115 HIS ** S 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 85 ASN ** 4 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 442 ASN ** 5 617 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 140 ASN D 76 HIS E 165 HIS J 149 GLN ** M 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 63 HIS Q 128 GLN ** U 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 18 GLN 8 52 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.3527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.057 66377 Z= 0.295 Angle : 0.600 13.497 89844 Z= 0.302 Chirality : 0.043 0.216 9939 Planarity : 0.005 0.058 11205 Dihedral : 10.239 166.417 9760 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.84 % Favored : 96.14 % Rotamer Outliers : 1.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.09), residues: 7814 helix: 1.05 (0.08), residues: 4146 sheet: -0.57 (0.25), residues: 417 loop : -0.71 (0.11), residues: 3251 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15628 Ramachandran restraints generated. 7814 Oldfield, 0 Emsley, 7814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15628 Ramachandran restraints generated. 7814 Oldfield, 0 Emsley, 7814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1039 residues out of total 6770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 951 time to evaluate : 5.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 88 outliers final: 56 residues processed: 1002 average time/residue: 0.6572 time to fit residues: 1101.7184 Evaluate side-chains 961 residues out of total 6770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 905 time to evaluate : 5.661 Switching outliers to nearest non-outliers outliers start: 56 outliers final: 0 residues processed: 56 average time/residue: 0.4985 time to fit residues: 59.6536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 776 random chunks: chunk 462 optimal weight: 0.8980 chunk 298 optimal weight: 0.6980 chunk 446 optimal weight: 5.9990 chunk 225 optimal weight: 4.9990 chunk 146 optimal weight: 0.9980 chunk 144 optimal weight: 0.9990 chunk 475 optimal weight: 0.0270 chunk 509 optimal weight: 7.9990 chunk 369 optimal weight: 3.9990 chunk 69 optimal weight: 0.0070 chunk 587 optimal weight: 10.0000 overall best weight: 0.5256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 380 ASN ** A 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 115 HIS ** S 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 29 ASN ** 2 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 85 ASN ** 4 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 429 ASN ** 4 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 52 GLN 5 251 HIS ** 5 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 617 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 140 ASN D 44 GLN ** E 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 149 GLN ** M 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 73 ASN n 18 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.3685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.063 66377 Z= 0.152 Angle : 0.548 14.325 89844 Z= 0.275 Chirality : 0.040 0.255 9939 Planarity : 0.004 0.059 11205 Dihedral : 9.720 167.414 9760 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.52 % Favored : 97.45 % Rotamer Outliers : 0.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.35 % 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: 0.56 (0.10), residues: 7814 helix: 1.24 (0.08), residues: 4152 sheet: -0.46 (0.25), residues: 427 loop : -0.59 (0.11), residues: 3235 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15628 Ramachandran restraints generated. 7814 Oldfield, 0 Emsley, 7814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15628 Ramachandran restraints generated. 7814 Oldfield, 0 Emsley, 7814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1085 residues out of total 6770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 1042 time to evaluate : 5.838 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 43 outliers final: 19 residues processed: 1061 average time/residue: 0.6778 time to fit residues: 1205.6568 Evaluate side-chains 957 residues out of total 6770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 938 time to evaluate : 5.810 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.5622 time to fit residues: 27.2681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 776 random chunks: chunk 680 optimal weight: 10.0000 chunk 716 optimal weight: 0.0870 chunk 653 optimal weight: 7.9990 chunk 696 optimal weight: 20.0000 chunk 419 optimal weight: 3.9990 chunk 303 optimal weight: 5.9990 chunk 547 optimal weight: 30.0000 chunk 213 optimal weight: 0.5980 chunk 629 optimal weight: 4.9990 chunk 659 optimal weight: 9.9990 chunk 694 optimal weight: 5.9990 overall best weight: 3.1364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 HIS ** A 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 149 HIS S 115 HIS ** S 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 29 ASN ** 2 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 469 GLN ** 5 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 617 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 140 ASN D 76 HIS ** M 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 128 GLN R 104 HIS ** U 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 18 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.3770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.070 66377 Z= 0.269 Angle : 0.593 14.258 89844 Z= 0.297 Chirality : 0.042 0.276 9939 Planarity : 0.004 0.053 11205 Dihedral : 9.719 166.694 9760 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.57 % Favored : 96.40 % Rotamer Outliers : 0.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.35 % 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: 0.45 (0.10), residues: 7814 helix: 1.12 (0.08), residues: 4157 sheet: -0.48 (0.25), residues: 411 loop : -0.62 (0.11), residues: 3246 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15628 Ramachandran restraints generated. 7814 Oldfield, 0 Emsley, 7814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15628 Ramachandran restraints generated. 7814 Oldfield, 0 Emsley, 7814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 995 residues out of total 6770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 950 time to evaluate : 6.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 45 outliers final: 28 residues processed: 969 average time/residue: 0.6781 time to fit residues: 1102.9883 Evaluate side-chains 951 residues out of total 6770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 923 time to evaluate : 5.693 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.4950 time to fit residues: 34.0981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 776 random chunks: chunk 457 optimal weight: 20.0000 chunk 737 optimal weight: 8.9990 chunk 449 optimal weight: 20.0000 chunk 349 optimal weight: 4.9990 chunk 512 optimal weight: 5.9990 chunk 773 optimal weight: 5.9990 chunk 711 optimal weight: 0.5980 chunk 615 optimal weight: 1.9990 chunk 63 optimal weight: 20.0000 chunk 475 optimal weight: 0.4980 chunk 377 optimal weight: 2.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 ASN ** A 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 115 HIS ** S 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 48 ASN 2 50 GLN ** 3 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 113 GLN 5 251 HIS ** 5 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 617 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 131 ASN D 76 HIS J 97 HIS J 149 GLN ** M 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 18 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.3866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 66377 Z= 0.217 Angle : 0.578 14.780 89844 Z= 0.290 Chirality : 0.042 0.270 9939 Planarity : 0.004 0.055 11205 Dihedral : 9.604 166.965 9760 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.11 % Favored : 96.86 % Rotamer Outliers : 0.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.35 % 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: 0.48 (0.10), residues: 7814 helix: 1.15 (0.08), residues: 4151 sheet: -0.42 (0.26), residues: 411 loop : -0.60 (0.11), residues: 3252 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15628 Ramachandran restraints generated. 7814 Oldfield, 0 Emsley, 7814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15628 Ramachandran restraints generated. 7814 Oldfield, 0 Emsley, 7814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 978 residues out of total 6770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 954 time to evaluate : 6.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 10 residues processed: 961 average time/residue: 0.7149 time to fit residues: 1159.3579 Evaluate side-chains 940 residues out of total 6770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 930 time to evaluate : 5.788 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.5522 time to fit residues: 18.2734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 776 random chunks: chunk 488 optimal weight: 9.9990 chunk 655 optimal weight: 1.9990 chunk 188 optimal weight: 2.9990 chunk 567 optimal weight: 0.0000 chunk 90 optimal weight: 2.9990 chunk 171 optimal weight: 6.9990 chunk 616 optimal weight: 9.9990 chunk 258 optimal weight: 5.9990 chunk 633 optimal weight: 5.9990 chunk 78 optimal weight: 7.9990 chunk 113 optimal weight: 10.0000 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 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 115 HIS ** S 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 50 GLN ** 3 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 251 HIS 5 452 HIS ** 5 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 617 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 140 ASN D 76 HIS ** M 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 18 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.137764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.113909 restraints weight = 109798.505| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 2.12 r_work: 0.3299 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3204 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3204 r_free = 0.3204 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3203 r_free = 0.3203 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3203 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.3942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.076 66377 Z= 0.249 Angle : 0.596 14.610 89844 Z= 0.298 Chirality : 0.042 0.281 9939 Planarity : 0.004 0.055 11205 Dihedral : 9.574 166.641 9760 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.54 % Favored : 96.43 % Rotamer Outliers : 0.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.35 % 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: 0.44 (0.09), residues: 7814 helix: 1.12 (0.08), residues: 4142 sheet: -0.47 (0.26), residues: 414 loop : -0.61 (0.11), residues: 3258 =============================================================================== Job complete usr+sys time: 18508.30 seconds wall clock time: 324 minutes 1.64 seconds (19441.64 seconds total)