Starting phenix.real_space_refine (version: dev) on Sun Feb 26 07:09:11 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qsd_14127/02_2023/7qsd_14127_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qsd_14127/02_2023/7qsd_14127.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qsd_14127/02_2023/7qsd_14127_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qsd_14127/02_2023/7qsd_14127_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qsd_14127/02_2023/7qsd_14127_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qsd_14127/02_2023/7qsd_14127.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qsd_14127/02_2023/7qsd_14127.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qsd_14127/02_2023/7qsd_14127_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qsd_14127/02_2023/7qsd_14127_updated.pdb" } resolution = 3.1 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= -0.003 sd= 0.973 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "A TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 32": "OE1" <-> "OE2" Residue "A PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 112": "OE1" <-> "OE2" Residue "B ASP 35": "OD1" <-> "OD2" Residue "B GLU 58": "OE1" <-> "OE2" Residue "B ASP 68": "OD1" <-> "OD2" Residue "B ARG 71": "NH1" <-> "NH2" Residue "B ARG 111": "NH1" <-> "NH2" Residue "B TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 8": "NH1" <-> "NH2" Residue "C ARG 12": "NH1" <-> "NH2" Residue "C ASP 16": "OD1" <-> "OD2" Residue "C GLU 27": "OE1" <-> "OE2" Residue "C GLU 31": "OE1" <-> "OE2" Residue "C GLU 47": "OE1" <-> "OE2" Residue "C GLU 49": "OE1" <-> "OE2" Residue "C GLU 131": "OE1" <-> "OE2" Residue "C GLU 133": "OE1" <-> "OE2" Residue "C PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 149": "NH1" <-> "NH2" Residue "C PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 177": "OD1" <-> "OD2" Residue "C GLU 179": "OE1" <-> "OE2" Residue "D ARG 2": "NH1" <-> "NH2" Residue "D TYR 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 88": "OE1" <-> "OE2" Residue "D GLU 92": "OE1" <-> "OE2" Residue "D TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 107": "OD1" <-> "OD2" Residue "D GLU 123": "OE1" <-> "OE2" Residue "D PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 143": "OE1" <-> "OE2" Residue "D PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 175": "OE1" <-> "OE2" Residue "D GLU 179": "OE1" <-> "OE2" Residue "D PHE 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 221": "NH1" <-> "NH2" Residue "D GLU 227": "OE1" <-> "OE2" Residue "D ARG 233": "NH1" <-> "NH2" Residue "D TYR 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 343": "OE1" <-> "OE2" Residue "D GLU 368": "OE1" <-> "OE2" Residue "D PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 403": "OD1" <-> "OD2" Residue "D GLU 427": "OE1" <-> "OE2" Residue "E PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 26": "OE1" <-> "OE2" Residue "E GLU 32": "OE1" <-> "OE2" Residue "E TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 52": "OD1" <-> "OD2" Residue "E GLU 71": "OE1" <-> "OE2" Residue "E PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 118": "OE1" <-> "OE2" Residue "E GLU 143": "OE1" <-> "OE2" Residue "E ASP 168": "OD1" <-> "OD2" Residue "E GLU 170": "OE1" <-> "OE2" Residue "E GLU 171": "OE1" <-> "OE2" Residue "E ARG 190": "NH1" <-> "NH2" Residue "F PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 32": "NH1" <-> "NH2" Residue "F ASP 98": "OD1" <-> "OD2" Residue "F GLU 109": "OE1" <-> "OE2" Residue "F ARG 112": "NH1" <-> "NH2" Residue "F ARG 132": "NH1" <-> "NH2" Residue "F TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 139": "NH1" <-> "NH2" Residue "F PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 189": "OE1" <-> "OE2" Residue "F GLU 194": "OE1" <-> "OE2" Residue "F GLU 197": "OE1" <-> "OE2" Residue "F PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 248": "OE1" <-> "OE2" Residue "F ARG 249": "NH1" <-> "NH2" Residue "F PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 269": "OE1" <-> "OE2" Residue "F GLU 270": "OE1" <-> "OE2" Residue "F GLU 278": "OE1" <-> "OE2" Residue "F ASP 292": "OD1" <-> "OD2" Residue "F GLU 313": "OE1" <-> "OE2" Residue "F ARG 349": "NH1" <-> "NH2" Residue "F PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 357": "OE1" <-> "OE2" Residue "F GLU 394": "OE1" <-> "OE2" Residue "F PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 427": "OE1" <-> "OE2" Residue "F GLU 428": "OE1" <-> "OE2" Residue "F ARG 429": "NH1" <-> "NH2" Residue "F PHE 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 10": "OE1" <-> "OE2" Residue "G ARG 39": "NH1" <-> "NH2" Residue "G GLU 44": "OE1" <-> "OE2" Residue "G ARG 53": "NH1" <-> "NH2" Residue "G GLU 60": "OE1" <-> "OE2" Residue "G GLU 84": "OE1" <-> "OE2" Residue "G GLU 165": "OE1" <-> "OE2" Residue "G ASP 180": "OD1" <-> "OD2" Residue "G GLU 188": "OE1" <-> "OE2" Residue "G GLU 194": "OE1" <-> "OE2" Residue "G ARG 218": "NH1" <-> "NH2" Residue "G GLU 226": "OE1" <-> "OE2" Residue "G ARG 243": "NH1" <-> "NH2" Residue "G ARG 253": "NH1" <-> "NH2" Residue "G GLU 256": "OE1" <-> "OE2" Residue "G ASP 265": "OD1" <-> "OD2" Residue "G ARG 285": "NH1" <-> "NH2" Residue "G ARG 302": "NH1" <-> "NH2" Residue "G ASP 314": "OD1" <-> "OD2" Residue "G ASP 341": "OD1" <-> "OD2" Residue "G GLU 346": "OE1" <-> "OE2" Residue "G ASP 357": "OD1" <-> "OD2" Residue "G GLU 372": "OE1" <-> "OE2" Residue "G GLU 373": "OE1" <-> "OE2" Residue "G ARG 385": "NH1" <-> "NH2" Residue "G ARG 418": "NH1" <-> "NH2" Residue "G ASP 420": "OD1" <-> "OD2" Residue "G GLU 512": "OE1" <-> "OE2" Residue "G PHE 523": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 596": "OD1" <-> "OD2" Residue "G GLU 605": "OE1" <-> "OE2" Residue "G ASP 617": "OD1" <-> "OD2" Residue "G GLU 625": "OE1" <-> "OE2" Residue "G GLU 637": "OE1" <-> "OE2" Residue "G GLU 647": "OE1" <-> "OE2" Residue "H PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 24": "OE1" <-> "OE2" Residue "H ARG 25": "NH1" <-> "NH2" Residue "H ARG 34": "NH1" <-> "NH2" Residue "H ARG 62": "NH1" <-> "NH2" Residue "H PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 199": "OD1" <-> "OD2" Residue "H PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 283": "OD1" <-> "OD2" Residue "I ARG 8": "NH1" <-> "NH2" Residue "I TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 44": "OE1" <-> "OE2" Residue "I TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 95": "OE1" <-> "OE2" Residue "I ARG 108": "NH1" <-> "NH2" Residue "I ASP 110": "OD1" <-> "OD2" Residue "I PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 138": "OE1" <-> "OE2" Residue "I GLU 145": "OE1" <-> "OE2" Residue "I GLU 152": "OE1" <-> "OE2" Residue "J PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 77": "OE1" <-> "OE2" Residue "J PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 139": "OE1" <-> "OE2" Residue "J GLU 170": "OE1" <-> "OE2" Residue "J ARG 173": "NH1" <-> "NH2" Residue "K GLU 34": "OE1" <-> "OE2" Residue "K TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 60": "OE1" <-> "OE2" Residue "L TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 161": "NH1" <-> "NH2" Residue "L ARG 262": "NH1" <-> "NH2" Residue "L PHE 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 268": "OE1" <-> "OE2" Residue "L ASP 297": "OD1" <-> "OD2" Residue "L PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 393": "OD1" <-> "OD2" Residue "L TYR 403": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 429": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 437": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 463": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 498": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 503": "OE1" <-> "OE2" Residue "L PHE 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 559": "OE1" <-> "OE2" Residue "L GLU 606": "OE1" <-> "OE2" Residue "M ASP 59": "OD1" <-> "OD2" Residue "M PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 142": "NH1" <-> "NH2" Residue "M TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 255": "OD1" <-> "OD2" Residue "M PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 432": "NH1" <-> "NH2" Residue "M GLU 433": "OE1" <-> "OE2" Residue "N TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 295": "NH1" <-> "NH2" Residue "N PHE 325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 347": "OE1" <-> "OE2" Residue "O TYR 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 44": "OE1" <-> "OE2" Residue "O GLU 53": "OE1" <-> "OE2" Residue "O GLU 125": "OE1" <-> "OE2" Residue "O TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 131": "OD1" <-> "OD2" Residue "O GLU 178": "OE1" <-> "OE2" Residue "O GLU 216": "OE1" <-> "OE2" Residue "O TYR 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 237": "OD1" <-> "OD2" Residue "O ASP 244": "OD1" <-> "OD2" Residue "O ASP 250": "OD1" <-> "OD2" Residue "O PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 302": "NH1" <-> "NH2" Residue "O TYR 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 305": "NH1" <-> "NH2" Residue "O TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 314": "OD1" <-> "OD2" Residue "P ARG 40": "NH1" <-> "NH2" Residue "P ARG 50": "NH1" <-> "NH2" Residue "P TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 82": "NH1" <-> "NH2" Residue "P ARG 97": "NH1" <-> "NH2" Residue "P GLU 98": "OE1" <-> "OE2" Residue "P ASP 108": "OD1" <-> "OD2" Residue "P GLU 123": "OE1" <-> "OE2" Residue "P GLU 127": "OE1" <-> "OE2" Residue "P TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 147": "NH1" <-> "NH2" Residue "P ARG 157": "NH1" <-> "NH2" Residue "P GLU 158": "OE1" <-> "OE2" Residue "P GLU 162": "OE1" <-> "OE2" Residue "P PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 175": "OE1" <-> "OE2" Residue "P ASP 176": "OD1" <-> "OD2" Residue "P TYR 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 220": "OD1" <-> "OD2" Residue "P ARG 235": "NH1" <-> "NH2" Residue "P TYR 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 251": "NH1" <-> "NH2" Residue "P TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 276": "OE1" <-> "OE2" Residue "P ARG 325": "NH1" <-> "NH2" Residue "Q ASP 18": "OD1" <-> "OD2" Residue "Q GLU 27": "OE1" <-> "OE2" Residue "Q GLU 28": "OE1" <-> "OE2" Residue "Q GLU 58": "OE1" <-> "OE2" Residue "Q PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 77": "OD1" <-> "OD2" Residue "Q PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 107": "OE1" <-> "OE2" Residue "Q TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 19": "OD1" <-> "OD2" Residue "R TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 31": "NH1" <-> "NH2" Residue "R ASP 42": "OD1" <-> "OD2" Residue "R ASP 60": "OD1" <-> "OD2" Residue "R TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 42": "OE1" <-> "OE2" Residue "S ASP 59": "OD1" <-> "OD2" Residue "S PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 84": "OD1" <-> "OD2" Residue "S GLU 91": "OE1" <-> "OE2" Residue "T GLU 9": "OE1" <-> "OE2" Residue "T TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 26": "OD1" <-> "OD2" Residue "T ASP 56": "OD1" <-> "OD2" Residue "T GLU 57": "OE1" <-> "OE2" Residue "T PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 23": "OD1" <-> "OD2" Residue "U ASP 43": "OD1" <-> "OD2" Residue "U GLU 49": "OE1" <-> "OE2" Residue "U GLU 55": "OE1" <-> "OE2" Residue "U GLU 57": "OE1" <-> "OE2" Residue "U PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 68": "OE1" <-> "OE2" Residue "U TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 82": "OD1" <-> "OD2" Residue "U TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 22": "NH1" <-> "NH2" Residue "V GLU 48": "OE1" <-> "OE2" Residue "V GLU 53": "OE1" <-> "OE2" Residue "V ASP 63": "OD1" <-> "OD2" Residue "V GLU 78": "OE1" <-> "OE2" Residue "V GLU 84": "OE1" <-> "OE2" Residue "W GLU 27": "OE1" <-> "OE2" Residue "W TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 42": "OE1" <-> "OE2" Residue "W ASP 61": "OD1" <-> "OD2" Residue "W ASP 75": "OD1" <-> "OD2" Residue "W ASP 80": "OD1" <-> "OD2" Residue "W GLU 91": "OE1" <-> "OE2" Residue "W PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 111": "OE1" <-> "OE2" Residue "X GLU 10": "OE1" <-> "OE2" Residue "X GLU 16": "OE1" <-> "OE2" Residue "X GLU 41": "OE1" <-> "OE2" Residue "X GLU 48": "OE1" <-> "OE2" Residue "X GLU 49": "OE1" <-> "OE2" Residue "X GLU 57": "OE1" <-> "OE2" Residue "X PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 79": "OE1" <-> "OE2" Residue "X TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 97": "NH1" <-> "NH2" Residue "X ARG 118": "NH1" <-> "NH2" Residue "X ARG 134": "NH1" <-> "NH2" Residue "X ARG 144": "NH1" <-> "NH2" Residue "X ARG 146": "NH1" <-> "NH2" Residue "X ASP 156": "OD1" <-> "OD2" Residue "X PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 13": "OE1" <-> "OE2" Residue "Y ARG 57": "NH1" <-> "NH2" Residue "Y PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 85": "OD1" <-> "OD2" Residue "Y ARG 103": "NH1" <-> "NH2" Residue "Y GLU 130": "OE1" <-> "OE2" Residue "Y GLU 137": "OE1" <-> "OE2" Residue "Z TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 66": "OE1" <-> "OE2" Residue "Z ASP 80": "OD1" <-> "OD2" Residue "Z ARG 82": "NH1" <-> "NH2" Residue "Z GLU 92": "OE1" <-> "OE2" Residue "Z GLU 93": "OE1" <-> "OE2" Residue "Z GLU 94": "OE1" <-> "OE2" Residue "Z GLU 108": "OE1" <-> "OE2" Residue "a GLU 4": "OE1" <-> "OE2" Residue "a PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 49": "OE1" <-> "OE2" Residue "a ARG 59": "NH1" <-> "NH2" Residue "a GLU 67": "OE1" <-> "OE2" Residue "b ARG 3": "NH1" <-> "NH2" Residue "b TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 57": "NH1" <-> "NH2" Residue "b ASP 59": "OD1" <-> "OD2" Residue "b ASP 64": "OD1" <-> "OD2" Residue "b GLU 78": "OE1" <-> "OE2" Residue "c GLU 6": "OE1" <-> "OE2" Residue "c PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 41": "OE1" <-> "OE2" Residue "c ARG 44": "NH1" <-> "NH2" Residue "d ARG 5": "NH1" <-> "NH2" Residue "d ASP 28": "OD1" <-> "OD2" Residue "d TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 51": "NH1" <-> "NH2" Residue "d ASP 87": "OD1" <-> "OD2" Residue "d GLU 99": "OE1" <-> "OE2" Residue "d ASP 100": "OD1" <-> "OD2" Residue "d PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 103": "OE1" <-> "OE2" Residue "d TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 115": "OE1" <-> "OE2" Residue "e ARG 8": "NH1" <-> "NH2" Residue "e GLU 23": "OE1" <-> "OE2" Residue "e ARG 50": "NH1" <-> "NH2" Residue "e ASP 61": "OD1" <-> "OD2" Residue "e GLU 83": "OE1" <-> "OE2" Residue "e GLU 88": "OE1" <-> "OE2" Residue "f PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ARG 28": "NH1" <-> "NH2" Residue "f ARG 46": "NH1" <-> "NH2" Residue "f GLU 53": "OE1" <-> "OE2" Residue "g PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ASP 82": "OD1" <-> "OD2" Residue "g TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 101": "OE1" <-> "OE2" Residue "g GLU 109": "OE1" <-> "OE2" Residue "g ASP 114": "OD1" <-> "OD2" Residue "h PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ARG 20": "NH1" <-> "NH2" Residue "h TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 62": "OE1" <-> "OE2" Residue "h TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ARG 77": "NH1" <-> "NH2" Residue "h GLU 88": "OE1" <-> "OE2" Residue "h GLU 102": "OE1" <-> "OE2" Residue "h GLU 109": "OE1" <-> "OE2" Residue "h ARG 112": "NH1" <-> "NH2" Residue "h ASP 142": "OD1" <-> "OD2" Residue "i ARG 18": "NH1" <-> "NH2" Residue "i GLU 26": "OE1" <-> "OE2" Residue "i GLU 31": "OE1" <-> "OE2" Residue "i PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i GLU 114": "OE1" <-> "OE2" Residue "i GLU 121": "OE1" <-> "OE2" Residue "i PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j TYR 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ASP 55": "OD1" <-> "OD2" Residue "j GLU 62": "OE1" <-> "OE2" Residue "j ASP 69": "OD1" <-> "OD2" Residue "k ASP 17": "OD1" <-> "OD2" Residue "k GLU 24": "OE1" <-> "OE2" Residue "k ARG 38": "NH1" <-> "NH2" Residue "k ARG 41": "NH1" <-> "NH2" Residue "k TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ASP 7": "OD1" <-> "OD2" Residue "l TYR 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l GLU 18": "OE1" <-> "OE2" Residue "l GLU 19": "OE1" <-> "OE2" Residue "l TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ARG 30": "NH1" <-> "NH2" Residue "l GLU 35": "OE1" <-> "OE2" Residue "l PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ARG 142": "NH1" <-> "NH2" Residue "m TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m GLU 21": "OE1" <-> "OE2" Residue "m TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m ASP 23": "OD1" <-> "OD2" Residue "m GLU 27": "OE1" <-> "OE2" Residue "m GLU 34": "OE1" <-> "OE2" Residue "m ARG 39": "NH1" <-> "NH2" Residue "m GLU 45": "OE1" <-> "OE2" Residue "m ARG 71": "NH1" <-> "NH2" Residue "m TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m ASP 107": "OD1" <-> "OD2" Residue "m ASP 109": "OD1" <-> "OD2" Residue "n TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ARG 21": "NH1" <-> "NH2" Residue "n ASP 34": "OD1" <-> "OD2" Residue "n TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ASP 48": "OD1" <-> "OD2" Residue "n ASP 55": "OD1" <-> "OD2" Residue "n ARG 64": "NH1" <-> "NH2" Residue "n GLU 68": "OE1" <-> "OE2" Residue "n GLU 83": "OE1" <-> "OE2" Residue "n GLU 91": "OE1" <-> "OE2" Residue "n ARG 92": "NH1" <-> "NH2" Residue "n TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ASP 105": "OD1" <-> "OD2" Residue "n GLU 110": "OE1" <-> "OE2" Residue "n TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ARG 134": "NH1" <-> "NH2" Residue "n ARG 149": "NH1" <-> "NH2" Residue "n GLU 151": "OE1" <-> "OE2" Residue "o ARG 6": "NH1" <-> "NH2" Residue "o ASP 11": "OD1" <-> "OD2" Residue "o GLU 15": "OE1" <-> "OE2" Residue "o ASP 17": "OD1" <-> "OD2" Residue "o PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ASP 27": "OD1" <-> "OD2" Residue "o GLU 35": "OE1" <-> "OE2" Residue "o ARG 36": "NH1" <-> "NH2" Residue "o GLU 44": "OE1" <-> "OE2" Residue "o ASP 56": "OD1" <-> "OD2" Residue "o TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o GLU 82": "OE1" <-> "OE2" Residue "o TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ARG 97": "NH1" <-> "NH2" Residue "o GLU 100": "OE1" <-> "OE2" Residue "o ARG 103": "NH1" <-> "NH2" Residue "o GLU 104": "OE1" <-> "OE2" Residue "o ARG 105": "NH1" <-> "NH2" Residue "o ARG 106": "NH1" <-> "NH2" Residue "o GLU 118": "OE1" <-> "OE2" Residue "p ASP 7": "OD1" <-> "OD2" Residue "p TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p GLU 49": "OE1" <-> "OE2" Residue "p GLU 52": "OE1" <-> "OE2" Residue "p TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p GLU 66": "OE1" <-> "OE2" Residue "p ASP 80": "OD1" <-> "OD2" Residue "p GLU 88": "OE1" <-> "OE2" Residue "p GLU 100": "OE1" <-> "OE2" Residue "p GLU 116": "OE1" <-> "OE2" Residue "p GLU 127": "OE1" <-> "OE2" Residue "p ASP 144": "OD1" <-> "OD2" Residue "p TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ARG 21": "NH1" <-> "NH2" Residue "q ARG 29": "NH1" <-> "NH2" Residue "q GLU 50": "OE1" <-> "OE2" Residue "q ARG 88": "NH1" <-> "NH2" Residue "q PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r GLU 29": "OE1" <-> "OE2" Residue "r ARG 59": "NH1" <-> "NH2" Residue "r GLU 61": "OE1" <-> "OE2" Residue "r TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s ASP 34": "OD1" <-> "OD2" Residue "s TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s ASP 45": "OD1" <-> "OD2" Residue "s ASP 53": "OD1" <-> "OD2" Residue "s GLU 71": "OE1" <-> "OE2" Time to flip residues: 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 67259 Number of models: 1 Model: "" Number of chains: 69 Chain: "A" Number of atoms: 921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 921 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} 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: "B" Number of atoms: 1241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1241 Classifications: {'peptide': 155} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 144} Chain: "C" Number of atoms: 1721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1721 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 16, 'TRANS': 190} Chain: "D" Number of atoms: 3459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3459 Classifications: {'peptide': 430} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 401} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'2MR:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 1655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1655 Classifications: {'peptide': 213} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 191} Chain: "F" Number of atoms: 3319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3319 Classifications: {'peptide': 431} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 409} Chain: "G" Number of atoms: 5279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 688, 5279 Classifications: {'peptide': 688} Link IDs: {'PTRANS': 32, 'TRANS': 655} Chain: "H" Number of atoms: 2509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2509 Classifications: {'peptide': 318} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 295} 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: "I" Number of atoms: 1414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1414 Classifications: {'peptide': 176} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 165} Chain: "J" Number of atoms: 1337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1337 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 3, 'TRANS': 170} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "K" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 745 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 1, 'TRANS': 96} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 4802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4802 Classifications: {'peptide': 606} Link IDs: {'PTRANS': 27, 'TRANS': 578} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "M" Number of atoms: 3654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3654 Classifications: {'peptide': 459} Link IDs: {'PCIS': 3, 'PTRANS': 17, 'TRANS': 438} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "N" Number of atoms: 2733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2733 Classifications: {'peptide': 347} Link IDs: {'PCIS': 2, 'PTRANS': 19, '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: "O" Number of atoms: 2589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2589 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 15, 'TRANS': 304} Chain: "P" Number of atoms: 2747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2747 Classifications: {'peptide': 341} Link IDs: {'PTRANS': 22, 'TRANS': 318} Chain: "Q" Number of atoms: 1016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1016 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 6, 'TRANS': 118} Chain: "R" Number of atoms: 730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 730 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "S" Number of atoms: 677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 677 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "T" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 612 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "U" Number of atoms: 692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 692 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 5, 'TRANS': 80} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "V" Number of atoms: 919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 919 Classifications: {'peptide': 113} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 104} Chain: "W" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 971 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 6, 'TRANS': 107} Chain: "X" Number of atoms: 1402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1402 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 12, 'TRANS': 158} Chain: "Y" Number of atoms: 1030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1030 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 5, 'TRANS': 134} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'AYA:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "Z" Number of atoms: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1152 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 7, 'TRANS': 133} Chain: "a" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 569 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "b" Number of atoms: 651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 651 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 11, 'TRANS': 71} Chain: "c" Number of atoms: 405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 405 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 3, 'TRANS': 44} Chain: "d" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 994 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 110} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "e" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 819 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 5, 'TRANS': 91} Chain: "f" Number of atoms: 437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 437 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "g" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 824 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 8, 'TRANS': 89} Chain: "h" Number of atoms: 1154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1154 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 10, 'TRANS': 127} Chain: "i" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 920 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 94} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'SAC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "j" Number of atoms: 556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 556 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 7, 'TRANS': 56} Chain: "k" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 644 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 3, 'TRANS': 76} Chain: "l" Number of atoms: 1304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1304 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 20, 'TRANS': 134} Chain: "m" Number of atoms: 1061 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1061 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 8, 'TRANS': 118} Chain: "n" Number of atoms: 1492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1492 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 15, 'TRANS': 156} Chain: "o" Number of atoms: 1048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1048 Classifications: {'peptide': 122} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 114} Chain: "p" Number of atoms: 1443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1443 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 10, 'TRANS': 160} Chain: "q" Number of atoms: 1201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1201 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 11, 'TRANS': 132} Chain: "r" Number of atoms: 767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 767 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 11, 'TRANS': 82} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'AYA:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "s" Number of atoms: 371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 371 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 3, 'TRANS': 40} Chain: "A" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 60 Unusual residues: {'3PE': 1, 'PC1': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 44 Planarities with less than four sites: {'PC1:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 86 Unusual residues: {'PC1': 2, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 30 Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'FMN': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 20 Unusual residues: {'FES': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 58 Unusual residues: {'3PE': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 23 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 39 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "L" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 180 Unusual residues: {'3PE': 3, 'CDL': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 73 Chain: "M" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 121 Unusual residues: {'3PE': 2, 'LMT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Chain: "N" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 120 Unusual residues: {'3PE': 2, 'LMT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 17 Chain: "O" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "P" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NDP': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'EHZ': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "U" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'EHZ': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "X" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 20 Chain: "Y" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 50 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 50 Chain: "b" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'LMT': 1} Classifications: {'undetermined': 1} Chain: "c" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 38 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Chain: "d" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 28 Chain: "g" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "h" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 64 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 36 Chain: "q" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 69 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 31 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1668 SG CYS B 119 96.446 93.138 203.255 1.00 28.89 S ATOM 1898 SG CYS B 149 94.033 90.603 207.613 1.00 29.19 S ATOM 1164 SG CYS B 54 91.087 89.408 201.924 1.00 31.54 S ATOM 1170 SG CYS B 55 90.272 94.978 204.865 1.00 31.37 S ATOM 8146 SG CYS E 103 114.454 43.361 257.422 1.00 47.37 S ATOM 8180 SG CYS E 108 112.992 40.553 259.236 1.00 47.74 S ATOM 8460 SG CYS E 144 116.935 40.022 253.974 1.00 46.87 S ATOM 8483 SG CYS E 148 115.829 37.372 254.898 1.00 49.70 S ATOM 11701 SG CYS F 362 119.823 51.006 234.160 1.00 32.50 S ATOM 11721 SG CYS F 365 116.824 49.933 238.924 1.00 34.78 S ATOM 12045 SG CYS F 405 121.440 45.840 237.973 1.00 36.22 S ATOM 11682 SG CYS F 359 123.245 51.733 239.712 1.00 34.68 S ATOM 13142 SG CYS G 114 116.043 69.702 225.665 1.00 28.75 S ATOM 13081 SG CYS G 105 110.053 71.755 227.080 1.00 27.64 S ATOM 13102 SG CYS G 108 115.341 74.495 229.651 1.00 28.53 S ATOM 13474 SG CYS G 156 124.370 63.676 230.395 1.00 30.51 S ATOM 13451 SG CYS G 153 121.412 65.628 235.938 1.00 30.39 S ATOM 13498 SG CYS G 159 127.566 66.839 234.848 1.00 31.97 S ATOM 13828 SG CYS G 203 123.055 69.696 231.074 1.00 31.36 S ATOM 12587 SG CYS G 41 125.151 57.193 227.854 1.00 31.57 S ATOM 12673 SG CYS G 52 121.253 57.316 226.777 1.00 31.74 S ATOM 12698 SG CYS G 55 123.256 53.082 223.620 1.00 32.96 S ATOM 12799 SG CYS G 69 126.211 53.856 224.745 1.00 32.70 S ATOM 21058 SG CYS I 119 97.149 84.480 213.600 1.00 27.53 S ATOM 21032 SG CYS I 116 97.159 90.944 214.635 1.00 27.92 S ATOM 21079 SG CYS I 122 98.521 86.589 219.283 1.00 26.49 S ATOM 20806 SG CYS I 87 102.669 87.595 214.315 1.00 26.65 S ATOM 21108 SG CYS I 126 101.083 83.199 226.709 1.00 26.68 S ATOM 20737 SG CYS I 77 105.731 87.646 227.971 1.00 28.28 S ATOM 20779 SG CYS I 83 104.544 86.022 221.941 1.00 27.02 S ATOM 20756 SG CYS I 80 106.656 81.377 225.456 1.00 28.03 S ATOM 41600 SG CYS R 59 102.474 78.144 241.645 1.00 32.49 S ATOM 41778 SG CYS R 84 105.638 79.063 239.712 1.00 33.62 S ATOM 41800 SG CYS R 87 103.198 81.358 240.616 1.00 31.92 S Time building chain proxies: 28.41, per 1000 atoms: 0.42 Number of scatterers: 67259 At special positions: 0 Unit cell: (186.912, 201.696, 291.456, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 1 29.99 Fe 28 26.01 S 470 16.00 P 35 15.00 Mg 1 11.99 O 12096 8.00 N 11182 7.00 C 43446 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS X 45 " - pdb=" SG CYS X 55 " distance=2.04 Simple disulfide: pdb=" SG CYS X 77 " - pdb=" SG CYS X 109 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 17 " - pdb=" SG CYS Y 74 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 94 " - pdb=" SG CYS Y 114 " distance=2.03 Simple disulfide: pdb=" SG CYS e 32 " - pdb=" SG CYS e 65 " distance=2.03 Simple disulfide: pdb=" SG CYS e 42 " - pdb=" SG CYS e 55 " distance=2.04 Simple disulfide: pdb=" SG CYS p 112 " - pdb=" SG CYS p 124 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 20.93 Conformation dependent library (CDL) restraints added in 7.2 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E 301 " pdb="FE1 FES E 301 " - pdb=" SG CYS E 108 " pdb="FE1 FES E 301 " - pdb=" SG CYS E 103 " pdb="FE2 FES E 301 " - pdb=" SG CYS E 144 " pdb="FE2 FES E 301 " - pdb=" SG CYS E 148 " pdb=" FES G 803 " pdb="FE2 FES G 803 " - pdb=" SG CYS G 55 " pdb="FE2 FES G 803 " - pdb=" SG CYS G 69 " pdb="FE1 FES G 803 " - pdb=" SG CYS G 52 " pdb="FE1 FES G 803 " - pdb=" SG CYS G 41 " pdb=" SF4 B 201 " pdb="FE2 SF4 B 201 " - pdb=" SG CYS B 149 " pdb="FE1 SF4 B 201 " - pdb=" SG CYS B 119 " pdb="FE3 SF4 B 201 " - pdb=" SG CYS B 54 " pdb="FE4 SF4 B 201 " - pdb=" SG CYS B 55 " pdb=" SF4 F 502 " pdb="FE2 SF4 F 502 " - pdb=" SG CYS F 365 " pdb="FE3 SF4 F 502 " - pdb=" SG CYS F 405 " pdb="FE4 SF4 F 502 " - pdb=" SG CYS F 359 " pdb="FE1 SF4 F 502 " - pdb=" SG CYS F 362 " pdb=" SF4 G 801 " pdb="FE3 SF4 G 801 " - pdb=" NE2 HIS G 101 " pdb="FE4 SF4 G 801 " - pdb=" SG CYS G 108 " pdb="FE1 SF4 G 801 " - pdb=" SG CYS G 114 " pdb="FE2 SF4 G 801 " - pdb=" SG CYS G 105 " pdb=" SF4 G 802 " pdb="FE2 SF4 G 802 " - pdb=" SG CYS G 153 " pdb="FE3 SF4 G 802 " - pdb=" SG CYS G 159 " pdb="FE4 SF4 G 802 " - pdb=" SG CYS G 203 " pdb="FE1 SF4 G 802 " - pdb=" SG CYS G 156 " pdb=" SF4 I 202 " pdb="FE2 SF4 I 202 " - pdb=" SG CYS I 116 " pdb="FE4 SF4 I 202 " - pdb=" SG CYS I 87 " pdb="FE3 SF4 I 202 " - pdb=" SG CYS I 122 " pdb="FE1 SF4 I 202 " - pdb=" SG CYS I 119 " pdb=" SF4 I 203 " pdb="FE3 SF4 I 203 " - pdb=" SG CYS I 83 " pdb="FE4 SF4 I 203 " - pdb=" SG CYS I 80 " pdb="FE2 SF4 I 203 " - pdb=" SG CYS I 77 " pdb="FE1 SF4 I 203 " - pdb=" SG CYS I 126 " Number of angles added : 81 Zn2+ tetrahedral coordination pdb=" ZN R 201 " pdb="ZN ZN R 201 " - pdb=" NE2 HIS R 68 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 87 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 84 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 59 " Number of angles added : 3 16198 Ramachandran restraints generated. 8099 Oldfield, 0 Emsley, 8099 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15420 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 343 helices and 29 sheets defined 52.0% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.90 Creating SS restraints... Processing helix chain 'A' and resid 3 through 24 Processing helix chain 'A' and resid 56 through 80 removed outlier: 3.552A pdb=" N LEU A 63 " --> pdb=" O ALA A 59 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU A 64 " --> pdb=" O ILE A 60 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA A 70 " --> pdb=" O ASP A 66 " (cutoff:3.500A) Proline residue: A 74 - end of helix removed outlier: 5.107A pdb=" N TRP A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N GLN A 80 " --> pdb=" O PRO A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 107 Processing helix chain 'B' and resid 26 through 42 Processing helix chain 'B' and resid 54 through 63 Processing helix chain 'B' and resid 69 through 72 Processing helix chain 'B' and resid 80 through 82 No H-bonds generated for 'chain 'B' and resid 80 through 82' Processing helix chain 'B' and resid 94 through 105 Proline residue: B 98 - end of helix Processing helix chain 'B' and resid 118 through 122 Processing helix chain 'B' and resid 124 through 126 No H-bonds generated for 'chain 'B' and resid 124 through 126' Processing helix chain 'B' and resid 136 through 138 No H-bonds generated for 'chain 'B' and resid 136 through 138' Processing helix chain 'B' and resid 153 through 169 Processing helix chain 'B' and resid 172 through 177 Processing helix chain 'C' and resid 16 through 32 removed outlier: 3.569A pdb=" N GLU C 27 " --> pdb=" O SER C 23 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 66 removed outlier: 3.587A pdb=" N VAL C 57 " --> pdb=" O PRO C 54 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N ILE C 58 " --> pdb=" O ASP C 55 " (cutoff:3.500A) Proline residue: C 59 - end of helix removed outlier: 3.512A pdb=" N THR C 62 " --> pdb=" O PRO C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 138 removed outlier: 3.647A pdb=" N ASN C 128 " --> pdb=" O LYS C 125 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N TRP C 129 " --> pdb=" O ALA C 126 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TYR C 130 " --> pdb=" O ALA C 127 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU C 131 " --> pdb=" O ASN C 128 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLU C 133 " --> pdb=" O TYR C 130 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N MET C 137 " --> pdb=" O ILE C 134 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N PHE C 138 " --> pdb=" O TRP C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 209 No H-bonds generated for 'chain 'C' and resid 207 through 209' Processing helix chain 'D' and resid 8 through 14 removed outlier: 4.089A pdb=" N GLN D 13 " --> pdb=" O GLU D 9 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N TYR D 14 " --> pdb=" O TRP D 10 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 25 No H-bonds generated for 'chain 'D' and resid 23 through 25' Processing helix chain 'D' and resid 56 through 58 No H-bonds generated for 'chain 'D' and resid 56 through 58' Processing helix chain 'D' and resid 87 through 93 removed outlier: 3.619A pdb=" N GLU D 92 " --> pdb=" O GLU D 88 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N TYR D 93 " --> pdb=" O LYS D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 104 Processing helix chain 'D' and resid 111 through 126 Processing helix chain 'D' and resid 132 through 161 Processing helix chain 'D' and resid 165 through 185 removed outlier: 3.944A pdb=" N GLU D 173 " --> pdb=" O TRP D 169 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LYS D 176 " --> pdb=" O GLU D 172 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N PHE D 180 " --> pdb=" O LYS D 176 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 229 removed outlier: 3.911A pdb=" N ASN D 217 " --> pdb=" O GLU D 213 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N PHE D 218 " --> pdb=" O PHE D 214 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N SER D 219 " --> pdb=" O SER D 215 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N LEU D 220 " --> pdb=" O LYS D 216 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG D 221 " --> pdb=" O ASN D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 237 Processing helix chain 'D' and resid 247 through 252 Processing helix chain 'D' and resid 257 through 263 removed outlier: 3.601A pdb=" N ARG D 261 " --> pdb=" O VAL D 258 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLY D 262 " --> pdb=" O MET D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 272 No H-bonds generated for 'chain 'D' and resid 269 through 272' Processing helix chain 'D' and resid 293 through 316 removed outlier: 3.926A pdb=" N GLN D 313 " --> pdb=" O ARG D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 339 removed outlier: 3.698A pdb=" N LYS D 339 " --> pdb=" O ARG D 335 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 335 through 339' Processing helix chain 'D' and resid 342 through 351 Processing helix chain 'D' and resid 394 through 406 removed outlier: 3.630A pdb=" N HIS D 398 " --> pdb=" O PRO D 394 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ASP D 403 " --> pdb=" O LEU D 399 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N LYS D 404 " --> pdb=" O ALA D 400 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 421 removed outlier: 3.518A pdb=" N VAL D 415 " --> pdb=" O LEU D 411 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY D 419 " --> pdb=" O VAL D 415 " (cutoff:3.500A) Processing helix chain 'D' and resid 425 through 429 Processing helix chain 'E' and resid 25 through 37 removed outlier: 3.644A pdb=" N ALA E 33 " --> pdb=" O LYS E 29 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS E 36 " --> pdb=" O GLU E 32 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASN E 37 " --> pdb=" O ALA E 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 45 No H-bonds generated for 'chain 'E' and resid 43 through 45' Processing helix chain 'E' and resid 48 through 58 Processing helix chain 'E' and resid 63 through 73 Processing helix chain 'E' and resid 77 through 86 Processing helix chain 'E' and resid 106 through 110 Processing helix chain 'E' and resid 113 through 124 Processing helix chain 'E' and resid 166 through 177 removed outlier: 3.852A pdb=" N GLU E 170 " --> pdb=" O PRO E 166 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU E 171 " --> pdb=" O LYS E 167 " (cutoff:3.500A) Processing helix chain 'F' and resid 17 through 19 No H-bonds generated for 'chain 'F' and resid 17 through 19' Processing helix chain 'F' and resid 33 through 38 removed outlier: 3.509A pdb=" N SER F 38 " --> pdb=" O LYS F 34 " (cutoff:3.500A) Processing helix chain 'F' and resid 45 through 51 Processing helix chain 'F' and resid 53 through 62 removed outlier: 3.664A pdb=" N LYS F 61 " --> pdb=" O LEU F 57 " (cutoff:3.500A) Processing helix chain 'F' and resid 75 through 82 removed outlier: 4.508A pdb=" N MET F 82 " --> pdb=" O LYS F 78 " (cutoff:3.500A) Processing helix chain 'F' and resid 106 through 113 removed outlier: 3.666A pdb=" N ILE F 110 " --> pdb=" O LYS F 106 " (cutoff:3.500A) Processing helix chain 'F' and resid 115 through 129 Processing helix chain 'F' and resid 143 through 158 Processing helix chain 'F' and resid 166 through 168 No H-bonds generated for 'chain 'F' and resid 166 through 168' Processing helix chain 'F' and resid 184 through 187 Processing helix chain 'F' and resid 189 through 196 Processing helix chain 'F' and resid 215 through 217 No H-bonds generated for 'chain 'F' and resid 215 through 217' Processing helix chain 'F' and resid 225 through 237 removed outlier: 3.586A pdb=" N VAL F 230 " --> pdb=" O GLU F 226 " (cutoff:3.500A) Proline residue: F 232 - end of helix Processing helix chain 'F' and resid 239 through 244 Processing helix chain 'F' and resid 276 through 282 Processing helix chain 'F' and resid 291 through 293 No H-bonds generated for 'chain 'F' and resid 291 through 293' Processing helix chain 'F' and resid 309 through 314 removed outlier: 4.699A pdb=" N THR F 314 " --> pdb=" O SER F 310 " (cutoff:3.500A) Processing helix chain 'F' and resid 319 through 325 Processing helix chain 'F' and resid 343 through 357 removed outlier: 3.609A pdb=" N LEU F 350 " --> pdb=" O ALA F 346 " (cutoff:3.500A) Processing helix chain 'F' and resid 363 through 366 No H-bonds generated for 'chain 'F' and resid 363 through 366' Processing helix chain 'F' and resid 368 through 381 removed outlier: 3.537A pdb=" N ARG F 378 " --> pdb=" O LYS F 374 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ARG F 381 " --> pdb=" O ALA F 377 " (cutoff:3.500A) Processing helix chain 'F' and resid 386 through 399 removed outlier: 3.841A pdb=" N ASP F 390 " --> pdb=" O ALA F 387 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU F 392 " --> pdb=" O ILE F 389 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N TRP F 393 " --> pdb=" O ASP F 390 " (cutoff:3.500A) Processing helix chain 'F' and resid 407 through 421 Proline residue: F 414 - end of helix Processing helix chain 'F' and resid 423 through 437 Processing helix chain 'G' and resid 26 through 33 removed outlier: 3.851A pdb=" N VAL G 33 " --> pdb=" O ALA G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 84 through 97 Processing helix chain 'G' and resid 105 through 107 No H-bonds generated for 'chain 'G' and resid 105 through 107' Processing helix chain 'G' and resid 115 through 122 Processing helix chain 'G' and resid 158 through 165 Processing helix chain 'G' and resid 178 through 180 No H-bonds generated for 'chain 'G' and resid 178 through 180' Processing helix chain 'G' and resid 196 through 202 removed outlier: 3.567A pdb=" N ILE G 202 " --> pdb=" O ILE G 199 " (cutoff:3.500A) Processing helix chain 'G' and resid 219 through 221 No H-bonds generated for 'chain 'G' and resid 219 through 221' Processing helix chain 'G' and resid 265 through 275 removed outlier: 4.696A pdb=" N TYR G 271 " --> pdb=" O THR G 267 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ASP G 272 " --> pdb=" O ARG G 268 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N GLY G 273 " --> pdb=" O PHE G 269 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N LEU G 274 " --> pdb=" O ALA G 270 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N LYS G 275 " --> pdb=" O TYR G 271 " (cutoff:3.500A) Processing helix chain 'G' and resid 296 through 309 Processing helix chain 'G' and resid 325 through 336 Processing helix chain 'G' and resid 359 through 362 Processing helix chain 'G' and resid 369 through 373 Processing helix chain 'G' and resid 384 through 387 No H-bonds generated for 'chain 'G' and resid 384 through 387' Processing helix chain 'G' and resid 389 through 400 Processing helix chain 'G' and resid 426 through 434 Processing helix chain 'G' and resid 438 through 444 removed outlier: 4.198A pdb=" N VAL G 442 " --> pdb=" O PRO G 438 " (cutoff:3.500A) Processing helix chain 'G' and resid 457 through 459 No H-bonds generated for 'chain 'G' and resid 457 through 459' Processing helix chain 'G' and resid 463 through 476 Processing helix chain 'G' and resid 499 through 505 Processing helix chain 'G' and resid 512 through 516 Processing helix chain 'G' and resid 534 through 536 No H-bonds generated for 'chain 'G' and resid 534 through 536' Processing helix chain 'G' and resid 554 through 556 No H-bonds generated for 'chain 'G' and resid 554 through 556' Processing helix chain 'G' and resid 596 through 606 removed outlier: 3.537A pdb=" N ILE G 600 " --> pdb=" O ASP G 596 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE G 606 " --> pdb=" O ALA G 602 " (cutoff:3.500A) Processing helix chain 'G' and resid 616 through 626 removed outlier: 3.549A pdb=" N GLU G 625 " --> pdb=" O ASN G 621 " (cutoff:3.500A) Processing helix chain 'G' and resid 628 through 631 removed outlier: 3.773A pdb=" N VAL G 631 " --> pdb=" O PRO G 628 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 628 through 631' Processing helix chain 'G' and resid 642 through 651 removed outlier: 3.771A pdb=" N LEU G 651 " --> pdb=" O GLU G 647 " (cutoff:3.500A) Processing helix chain 'G' and resid 676 through 680 Processing helix chain 'G' and resid 683 through 692 Processing helix chain 'H' and resid 3 through 32 Proline residue: H 12 - end of helix removed outlier: 3.883A pdb=" N LEU H 22 " --> pdb=" O ALA H 18 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ARG H 25 " --> pdb=" O THR H 21 " (cutoff:3.500A) Processing helix chain 'H' and resid 42 through 44 No H-bonds generated for 'chain 'H' and resid 42 through 44' Processing helix chain 'H' and resid 47 through 56 Processing helix chain 'H' and resid 68 through 86 Proline residue: H 75 - end of helix removed outlier: 4.404A pdb=" N TRP H 86 " --> pdb=" O ALA H 82 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 123 removed outlier: 3.861A pdb=" N VAL H 113 " --> pdb=" O SER H 109 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N TYR H 114 " --> pdb=" O SER H 110 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N SER H 115 " --> pdb=" O LEU H 111 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ILE H 116 " --> pdb=" O ALA H 112 " (cutoff:3.500A) Processing helix chain 'H' and resid 126 through 157 removed outlier: 3.577A pdb=" N VAL H 136 " --> pdb=" O ALA H 132 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N VAL H 144 " --> pdb=" O ILE H 140 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N THR H 145 " --> pdb=" O SER H 141 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL H 153 " --> pdb=" O ILE H 149 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N MET H 156 " --> pdb=" O SER H 152 " (cutoff:3.500A) Processing helix chain 'H' and resid 164 through 168 Processing helix chain 'H' and resid 179 through 192 Processing helix chain 'H' and resid 204 through 207 No H-bonds generated for 'chain 'H' and resid 204 through 207' Processing helix chain 'H' and resid 210 through 212 No H-bonds generated for 'chain 'H' and resid 210 through 212' Processing helix chain 'H' and resid 217 through 241 removed outlier: 3.647A pdb=" N PHE H 223 " --> pdb=" O PRO H 219 " (cutoff:3.500A) Processing helix chain 'H' and resid 249 through 274 Proline residue: H 252 - end of helix removed outlier: 3.533A pdb=" N ILE H 261 " --> pdb=" O ASN H 258 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU H 265 " --> pdb=" O LYS H 262 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LEU H 266 " --> pdb=" O SER H 263 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N MET H 268 " --> pdb=" O LEU H 265 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N PHE H 270 " --> pdb=" O THR H 267 " (cutoff:3.500A) Processing helix chain 'H' and resid 282 through 290 removed outlier: 3.945A pdb=" N MET H 286 " --> pdb=" O TYR H 282 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N HIS H 287 " --> pdb=" O ASP H 283 " (cutoff:3.500A) Processing helix chain 'H' and resid 293 through 311 Proline residue: H 308 - end of helix Processing helix chain 'I' and resid 15 through 26 Processing helix chain 'I' and resid 29 through 42 removed outlier: 3.527A pdb=" N THR I 37 " --> pdb=" O GLY I 33 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N PHE I 42 " --> pdb=" O LEU I 38 " (cutoff:3.500A) Processing helix chain 'I' and resid 82 through 86 Processing helix chain 'I' and resid 121 through 125 Processing helix chain 'I' and resid 145 through 147 No H-bonds generated for 'chain 'I' and resid 145 through 147' Processing helix chain 'I' and resid 151 through 175 removed outlier: 5.491A pdb=" N ALA I 163 " --> pdb=" O ASP I 159 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N GLU I 164 " --> pdb=" O LYS I 160 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N ALA I 167 " --> pdb=" O ALA I 163 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N LEU I 174 " --> pdb=" O GLN I 170 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N TYR I 175 " --> pdb=" O ALA I 171 " (cutoff:3.500A) Processing helix chain 'J' and resid 5 through 21 Processing helix chain 'J' and resid 26 through 46 Processing helix chain 'J' and resid 50 through 74 removed outlier: 3.515A pdb=" N ALA J 73 " --> pdb=" O GLY J 69 " (cutoff:3.500A) Processing helix chain 'J' and resid 87 through 110 removed outlier: 3.595A pdb=" N MET J 103 " --> pdb=" O MET J 99 " (cutoff:3.500A) Processing helix chain 'J' and resid 124 through 127 removed outlier: 3.613A pdb=" N ILE J 127 " --> pdb=" O ASP J 124 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 124 through 127' Processing helix chain 'J' and resid 138 through 146 removed outlier: 3.875A pdb=" N LEU J 146 " --> pdb=" O GLY J 142 " (cutoff:3.500A) Processing helix chain 'J' and resid 151 through 172 Processing helix chain 'K' and resid 5 through 20 Processing helix chain 'K' and resid 26 through 51 Processing helix chain 'K' and resid 54 through 85 removed outlier: 3.851A pdb=" N MET K 58 " --> pdb=" O LEU K 55 " (cutoff:3.500A) Proline residue: K 60 - end of helix removed outlier: 3.525A pdb=" N PHE K 66 " --> pdb=" O LEU K 63 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA K 68 " --> pdb=" O VAL K 65 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N CYS K 69 " --> pdb=" O PHE K 66 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER K 76 " --> pdb=" O LEU K 73 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASN K 83 " --> pdb=" O MET K 80 " (cutoff:3.500A) Processing helix chain 'K' and resid 95 through 97 No H-bonds generated for 'chain 'K' and resid 95 through 97' Processing helix chain 'L' and resid 3 through 24 removed outlier: 3.622A pdb=" N THR L 11 " --> pdb=" O LEU L 7 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N LEU L 12 " --> pdb=" O SER L 8 " (cutoff:3.500A) Proline residue: L 18 - end of helix Processing helix chain 'L' and resid 32 through 57 removed outlier: 3.690A pdb=" N ILE L 49 " --> pdb=" O ILE L 45 " (cutoff:3.500A) Proline residue: L 50 - end of helix Processing helix chain 'L' and resid 84 through 107 Proline residue: L 91 - end of helix removed outlier: 3.584A pdb=" N GLU L 102 " --> pdb=" O TRP L 98 " (cutoff:3.500A) Processing helix chain 'L' and resid 114 through 132 removed outlier: 4.079A pdb=" N MET L 128 " --> pdb=" O PHE L 124 " (cutoff:3.500A) Processing helix chain 'L' and resid 137 through 155 Processing helix chain 'L' and resid 162 through 192 removed outlier: 3.565A pdb=" N ILE L 172 " --> pdb=" O ALA L 168 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N GLY L 181 " --> pdb=" O ILE L 177 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE L 182 " --> pdb=" O GLY L 178 " (cutoff:3.500A) Processing helix chain 'L' and resid 198 through 204 Processing helix chain 'L' and resid 210 through 224 Processing helix chain 'L' and resid 232 through 236 Processing helix chain 'L' and resid 241 through 249 Processing helix chain 'L' and resid 253 through 261 removed outlier: 3.822A pdb=" N GLY L 256 " --> pdb=" O VAL L 253 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N ILE L 257 " --> pdb=" O VAL L 254 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N PHE L 258 " --> pdb=" O ALA L 255 " (cutoff:3.500A) Processing helix chain 'L' and resid 264 through 267 No H-bonds generated for 'chain 'L' and resid 264 through 267' Processing helix chain 'L' and resid 271 through 291 Processing helix chain 'L' and resid 298 through 318 Processing helix chain 'L' and resid 322 through 349 removed outlier: 4.022A pdb=" N PHE L 334 " --> pdb=" O CYS L 330 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N PHE L 335 " --> pdb=" O THR L 331 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA L 337 " --> pdb=" O ALA L 333 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N SER L 349 " --> pdb=" O SER L 345 " (cutoff:3.500A) Processing helix chain 'L' and resid 356 through 358 No H-bonds generated for 'chain 'L' and resid 356 through 358' Processing helix chain 'L' and resid 362 through 365 No H-bonds generated for 'chain 'L' and resid 362 through 365' Processing helix chain 'L' and resid 367 through 381 Processing helix chain 'L' and resid 389 through 400 removed outlier: 5.448A pdb=" N LEU L 394 " --> pdb=" O TYR L 390 " (cutoff:3.500A) Processing helix chain 'L' and resid 406 through 430 removed outlier: 3.650A pdb=" N ALA L 420 " --> pdb=" O THR L 416 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER L 423 " --> pdb=" O THR L 419 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ILE L 426 " --> pdb=" O TYR L 422 " (cutoff:3.500A) Processing helix chain 'L' and resid 448 through 471 removed outlier: 3.691A pdb=" N LEU L 457 " --> pdb=" O SER L 453 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N GLY L 465 " --> pdb=" O SER L 461 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N TYR L 466 " --> pdb=" O LEU L 462 " (cutoff:3.500A) Processing helix chain 'L' and resid 484 through 487 No H-bonds generated for 'chain 'L' and resid 484 through 487' Processing helix chain 'L' and resid 489 through 508 removed outlier: 3.505A pdb=" N ILE L 495 " --> pdb=" O LEU L 491 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLY L 497 " --> pdb=" O VAL L 493 " (cutoff:3.500A) Processing helix chain 'L' and resid 518 through 524 Processing helix chain 'L' and resid 526 through 547 Proline residue: L 530 - end of helix removed outlier: 4.002A pdb=" N MET L 533 " --> pdb=" O PRO L 530 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N HIS L 534 " --> pdb=" O THR L 531 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N ALA L 537 " --> pdb=" O HIS L 534 " (cutoff:3.500A) Proline residue: L 538 - end of helix removed outlier: 3.509A pdb=" N LEU L 542 " --> pdb=" O TYR L 539 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER L 543 " --> pdb=" O MET L 540 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LYS L 547 " --> pdb=" O MET L 544 " (cutoff:3.500A) Processing helix chain 'L' and resid 557 through 560 No H-bonds generated for 'chain 'L' and resid 557 through 560' Processing helix chain 'L' and resid 563 through 578 Processing helix chain 'L' and resid 584 through 600 removed outlier: 3.609A pdb=" N ILE L 593 " --> pdb=" O LEU L 589 " (cutoff:3.500A) Processing helix chain 'M' and resid 5 through 16 removed outlier: 4.431A pdb=" N MET M 12 " --> pdb=" O THR M 8 " (cutoff:3.500A) Proline residue: M 13 - end of helix Processing helix chain 'M' and resid 20 through 42 removed outlier: 4.216A pdb=" N ILE M 23 " --> pdb=" O ASN M 20 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N TRP M 24 " --> pdb=" O ASN M 21 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ASN M 26 " --> pdb=" O ILE M 23 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR M 28 " --> pdb=" O VAL M 25 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA M 29 " --> pdb=" O ASN M 26 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU M 32 " --> pdb=" O ALA M 29 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE M 34 " --> pdb=" O SER M 31 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER M 35 " --> pdb=" O LEU M 32 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU M 39 " --> pdb=" O PHE M 36 " (cutoff:3.500A) Processing helix chain 'M' and resid 60 through 79 Proline residue: M 64 - end of helix removed outlier: 3.747A pdb=" N LEU M 73 " --> pdb=" O THR M 69 " (cutoff:3.500A) Proline residue: M 74 - end of helix Processing helix chain 'M' and resid 89 through 109 removed outlier: 3.624A pdb=" N MET M 108 " --> pdb=" O LEU M 104 " (cutoff:3.500A) Processing helix chain 'M' and resid 115 through 136 removed outlier: 5.032A pdb=" N LEU M 126 " --> pdb=" O PHE M 122 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N VAL M 127 " --> pdb=" O GLU M 123 " (cutoff:3.500A) Proline residue: M 128 - end of helix Processing helix chain 'M' and resid 140 through 171 removed outlier: 3.616A pdb=" N LEU M 143 " --> pdb=" O THR M 140 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA M 145 " --> pdb=" O ARG M 142 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N TYR M 148 " --> pdb=" O ALA M 145 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE M 151 " --> pdb=" O TYR M 148 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N TYR M 152 " --> pdb=" O PHE M 149 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU M 154 " --> pdb=" O PHE M 151 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLY M 156 " --> pdb=" O THR M 153 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LEU M 158 " --> pdb=" O ALA M 155 " (cutoff:3.500A) Proline residue: M 159 - end of helix removed outlier: 3.520A pdb=" N LEU M 164 " --> pdb=" O LEU M 161 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N TYR M 166 " --> pdb=" O ALA M 163 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR M 170 " --> pdb=" O ILE M 167 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL M 171 " --> pdb=" O GLN M 168 " (cutoff:3.500A) Processing helix chain 'M' and resid 176 through 182 removed outlier: 3.871A pdb=" N TYR M 181 " --> pdb=" O LEU M 177 " (cutoff:3.500A) Processing helix chain 'M' and resid 190 through 204 removed outlier: 3.621A pdb=" N PHE M 194 " --> pdb=" O TRP M 190 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ALA M 202 " --> pdb=" O ALA M 198 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N PHE M 203 " --> pdb=" O CYS M 199 " (cutoff:3.500A) Processing helix chain 'M' and resid 214 through 221 removed outlier: 3.914A pdb=" N LYS M 218 " --> pdb=" O LEU M 214 " (cutoff:3.500A) Processing helix chain 'M' and resid 225 through 231 Processing helix chain 'M' and resid 236 through 249 removed outlier: 4.102A pdb=" N GLY M 240 " --> pdb=" O LEU M 236 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N LEU M 248 " --> pdb=" O LEU M 244 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N ILE M 249 " --> pdb=" O ARG M 245 " (cutoff:3.500A) Processing helix chain 'M' and resid 253 through 278 removed outlier: 3.701A pdb=" N MET M 257 " --> pdb=" O THR M 254 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N ALA M 258 " --> pdb=" O ASP M 255 " (cutoff:3.500A) Proline residue: M 260 - end of helix removed outlier: 3.679A pdb=" N MET M 263 " --> pdb=" O PRO M 260 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU M 264 " --> pdb=" O PHE M 261 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER M 265 " --> pdb=" O ILE M 262 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N TRP M 267 " --> pdb=" O LEU M 264 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N MET M 269 " --> pdb=" O LEU M 266 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N MET M 271 " --> pdb=" O GLY M 268 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N THR M 272 " --> pdb=" O MET M 269 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N SER M 274 " --> pdb=" O MET M 271 " (cutoff:3.500A) Processing helix chain 'M' and resid 283 through 303 removed outlier: 4.002A pdb=" N LEU M 296 " --> pdb=" O SER M 292 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL M 297 " --> pdb=" O HIS M 293 " (cutoff:3.500A) Processing helix chain 'M' and resid 306 through 337 removed outlier: 3.569A pdb=" N MET M 310 " --> pdb=" O PRO M 306 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ARG M 336 " --> pdb=" O SER M 332 " (cutoff:3.500A) Processing helix chain 'M' and resid 353 through 366 Processing helix chain 'M' and resid 373 through 388 removed outlier: 3.731A pdb=" N SER M 387 " --> pdb=" O MET M 383 " (cutoff:3.500A) Processing helix chain 'M' and resid 390 through 415 removed outlier: 3.617A pdb=" N MET M 396 " --> pdb=" O ILE M 393 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N THR M 403 " --> pdb=" O MET M 400 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N TYR M 406 " --> pdb=" O THR M 403 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N SER M 407 " --> pdb=" O ALA M 404 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU M 408 " --> pdb=" O LEU M 405 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR M 409 " --> pdb=" O TYR M 406 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N MET M 413 " --> pdb=" O MET M 410 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N THR M 414 " --> pdb=" O LEU M 411 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLN M 415 " --> pdb=" O ILE M 412 " (cutoff:3.500A) Processing helix chain 'M' and resid 431 through 448 removed outlier: 3.579A pdb=" N HIS M 440 " --> pdb=" O LEU M 436 " (cutoff:3.500A) Proline residue: M 443 - end of helix removed outlier: 4.325A pdb=" N THR M 448 " --> pdb=" O LEU M 444 " (cutoff:3.500A) Processing helix chain 'M' and resid 451 through 453 No H-bonds generated for 'chain 'M' and resid 451 through 453' Processing helix chain 'N' and resid 3 through 22 removed outlier: 3.509A pdb=" N VAL N 20 " --> pdb=" O GLY N 16 " (cutoff:3.500A) Processing helix chain 'N' and resid 26 through 44 Proline residue: N 42 - end of helix Processing helix chain 'N' and resid 50 through 81 Processing helix chain 'N' and resid 92 through 106 Processing helix chain 'N' and resid 112 through 121 Proline residue: N 116 - end of helix removed outlier: 3.914A pdb=" N THR N 119 " --> pdb=" O PRO N 116 " (cutoff:3.500A) Processing helix chain 'N' and resid 124 through 131 removed outlier: 3.839A pdb=" N ILE N 129 " --> pdb=" O SER N 125 " (cutoff:3.500A) Processing helix chain 'N' and resid 133 through 148 removed outlier: 3.889A pdb=" N ALA N 137 " --> pdb=" O GLN N 134 " (cutoff:3.500A) Proline residue: N 138 - end of helix removed outlier: 3.501A pdb=" N VAL N 141 " --> pdb=" O PRO N 138 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU N 142 " --> pdb=" O MET N 139 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N PHE N 146 " --> pdb=" O TYR N 143 " (cutoff:3.500A) Proline residue: N 147 - end of helix Processing helix chain 'N' and resid 151 through 171 removed outlier: 3.684A pdb=" N GLY N 169 " --> pdb=" O GLY N 165 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU N 170 " --> pdb=" O GLY N 166 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ASN N 171 " --> pdb=" O TRP N 167 " (cutoff:3.500A) Processing helix chain 'N' and resid 175 through 193 removed outlier: 3.511A pdb=" N ALA N 180 " --> pdb=" O ARG N 176 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLY N 188 " --> pdb=" O ILE N 184 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL N 193 " --> pdb=" O TRP N 189 " (cutoff:3.500A) Processing helix chain 'N' and resid 198 through 222 removed outlier: 3.557A pdb=" N ASN N 222 " --> pdb=" O MET N 218 " (cutoff:3.500A) Processing helix chain 'N' and resid 227 through 235 removed outlier: 3.528A pdb=" N HIS N 232 " --> pdb=" O LEU N 228 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N THR N 233 " --> pdb=" O SER N 229 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N TRP N 234 " --> pdb=" O LEU N 230 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N ASN N 235 " --> pdb=" O SER N 231 " (cutoff:3.500A) Processing helix chain 'N' and resid 238 through 251 Processing helix chain 'N' and resid 258 through 272 Proline residue: N 262 - end of helix removed outlier: 3.914A pdb=" N MET N 265 " --> pdb=" O PRO N 262 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N MET N 270 " --> pdb=" O ILE N 267 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N THR N 271 " --> pdb=" O GLN N 268 " (cutoff:3.500A) Processing helix chain 'N' and resid 277 through 300 removed outlier: 3.900A pdb=" N LEU N 287 " --> pdb=" O ALA N 283 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N LEU N 288 " --> pdb=" O ILE N 284 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N ASN N 289 " --> pdb=" O THR N 285 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU N 296 " --> pdb=" O PHE N 292 " (cutoff:3.500A) Processing helix chain 'N' and resid 309 through 316 Processing helix chain 'N' and resid 326 through 332 removed outlier: 3.754A pdb=" N VAL N 331 " --> pdb=" O PRO N 327 " (cutoff:3.500A) Processing helix chain 'N' and resid 340 through 346 Processing helix chain 'O' and resid 5 through 10 Processing helix chain 'O' and resid 14 through 17 No H-bonds generated for 'chain 'O' and resid 14 through 17' Processing helix chain 'O' and resid 35 through 46 Processing helix chain 'O' and resid 59 through 62 No H-bonds generated for 'chain 'O' and resid 59 through 62' Processing helix chain 'O' and resid 71 through 74 Processing helix chain 'O' and resid 80 through 84 Processing helix chain 'O' and resid 92 through 118 Processing helix chain 'O' and resid 132 through 141 Processing helix chain 'O' and resid 146 through 159 Processing helix chain 'O' and resid 176 through 186 Processing helix chain 'O' and resid 191 through 193 No H-bonds generated for 'chain 'O' and resid 191 through 193' Processing helix chain 'O' and resid 196 through 208 removed outlier: 3.613A pdb=" N ALA O 205 " --> pdb=" O ASP O 201 " (cutoff:3.500A) Processing helix chain 'O' and resid 210 through 216 removed outlier: 4.279A pdb=" N GLU O 216 " --> pdb=" O PRO O 212 " (cutoff:3.500A) Processing helix chain 'O' and resid 231 through 239 Processing helix chain 'O' and resid 247 through 249 No H-bonds generated for 'chain 'O' and resid 247 through 249' Processing helix chain 'O' and resid 253 through 263 Processing helix chain 'O' and resid 266 through 269 No H-bonds generated for 'chain 'O' and resid 266 through 269' Processing helix chain 'O' and resid 286 through 298 Processing helix chain 'O' and resid 310 through 312 No H-bonds generated for 'chain 'O' and resid 310 through 312' Processing helix chain 'P' and resid 3 through 5 No H-bonds generated for 'chain 'P' and resid 3 through 5' Processing helix chain 'P' and resid 29 through 40 removed outlier: 3.832A pdb=" N TYR P 33 " --> pdb=" O PHE P 29 " (cutoff:3.500A) Processing helix chain 'P' and resid 53 through 62 removed outlier: 4.818A pdb=" N HIS P 58 " --> pdb=" O ASP P 55 " (cutoff:3.500A) Proline residue: P 61 - end of helix Processing helix chain 'P' and resid 80 through 85 removed outlier: 3.772A pdb=" N ALA P 84 " --> pdb=" O SER P 80 " (cutoff:3.500A) Processing helix chain 'P' and resid 106 through 110 Processing helix chain 'P' and resid 112 through 124 removed outlier: 3.576A pdb=" N GLU P 123 " --> pdb=" O GLN P 119 " (cutoff:3.500A) Processing helix chain 'P' and resid 144 through 159 removed outlier: 3.516A pdb=" N ARG P 157 " --> pdb=" O GLU P 153 " (cutoff:3.500A) Processing helix chain 'P' and resid 179 through 188 removed outlier: 4.263A pdb=" N ARG P 186 " --> pdb=" O PHE P 182 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N TRP P 187 " --> pdb=" O ALA P 183 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N PHE P 188 " --> pdb=" O ASN P 184 " (cutoff:3.500A) Processing helix chain 'P' and resid 194 through 197 Processing helix chain 'P' and resid 207 through 218 Processing helix chain 'P' and resid 238 through 248 Processing helix chain 'P' and resid 260 through 270 removed outlier: 3.674A pdb=" N GLY P 267 " --> pdb=" O TYR P 263 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG P 268 " --> pdb=" O ARG P 264 " (cutoff:3.500A) Processing helix chain 'P' and resid 281 through 288 Processing helix chain 'P' and resid 310 through 321 removed outlier: 4.588A pdb=" N ILE P 315 " --> pdb=" O GLU P 311 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N GLU P 316 " --> pdb=" O LEU P 312 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL P 317 " --> pdb=" O LYS P 313 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N ARG P 320 " --> pdb=" O GLU P 316 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N HIS P 321 " --> pdb=" O VAL P 317 " (cutoff:3.500A) Processing helix chain 'P' and resid 324 through 326 No H-bonds generated for 'chain 'P' and resid 324 through 326' Processing helix chain 'Q' and resid 21 through 23 No H-bonds generated for 'chain 'Q' and resid 21 through 23' Processing helix chain 'Q' and resid 27 through 29 No H-bonds generated for 'chain 'Q' and resid 27 through 29' Processing helix chain 'Q' and resid 78 through 80 No H-bonds generated for 'chain 'Q' and resid 78 through 80' Processing helix chain 'Q' and resid 89 through 98 Processing helix chain 'Q' and resid 119 through 122 Processing helix chain 'R' and resid 23 through 28 Processing helix chain 'R' and resid 40 through 46 removed outlier: 3.554A pdb=" N ALA R 45 " --> pdb=" O ILE R 41 " (cutoff:3.500A) Processing helix chain 'S' and resid 30 through 46 removed outlier: 6.937A pdb=" N VAL S 41 " --> pdb=" O GLU S 37 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N GLU S 42 " --> pdb=" O LYS S 38 " (cutoff:3.500A) Processing helix chain 'S' and resid 83 through 95 removed outlier: 3.630A pdb=" N VAL S 93 " --> pdb=" O ALA S 89 " (cutoff:3.500A) Processing helix chain 'T' and resid 10 through 21 removed outlier: 4.055A pdb=" N VAL T 15 " --> pdb=" O ILE T 11 " (cutoff:3.500A) Processing helix chain 'T' and resid 36 through 39 No H-bonds generated for 'chain 'T' and resid 36 through 39' Processing helix chain 'T' and resid 44 through 57 Processing helix chain 'T' and resid 64 through 69 removed outlier: 4.505A pdb=" N LYS T 69 " --> pdb=" O ILE T 65 " (cutoff:3.500A) Processing helix chain 'T' and resid 73 through 81 Processing helix chain 'U' and resid 8 through 21 removed outlier: 3.594A pdb=" N LEU U 21 " --> pdb=" O TYR U 17 " (cutoff:3.500A) Processing helix chain 'U' and resid 27 through 29 No H-bonds generated for 'chain 'U' and resid 27 through 29' Processing helix chain 'U' and resid 45 through 58 Processing helix chain 'U' and resid 73 through 84 Processing helix chain 'V' and resid 19 through 36 removed outlier: 3.521A pdb=" N GLY V 35 " --> pdb=" O LEU V 31 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N HIS V 36 " --> pdb=" O ASP V 32 " (cutoff:3.500A) Processing helix chain 'V' and resid 42 through 60 Processing helix chain 'V' and resid 64 through 71 removed outlier: 3.917A pdb=" N GLU V 69 " --> pdb=" O LYS V 65 " (cutoff:3.500A) Processing helix chain 'V' and resid 76 through 96 removed outlier: 3.989A pdb=" N GLN V 95 " --> pdb=" O ARG V 91 " (cutoff:3.500A) Processing helix chain 'W' and resid 25 through 50 removed outlier: 3.536A pdb=" N ARG W 30 " --> pdb=" O ASN W 26 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ARG W 31 " --> pdb=" O GLU W 27 " (cutoff:3.500A) Proline residue: W 44 - end of helix Processing helix chain 'W' and resid 56 through 68 Processing helix chain 'W' and resid 76 through 94 removed outlier: 3.623A pdb=" N GLU W 89 " --> pdb=" O LYS W 85 " (cutoff:3.500A) Processing helix chain 'W' and resid 100 through 104 Processing helix chain 'W' and resid 118 through 124 Processing helix chain 'X' and resid 21 through 26 Processing helix chain 'X' and resid 29 through 34 removed outlier: 3.657A pdb=" N ALA X 33 " --> pdb=" O HIS X 29 " (cutoff:3.500A) Processing helix chain 'X' and resid 36 through 49 Processing helix chain 'X' and resid 57 through 75 removed outlier: 4.076A pdb=" N ASN X 63 " --> pdb=" O GLY X 59 " (cutoff:3.500A) Processing helix chain 'X' and resid 79 through 90 removed outlier: 4.016A pdb=" N CYS X 87 " --> pdb=" O GLU X 83 " (cutoff:3.500A) Processing helix chain 'X' and resid 100 through 113 removed outlier: 3.945A pdb=" N GLN X 105 " --> pdb=" O LYS X 101 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N PHE X 106 " --> pdb=" O GLN X 102 " (cutoff:3.500A) Processing helix chain 'Y' and resid 3 through 10 removed outlier: 3.540A pdb=" N TRP Y 9 " --> pdb=" O LEU Y 5 " (cutoff:3.500A) Processing helix chain 'Y' and resid 17 through 42 removed outlier: 3.522A pdb=" N TYR Y 22 " --> pdb=" O HIS Y 18 " (cutoff:3.500A) Processing helix chain 'Y' and resid 48 through 80 Processing helix chain 'Y' and resid 86 through 103 removed outlier: 3.508A pdb=" N ILE Y 99 " --> pdb=" O ALA Y 95 " (cutoff:3.500A) Processing helix chain 'Y' and resid 108 through 130 removed outlier: 3.601A pdb=" N ALA Y 115 " --> pdb=" O ALA Y 111 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLY Y 118 " --> pdb=" O CYS Y 114 " (cutoff:3.500A) Processing helix chain 'Z' and resid 32 through 95 Proline residue: Z 73 - end of helix Processing helix chain 'Z' and resid 121 through 124 No H-bonds generated for 'chain 'Z' and resid 121 through 124' Processing helix chain 'Z' and resid 130 through 142 removed outlier: 5.874A pdb=" N PHE Z 140 " --> pdb=" O ALA Z 136 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N ILE Z 141 " --> pdb=" O THR Z 137 " (cutoff:3.500A) Processing helix chain 'a' and resid 2 through 31 Proline residue: a 7 - end of helix removed outlier: 3.587A pdb=" N ALA a 10 " --> pdb=" O PRO a 7 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL a 14 " --> pdb=" O VAL a 11 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N PHE a 17 " --> pdb=" O VAL a 14 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ILE a 18 " --> pdb=" O CYS a 15 " (cutoff:3.500A) Proline residue: a 19 - end of helix removed outlier: 3.843A pdb=" N ALA a 22 " --> pdb=" O PRO a 19 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N THR a 23 " --> pdb=" O GLY a 20 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N HIS a 27 " --> pdb=" O ALA a 24 " (cutoff:3.500A) Processing helix chain 'a' and resid 42 through 55 Processing helix chain 'a' and resid 66 through 68 No H-bonds generated for 'chain 'a' and resid 66 through 68' Processing helix chain 'b' and resid 2 through 14 removed outlier: 3.981A pdb=" N LYS b 9 " --> pdb=" O ALA b 5 " (cutoff:3.500A) Processing helix chain 'b' and resid 16 through 30 Processing helix chain 'b' and resid 38 through 45 removed outlier: 4.105A pdb=" N LEU b 42 " --> pdb=" O THR b 38 " (cutoff:3.500A) Processing helix chain 'b' and resid 78 through 81 No H-bonds generated for 'chain 'b' and resid 78 through 81' Processing helix chain 'c' and resid 14 through 46 Processing helix chain 'd' and resid 16 through 20 Processing helix chain 'd' and resid 29 through 49 removed outlier: 3.547A pdb=" N ARG d 49 " --> pdb=" O ASP d 45 " (cutoff:3.500A) Processing helix chain 'd' and resid 58 through 96 removed outlier: 3.650A pdb=" N TYR d 74 " --> pdb=" O PHE d 70 " (cutoff:3.500A) Processing helix chain 'e' and resid 5 through 9 Processing helix chain 'e' and resid 15 through 17 No H-bonds generated for 'chain 'e' and resid 15 through 17' Processing helix chain 'e' and resid 25 through 27 No H-bonds generated for 'chain 'e' and resid 25 through 27' Processing helix chain 'e' and resid 33 through 42 Processing helix chain 'e' and resid 48 through 54 removed outlier: 3.907A pdb=" N LYS e 53 " --> pdb=" O ILE e 49 " (cutoff:3.500A) Processing helix chain 'e' and resid 56 through 67 Processing helix chain 'e' and resid 69 through 87 removed outlier: 3.625A pdb=" N LYS e 87 " --> pdb=" O GLU e 83 " (cutoff:3.500A) Processing helix chain 'f' and resid 11 through 34 removed outlier: 5.543A pdb=" N VAL f 16 " --> pdb=" O HIS f 13 " (cutoff:3.500A) Proline residue: f 17 - end of helix removed outlier: 3.705A pdb=" N PHE f 22 " --> pdb=" O GLY f 19 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU f 26 " --> pdb=" O GLY f 23 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLU f 32 " --> pdb=" O LYS f 29 " (cutoff:3.500A) Processing helix chain 'g' and resid 51 through 65 Processing helix chain 'g' and resid 69 through 78 Processing helix chain 'g' and resid 86 through 103 Processing helix chain 'g' and resid 115 through 117 No H-bonds generated for 'chain 'g' and resid 115 through 117' Processing helix chain 'h' and resid 16 through 46 removed outlier: 3.880A pdb=" N THR h 32 " --> pdb=" O TYR h 28 " (cutoff:3.500A) Proline residue: h 35 - end of helix Processing helix chain 'h' and resid 70 through 78 Processing helix chain 'h' and resid 83 through 117 removed outlier: 3.560A pdb=" N ARG h 115 " --> pdb=" O ARG h 111 " (cutoff:3.500A) Processing helix chain 'i' and resid 7 through 25 Processing helix chain 'i' and resid 58 through 73 removed outlier: 4.295A pdb=" N LYS i 62 " --> pdb=" O ASN i 58 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N THR i 63 " --> pdb=" O VAL i 59 " (cutoff:3.500A) Processing helix chain 'i' and resid 75 through 87 Processing helix chain 'i' and resid 89 through 91 No H-bonds generated for 'chain 'i' and resid 89 through 91' Processing helix chain 'j' and resid 19 through 42 removed outlier: 3.910A pdb=" N GLN j 24 " --> pdb=" O SER j 20 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N TRP j 33 " --> pdb=" O SER j 29 " (cutoff:3.500A) Processing helix chain 'j' and resid 44 through 48 Processing helix chain 'j' and resid 56 through 58 No H-bonds generated for 'chain 'j' and resid 56 through 58' Processing helix chain 'k' and resid 27 through 38 removed outlier: 4.193A pdb=" N ARG k 38 " --> pdb=" O LYS k 34 " (cutoff:3.500A) Processing helix chain 'k' and resid 47 through 49 No H-bonds generated for 'chain 'k' and resid 47 through 49' Processing helix chain 'k' and resid 62 through 66 Processing helix chain 'k' and resid 70 through 89 Processing helix chain 'l' and resid 17 through 26 removed outlier: 3.888A pdb=" N ALA l 21 " --> pdb=" O PRO l 17 " (cutoff:3.500A) Processing helix chain 'l' and resid 81 through 84 No H-bonds generated for 'chain 'l' and resid 81 through 84' Processing helix chain 'l' and resid 98 through 121 Processing helix chain 'l' and resid 134 through 142 removed outlier: 5.586A pdb=" N LEU l 140 " --> pdb=" O ASN l 136 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N GLU l 141 " --> pdb=" O ASN l 137 " (cutoff:3.500A) Processing helix chain 'm' and resid 19 through 22 No H-bonds generated for 'chain 'm' and resid 19 through 22' Processing helix chain 'm' and resid 26 through 51 removed outlier: 3.833A pdb=" N GLN m 49 " --> pdb=" O GLU m 45 " (cutoff:3.500A) Processing helix chain 'm' and resid 62 through 70 Processing helix chain 'm' and resid 83 through 91 Processing helix chain 'm' and resid 95 through 117 Processing helix chain 'n' and resid 11 through 30 Processing helix chain 'n' and resid 33 through 50 removed outlier: 3.535A pdb=" N PHE n 47 " --> pdb=" O LEU n 43 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N HIS n 50 " --> pdb=" O ARG n 46 " (cutoff:3.500A) Processing helix chain 'n' and resid 56 through 73 removed outlier: 3.541A pdb=" N GLU n 65 " --> pdb=" O GLN n 61 " (cutoff:3.500A) Processing helix chain 'n' and resid 100 through 105 Processing helix chain 'n' and resid 108 through 113 removed outlier: 3.977A pdb=" N MET n 113 " --> pdb=" O SER n 109 " (cutoff:3.500A) Processing helix chain 'n' and resid 115 through 142 removed outlier: 3.502A pdb=" N ARG n 128 " --> pdb=" O TRP n 124 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N GLU n 133 " --> pdb=" O ARG n 129 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N ARG n 134 " --> pdb=" O GLU n 130 " (cutoff:3.500A) Processing helix chain 'n' and resid 167 through 170 No H-bonds generated for 'chain 'n' and resid 167 through 170' Processing helix chain 'o' and resid 3 through 8 Processing helix chain 'o' and resid 12 through 14 No H-bonds generated for 'chain 'o' and resid 12 through 14' Processing helix chain 'o' and resid 42 through 48 Processing helix chain 'o' and resid 52 through 54 No H-bonds generated for 'chain 'o' and resid 52 through 54' Processing helix chain 'o' and resid 59 through 71 Processing helix chain 'o' and resid 80 through 120 removed outlier: 3.778A pdb=" N LYS o 112 " --> pdb=" O LEU o 108 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG o 113 " --> pdb=" O GLN o 109 " (cutoff:3.500A) Processing helix chain 'p' and resid 28 through 39 Processing helix chain 'p' and resid 41 through 57 Processing helix chain 'p' and resid 73 through 75 No H-bonds generated for 'chain 'p' and resid 73 through 75' Processing helix chain 'p' and resid 81 through 115 removed outlier: 3.602A pdb=" N GLU p 86 " --> pdb=" O LEU p 82 " (cutoff:3.500A) Processing helix chain 'p' and resid 117 through 123 removed outlier: 3.727A pdb=" N HIS p 120 " --> pdb=" O GLY p 117 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N ARG p 121 " --> pdb=" O GLU p 118 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLN p 122 " --> pdb=" O SER p 119 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASN p 123 " --> pdb=" O HIS p 120 " (cutoff:3.500A) No H-bonds generated for 'chain 'p' and resid 117 through 123' Processing helix chain 'p' and resid 126 through 142 Processing helix chain 'p' and resid 151 through 171 Processing helix chain 'q' and resid 3 through 16 removed outlier: 3.559A pdb=" N VAL q 14 " --> pdb=" O GLY q 10 " (cutoff:3.500A) Processing helix chain 'q' and resid 20 through 30 Processing helix chain 'q' and resid 79 through 81 No H-bonds generated for 'chain 'q' and resid 79 through 81' Processing helix chain 'q' and resid 84 through 90 removed outlier: 4.531A pdb=" N TRP q 89 " --> pdb=" O GLU q 85 " (cutoff:3.500A) Processing helix chain 'r' and resid 5 through 13 Processing helix chain 'r' and resid 19 through 21 No H-bonds generated for 'chain 'r' and resid 19 through 21' Processing helix chain 'r' and resid 53 through 56 Processing helix chain 'r' and resid 59 through 61 No H-bonds generated for 'chain 'r' and resid 59 through 61' Processing helix chain 's' and resid 42 through 45 Processing helix chain 's' and resid 51 through 61 removed outlier: 4.811A pdb=" N LYS s 60 " --> pdb=" O LEU s 56 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N PHE s 61 " --> pdb=" O ASP s 57 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 85 through 89 removed outlier: 6.572A pdb=" N TYR B 112 " --> pdb=" O MET B 86 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N VAL B 88 " --> pdb=" O TYR B 112 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N VAL B 114 " --> pdb=" O VAL B 88 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N ILE B 144 " --> pdb=" O SER B 115 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'C' and resid 74 through 82 removed outlier: 6.757A pdb=" N ASN C 95 " --> pdb=" O ALA C 76 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N LEU C 78 " --> pdb=" O VAL C 93 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N VAL C 93 " --> pdb=" O LEU C 78 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ALA C 80 " --> pdb=" O GLU C 91 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N GLU C 91 " --> pdb=" O ALA C 80 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LEU C 48 " --> pdb=" O ARG C 106 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N LYS C 108 " --> pdb=" O LEU C 48 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ILE C 50 " --> pdb=" O LYS C 108 " (cutoff:3.500A) removed outlier: 8.798A pdb=" N TYR C 110 " --> pdb=" O ILE C 50 " (cutoff:3.500A) removed outlier: 8.876A pdb=" N ILE C 52 " --> pdb=" O TYR C 110 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 172 through 177 removed outlier: 3.551A pdb=" N ARG C 182 " --> pdb=" O ASP C 177 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 47 through 51 removed outlier: 3.792A pdb=" N ARG D 63 " --> pdb=" O HIS D 79 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N SER D 69 " --> pdb=" O VAL D 73 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N VAL D 73 " --> pdb=" O SER D 69 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'D' and resid 361 through 369 Processing sheet with id= F, first strand: chain 'E' and resid 137 through 142 removed outlier: 6.664A pdb=" N TYR E 98 " --> pdb=" O THR E 138 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N ILE E 140 " --> pdb=" O TYR E 98 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ILE E 100 " --> pdb=" O ILE E 140 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N VAL E 142 " --> pdb=" O ILE E 100 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N VAL E 102 " --> pdb=" O VAL E 142 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'F' and resid 219 through 224 removed outlier: 6.355A pdb=" N ALA F 133 " --> pdb=" O LEU F 93 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N VAL F 95 " --> pdb=" O ALA F 133 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N TYR F 135 " --> pdb=" O VAL F 95 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ALA F 97 " --> pdb=" O TYR F 135 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N TYR F 137 " --> pdb=" O ALA F 97 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ASP F 174 " --> pdb=" O ALA F 134 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N ILE F 136 " --> pdb=" O ASP F 174 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N PHE F 176 " --> pdb=" O ILE F 136 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N ILE F 138 " --> pdb=" O PHE F 176 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N VAL F 178 " --> pdb=" O ILE F 138 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'F' and resid 266 through 271 Processing sheet with id= I, first strand: chain 'G' and resid 9 through 13 Processing sheet with id= J, first strand: chain 'G' and resid 146 through 148 Processing sheet with id= K, first strand: chain 'G' and resid 173 through 175 Processing sheet with id= L, first strand: chain 'G' and resid 223 through 228 removed outlier: 3.635A pdb=" N ARG G 249 " --> pdb=" O SER G 241 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'G' and resid 283 through 285 Processing sheet with id= N, first strand: chain 'G' and resid 343 through 345 removed outlier: 8.496A pdb=" N CYS G 344 " --> pdb=" O VAL G 315 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ALA G 317 " --> pdb=" O CYS G 344 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N MET G 521 " --> pdb=" O ALA G 316 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N ILE G 318 " --> pdb=" O MET G 521 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N PHE G 523 " --> pdb=" O ILE G 318 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N PHE G 542 " --> pdb=" O LEU G 522 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N LEU G 524 " --> pdb=" O PHE G 542 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N VAL G 544 " --> pdb=" O LEU G 524 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'G' and resid 405 through 409 Processing sheet with id= P, first strand: chain 'G' and resid 572 through 574 Processing sheet with id= Q, first strand: chain 'I' and resid 65 through 67 Processing sheet with id= R, first strand: chain 'I' and resid 92 through 98 removed outlier: 5.762A pdb=" N GLU I 97 " --> pdb=" O THR I 106 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N THR I 106 " --> pdb=" O GLU I 97 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'L' and resid 61 through 64 removed outlier: 3.624A pdb=" N LEU L 61 " --> pdb=" O MET L 82 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'L' and resid 67 through 71 removed outlier: 6.863A pdb=" N LEU L 76 " --> pdb=" O TRP L 68 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N THR L 70 " --> pdb=" O LEU L 74 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N LEU L 74 " --> pdb=" O THR L 70 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'O' and resid 219 through 224 removed outlier: 6.113A pdb=" N VAL O 122 " --> pdb=" O ILE O 25 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N VAL O 27 " --> pdb=" O VAL O 122 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N LEU O 124 " --> pdb=" O VAL O 27 " (cutoff:3.500A) removed outlier: 8.676A pdb=" N GLY O 29 " --> pdb=" O LEU O 124 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N LYS O 49 " --> pdb=" O VAL O 123 " (cutoff:3.500A) removed outlier: 8.417A pdb=" N GLU O 125 " --> pdb=" O LYS O 49 " (cutoff:3.500A) removed outlier: 8.456A pdb=" N PHE O 51 " --> pdb=" O GLU O 125 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'P' and resid 227 through 230 removed outlier: 6.894A pdb=" N ILE P 165 " --> pdb=" O PHE P 228 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N PHE P 230 " --> pdb=" O ILE P 165 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N LYS P 167 " --> pdb=" O PHE P 230 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE P 132 " --> pdb=" O ASN P 93 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N GLN P 44 " --> pdb=" O ALA P 21 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N VAL P 23 " --> pdb=" O GLN P 44 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ILE P 46 " --> pdb=" O VAL P 23 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'P' and resid 191 through 193 removed outlier: 3.516A pdb=" N TYR P 256 " --> pdb=" O VAL P 191 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU P 193 " --> pdb=" O TYR P 256 " (cutoff:3.500A) No H-bonds generated for sheet with id= W Processing sheet with id= X, first strand: chain 'Q' and resid 102 through 105 Processing sheet with id= Y, first strand: chain 'Q' and resid 64 through 66 Processing sheet with id= Z, first strand: chain 'R' and resid 50 through 52 Processing sheet with id= AA, first strand: chain 'R' and resid 56 through 59 Processing sheet with id= AB, first strand: chain 'S' and resid 51 through 56 removed outlier: 3.782A pdb=" N LEU S 22 " --> pdb=" O ARG S 55 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLN S 72 " --> pdb=" O TYR S 68 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'q' and resid 60 through 63 removed outlier: 6.615A pdb=" N GLU q 50 " --> pdb=" O LEU q 38 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N LEU q 38 " --> pdb=" O GLU q 50 " (cutoff:3.500A) 2750 hydrogen bonds defined for protein. 7566 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: 21.04 Time building geometry restraints manager: 22.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.40: 27831 1.40 - 1.62: 40217 1.62 - 1.85: 830 1.85 - 2.07: 0 2.07 - 2.30: 80 Bond restraints: 68958 Sorted by residual: bond pdb=" C5 GTP O 401 " pdb=" N7 GTP O 401 " ideal model delta sigma weight residual 1.350 1.519 -0.169 2.00e-02 2.50e+03 7.17e+01 bond pdb=" C6 GTP O 401 " pdb=" O6 GTP O 401 " ideal model delta sigma weight residual 1.230 1.396 -0.166 2.00e-02 2.50e+03 6.91e+01 bond pdb=" CB7 CDL L 702 " pdb=" OB8 CDL L 702 " ideal model delta sigma weight residual 1.334 1.404 -0.070 1.10e-02 8.26e+03 4.00e+01 bond pdb=" CB7 CDL h1001 " pdb=" OB8 CDL h1001 " ideal model delta sigma weight residual 1.334 1.402 -0.068 1.10e-02 8.26e+03 3.80e+01 bond pdb=" CA7 CDL L 702 " pdb=" OA8 CDL L 702 " ideal model delta sigma weight residual 1.334 1.402 -0.068 1.10e-02 8.26e+03 3.77e+01 ... (remaining 68953 not shown) Histogram of bond angle deviations from ideal: 72.53 - 84.87: 76 84.87 - 97.20: 1 97.20 - 109.54: 8180 109.54 - 121.87: 72153 121.87 - 134.21: 12962 Bond angle restraints: 93372 Sorted by residual: angle pdb=" C51 CDL h1001 " pdb=" CB5 CDL h1001 " pdb=" OB6 CDL h1001 " ideal model delta sigma weight residual 111.33 122.30 -10.97 1.32e+00 5.72e-01 6.89e+01 angle pdb=" C51 CDL Y 701 " pdb=" CB5 CDL Y 701 " pdb=" OB6 CDL Y 701 " ideal model delta sigma weight residual 111.33 121.29 -9.96 1.32e+00 5.72e-01 5.68e+01 angle pdb=" C11 CDL L 702 " pdb=" CA5 CDL L 702 " pdb=" OA6 CDL L 702 " ideal model delta sigma weight residual 111.33 120.27 -8.94 1.32e+00 5.72e-01 4.57e+01 angle pdb=" C51 CDL q 201 " pdb=" CB5 CDL q 201 " pdb=" OB6 CDL q 201 " ideal model delta sigma weight residual 111.33 120.24 -8.91 1.32e+00 5.72e-01 4.54e+01 angle pdb=" C11 CDL h1001 " pdb=" CA5 CDL h1001 " pdb=" OA6 CDL h1001 " ideal model delta sigma weight residual 111.33 119.72 -8.39 1.32e+00 5.72e-01 4.03e+01 ... (remaining 93367 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.60: 40293 35.60 - 71.20: 944 71.20 - 106.81: 103 106.81 - 142.41: 3 142.41 - 178.01: 4 Dihedral angle restraints: 41347 sinusoidal: 17425 harmonic: 23922 Sorted by residual: dihedral pdb=" C10 FMN F 501 " pdb=" C1' FMN F 501 " pdb=" N10 FMN F 501 " pdb=" C2' FMN F 501 " ideal model delta sinusoidal sigma weight residual 257.59 79.58 178.01 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O3B GTP O 401 " pdb=" O3A GTP O 401 " pdb=" PB GTP O 401 " pdb=" PA GTP O 401 " ideal model delta sinusoidal sigma weight residual 291.08 115.77 175.31 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" O5' GTP O 401 " pdb=" O3A GTP O 401 " pdb=" PA GTP O 401 " pdb=" PB GTP O 401 " ideal model delta sinusoidal sigma weight residual -85.88 81.02 -166.89 1 2.00e+01 2.50e-03 4.74e+01 ... (remaining 41344 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.248: 10140 4.248 - 8.497: 0 8.497 - 12.745: 0 12.745 - 16.994: 0 16.994 - 21.242: 16 Chirality restraints: 10156 Sorted by residual: chirality pdb="FE1 SF4 I 202 " pdb=" S2 SF4 I 202 " pdb=" S3 SF4 I 202 " pdb=" S4 SF4 I 202 " both_signs ideal model delta sigma weight residual False -10.55 10.69 -21.24 2.00e-01 2.50e+01 1.13e+04 chirality pdb="FE4 SF4 F 502 " pdb=" S1 SF4 F 502 " pdb=" S2 SF4 F 502 " pdb=" S3 SF4 F 502 " both_signs ideal model delta sigma weight residual False 10.55 -10.67 21.22 2.00e-01 2.50e+01 1.13e+04 chirality pdb="FE2 SF4 G 801 " pdb=" S1 SF4 G 801 " pdb=" S3 SF4 G 801 " pdb=" S4 SF4 G 801 " both_signs ideal model delta sigma weight residual False 10.55 -10.66 21.21 2.00e-01 2.50e+01 1.12e+04 ... (remaining 10153 not shown) Planarity restraints: 11705 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 125 " 0.044 2.00e-02 2.50e+03 3.39e-02 2.29e+01 pdb=" CG TYR B 125 " -0.081 2.00e-02 2.50e+03 pdb=" CD1 TYR B 125 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TYR B 125 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR B 125 " -0.010 2.00e-02 2.50e+03 pdb=" CE2 TYR B 125 " 0.009 2.00e-02 2.50e+03 pdb=" CZ TYR B 125 " 0.009 2.00e-02 2.50e+03 pdb=" OH TYR B 125 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE K 53 " -0.014 2.00e-02 2.50e+03 2.31e-02 9.33e+00 pdb=" CG PHE K 53 " 0.048 2.00e-02 2.50e+03 pdb=" CD1 PHE K 53 " -0.030 2.00e-02 2.50e+03 pdb=" CD2 PHE K 53 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE K 53 " 0.014 2.00e-02 2.50e+03 pdb=" CE2 PHE K 53 " -0.007 2.00e-02 2.50e+03 pdb=" CZ PHE K 53 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE s 33 " -0.015 2.00e-02 2.50e+03 1.95e-02 6.68e+00 pdb=" CG PHE s 33 " 0.043 2.00e-02 2.50e+03 pdb=" CD1 PHE s 33 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 PHE s 33 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE s 33 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE s 33 " -0.005 2.00e-02 2.50e+03 pdb=" CZ PHE s 33 " -0.003 2.00e-02 2.50e+03 ... (remaining 11702 not shown) Histogram of nonbonded interaction distances: 1.43 - 2.12: 33 2.12 - 2.82: 20953 2.82 - 3.51: 92143 3.51 - 4.21: 169309 4.21 - 4.90: 297910 Nonbonded interactions: 580348 Sorted by model distance: nonbonded pdb=" OXT AME d 1 " pdb=" CA MET d 2 " model vdw 1.431 2.776 nonbonded pdb=" O LEU A 71 " pdb=" OH TYR J 147 " model vdw 1.826 2.440 nonbonded pdb=" OE1 GLU B 109 " pdb=" OH TYR P 54 " model vdw 1.913 2.440 nonbonded pdb=" OH TYR G 362 " pdb=" OD1 ASP G 504 " model vdw 1.914 2.440 nonbonded pdb=" O1G GTP O 401 " pdb="MG MG O 402 " model vdw 1.940 2.170 ... (remaining 580343 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'T' and (resid 7 through 65 or (resid 66 and (name N or name CA or name C \ or name CB or name CG or name OD1 or name OD2)) or resid 67 through 82 or resid \ 101)) selection = (chain 'U' and (resid 7 through 82 or resid 101)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Fe 28 7.16 5 Zn 1 6.06 5 P 35 5.49 5 Mg 1 5.21 5 S 470 5.16 5 C 43446 2.51 5 N 11182 2.21 5 O 12096 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 23.030 Check model and map are aligned: 0.730 Process input model: 147.060 Find NCS groups from input model: 2.310 Set up NCS constraints: 0.270 Set refine NCS operators: 0.000 Set scattering table: 0.480 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:2.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 180.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.169 68958 Z= 0.509 Angle : 0.787 17.286 93372 Z= 0.376 Chirality : 0.841 21.242 10156 Planarity : 0.004 0.059 11705 Dihedral : 15.687 178.012 25906 Min Nonbonded Distance : 1.431 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.69 % Favored : 94.21 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.66 % 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: -1.37 (0.09), residues: 8099 helix: -0.83 (0.08), residues: 4226 sheet: -0.99 (0.25), residues: 423 loop : -0.80 (0.11), residues: 3450 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16198 Ramachandran restraints generated. 8099 Oldfield, 0 Emsley, 8099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16198 Ramachandran restraints generated. 8099 Oldfield, 0 Emsley, 8099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1622 residues out of total 7157 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1620 time to evaluate : 7.006 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "ASP U 66 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 1622 average time/residue: 0.7039 time to fit residues: 1907.9417 Evaluate side-chains 1335 residues out of total 7157 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1333 time to evaluate : 5.950 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.5092 time to fit residues: 10.2564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 802 random chunks: chunk 677 optimal weight: 0.6980 chunk 607 optimal weight: 4.9990 chunk 337 optimal weight: 0.6980 chunk 207 optimal weight: 5.9990 chunk 410 optimal weight: 2.9990 chunk 324 optimal weight: 0.9990 chunk 628 optimal weight: 2.9990 chunk 243 optimal weight: 3.9990 chunk 382 optimal weight: 5.9990 chunk 467 optimal weight: 0.4980 chunk 728 optimal weight: 4.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 211 GLN F 150 GLN H 5 ASN L 226 GLN L 541 ASN N 268 GLN P 87 HIS Q 44 ASN Q 46 GLN Q 121 ASN S 79 ASN S 92 ASN W 48 HIS f 13 HIS i 82 HIS m 78 ASN n 77 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.289 68958 Z= 0.438 Angle : 1.324 50.932 93372 Z= 0.845 Chirality : 0.255 6.640 10156 Planarity : 0.005 0.056 11705 Dihedral : 10.067 178.835 9696 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.75 % Favored : 97.20 % Rotamer Outliers : 0.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.09), residues: 8099 helix: 0.49 (0.08), residues: 4250 sheet: -0.67 (0.25), residues: 419 loop : -0.53 (0.11), residues: 3430 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16198 Ramachandran restraints generated. 8099 Oldfield, 0 Emsley, 8099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16198 Ramachandran restraints generated. 8099 Oldfield, 0 Emsley, 8099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1549 residues out of total 7157 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 1481 time to evaluate : 6.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 68 outliers final: 41 residues processed: 1503 average time/residue: 0.6653 time to fit residues: 1690.6315 Evaluate side-chains 1365 residues out of total 7157 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 1324 time to evaluate : 5.950 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 0 residues processed: 41 average time/residue: 0.5168 time to fit residues: 47.8379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 802 random chunks: chunk 404 optimal weight: 0.0370 chunk 226 optimal weight: 0.7980 chunk 606 optimal weight: 4.9990 chunk 495 optimal weight: 7.9990 chunk 200 optimal weight: 3.9990 chunk 729 optimal weight: 0.8980 chunk 788 optimal weight: 0.0970 chunk 649 optimal weight: 1.9990 chunk 723 optimal weight: 0.9980 chunk 248 optimal weight: 6.9990 chunk 585 optimal weight: 9.9990 overall best weight: 0.5656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 162 GLN D 273 GLN L 434 GLN L 541 ASN M 304 GLN N 63 GLN ** O 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 95 HIS S 24 GLN S 79 ASN W 48 HIS Y 7 GLN Z 76 GLN l 87 ASN ** n 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 35 GLN r 50 ASN s 44 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.250 68958 Z= 0.413 Angle : 1.293 50.496 93372 Z= 0.833 Chirality : 0.254 6.381 10156 Planarity : 0.004 0.050 11705 Dihedral : 9.541 177.899 9696 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.94 % Favored : 97.04 % Rotamer Outliers : 0.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.66 % 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 (0.09), residues: 8099 helix: 1.08 (0.08), residues: 4232 sheet: -0.58 (0.25), residues: 444 loop : -0.29 (0.11), residues: 3423 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16198 Ramachandran restraints generated. 8099 Oldfield, 0 Emsley, 8099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16198 Ramachandran restraints generated. 8099 Oldfield, 0 Emsley, 8099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1495 residues out of total 7157 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 1433 time to evaluate : 5.883 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 62 outliers final: 27 residues processed: 1462 average time/residue: 0.6703 time to fit residues: 1658.6527 Evaluate side-chains 1368 residues out of total 7157 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 1341 time to evaluate : 5.930 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.5618 time to fit residues: 35.4579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 802 random chunks: chunk 720 optimal weight: 2.9990 chunk 548 optimal weight: 2.9990 chunk 378 optimal weight: 2.9990 chunk 80 optimal weight: 5.9990 chunk 348 optimal weight: 0.0670 chunk 489 optimal weight: 0.9990 chunk 732 optimal weight: 8.9990 chunk 775 optimal weight: 2.9990 chunk 382 optimal weight: 2.9990 chunk 693 optimal weight: 0.1980 chunk 208 optimal weight: 0.3980 overall best weight: 0.9322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 273 GLN L 541 ASN S 30 GLN S 79 ASN X 94 GLN X 150 ASN ** g 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 58 ASN l 87 ASN ** n 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 24 GLN r 35 GLN s 43 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.246 68958 Z= 0.415 Angle : 1.293 50.536 93372 Z= 0.832 Chirality : 0.254 6.387 10156 Planarity : 0.004 0.057 11705 Dihedral : 9.297 179.900 9696 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.63 % Favored : 97.35 % Rotamer Outliers : 0.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.66 % 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: 0.80 (0.09), residues: 8099 helix: 1.29 (0.08), residues: 4233 sheet: -0.43 (0.24), residues: 462 loop : -0.20 (0.11), residues: 3404 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16198 Ramachandran restraints generated. 8099 Oldfield, 0 Emsley, 8099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16198 Ramachandran restraints generated. 8099 Oldfield, 0 Emsley, 8099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1419 residues out of total 7157 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 1353 time to evaluate : 7.593 Fit side-chains revert: symmetry clash outliers start: 66 outliers final: 33 residues processed: 1385 average time/residue: 0.6901 time to fit residues: 1629.4328 Evaluate side-chains 1333 residues out of total 7157 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 1300 time to evaluate : 6.069 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 0 residues processed: 33 average time/residue: 0.5199 time to fit residues: 41.0879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 802 random chunks: chunk 645 optimal weight: 4.9990 chunk 440 optimal weight: 0.9990 chunk 11 optimal weight: 5.9990 chunk 577 optimal weight: 1.9990 chunk 319 optimal weight: 2.9990 chunk 661 optimal weight: 6.9990 chunk 535 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 395 optimal weight: 3.9990 chunk 695 optimal weight: 4.9990 chunk 195 optimal weight: 0.8980 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 273 GLN N 152 ASN S 79 ASN X 94 GLN a 31 ASN b 51 ASN ** l 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 35 GLN r 50 ASN s 44 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.245 68958 Z= 0.430 Angle : 1.297 50.543 93372 Z= 0.834 Chirality : 0.254 6.409 10156 Planarity : 0.004 0.053 11705 Dihedral : 9.191 177.723 9696 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.91 % Favored : 97.06 % Rotamer Outliers : 0.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.66 % 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: 0.87 (0.09), residues: 8099 helix: 1.33 (0.08), residues: 4254 sheet: -0.35 (0.25), residues: 433 loop : -0.16 (0.11), residues: 3412 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16198 Ramachandran restraints generated. 8099 Oldfield, 0 Emsley, 8099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16198 Ramachandran restraints generated. 8099 Oldfield, 0 Emsley, 8099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1400 residues out of total 7157 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 1344 time to evaluate : 6.210 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 56 outliers final: 30 residues processed: 1368 average time/residue: 0.6861 time to fit residues: 1591.1034 Evaluate side-chains 1320 residues out of total 7157 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 1290 time to evaluate : 5.997 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 0 residues processed: 30 average time/residue: 0.5497 time to fit residues: 38.3538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 802 random chunks: chunk 260 optimal weight: 0.9990 chunk 698 optimal weight: 6.9990 chunk 153 optimal weight: 7.9990 chunk 455 optimal weight: 5.9990 chunk 191 optimal weight: 2.9990 chunk 775 optimal weight: 1.9990 chunk 644 optimal weight: 3.9990 chunk 359 optimal weight: 0.9990 chunk 64 optimal weight: 3.9990 chunk 256 optimal weight: 2.9990 chunk 407 optimal weight: 0.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 273 GLN ** L 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 44 ASN S 79 ASN Y 7 GLN a 31 ASN b 51 ASN ** g 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 25 GLN ** l 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 87 ASN r 35 GLN s 44 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.245 68958 Z= 0.430 Angle : 1.298 50.548 93372 Z= 0.834 Chirality : 0.254 6.404 10156 Planarity : 0.004 0.053 11705 Dihedral : 9.093 179.292 9696 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.69 % Favored : 97.28 % Rotamer Outliers : 0.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.66 % 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: 0.93 (0.09), residues: 8099 helix: 1.38 (0.08), residues: 4257 sheet: -0.34 (0.25), residues: 439 loop : -0.13 (0.11), residues: 3403 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16198 Ramachandran restraints generated. 8099 Oldfield, 0 Emsley, 8099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16198 Ramachandran restraints generated. 8099 Oldfield, 0 Emsley, 8099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1372 residues out of total 7157 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 1324 time to evaluate : 6.316 Fit side-chains revert: symmetry clash outliers start: 48 outliers final: 35 residues processed: 1345 average time/residue: 0.6954 time to fit residues: 1588.1591 Evaluate side-chains 1326 residues out of total 7157 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 1291 time to evaluate : 5.974 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 0 residues processed: 35 average time/residue: 0.5354 time to fit residues: 43.4733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 802 random chunks: chunk 748 optimal weight: 0.0980 chunk 87 optimal weight: 0.5980 chunk 442 optimal weight: 0.8980 chunk 566 optimal weight: 0.5980 chunk 439 optimal weight: 8.9990 chunk 653 optimal weight: 5.9990 chunk 433 optimal weight: 5.9990 chunk 772 optimal weight: 7.9990 chunk 483 optimal weight: 0.9980 chunk 471 optimal weight: 10.0000 chunk 356 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 273 GLN F 435 GLN ** L 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 99 GLN X 94 GLN Y 7 GLN b 51 ASN l 28 ASN q 123 GLN r 35 GLN r 50 ASN s 44 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.246 68958 Z= 0.409 Angle : 1.288 50.565 93372 Z= 0.830 Chirality : 0.253 6.363 10156 Planarity : 0.004 0.054 11705 Dihedral : 8.862 178.531 9696 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.68 % Favored : 97.30 % Rotamer Outliers : 0.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.66 % 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: 1.05 (0.09), residues: 8099 helix: 1.51 (0.08), residues: 4237 sheet: -0.32 (0.24), residues: 458 loop : -0.10 (0.11), residues: 3404 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16198 Ramachandran restraints generated. 8099 Oldfield, 0 Emsley, 8099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16198 Ramachandran restraints generated. 8099 Oldfield, 0 Emsley, 8099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1410 residues out of total 7157 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 1386 time to evaluate : 5.940 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 10 residues processed: 1398 average time/residue: 0.6953 time to fit residues: 1655.7196 Evaluate side-chains 1313 residues out of total 7157 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 1303 time to evaluate : 6.018 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.5143 time to fit residues: 17.9771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 802 random chunks: chunk 478 optimal weight: 5.9990 chunk 308 optimal weight: 6.9990 chunk 461 optimal weight: 4.9990 chunk 232 optimal weight: 5.9990 chunk 151 optimal weight: 0.9980 chunk 149 optimal weight: 6.9990 chunk 491 optimal weight: 3.9990 chunk 526 optimal weight: 6.9990 chunk 382 optimal weight: 4.9990 chunk 72 optimal weight: 4.9990 chunk 607 optimal weight: 8.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 273 GLN J 46 ASN L 175 ASN L 248 HIS N 91 ASN N 309 ASN S 30 GLN S 79 ASN ** b 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 51 ASN c 46 ASN ** g 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 123 GLN r 35 GLN s 44 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.2248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.242 68958 Z= 0.541 Angle : 1.343 50.526 93372 Z= 0.850 Chirality : 0.257 6.480 10156 Planarity : 0.005 0.057 11705 Dihedral : 9.196 177.723 9696 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.43 % Favored : 96.54 % Rotamer Outliers : 0.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.66 % 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: 0.68 (0.09), residues: 8099 helix: 1.14 (0.08), residues: 4262 sheet: -0.39 (0.25), residues: 433 loop : -0.22 (0.11), residues: 3404 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16198 Ramachandran restraints generated. 8099 Oldfield, 0 Emsley, 8099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16198 Ramachandran restraints generated. 8099 Oldfield, 0 Emsley, 8099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1364 residues out of total 7157 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 1305 time to evaluate : 6.043 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 59 outliers final: 43 residues processed: 1334 average time/residue: 0.6963 time to fit residues: 1573.8583 Evaluate side-chains 1303 residues out of total 7157 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 1260 time to evaluate : 5.987 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 0 residues processed: 43 average time/residue: 0.5245 time to fit residues: 50.7305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 802 random chunks: chunk 703 optimal weight: 4.9990 chunk 740 optimal weight: 1.9990 chunk 675 optimal weight: 3.9990 chunk 720 optimal weight: 1.9990 chunk 433 optimal weight: 0.9990 chunk 313 optimal weight: 0.9990 chunk 565 optimal weight: 0.9980 chunk 221 optimal weight: 0.9980 chunk 650 optimal weight: 3.9990 chunk 681 optimal weight: 6.9990 chunk 717 optimal weight: 7.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 273 GLN F 257 ASN H 292 ASN ** L 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 79 ASN X 94 GLN b 45 ASN ** g 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 50 ASN s 44 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.246 68958 Z= 0.422 Angle : 1.303 50.566 93372 Z= 0.836 Chirality : 0.254 6.389 10156 Planarity : 0.004 0.056 11705 Dihedral : 8.948 177.411 9696 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.67 % Favored : 97.31 % Rotamer Outliers : 0.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.66 % 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: 0.90 (0.09), residues: 8099 helix: 1.34 (0.08), residues: 4248 sheet: -0.33 (0.25), residues: 437 loop : -0.12 (0.11), residues: 3414 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16198 Ramachandran restraints generated. 8099 Oldfield, 0 Emsley, 8099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16198 Ramachandran restraints generated. 8099 Oldfield, 0 Emsley, 8099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1340 residues out of total 7157 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 1322 time to evaluate : 6.086 Fit side-chains revert: symmetry clash outliers start: 18 outliers final: 11 residues processed: 1330 average time/residue: 0.7108 time to fit residues: 1604.9304 Evaluate side-chains 1309 residues out of total 7157 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 1298 time to evaluate : 5.907 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.5443 time to fit residues: 19.2538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 802 random chunks: chunk 473 optimal weight: 0.8980 chunk 761 optimal weight: 1.9990 chunk 464 optimal weight: 0.8980 chunk 361 optimal weight: 0.9980 chunk 529 optimal weight: 0.4980 chunk 798 optimal weight: 2.9990 chunk 735 optimal weight: 8.9990 chunk 636 optimal weight: 2.9990 chunk 66 optimal weight: 6.9990 chunk 491 optimal weight: 2.9990 chunk 390 optimal weight: 3.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 273 GLN ** L 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 44 ASN ** R 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 79 ASN ** X 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 51 ASN ** g 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 44 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.246 68958 Z= 0.420 Angle : 1.301 50.551 93372 Z= 0.835 Chirality : 0.254 6.379 10156 Planarity : 0.004 0.054 11705 Dihedral : 8.767 175.266 9696 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.84 % Favored : 97.14 % Rotamer Outliers : 0.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.66 % 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: 1.00 (0.09), residues: 8099 helix: 1.44 (0.08), residues: 4225 sheet: -0.27 (0.25), residues: 419 loop : -0.08 (0.11), residues: 3455 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16198 Ramachandran restraints generated. 8099 Oldfield, 0 Emsley, 8099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16198 Ramachandran restraints generated. 8099 Oldfield, 0 Emsley, 8099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1340 residues out of total 7157 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 1322 time to evaluate : 6.130 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 10 residues processed: 1327 average time/residue: 0.6973 time to fit residues: 1575.3505 Evaluate side-chains 1301 residues out of total 7157 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 1291 time to evaluate : 6.162 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.5604 time to fit residues: 18.8102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 802 random chunks: chunk 505 optimal weight: 0.9990 chunk 677 optimal weight: 2.9990 chunk 194 optimal weight: 8.9990 chunk 586 optimal weight: 10.0000 chunk 93 optimal weight: 0.6980 chunk 176 optimal weight: 3.9990 chunk 637 optimal weight: 2.9990 chunk 266 optimal weight: 4.9990 chunk 654 optimal weight: 6.9990 chunk 80 optimal weight: 3.9990 chunk 117 optimal weight: 0.1980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 273 GLN ** L 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 79 ASN X 15 GLN Y 7 GLN b 51 ASN ** g 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 50 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.114995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.101488 restraints weight = 92598.759| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 1.27 r_work: 0.3047 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.245 68958 Z= 0.432 Angle : 1.307 50.550 93372 Z= 0.837 Chirality : 0.254 6.394 10156 Planarity : 0.004 0.054 11705 Dihedral : 8.738 174.450 9696 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.83 % Favored : 97.16 % Rotamer Outliers : 0.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.66 % 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: 0.97 (0.09), residues: 8099 helix: 1.41 (0.08), residues: 4229 sheet: -0.29 (0.25), residues: 437 loop : -0.09 (0.11), residues: 3433 =============================================================================== Job complete usr+sys time: 22595.19 seconds wall clock time: 394 minutes 19.61 seconds (23659.61 seconds total)