Starting phenix.real_space_refine on Fri Mar 15 03:44:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r44_14266/03_2024/7r44_14266_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r44_14266/03_2024/7r44_14266.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r44_14266/03_2024/7r44_14266_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r44_14266/03_2024/7r44_14266_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r44_14266/03_2024/7r44_14266_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r44_14266/03_2024/7r44_14266.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r44_14266/03_2024/7r44_14266.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r44_14266/03_2024/7r44_14266_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r44_14266/03_2024/7r44_14266_updated.pdb" } resolution = 2.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.008 sd= 1.039 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 11 Type Number sf(0) Gaussians I 1 10.91 5 K 1 8.98 5 Fe 28 7.16 5 Zn 1 6.06 5 P 35 5.49 5 Mg 1 5.21 5 S 467 5.16 5 Cl 1 4.86 5 C 43528 2.51 5 N 11125 2.21 5 O 13025 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 32": "OE1" <-> "OE2" Residue "A ASP 42": "OD1" <-> "OD2" Residue "A PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 115": "OE1" <-> "OE2" Residue "B ASP 34": "OD1" <-> "OD2" Residue "B ARG 71": "NH1" <-> "NH2" Residue "B ARG 111": "NH1" <-> "NH2" Residue "B GLU 154": "OE1" <-> "OE2" Residue "B GLU 170": "OE1" <-> "OE2" Residue "C ARG 8": "NH1" <-> "NH2" Residue "C ARG 12": "NH1" <-> "NH2" Residue "C PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 49": "OE1" <-> "OE2" Residue "C GLU 91": "OE1" <-> "OE2" Residue "C ASP 112": "OD1" <-> "OD2" Residue "C ARG 149": "NH1" <-> "NH2" Residue "C GLU 158": "OE1" <-> "OE2" Residue "C PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 186": "OE1" <-> "OE2" Residue "C ASP 198": "OD1" <-> "OD2" Residue "C GLU 204": "OE1" <-> "OE2" Residue "D ARG 2": "NH1" <-> "NH2" Residue "D GLU 123": "OE1" <-> "OE2" 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 226": "OE1" <-> "OE2" Residue "D GLU 227": "OE1" <-> "OE2" Residue "D ARG 233": "NH1" <-> "NH2" Residue "D GLU 248": "OE1" <-> "OE2" Residue "D ASP 249": "OD1" <-> "OD2" Residue "D GLU 343": "OE1" <-> "OE2" Residue "D PHE 425": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 427": "OE1" <-> "OE2" Residue "D ASP 429": "OD1" <-> "OD2" Residue "E GLU 40": "OE1" <-> "OE2" Residue "E ASP 52": "OD1" <-> "OD2" Residue "E GLU 82": "OE1" <-> "OE2" Residue "E GLU 162": "OE1" <-> "OE2" 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 54": "OD1" <-> "OD2" Residue "F ARG 112": "NH1" <-> "NH2" Residue "F ARG 132": "NH1" <-> "NH2" Residue "F TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 139": "NH1" <-> "NH2" Residue "F GLU 194": "OE1" <-> "OE2" Residue "F ARG 249": "NH1" <-> "NH2" Residue "F GLU 278": "OE1" <-> "OE2" Residue "F ARG 349": "NH1" <-> "NH2" Residue "F GLU 352": "OE1" <-> "OE2" Residue "F GLU 357": "OE1" <-> "OE2" Residue "F GLU 425": "OE1" <-> "OE2" Residue "F ARG 429": "NH1" <-> "NH2" Residue "G GLU 10": "OE1" <-> "OE2" Residue "G PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 21": "OE1" <-> "OE2" Residue "G ARG 39": "NH1" <-> "NH2" Residue "G ARG 53": "NH1" <-> "NH2" Residue "G GLU 138": "OE1" <-> "OE2" Residue "G GLU 165": "OE1" <-> "OE2" Residue "G ASP 171": "OD1" <-> "OD2" Residue "G ASP 180": "OD1" <-> "OD2" Residue "G ARG 218": "NH1" <-> "NH2" Residue "G ARG 243": "NH1" <-> "NH2" Residue "G GLU 246": "OE1" <-> "OE2" Residue "G ARG 253": "NH1" <-> "NH2" Residue "G GLU 260": "OE1" <-> "OE2" Residue "G GLU 261": "OE1" <-> "OE2" Residue "G ARG 285": "NH1" <-> "NH2" Residue "G GLU 287": "OE1" <-> "OE2" Residue "G GLU 297": "OE1" <-> "OE2" Residue "G ARG 302": "NH1" <-> "NH2" Residue "G ASP 314": "OD1" <-> "OD2" Residue "G GLU 346": "OE1" <-> "OE2" Residue "G GLU 347": "OE1" <-> "OE2" Residue "G ASP 375": "OD1" <-> "OD2" Residue "G ARG 385": "NH1" <-> "NH2" Residue "G ARG 418": "NH1" <-> "NH2" Residue "G ASP 431": "OD1" <-> "OD2" Residue "G ASP 536": "OD1" <-> "OD2" Residue "G GLU 595": "OE1" <-> "OE2" Residue "G GLU 605": "OE1" <-> "OE2" Residue "G ASP 614": "OD1" <-> "OD2" Residue "G GLU 625": "OE1" <-> "OE2" Residue "G ASP 634": "OD1" <-> "OD2" Residue "G GLU 637": "OE1" <-> "OE2" Residue "G PHE 642": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 693": "OE1" <-> "OE2" Residue "H ARG 25": "NH1" <-> "NH2" Residue "H ARG 34": "NH1" <-> "NH2" Residue "H TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 62": "NH1" <-> "NH2" Residue "H GLU 192": "OE1" <-> "OE2" Residue "H PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 214": "OE1" <-> "OE2" Residue "H PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 227": "OE1" <-> "OE2" Residue "I ARG 8": "NH1" <-> "NH2" Residue "I TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 74": "OE1" <-> "OE2" Residue "I GLU 84": "OE1" <-> "OE2" Residue "I GLU 95": "OE1" <-> "OE2" Residue "I ARG 108": "NH1" <-> "NH2" Residue "J GLU 81": "OE1" <-> "OE2" Residue "J GLU 100": "OE1" <-> "OE2" Residue "J PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 170": "OE1" <-> "OE2" Residue "J ARG 173": "NH1" <-> "NH2" Residue "L TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 102": "OE1" <-> "OE2" Residue "L PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 111": "OD1" <-> "OD2" Residue "L ARG 161": "NH1" <-> "NH2" Residue "L ASP 179": "OD1" <-> "OD2" Residue "L PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 262": "NH1" <-> "NH2" Residue "L TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 268": "OE1" <-> "OE2" Residue "L GLU 353": "OE1" <-> "OE2" Residue "L ASP 393": "OD1" <-> "OD2" Residue "L TYR 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 606": "OE1" <-> "OE2" Residue "M ASP 59": "OD1" <-> "OD2" Residue "M PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 142": "NH1" <-> "NH2" Residue "M GLU 222": "OE1" <-> "OE2" 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 "N GLU 34": "OE1" <-> "OE2" Residue "N GLU 117": "OE1" <-> "OE2" Residue "N TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 269": "OE1" <-> "OE2" Residue "N PHE 281": "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 GLU 12": "OE1" <-> "OE2" Residue "O GLU 44": "OE1" <-> "OE2" Residue "O GLU 53": "OE1" <-> "OE2" Residue "O ASP 85": "OD1" <-> "OD2" Residue "O TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 216": "OE1" <-> "OE2" Residue "O ASP 237": "OD1" <-> "OD2" Residue "O GLU 239": "OE1" <-> "OE2" Residue "O ARG 302": "NH1" <-> "NH2" Residue "O ARG 305": "NH1" <-> "NH2" Residue "O ASP 311": "OD1" <-> "OD2" Residue "P ARG 40": "NH1" <-> "NH2" Residue "P ARG 50": "NH1" <-> "NH2" Residue "P ASP 72": "OD1" <-> "OD2" 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 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 162": "OE1" <-> "OE2" Residue "P PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 175": "OE1" <-> "OE2" Residue "P PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 235": "NH1" <-> "NH2" Residue "P PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 251": "NH1" <-> "NH2" Residue "P PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 285": "OE1" <-> "OE2" Residue "P GLU 306": "OE1" <-> "OE2" Residue "P ARG 325": "NH1" <-> "NH2" Residue "Q ASP 14": "OD1" <-> "OD2" Residue "Q GLU 15": "OE1" <-> "OE2" Residue "Q GLU 27": "OE1" <-> "OE2" Residue "Q GLU 58": "OE1" <-> "OE2" Residue "Q TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 106": "OE1" <-> "OE2" Residue "R ARG 31": "NH1" <-> "NH2" Residue "R GLU 37": "OE1" <-> "OE2" Residue "R GLU 78": "OE1" <-> "OE2" Residue "S GLU 17": "OE1" <-> "OE2" Residue "S ASP 34": "OD1" <-> "OD2" Residue "S PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 37": "OE1" <-> "OE2" Residue "S ASP 59": "OD1" <-> "OD2" Residue "S ASP 84": "OD1" <-> "OD2" Residue "T ASP 13": "OD1" <-> "OD2" Residue "T ASP 23": "OD1" <-> "OD2" Residue "T ASP 56": "OD1" <-> "OD2" Residue "T GLU 57": "OE1" <-> "OE2" Residue "T ASP 66": "OD1" <-> "OD2" Residue "T ASP 78": "OD1" <-> "OD2" Residue "T ASP 82": "OD1" <-> "OD2" Residue "U GLU 9": "OE1" <-> "OE2" Residue "U GLU 28": "OE1" <-> "OE2" Residue "U ASP 43": "OD1" <-> "OD2" Residue "U GLU 49": "OE1" <-> "OE2" Residue "U GLU 61": "OE1" <-> "OE2" Residue "U GLU 68": "OE1" <-> "OE2" Residue "V ARG 22": "NH1" <-> "NH2" Residue "V ASP 32": "OD1" <-> "OD2" Residue "V GLU 61": "OE1" <-> "OE2" Residue "V GLU 84": "OE1" <-> "OE2" Residue "W ASP 24": "OD1" <-> "OD2" Residue "W GLU 27": "OE1" <-> "OE2" Residue "W GLU 34": "OE1" <-> "OE2" Residue "W TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 42": "OE1" <-> "OE2" Residue "W ASP 53": "OD1" <-> "OD2" 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 PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 97": "NH1" <-> "NH2" Residue "X ARG 118": "NH1" <-> "NH2" Residue "X ASP 133": "OD1" <-> "OD2" Residue "X ARG 134": "NH1" <-> "NH2" Residue "X ARG 144": "NH1" <-> "NH2" Residue "X ARG 146": "NH1" <-> "NH2" Residue "X GLU 148": "OE1" <-> "OE2" Residue "Y TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 13": "OE1" <-> "OE2" Residue "Y GLU 16": "OE1" <-> "OE2" Residue "Y TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 57": "NH1" <-> "NH2" Residue "Y PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 85": "OD1" <-> "OD2" Residue "Y ARG 103": "NH1" <-> "NH2" Residue "Z TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 78": "OE1" <-> "OE2" Residue "Z ARG 82": "NH1" <-> "NH2" Residue "a GLU 4": "OE1" <-> "OE2" Residue "a TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 51": "OD1" <-> "OD2" Residue "a ARG 59": "NH1" <-> "NH2" Residue "a TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 2": "OE1" <-> "OE2" Residue "b ARG 3": "NH1" <-> "NH2" Residue "b ARG 57": "NH1" <-> "NH2" Residue "b ASP 58": "OD1" <-> "OD2" Residue "c PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 44": "NH1" <-> "NH2" Residue "d GLU 17": "OE1" <-> "OE2" Residue "d ASP 45": "OD1" <-> "OD2" Residue "d ARG 51": "NH1" <-> "NH2" Residue "d ASP 87": "OD1" <-> "OD2" Residue "d GLU 114": "OE1" <-> "OE2" Residue "e ASP 4": "OD1" <-> "OD2" Residue "e ARG 8": "NH1" <-> "NH2" Residue "e GLU 38": "OE1" <-> "OE2" Residue "e ARG 50": "NH1" <-> "NH2" Residue "e GLU 83": "OE1" <-> "OE2" Residue "f TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ASP 27": "OD1" <-> "OD2" Residue "f ARG 28": "NH1" <-> "NH2" Residue "f ASP 31": "OD1" <-> "OD2" Residue "f ARG 46": "NH1" <-> "NH2" Residue "f GLU 47": "OE1" <-> "OE2" Residue "g GLU 33": "OE1" <-> "OE2" Residue "g ASP 50": "OD1" <-> "OD2" Residue "g GLU 92": "OE1" <-> "OE2" Residue "h ARG 20": "NH1" <-> "NH2" Residue "h GLU 51": "OE1" <-> "OE2" Residue "h TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 62": "OE1" <-> "OE2" Residue "h ARG 77": "NH1" <-> "NH2" Residue "h GLU 88": "OE1" <-> "OE2" Residue "h ARG 112": "NH1" <-> "NH2" Residue "h GLU 131": "OE1" <-> "OE2" Residue "i GLU 16": "OE1" <-> "OE2" Residue "i ARG 18": "NH1" <-> "NH2" Residue "i GLU 111": "OE1" <-> "OE2" Residue "i GLU 121": "OE1" <-> "OE2" Residue "j PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j GLU 26": "OE1" <-> "OE2" Residue "j ASP 69": "OD1" <-> "OD2" Residue "k ARG 38": "NH1" <-> "NH2" Residue "k ARG 41": "NH1" <-> "NH2" Residue "k TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ASP 7": "OD1" <-> "OD2" Residue "l TYR 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ARG 30": "NH1" <-> "NH2" Residue "l GLU 32": "OE1" <-> "OE2" Residue "l ASP 63": "OD1" <-> "OD2" Residue "l GLU 75": "OE1" <-> "OE2" Residue "l GLU 141": "OE1" <-> "OE2" Residue "l ARG 142": "NH1" <-> "NH2" Residue "l GLU 151": "OE1" <-> "OE2" Residue "l GLU 157": "OE1" <-> "OE2" Residue "m PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m GLU 6": "OE1" <-> "OE2" Residue "m TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 109": "OD1" <-> "OD2" Residue "n ARG 21": "NH1" <-> "NH2" Residue "n GLU 27": "OE1" <-> "OE2" Residue "n ARG 64": "NH1" <-> "NH2" Residue "n GLU 65": "OE1" <-> "OE2" Residue "n GLU 68": "OE1" <-> "OE2" Residue "n GLU 69": "OE1" <-> "OE2" Residue "n GLU 91": "OE1" <-> "OE2" Residue "n ARG 92": "NH1" <-> "NH2" Residue "n TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n GLU 94": "OE1" <-> "OE2" Residue "n TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ASP 104": "OD1" <-> "OD2" Residue "n TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ARG 134": "NH1" <-> "NH2" Residue "n ARG 149": "NH1" <-> "NH2" Residue "n GLU 151": "OE1" <-> "OE2" Residue "n ASP 161": "OD1" <-> "OD2" Residue "o ARG 6": "NH1" <-> "NH2" Residue "o ARG 36": "NH1" <-> "NH2" Residue "o PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ARG 97": "NH1" <-> "NH2" Residue "o ARG 103": "NH1" <-> "NH2" Residue "o ARG 105": "NH1" <-> "NH2" Residue "o ARG 106": "NH1" <-> "NH2" Residue "o GLU 115": "OE1" <-> "OE2" Residue "o ASP 120": "OD1" <-> "OD2" Residue "p ASP 5": "OD1" <-> "OD2" Residue "p PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p GLU 75": "OE1" <-> "OE2" Residue "p GLU 86": "OE1" <-> "OE2" Residue "p GLU 100": "OE1" <-> "OE2" Residue "p GLU 107": "OE1" <-> "OE2" Residue "p GLU 116": "OE1" <-> "OE2" Residue "p TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ARG 21": "NH1" <-> "NH2" Residue "q TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ARG 29": "NH1" <-> "NH2" Residue "q TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q GLU 50": "OE1" <-> "OE2" Residue "q ASP 76": "OD1" <-> "OD2" Residue "q ASP 78": "OD1" <-> "OD2" Residue "q ARG 88": "NH1" <-> "NH2" Residue "q ASP 96": "OD1" <-> "OD2" 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 PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s ASP 53": "OD1" <-> "OD2" Residue "s GLU 71": "OE1" <-> "OE2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 68213 Number of models: 1 Model: "" Number of chains: 113 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: 4692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4692 Classifications: {'peptide': 595} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 27, 'TRANS': 567} Chain breaks: 1 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'FME:plan-2': 1, 'PHE:plan': 1, 'ASN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 17 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: 663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 663 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 4, 'TRANS': 77} 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: 693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 693 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 5, 'TRANS': 80} Chain: "V" Number of atoms: 911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 911 Classifications: {'peptide': 112} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 103} 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: 1146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1146 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 7, 'TRANS': 132} 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: 934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 934 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 9, 'TRANS': 102} Chain: "e" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 799 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 5, 'TRANS': 89} Chain: "f" Number of atoms: 451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 451 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 2, 'TRANS': 49} 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: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 876 Classifications: {'peptide': 102} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 89} 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: 580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 580 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 7, 'TRANS': 59} Chain: "k" Number of atoms: 647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 647 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: 954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 954 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 7, 'TRANS': 105} Chain breaks: 1 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: 1035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 1035 Classifications: {'peptide': 120} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 112} Chain: "p" Number of atoms: 1435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1435 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 10, 'TRANS': 159} 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: 353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 353 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 3, 'TRANS': 38} Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 70 Unusual residues: {'LMT': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 85 Unusual residues: {'PC1': 2, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 31 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: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 21 Unusual residues: {' K': 1, 'FES': 1, 'SF4': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "H" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 78 Unusual residues: {'3PE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'3PE:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "I" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Unusual residues: {'3PE': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "J" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 62 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 38 Chain: "K" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 71 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 29 Chain: "L" Number of atoms: 198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 198 Unusual residues: {'3PE': 2, 'CDL': 1, 'LMT': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 39 Chain: "M" Number of atoms: 216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 216 Unusual residues: {'3PE': 2, 'LMT': 2, 'PC1': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Chain: "N" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 109 Unusual residues: {'3PE': 2, 'I49': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 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: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 69 Unusual residues: {'NDP': 1, 'PC1': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 32 Planarities with less than four sites: {'PC1:plan-1': 1} Unresolved non-hydrogen planarities: 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 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 Chain: "X" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 45 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Chain: "Y" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 70 Unusual residues: {'3PE': 1, 'LMT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Chain: "Z" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'LMT': 1} Classifications: {'undetermined': 1} Chain: "a" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 76 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 24 Chain: "d" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Chain: "e" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'LMT': 1} Classifications: {'undetermined': 1} Chain: "h" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 102 Unusual residues: {'CDL': 1, 'LMT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 33 Chain: "k" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'LMT': 1} Classifications: {'undetermined': 1} Chain: "l" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'LMT': 1} Classifications: {'undetermined': 1} Chain: "o" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'MYR': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'MYR:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "B" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 48 Classifications: {'water': 48} Link IDs: {None: 47} Chain: "C" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 61 Classifications: {'water': 61} Link IDs: {None: 60} Chain: "D" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 123 Classifications: {'water': 123} Link IDs: {None: 122} Chain: "E" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "F" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 36 Classifications: {'water': 36} Link IDs: {None: 35} Chain: "G" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 132 Classifications: {'water': 132} Link IDs: {None: 131} Chain: "H" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 42 Classifications: {'water': 42} Link IDs: {None: 41} Chain: "I" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 76 Classifications: {'water': 76} Link IDs: {None: 75} Chain: "J" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "K" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "L" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 23 Classifications: {'water': 23} Link IDs: {None: 22} Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 28 Classifications: {'water': 28} Link IDs: {None: 27} Chain: "N" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 30 Classifications: {'water': 30} Link IDs: {None: 29} Chain: "O" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "P" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 35 Classifications: {'water': 35} Link IDs: {None: 34} Chain: "Q" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 45 Classifications: {'water': 45} Link IDs: {None: 44} Chain: "R" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Chain: "S" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "V" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "W" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "X" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "Y" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "Z" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "a" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "d" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "e" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "f" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "g" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "h" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "i" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "j" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "k" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "l" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "m" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "n" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "o" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "p" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "q" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "r" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "s" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1668 SG CYS B 119 95.240 94.169 204.600 1.00 27.94 S ATOM 1898 SG CYS B 149 93.022 91.562 209.269 1.00 27.69 S ATOM 1164 SG CYS B 54 89.702 90.461 203.738 1.00 30.79 S ATOM 1170 SG CYS B 55 89.266 96.012 206.757 1.00 30.49 S ATOM 8146 SG CYS E 103 113.636 43.863 258.335 1.00 46.22 S ATOM 8180 SG CYS E 108 111.985 41.056 260.186 1.00 46.84 S ATOM 8460 SG CYS E 144 115.785 40.622 254.798 1.00 44.50 S ATOM 8483 SG CYS E 148 114.553 37.853 255.850 1.00 48.37 S ATOM 11701 SG CYS F 362 118.433 51.326 234.865 1.00 31.83 S ATOM 11721 SG CYS F 365 115.538 50.503 239.746 1.00 33.10 S ATOM 12045 SG CYS F 405 120.109 46.143 238.678 1.00 35.16 S ATOM 11682 SG CYS F 359 122.082 51.810 240.349 1.00 34.70 S ATOM 13142 SG CYS G 114 114.748 70.111 226.322 1.00 28.27 S ATOM 13081 SG CYS G 105 108.875 72.440 228.262 1.00 27.34 S ATOM 13102 SG CYS G 108 114.447 74.872 230.461 1.00 28.39 S ATOM 13474 SG CYS G 156 123.148 63.887 230.855 1.00 29.96 S ATOM 13451 SG CYS G 153 120.436 65.983 236.585 1.00 29.32 S ATOM 13498 SG CYS G 159 126.518 67.045 235.145 1.00 32.81 S ATOM 13828 SG CYS G 203 121.963 69.884 231.398 1.00 30.14 S ATOM 12587 SG CYS G 41 123.543 57.211 228.427 1.00 30.02 S ATOM 12673 SG CYS G 52 119.747 57.720 227.470 1.00 29.90 S ATOM 12698 SG CYS G 55 121.297 53.364 223.905 1.00 31.72 S ATOM 12799 SG CYS G 69 124.502 53.996 225.103 1.00 32.57 S ATOM 21058 SG CYS I 119 96.150 85.527 214.964 1.00 24.89 S ATOM 21032 SG CYS I 116 96.468 92.078 216.100 1.00 25.15 S ATOM 21079 SG CYS I 122 97.722 87.517 220.532 1.00 25.61 S ATOM 20806 SG CYS I 87 101.802 88.437 215.473 1.00 25.60 S ATOM 21108 SG CYS I 126 100.346 84.073 227.902 1.00 27.28 S ATOM 20737 SG CYS I 77 105.277 88.306 229.034 1.00 28.83 S ATOM 20779 SG CYS I 83 103.693 86.754 223.028 1.00 26.20 S ATOM 20756 SG CYS I 80 105.899 82.012 226.399 1.00 27.30 S ATOM 41490 SG CYS R 59 102.289 79.071 242.914 1.00 33.64 S ATOM 41668 SG CYS R 84 105.263 79.742 240.796 1.00 33.55 S ATOM 41690 SG CYS R 87 102.927 82.446 241.661 1.00 32.29 S Time building chain proxies: 27.05, per 1000 atoms: 0.40 Number of scatterers: 68213 At special positions: 0 Unit cell: (184.943, 198.832, 290.938, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 11 Type Number sf(0) I 1 52.95 Zn 1 29.99 Fe 28 26.01 K 1 19.00 Cl 1 17.00 S 467 16.00 P 35 15.00 Mg 1 11.99 O 13025 8.00 N 11125 7.00 C 43528 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 21.83 Conformation dependent library (CDL) restraints added in 10.3 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E 301 " pdb="FE1 FES E 301 " - pdb=" SG CYS E 103 " pdb="FE1 FES E 301 " - pdb=" SG CYS E 108 " 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="FE1 FES G 803 " - pdb=" SG CYS G 52 " pdb="FE2 FES G 803 " - pdb=" SG CYS G 55 " pdb="FE1 FES G 803 " - pdb=" SG CYS G 41 " pdb="FE2 FES G 803 " - pdb=" SG CYS G 69 " 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="FE4 SF4 B 201 " - pdb=" SG CYS B 55 " pdb="FE3 SF4 B 201 " - pdb=" SG CYS B 54 " pdb=" SF4 F 502 " pdb="FE2 SF4 F 502 " - pdb=" SG CYS F 365 " pdb="FE4 SF4 F 502 " - pdb=" SG CYS F 359 " pdb="FE3 SF4 F 502 " - pdb=" SG CYS F 405 " 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="FE1 SF4 G 801 " - pdb=" SG CYS G 114 " pdb="FE4 SF4 G 801 " - pdb=" SG CYS G 108 " pdb="FE2 SF4 G 801 " - pdb=" SG CYS G 105 " pdb=" SF4 G 802 " pdb="FE4 SF4 G 802 " - pdb=" SG CYS G 203 " pdb="FE3 SF4 G 802 " - pdb=" SG CYS G 159 " pdb="FE2 SF4 G 802 " - pdb=" SG CYS G 153 " pdb="FE1 SF4 G 802 " - pdb=" SG CYS G 156 " pdb=" SF4 I 202 " pdb="FE3 SF4 I 202 " - pdb=" SG CYS I 122 " pdb="FE2 SF4 I 202 " - pdb=" SG CYS I 116 " pdb="FE4 SF4 I 202 " - pdb=" SG CYS I 87 " 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="FE1 SF4 I 203 " - pdb=" SG CYS I 126 " pdb="FE2 SF4 I 203 " - pdb=" SG CYS I 77 " pdb="FE4 SF4 I 203 " - pdb=" SG CYS I 80 " 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 84 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 87 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 59 " Number of angles added : 3 16104 Ramachandran restraints generated. 8052 Oldfield, 0 Emsley, 8052 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15338 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 361 helices and 30 sheets defined 54.0% alpha, 4.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 10.10 Creating SS restraints... Processing helix chain 'A' and resid 3 through 23 Processing helix chain 'A' and resid 31 through 34 No H-bonds generated for 'chain 'A' and resid 31 through 34' Processing helix chain 'A' and resid 56 through 80 removed outlier: 3.523A pdb=" N LEU A 64 " --> pdb=" O ILE A 60 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU A 68 " --> pdb=" O LEU A 64 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE A 69 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA A 70 " --> pdb=" O ASP A 66 " (cutoff:3.500A) Proline residue: A 74 - end of helix removed outlier: 5.375A pdb=" N TRP A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 4.287A 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 43 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 117 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 Processing helix chain 'C' and resid 54 through 66 removed outlier: 4.772A pdb=" N ILE C 58 " --> pdb=" O ASP C 55 " (cutoff:3.500A) Proline residue: C 59 - end of helix removed outlier: 3.604A pdb=" N THR C 62 " --> pdb=" O PRO C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 138 removed outlier: 3.987A pdb=" N TRP C 129 " --> pdb=" O ALA C 126 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU C 131 " --> pdb=" O ASN C 128 " (cutoff:3.500A) removed outlier: 3.892A 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: 3.976A pdb=" N GLN D 13 " --> pdb=" O GLU D 9 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N TYR D 14 " --> pdb=" O TRP D 10 " (cutoff:3.500A) 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: 3.868A pdb=" N GLU D 92 " --> pdb=" O GLU D 88 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N TYR D 93 " --> pdb=" O LYS D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 104 removed outlier: 3.569A pdb=" N LEU D 100 " --> pdb=" O TYR D 96 " (cutoff:3.500A) Proline residue: D 101 - end of helix removed outlier: 3.802A pdb=" N ASP D 104 " --> pdb=" O LEU D 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 96 through 104' Processing helix chain 'D' and resid 111 through 126 Processing helix chain 'D' and resid 132 through 160 Processing helix chain 'D' and resid 165 through 185 removed outlier: 3.519A pdb=" N GLU D 172 " --> pdb=" O PHE D 168 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLU D 173 " --> pdb=" O TRP D 169 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE D 180 " --> pdb=" O LYS D 176 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 229 removed outlier: 3.859A pdb=" N ASN D 217 " --> pdb=" O GLU D 213 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N SER D 219 " --> pdb=" O SER D 215 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N LEU D 220 " --> pdb=" O LYS D 216 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG D 221 " --> pdb=" O ASN D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 239 Processing helix chain 'D' and resid 247 through 252 Processing helix chain 'D' and resid 257 through 263 removed outlier: 4.677A 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 278 through 280 No H-bonds generated for 'chain 'D' and resid 278 through 280' Processing helix chain 'D' and resid 293 through 317 Processing helix chain 'D' and resid 335 through 338 No H-bonds generated for 'chain 'D' and resid 335 through 338' Processing helix chain 'D' and resid 342 through 353 Processing helix chain 'D' and resid 394 through 405 removed outlier: 3.500A pdb=" N LEU D 402 " --> pdb=" O HIS D 398 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N ASP D 403 " --> pdb=" O LEU D 399 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N LYS D 404 " --> pdb=" O ALA D 400 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 421 Processing helix chain 'D' and resid 425 through 429 Processing helix chain 'E' and resid 25 through 37 removed outlier: 3.538A pdb=" N ASN E 37 " --> pdb=" O ALA E 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 58 removed outlier: 4.476A pdb=" N LEU E 48 " --> pdb=" O ALA E 45 " (cutoff:3.500A) Proline residue: E 49 - end of helix Processing helix chain 'E' and resid 63 through 73 Processing helix chain 'E' and resid 77 through 86 removed outlier: 3.655A pdb=" N VAL E 83 " --> pdb=" O ARG E 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 110 Processing helix chain 'E' and resid 113 through 124 Processing helix chain 'E' and resid 148 through 150 No H-bonds generated for 'chain 'E' and resid 148 through 150' Processing helix chain 'E' and resid 166 through 178 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 Processing helix chain 'F' and resid 45 through 63 removed outlier: 3.879A pdb=" N GLY F 52 " --> pdb=" O ILE F 48 " (cutoff:3.500A) Proline residue: F 53 - end of helix Processing helix chain 'F' and resid 75 through 82 removed outlier: 3.736A pdb=" N PHE F 81 " --> pdb=" O LEU F 77 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N MET F 82 " --> pdb=" O LYS F 78 " (cutoff:3.500A) Processing helix chain 'F' and resid 107 through 113 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: 3.761A pdb=" N SER F 231 " --> pdb=" O THR F 227 " (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 284 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 313 Processing helix chain 'F' and resid 319 through 324 Processing helix chain 'F' and resid 343 through 357 Processing helix chain 'F' and resid 363 through 381 removed outlier: 4.319A pdb=" N ASP F 370 " --> pdb=" O ARG F 366 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ARG F 381 " --> pdb=" O ALA F 377 " (cutoff:3.500A) Processing helix chain 'F' and resid 386 through 399 removed outlier: 3.789A pdb=" N ASP F 390 " --> pdb=" O ALA F 387 " (cutoff:3.500A) Processing helix chain 'F' and resid 407 through 437 Proline residue: F 414 - end of helix removed outlier: 3.690A pdb=" N ARG F 423 " --> pdb=" O ILE F 419 " (cutoff:3.500A) Proline residue: F 424 - end of helix Processing helix chain 'G' and resid 26 through 33 removed outlier: 3.956A pdb=" N VAL G 33 " --> pdb=" O ALA G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 84 through 99 Processing helix chain 'G' and resid 115 through 123 Processing helix chain 'G' and resid 150 through 152 No H-bonds generated for 'chain 'G' and resid 150 through 152' 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: 3.790A 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: 5.175A pdb=" N TYR G 271 " --> pdb=" O THR G 267 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ASP G 272 " --> pdb=" O ARG G 268 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N GLY G 273 " --> pdb=" O PHE G 269 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N LEU G 274 " --> pdb=" O ALA G 270 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LYS G 275 " --> pdb=" O TYR G 271 " (cutoff:3.500A) Processing helix chain 'G' and resid 296 through 309 removed outlier: 3.577A pdb=" N SER G 309 " --> pdb=" O GLY G 305 " (cutoff:3.500A) Processing helix chain 'G' and resid 312 through 314 No H-bonds generated for 'chain 'G' and resid 312 through 314' Processing helix chain 'G' and resid 325 through 338 removed outlier: 3.609A pdb=" N VAL G 338 " --> pdb=" O LEU G 334 " (cutoff:3.500A) 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 401 Processing helix chain 'G' and resid 426 through 434 Processing helix chain 'G' and resid 438 through 445 Processing helix chain 'G' and resid 455 through 459 Processing helix chain 'G' and resid 463 through 479 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 566 through 568 No H-bonds generated for 'chain 'G' and resid 566 through 568' Processing helix chain 'G' and resid 596 through 606 Processing helix chain 'G' and resid 616 through 626 Processing helix chain 'G' and resid 628 through 631 removed outlier: 3.573A 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 650 Processing helix chain 'G' and resid 668 through 670 No H-bonds generated for 'chain 'G' and resid 668 through 670' Processing helix chain 'G' and resid 676 through 679 No H-bonds generated for 'chain 'G' and resid 676 through 679' Processing helix chain 'G' and resid 682 through 691 Processing helix chain 'H' and resid 3 through 31 Proline residue: H 12 - end of helix removed outlier: 3.613A pdb=" N LEU H 22 " --> pdb=" O ALA H 18 " (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 57 Processing helix chain 'H' and resid 68 through 86 Proline residue: H 75 - end of helix removed outlier: 4.240A pdb=" N TRP H 86 " --> pdb=" O ALA H 82 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 122 removed outlier: 3.526A pdb=" N VAL H 113 " --> pdb=" O SER H 109 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N TYR H 114 " --> pdb=" O SER H 110 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N SER H 115 " --> pdb=" O LEU H 111 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ILE H 116 " --> pdb=" O ALA H 112 " (cutoff:3.500A) Processing helix chain 'H' and resid 126 through 157 removed outlier: 5.166A pdb=" N VAL H 144 " --> pdb=" O ILE H 140 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N THR H 145 " --> pdb=" O SER H 141 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N MET H 156 " --> pdb=" O SER H 152 " (cutoff:3.500A) Processing helix chain 'H' and resid 162 through 168 removed outlier: 4.053A pdb=" N ILE H 166 " --> pdb=" O LEU H 162 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR H 167 " --> pdb=" O SER H 163 " (cutoff:3.500A) Processing helix chain 'H' and resid 174 through 177 No H-bonds generated for 'chain 'H' and resid 174 through 177' 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 242 removed outlier: 3.604A pdb=" N PHE H 223 " --> pdb=" O PRO H 219 " (cutoff:3.500A) Processing helix chain 'H' and resid 252 through 274 removed outlier: 3.557A pdb=" N LEU H 271 " --> pdb=" O THR H 267 " (cutoff:3.500A) Processing helix chain 'H' and resid 282 through 291 removed outlier: 3.501A pdb=" N MET H 286 " --> pdb=" O TYR H 282 " (cutoff:3.500A) Processing helix chain 'H' and resid 293 through 310 Proline residue: H 308 - end of helix Processing helix chain 'I' and resid 14 through 26 Processing helix chain 'I' and resid 28 through 41 removed outlier: 3.521A pdb=" N MET I 36 " --> pdb=" O ARG I 32 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR I 37 " --> pdb=" O GLY I 33 " (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: 5.733A pdb=" N ALA I 163 " --> pdb=" O ASP I 159 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N GLU I 164 " --> pdb=" O LYS I 160 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA I 167 " --> pdb=" O ALA I 163 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N LEU I 174 " --> pdb=" O GLN I 170 " (cutoff:3.500A) removed outlier: 5.803A 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 47 removed outlier: 3.630A pdb=" N PHE J 47 " --> pdb=" O ILE J 43 " (cutoff:3.500A) Processing helix chain 'J' and resid 50 through 74 Processing helix chain 'J' and resid 87 through 110 Processing helix chain 'J' and resid 124 through 127 Processing helix chain 'J' and resid 138 through 147 removed outlier: 4.089A pdb=" N LEU J 146 " --> pdb=" O GLY J 142 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N TYR J 147 " --> pdb=" O ILE J 143 " (cutoff:3.500A) Processing helix chain 'J' and resid 151 through 171 Processing helix chain 'K' and resid 3 through 20 removed outlier: 3.798A pdb=" N ASN K 7 " --> pdb=" O MET K 3 " (cutoff:3.500A) Processing helix chain 'K' and resid 26 through 51 removed outlier: 3.503A pdb=" N CYS K 32 " --> pdb=" O SER K 28 " (cutoff:3.500A) Processing helix chain 'K' and resid 55 through 85 removed outlier: 3.526A pdb=" N MET K 58 " --> pdb=" O LEU K 55 " (cutoff:3.500A) Proline residue: K 60 - end of helix removed outlier: 3.589A pdb=" N CYS K 69 " --> pdb=" O PHE K 66 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU K 73 " --> pdb=" O GLU K 70 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL K 79 " --> pdb=" O SER K 76 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASN K 83 " --> pdb=" O MET K 80 " (cutoff:3.500A) Processing helix chain 'K' and resid 90 through 92 No H-bonds generated for 'chain 'K' and resid 90 through 92' 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 23 removed outlier: 3.521A pdb=" N THR L 11 " --> pdb=" O LEU L 7 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU L 12 " --> pdb=" O SER L 8 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR L 16 " --> pdb=" O LEU L 12 " (cutoff:3.500A) Proline residue: L 18 - end of helix Processing helix chain 'L' and resid 29 through 57 removed outlier: 3.855A pdb=" N TYR L 32 " --> pdb=" O PRO L 29 " (cutoff:3.500A) Proline residue: L 33 - end of helix removed outlier: 3.584A pdb=" N PHE L 44 " --> pdb=" O SER L 41 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR L 46 " --> pdb=" O ALA L 43 " (cutoff:3.500A) Proline residue: L 50 - end of helix removed outlier: 3.632A pdb=" N SER L 57 " --> pdb=" O PHE L 54 " (cutoff:3.500A) Processing helix chain 'L' and resid 84 through 107 Proline residue: L 91 - end of helix removed outlier: 3.753A pdb=" N TRP L 106 " --> pdb=" O GLU L 102 " (cutoff:3.500A) Processing helix chain 'L' and resid 114 through 133 removed outlier: 3.625A pdb=" N MET L 128 " --> pdb=" O PHE L 124 " (cutoff:3.500A) Processing helix chain 'L' and resid 137 through 155 removed outlier: 3.529A pdb=" N GLY L 143 " --> pdb=" O GLN L 139 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLY L 148 " --> pdb=" O TRP L 144 " (cutoff:3.500A) Processing helix chain 'L' and resid 162 through 193 removed outlier: 4.247A pdb=" N GLY L 181 " --> pdb=" O ILE L 177 " (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 231 through 238 removed outlier: 4.197A pdb=" N MET L 237 " --> pdb=" O LEU L 233 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N GLU L 238 " --> pdb=" O PRO L 234 " (cutoff:3.500A) Processing helix chain 'L' and resid 241 through 249 Processing helix chain 'L' and resid 252 through 262 removed outlier: 4.245A pdb=" N GLY L 256 " --> pdb=" O MET L 252 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ILE L 257 " --> pdb=" O VAL L 253 " (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 294 removed outlier: 4.472A pdb=" N THR L 294 " --> pdb=" O MET L 290 " (cutoff:3.500A) Processing helix chain 'L' and resid 298 through 319 Processing helix chain 'L' and resid 322 through 349 removed outlier: 3.900A pdb=" N PHE L 334 " --> pdb=" O CYS L 330 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N PHE L 335 " --> pdb=" O THR L 331 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ALA L 337 " --> pdb=" O ALA L 333 " (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 367 through 381 Processing helix chain 'L' and resid 387 through 400 removed outlier: 3.535A pdb=" N TYR L 390 " --> pdb=" O THR L 387 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N SER L 391 " --> pdb=" O GLY L 388 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N LYS L 392 " --> pdb=" O PHE L 389 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N ASP L 393 " --> pdb=" O TYR L 390 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLU L 397 " --> pdb=" O LEU L 394 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASN L 400 " --> pdb=" O GLU L 397 " (cutoff:3.500A) Processing helix chain 'L' and resid 406 through 431 removed outlier: 3.651A pdb=" N ALA L 420 " --> pdb=" O THR L 416 " (cutoff:3.500A) Processing helix chain 'L' and resid 448 through 469 removed outlier: 3.502A pdb=" N LEU L 457 " --> pdb=" O SER L 453 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N GLY L 465 " --> pdb=" O SER L 461 " (cutoff:3.500A) removed outlier: 5.260A 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 509 removed outlier: 3.687A pdb=" N THR L 508 " --> pdb=" O ILE L 504 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N LYS L 509 " --> pdb=" O SER L 505 " (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: 3.750A pdb=" N MET L 533 " --> pdb=" O PRO L 530 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N HIS L 534 " --> pdb=" O THR L 531 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU L 536 " --> pdb=" O MET L 533 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N ALA L 537 " --> pdb=" O HIS L 534 " (cutoff:3.500A) Proline residue: L 538 - end of helix removed outlier: 3.651A pdb=" N ASN L 541 " --> pdb=" O PRO L 538 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU L 542 " --> pdb=" O TYR L 539 " (cutoff:3.500A) Processing helix chain 'L' and resid 563 through 578 Processing helix chain 'L' and resid 584 through 600 Processing helix chain 'M' and resid 5 through 16 removed outlier: 4.189A 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 23 through 42 removed outlier: 4.026A pdb=" N LEU M 39 " --> pdb=" O SER M 35 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N LEU M 40 " --> pdb=" O PHE M 36 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N LEU M 41 " --> pdb=" O THR M 37 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N MET M 42 " --> pdb=" O SER M 38 " (cutoff:3.500A) Processing helix chain 'M' and resid 62 through 80 Proline residue: M 74 - end of helix Processing helix chain 'M' and resid 89 through 109 Processing helix chain 'M' and resid 115 through 136 removed outlier: 4.804A pdb=" N LEU M 126 " --> pdb=" O PHE M 122 " (cutoff:3.500A) removed outlier: 4.348A 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: 3.581A pdb=" N ALA M 145 " --> pdb=" O ARG M 142 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLY M 146 " --> pdb=" O LEU M 143 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE M 149 " --> pdb=" O GLY M 146 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE M 151 " --> pdb=" O TYR M 148 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N TYR M 152 " --> pdb=" O PHE M 149 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR M 153 " --> pdb=" O LEU M 150 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU M 154 " --> pdb=" O PHE M 151 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA M 155 " --> pdb=" O TYR M 152 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N LEU M 158 " --> pdb=" O ALA M 155 " (cutoff:3.500A) Proline residue: M 159 - end of helix removed outlier: 3.807A pdb=" N VAL M 171 " --> pdb=" O GLN M 168 " (cutoff:3.500A) Processing helix chain 'M' and resid 176 through 182 removed outlier: 3.965A pdb=" N TYR M 181 " --> pdb=" O LEU M 177 " (cutoff:3.500A) Processing helix chain 'M' and resid 190 through 206 removed outlier: 4.528A pdb=" N ALA M 202 " --> pdb=" O ALA M 198 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N PHE M 203 " --> pdb=" O CYS M 199 " (cutoff:3.500A) Processing helix chain 'M' and resid 214 through 222 removed outlier: 3.994A pdb=" N LYS M 218 " --> pdb=" O LEU M 214 " (cutoff:3.500A) Processing helix chain 'M' and resid 225 through 233 Processing helix chain 'M' and resid 235 through 249 removed outlier: 4.280A pdb=" N GLY M 239 " --> pdb=" O LEU M 235 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLY M 240 " --> pdb=" O LEU M 236 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N LEU M 248 " --> pdb=" O LEU M 244 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N ILE M 249 " --> pdb=" O ARG M 245 " (cutoff:3.500A) Processing helix chain 'M' and resid 253 through 257 removed outlier: 3.736A pdb=" N MET M 257 " --> pdb=" O THR M 254 " (cutoff:3.500A) Processing helix chain 'M' and resid 259 through 278 removed outlier: 3.854A pdb=" N ILE M 270 " --> pdb=" O LEU M 266 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU M 277 " --> pdb=" O SER M 273 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ARG M 278 " --> pdb=" O SER M 274 " (cutoff:3.500A) Processing helix chain 'M' and resid 282 through 303 removed outlier: 3.772A pdb=" N LEU M 296 " --> pdb=" O SER M 292 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL M 297 " --> pdb=" O HIS M 293 " (cutoff:3.500A) Processing helix chain 'M' and resid 306 through 337 removed outlier: 3.690A 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 Processing helix chain 'M' and resid 390 through 415 removed outlier: 3.562A pdb=" N MET M 396 " --> pdb=" O ILE M 393 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N TYR M 406 " --> pdb=" O THR M 403 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER M 407 " --> pdb=" O ALA M 404 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU M 408 " --> pdb=" O LEU M 405 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N MET M 410 " --> pdb=" O SER M 407 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N MET M 413 " --> pdb=" O MET M 410 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N THR M 414 " --> pdb=" O LEU M 411 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLN M 415 " --> pdb=" O ILE M 412 " (cutoff:3.500A) Processing helix chain 'M' and resid 431 through 448 removed outlier: 3.575A pdb=" N HIS M 440 " --> pdb=" O LEU M 436 " (cutoff:3.500A) Proline residue: M 443 - end of helix removed outlier: 4.165A pdb=" N THR M 448 " --> pdb=" O LEU M 444 " (cutoff:3.500A) Processing helix chain 'M' and resid 451 through 454 Processing helix chain 'N' and resid 3 through 22 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 113 through 120 removed outlier: 4.167A pdb=" N GLU N 117 " --> pdb=" O PHE N 113 " (cutoff:3.500A) Processing helix chain 'N' and resid 124 through 131 removed outlier: 3.501A pdb=" N ILE N 129 " --> pdb=" O SER N 125 " (cutoff:3.500A) Processing helix chain 'N' and resid 133 through 148 removed outlier: 4.416A pdb=" N ALA N 137 " --> pdb=" O GLN N 134 " (cutoff:3.500A) Proline residue: N 138 - end of helix removed outlier: 3.556A pdb=" N TYR N 143 " --> pdb=" O SER N 140 " (cutoff:3.500A) removed outlier: 4.531A 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: 3.883A pdb=" N LEU N 170 " --> pdb=" O GLY N 166 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ASN N 171 " --> pdb=" O TRP N 167 " (cutoff:3.500A) Processing helix chain 'N' and resid 175 through 192 removed outlier: 3.717A pdb=" N TRP N 189 " --> pdb=" O ALA N 185 " (cutoff:3.500A) Processing helix chain 'N' and resid 198 through 222 removed outlier: 3.564A pdb=" N ASN N 222 " --> pdb=" O MET N 218 " (cutoff:3.500A) Processing helix chain 'N' and resid 227 through 235 removed outlier: 3.613A pdb=" N HIS N 232 " --> pdb=" O LEU N 228 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N THR N 233 " --> pdb=" O SER N 229 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N TRP N 234 " --> pdb=" O LEU N 230 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N ASN N 235 " --> pdb=" O SER N 231 " (cutoff:3.500A) Processing helix chain 'N' and resid 238 through 251 removed outlier: 3.523A pdb=" N VAL N 242 " --> pdb=" O PRO N 238 " (cutoff:3.500A) Processing helix chain 'N' and resid 258 through 272 Proline residue: N 262 - end of helix removed outlier: 3.646A pdb=" N ILE N 266 " --> pdb=" O LYS N 263 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYS N 272 " --> pdb=" O GLU N 269 " (cutoff:3.500A) Processing helix chain 'N' and resid 277 through 300 removed outlier: 3.524A pdb=" N LEU N 287 " --> pdb=" O ALA N 283 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N LEU N 288 " --> pdb=" O ILE N 284 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ASN N 289 " --> pdb=" O THR N 285 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LEU N 296 " --> pdb=" O PHE N 292 " (cutoff:3.500A) Processing helix chain 'N' and resid 309 through 316 removed outlier: 3.623A pdb=" N GLN N 316 " --> pdb=" O MET N 313 " (cutoff:3.500A) Processing helix chain 'N' and resid 326 through 332 removed outlier: 3.522A pdb=" N VAL N 331 " --> pdb=" O PRO N 327 " (cutoff:3.500A) Processing helix chain 'N' and resid 337 through 346 Proline residue: N 341 - end of helix 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 60 through 62 No H-bonds generated for 'chain 'O' and resid 60 through 62' Processing helix chain 'O' and resid 71 through 74 Processing helix chain 'O' and resid 79 through 84 Processing helix chain 'O' and resid 92 through 118 Processing helix chain 'O' and resid 131 through 140 removed outlier: 3.557A pdb=" N GLU O 136 " --> pdb=" O VAL O 133 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG O 140 " --> pdb=" O ALA O 137 " (cutoff:3.500A) Processing helix chain 'O' and resid 146 through 157 Processing helix chain 'O' and resid 160 through 162 No H-bonds generated for 'chain 'O' and resid 160 through 162' 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 Processing helix chain 'O' and resid 210 through 216 removed outlier: 3.963A pdb=" N GLU O 216 " --> pdb=" O PRO O 212 " (cutoff:3.500A) Processing helix chain 'O' and resid 227 through 229 No H-bonds generated for 'chain 'O' and resid 227 through 229' Processing helix chain 'O' and resid 231 through 240 removed outlier: 3.698A pdb=" N TYR O 240 " --> pdb=" O GLU O 236 " (cutoff:3.500A) Processing helix chain 'O' and resid 247 through 250 Processing helix chain 'O' and resid 253 through 264 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 271 through 274 removed outlier: 3.814A pdb=" N SER O 274 " --> pdb=" O ASN O 271 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 271 through 274' Processing helix chain 'O' and resid 286 through 298 Processing helix chain 'O' and resid 317 through 319 No H-bonds generated for 'chain 'O' and resid 317 through 319' 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: 4.178A pdb=" N TYR P 33 " --> pdb=" O PHE P 29 " (cutoff:3.500A) Processing helix chain 'P' and resid 53 through 62 removed outlier: 5.027A 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 78 through 85 Processing helix chain 'P' and resid 106 through 110 Processing helix chain 'P' and resid 112 through 123 Processing helix chain 'P' and resid 144 through 159 Processing helix chain 'P' and resid 179 through 188 removed outlier: 3.554A pdb=" N ILE P 185 " --> pdb=" O TYR P 181 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N ARG P 186 " --> pdb=" O PHE P 182 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N TRP P 187 " --> pdb=" O ALA P 183 " (cutoff:3.500A) removed outlier: 4.974A 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 219 Processing helix chain 'P' and resid 221 through 223 No H-bonds generated for 'chain 'P' and resid 221 through 223' Processing helix chain 'P' and resid 238 through 248 Processing helix chain 'P' and resid 260 through 272 removed outlier: 3.669A pdb=" N ILE P 272 " --> pdb=" O ARG P 268 " (cutoff:3.500A) Processing helix chain 'P' and resid 281 through 287 Processing helix chain 'P' and resid 300 through 303 Processing helix chain 'P' and resid 310 through 312 No H-bonds generated for 'chain 'P' and resid 310 through 312' Processing helix chain 'P' and resid 314 through 321 removed outlier: 5.840A pdb=" N ARG P 320 " --> pdb=" O GLU P 316 " (cutoff:3.500A) removed outlier: 5.301A 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 27 through 31 removed outlier: 4.078A pdb=" N LYS Q 31 " --> pdb=" O GLU Q 28 " (cutoff:3.500A) Processing helix chain 'Q' and resid 50 through 52 No H-bonds generated for 'chain 'Q' and resid 50 through 52' Processing helix chain 'Q' and resid 89 through 99 Processing helix chain 'Q' and resid 118 through 122 Processing helix chain 'R' and resid 23 through 28 Processing helix chain 'R' and resid 40 through 46 removed outlier: 3.639A pdb=" N ALA R 45 " --> pdb=" O ILE R 41 " (cutoff:3.500A) Processing helix chain 'R' and resid 64 through 66 No H-bonds generated for 'chain 'R' and resid 64 through 66' Processing helix chain 'S' and resid 27 through 46 removed outlier: 5.198A pdb=" N GLY S 31 " --> pdb=" O GLY S 28 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ARG S 39 " --> pdb=" O ILE S 36 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N TYR S 40 " --> pdb=" O GLU S 37 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N VAL S 41 " --> pdb=" O LYS S 38 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLU S 42 " --> pdb=" O ARG S 39 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LYS S 44 " --> pdb=" O VAL S 41 " (cutoff:3.500A) Processing helix chain 'S' and resid 69 through 71 No H-bonds generated for 'chain 'S' and resid 69 through 71' Processing helix chain 'S' and resid 83 through 94 Processing helix chain 'T' and resid 8 through 21 removed outlier: 3.719A pdb=" N LEU T 21 " --> pdb=" O TYR T 17 " (cutoff:3.500A) Processing helix chain 'T' and resid 27 through 29 No H-bonds generated for 'chain 'T' and resid 27 through 29' Processing helix chain 'T' and resid 44A through 58 Processing helix chain 'T' and resid 64 through 69 removed outlier: 4.586A 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 20 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 44A through 58 Processing helix chain 'U' and resid 64 through 69 removed outlier: 4.436A pdb=" N LYS U 69 " --> pdb=" O ILE U 65 " (cutoff:3.500A) Processing helix chain 'U' and resid 73 through 83 Processing helix chain 'V' and resid 19 through 36 removed outlier: 3.950A 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 Processing helix chain 'V' and resid 76 through 96 removed outlier: 3.866A pdb=" N GLN V 95 " --> pdb=" O ARG V 91 " (cutoff:3.500A) Processing helix chain 'W' and resid 25 through 49 Proline residue: W 44 - end of helix Processing helix chain 'W' and resid 56 through 70 removed outlier: 4.303A pdb=" N ASN W 70 " --> pdb=" O MET W 66 " (cutoff:3.500A) Processing helix chain 'W' and resid 76 through 94 Processing helix chain 'W' and resid 100 through 106 removed outlier: 4.423A pdb=" N PHE W 106 " --> pdb=" O HIS W 102 " (cutoff:3.500A) Processing helix chain 'W' and resid 118 through 124 Processing helix chain 'X' and resid 9 through 12 Processing helix chain 'X' and resid 21 through 34 removed outlier: 4.722A pdb=" N HIS X 29 " --> pdb=" O LYS X 25 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N HIS X 30 " --> pdb=" O ALA X 26 " (cutoff:3.500A) Processing helix chain 'X' and resid 36 through 49 Processing helix chain 'X' and resid 52 through 54 No H-bonds generated for 'chain 'X' and resid 52 through 54' Processing helix chain 'X' and resid 56 through 76 Processing helix chain 'X' and resid 78 through 90 Processing helix chain 'X' and resid 96 through 98 No H-bonds generated for 'chain 'X' and resid 96 through 98' Processing helix chain 'X' and resid 100 through 114 Processing helix chain 'Y' and resid 3 through 10 Processing helix chain 'Y' and resid 17 through 42 Processing helix chain 'Y' and resid 48 through 80 removed outlier: 3.692A pdb=" N CYS Y 74 " --> pdb=" O GLY Y 70 " (cutoff:3.500A) Processing helix chain 'Y' and resid 86 through 103 Processing helix chain 'Y' and resid 107 through 130 Processing helix chain 'Z' and resid 32 through 97 Proline residue: Z 73 - end of helix removed outlier: 3.696A pdb=" N THR Z 96 " --> pdb=" O GLU Z 92 " (cutoff:3.500A) 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: 5.833A pdb=" N PHE Z 140 " --> pdb=" O ALA Z 136 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N ILE Z 141 " --> pdb=" O THR Z 137 " (cutoff:3.500A) Processing helix chain 'a' and resid 2 through 30 Proline residue: a 7 - end of helix removed outlier: 3.506A pdb=" N ALA a 10 " --> pdb=" O PRO a 7 " (cutoff:3.500A) Proline residue: a 19 - end of helix removed outlier: 3.577A pdb=" N ALA a 22 " --> pdb=" O PRO a 19 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N THR a 23 " --> pdb=" O GLY a 20 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE a 26 " --> pdb=" O THR a 23 " (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 Processing helix chain 'b' and resid 16 through 34 Proline residue: b 32 - end of helix Processing helix chain 'b' and resid 36 through 47 removed outlier: 4.210A pdb=" N LYS b 39 " --> pdb=" O PRO b 36 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE b 44 " --> pdb=" O SER b 41 " (cutoff:3.500A) Processing helix chain 'b' and resid 78 through 82 Processing helix chain 'c' and resid 14 through 45 Processing helix chain 'd' and resid 16 through 20 Processing helix chain 'd' and resid 29 through 48 Processing helix chain 'd' and resid 58 through 96 removed outlier: 3.705A pdb=" N TYR d 74 " --> pdb=" O PHE d 70 " (cutoff:3.500A) Processing helix chain 'd' and resid 98 through 100 No H-bonds generated for 'chain 'd' and resid 98 through 100' 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 43 Processing helix chain 'e' and resid 48 through 54 removed outlier: 3.995A 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 Processing helix chain 'f' and resid 8 through 10 No H-bonds generated for 'chain 'f' and resid 8 through 10' Processing helix chain 'f' and resid 12 through 33 removed outlier: 4.899A pdb=" N VAL f 16 " --> pdb=" O HIS f 13 " (cutoff:3.500A) Proline residue: f 17 - end of helix Processing helix chain 'g' and resid 37 through 40 No H-bonds generated for 'chain 'g' and resid 37 through 40' Processing helix chain 'g' and resid 51 through 65 Processing helix chain 'g' and resid 69 through 78 Processing helix chain 'g' and resid 83 through 102 removed outlier: 3.736A pdb=" N GLN g 86 " --> pdb=" O TYR g 83 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N GLU g 87 " --> pdb=" O ARG g 84 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TRP g 88 " --> pdb=" O MET g 85 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS g 98 " --> pdb=" O ARG g 95 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLU g 101 " --> pdb=" O LYS g 98 " (cutoff:3.500A) 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: 4.050A 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 63 through 66 removed outlier: 3.861A pdb=" N TYR h 66 " --> pdb=" O HIS h 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 63 through 66' Processing helix chain 'h' and resid 70 through 78 Processing helix chain 'h' and resid 83 through 117 Processing helix chain 'h' and resid 130 through 132 No H-bonds generated for 'chain 'h' and resid 130 through 132' Processing helix chain 'i' and resid 5 through 25 Processing helix chain 'i' and resid 63 through 73 Processing helix chain 'i' and resid 75 through 87 Processing helix chain 'j' and resid 19 through 42 removed outlier: 3.587A pdb=" N HIS j 42 " --> pdb=" O TRP j 38 " (cutoff:3.500A) Processing helix chain 'j' and resid 44 through 48 Processing helix chain 'j' and resid 61 through 64 No H-bonds generated for 'chain 'j' and resid 61 through 64' Processing helix chain 'k' and resid 18 through 20 No H-bonds generated for 'chain 'k' and resid 18 through 20' Processing helix chain 'k' and resid 27 through 38 removed outlier: 4.387A pdb=" N ARG k 38 " --> pdb=" O LYS k 34 " (cutoff:3.500A) Processing helix chain 'k' and resid 46 through 52 removed outlier: 4.991A pdb=" N TRP k 50 " --> pdb=" O ASN k 47 " (cutoff:3.500A) Processing helix chain 'k' and resid 54 through 56 No H-bonds generated for 'chain 'k' and resid 54 through 56' Processing helix chain 'k' and resid 62 through 66 Processing helix chain 'k' and resid 70 through 89 Processing helix chain 'l' and resid 6 through 8 No H-bonds generated for 'chain 'l' and resid 6 through 8' Processing helix chain 'l' and resid 19 through 26 removed outlier: 3.915A pdb=" N ALA l 24 " --> pdb=" O ARG l 20 " (cutoff:3.500A) Processing helix chain 'l' and resid 55 through 57 No H-bonds generated for 'chain 'l' and resid 55 through 57' 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 138 Processing helix chain 'm' and resid 15 through 17 No H-bonds generated for 'chain 'm' and resid 15 through 17' 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 50 removed outlier: 3.772A pdb=" N GLN m 49 " --> pdb=" O GLU m 45 " (cutoff:3.500A) Processing helix chain 'm' and resid 62 through 71 Processing helix chain 'm' and resid 95 through 117 removed outlier: 3.554A pdb=" N LEU m 114 " --> pdb=" O ARG m 110 " (cutoff:3.500A) Processing helix chain 'n' and resid 11 through 30 Processing helix chain 'n' and resid 33 through 49 Processing helix chain 'n' and resid 56 through 73 Processing helix chain 'n' and resid 94 through 96 No H-bonds generated for 'chain 'n' and resid 94 through 96' Processing helix chain 'n' and resid 100 through 105 Processing helix chain 'n' and resid 108 through 142 removed outlier: 3.666A pdb=" N MET n 113 " --> pdb=" O SER n 109 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N TYR n 114 " --> pdb=" O GLU n 110 " (cutoff:3.500A) Proline residue: n 115 - end of helix removed outlier: 3.579A pdb=" N GLN n 123 " --> pdb=" O ALA n 119 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N GLU n 133 " --> pdb=" O ARG n 129 " (cutoff:3.500A) removed outlier: 5.106A 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 2 through 9 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 119 removed outlier: 3.529A pdb=" N ARG o 97 " --> pdb=" O ASP o 93 " (cutoff:3.500A) Processing helix chain 'p' and resid 28 through 39 Processing helix chain 'p' and resid 41 through 57 removed outlier: 3.521A pdb=" N LYS p 57 " --> pdb=" O ARG p 53 " (cutoff:3.500A) 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 123 removed outlier: 3.577A pdb=" N GLU p 86 " --> pdb=" O LEU p 82 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLY p 117 " --> pdb=" O GLN p 113 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N GLU p 118 " --> pdb=" O GLN p 114 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N SER p 119 " --> pdb=" O ARG p 115 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N HIS p 120 " --> pdb=" O GLU p 116 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N ARG p 121 " --> pdb=" O GLY p 117 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N GLN p 122 " --> pdb=" O GLU p 118 " (cutoff:3.500A) Processing helix chain 'p' and resid 125 through 142 Processing helix chain 'p' and resid 151 through 170 Processing helix chain 'q' and resid 3 through 17 removed outlier: 3.792A pdb=" N VAL q 14 " --> pdb=" O GLY q 10 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER q 15 " --> pdb=" O LEU q 11 " (cutoff:3.500A) Processing helix chain 'q' and resid 19 through 29 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: 4.043A pdb=" N TRP q 89 " --> pdb=" O GLU q 85 " (cutoff:3.500A) Processing helix chain 'r' and resid 5 through 15 Processing helix chain 'r' and resid 20 through 22 No H-bonds generated for 'chain 'r' and resid 20 through 22' Processing helix chain 'r' and resid 53 through 55 No H-bonds generated for 'chain 'r' and resid 53 through 55' 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 50 through 61 removed outlier: 4.712A pdb=" N LYS s 60 " --> pdb=" O LEU s 56 " (cutoff:3.500A) removed outlier: 5.130A 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: 6.695A pdb=" N TYR B 112 " --> pdb=" O MET B 86 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N VAL B 88 " --> pdb=" O TYR B 112 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N VAL B 114 " --> pdb=" O VAL B 88 " (cutoff:3.500A) removed outlier: 6.385A 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: 6.722A pdb=" N ASN C 95 " --> pdb=" O ALA C 76 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N LEU C 78 " --> pdb=" O VAL C 93 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N VAL C 93 " --> pdb=" O LEU C 78 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ALA C 80 " --> pdb=" O GLU C 91 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N GLU C 91 " --> pdb=" O ALA C 80 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N LEU C 48 " --> pdb=" O ARG C 104 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N TYR C 110 " --> pdb=" O ILE C 52 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 172 through 177 Processing sheet with id= D, first strand: chain 'D' and resid 47 through 51 removed outlier: 6.315A pdb=" N SER D 69 " --> pdb=" O VAL D 73 " (cutoff:3.500A) removed outlier: 5.232A 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: 6.557A pdb=" N TYR E 98 " --> pdb=" O THR E 138 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N ILE E 140 " --> pdb=" O TYR E 98 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ILE E 100 " --> pdb=" O ILE E 140 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N VAL E 142 " --> pdb=" O ILE E 100 " (cutoff:3.500A) removed outlier: 6.121A 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: 6.444A pdb=" N ALA F 133 " --> pdb=" O LEU F 93 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N VAL F 95 " --> pdb=" O ALA F 133 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N TYR F 135 " --> pdb=" O VAL F 95 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ALA F 97 " --> pdb=" O TYR F 135 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N TYR F 137 " --> pdb=" O ALA F 97 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ASP F 174 " --> pdb=" O ALA F 134 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N ILE F 136 " --> pdb=" O ASP F 174 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N PHE F 176 " --> pdb=" O ILE F 136 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N ILE F 138 " --> pdb=" O PHE F 176 " (cutoff:3.500A) removed outlier: 6.174A 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 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 342 through 345 removed outlier: 4.660A pdb=" N THR G 342 " --> pdb=" O VAL G 315 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N MET G 521 " --> pdb=" O ALA G 316 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N ILE G 318 " --> pdb=" O MET G 521 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N PHE G 523 " --> pdb=" O ILE G 318 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N PHE G 542 " --> pdb=" O LEU G 522 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N LEU G 524 " --> pdb=" O PHE G 542 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N VAL G 544 " --> pdb=" O LEU G 524 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N VAL G 559 " --> pdb=" O TYR G 545 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N GLY G 547 " --> pdb=" O VAL G 559 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N LEU G 561 " --> pdb=" O GLY G 547 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'G' and resid 490 through 493 removed outlier: 8.209A pdb=" N ASN G 491 " --> pdb=" O PRO G 449 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N VAL G 451 " --> pdb=" O ASN G 491 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N LEU G 493 " --> pdb=" O VAL G 451 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N LEU G 453 " --> pdb=" O LEU G 493 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N VAL G 376 " --> pdb=" O MET G 450 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N ILE G 452 " --> pdb=" O VAL G 376 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU G 378 " --> pdb=" O ILE G 452 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N GLY G 454 " --> pdb=" O LEU G 378 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N VAL G 380 " --> pdb=" O GLY G 454 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N LYS G 405 " --> pdb=" O VAL G 377 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N LEU G 379 " --> pdb=" O LYS G 405 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ALA G 407 " --> pdb=" O LEU G 379 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ASP G 420 " --> pdb=" O LEU G 408 " (cutoff:3.500A) No H-bonds generated for sheet with id= O 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: 5.979A pdb=" N GLU I 97 " --> pdb=" O THR I 106 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N THR I 106 " --> pdb=" O GLU I 97 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'J' and resid 112 through 115 Processing sheet with id= T, first strand: chain 'L' and resid 69 through 71 Processing sheet with id= U, first strand: chain 'L' and resid 61 through 67 removed outlier: 6.814A pdb=" N LEU L 78 " --> pdb=" O ASN L 65 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'O' and resid 219 through 223 removed outlier: 6.147A pdb=" N VAL O 122 " --> pdb=" O ILE O 25 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N VAL O 27 " --> pdb=" O VAL O 122 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N LEU O 124 " --> pdb=" O VAL O 27 " (cutoff:3.500A) removed outlier: 8.615A pdb=" N GLY O 29 " --> pdb=" O LEU O 124 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N LYS O 49 " --> pdb=" O VAL O 123 " (cutoff:3.500A) removed outlier: 8.400A pdb=" N GLU O 125 " --> pdb=" O LYS O 49 " (cutoff:3.500A) removed outlier: 8.442A pdb=" N PHE O 51 " --> pdb=" O GLU O 125 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'P' and resid 227 through 230 removed outlier: 6.610A pdb=" N ILE P 165 " --> pdb=" O PHE P 228 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N PHE P 230 " --> pdb=" O ILE P 165 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N LYS P 167 " --> pdb=" O PHE P 230 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE P 132 " --> pdb=" O ASN P 93 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N GLN P 44 " --> pdb=" O ALA P 21 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N VAL P 23 " --> pdb=" O GLN P 44 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ILE P 46 " --> pdb=" O VAL P 23 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'P' and resid 191 through 193 Processing sheet with id= Y, first strand: chain 'Q' and resid 102 through 105 Processing sheet with id= Z, first strand: chain 'Q' and resid 64 through 66 Processing sheet with id= AA, first strand: chain 'R' and resid 50 through 52 Processing sheet with id= AB, first strand: chain 'R' and resid 56 through 59 Processing sheet with id= AC, first strand: chain 'S' and resid 51 through 56 removed outlier: 6.496A pdb=" N ARG S 67 " --> pdb=" O ARG S 16 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ILE S 18 " --> pdb=" O TRP S 65 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N TRP S 65 " --> pdb=" O ILE S 18 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N ILE S 20 " --> pdb=" O LYS S 63 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LYS S 63 " --> pdb=" O ILE S 20 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'q' and resid 60 through 63 removed outlier: 3.534A pdb=" N GLY q 40 " --> pdb=" O TYR q 48 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N GLU q 50 " --> pdb=" O LEU q 38 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N LEU q 38 " --> pdb=" O GLU q 50 " (cutoff:3.500A) 2890 hydrogen bonds defined for protein. 7824 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: 21.51 Time building geometry restraints manager: 23.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.40: 27767 1.40 - 1.63: 40329 1.63 - 1.85: 825 1.85 - 2.08: 0 2.08 - 2.30: 81 Bond restraints: 69002 Sorted by residual: bond pdb=" C5 GTP O 401 " pdb=" N7 GTP O 401 " ideal model delta sigma weight residual 1.350 1.520 -0.170 2.00e-02 2.50e+03 7.23e+01 bond pdb=" C6 GTP O 401 " pdb=" O6 GTP O 401 " ideal model delta sigma weight residual 1.230 1.392 -0.162 2.00e-02 2.50e+03 6.59e+01 bond pdb=" CA7 CDL J 701 " pdb=" OA8 CDL J 701 " ideal model delta sigma weight residual 1.334 1.402 -0.068 1.10e-02 8.26e+03 3.81e+01 bond pdb=" CB7 CDL L 703 " pdb=" OB8 CDL L 703 " ideal model delta sigma weight residual 1.334 1.400 -0.066 1.10e-02 8.26e+03 3.65e+01 bond pdb=" C 2MR D 85 " pdb=" O 2MR D 85 " ideal model delta sigma weight residual 1.231 1.352 -0.121 2.00e-02 2.50e+03 3.63e+01 ... (remaining 68997 not shown) Histogram of bond angle deviations from ideal: 72.62 - 84.92: 76 84.92 - 97.21: 2 97.21 - 109.51: 7681 109.51 - 121.81: 72351 121.81 - 134.10: 13261 Bond angle restraints: 93371 Sorted by residual: angle pdb=" O 2MR D 85 " pdb=" C 2MR D 85 " pdb=" N GLY D 86 " ideal model delta sigma weight residual 123.00 103.45 19.55 1.60e+00 3.91e-01 1.49e+02 angle pdb=" C51 CDL J 701 " pdb=" CB5 CDL J 701 " pdb=" OB6 CDL J 701 " ideal model delta sigma weight residual 111.33 121.22 -9.89 1.32e+00 5.72e-01 5.60e+01 angle pdb=" C51 CDL h1001 " pdb=" CB5 CDL h1001 " pdb=" OB6 CDL h1001 " ideal model delta sigma weight residual 111.33 120.82 -9.49 1.32e+00 5.72e-01 5.16e+01 angle pdb=" C11 CDL a 101 " pdb=" CA5 CDL a 101 " pdb=" OA6 CDL a 101 " ideal model delta sigma weight residual 111.33 120.31 -8.98 1.32e+00 5.72e-01 4.62e+01 angle pdb=" C11 CDL h1001 " pdb=" CA5 CDL h1001 " pdb=" OA6 CDL h1001 " ideal model delta sigma weight residual 111.33 120.15 -8.82 1.32e+00 5.72e-01 4.45e+01 ... (remaining 93366 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.48: 40916 35.48 - 70.96: 1015 70.96 - 106.44: 155 106.44 - 141.92: 22 141.92 - 177.41: 5 Dihedral angle restraints: 42113 sinusoidal: 18321 harmonic: 23792 Sorted by residual: 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 274.12 98.47 175.65 1 2.00e+01 2.50e-03 4.79e+01 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 89.05 168.54 1 2.00e+01 2.50e-03 4.75e+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 -68.92 81.26 -150.18 1 2.00e+01 2.50e-03 4.48e+01 ... (remaining 42110 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.264: 10170 4.264 - 8.528: 0 8.528 - 12.792: 0 12.792 - 17.056: 0 17.056 - 21.320: 16 Chirality restraints: 10186 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 10.77 -21.32 2.00e-01 2.50e+01 1.14e+04 chirality pdb="FE4 SF4 I 202 " pdb=" S1 SF4 I 202 " pdb=" S2 SF4 I 202 " pdb=" S3 SF4 I 202 " both_signs ideal model delta sigma weight residual False 10.55 -10.73 21.29 2.00e-01 2.50e+01 1.13e+04 chirality pdb="FE2 SF4 I 202 " pdb=" S1 SF4 I 202 " pdb=" S3 SF4 I 202 " pdb=" S4 SF4 I 202 " both_signs ideal model delta sigma weight residual False 10.55 -10.72 21.27 2.00e-01 2.50e+01 1.13e+04 ... (remaining 10183 not shown) Planarity restraints: 11642 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C08 I49 N1303 " 0.149 2.00e-02 2.50e+03 5.90e-01 6.97e+03 pdb=" C14 I49 N1303 " 0.113 2.00e-02 2.50e+03 pdb=" C15 I49 N1303 " 0.022 2.00e-02 2.50e+03 pdb=" N01 I49 N1303 " -0.177 2.00e-02 2.50e+03 pdb=" N02 I49 N1303 " 0.722 2.00e-02 2.50e+03 pdb=" N03 I49 N1303 " -0.132 2.00e-02 2.50e+03 pdb=" N04 I49 N1303 " -1.333 2.00e-02 2.50e+03 pdb=" N05 I49 N1303 " 0.637 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA 2MR D 85 " 0.103 2.00e-02 2.50e+03 1.80e-01 3.26e+02 pdb=" C 2MR D 85 " -0.313 2.00e-02 2.50e+03 pdb=" O 2MR D 85 " 0.101 2.00e-02 2.50e+03 pdb=" N GLY D 86 " 0.108 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 125 " 0.047 2.00e-02 2.50e+03 3.65e-02 2.66e+01 pdb=" CG TYR B 125 " -0.087 2.00e-02 2.50e+03 pdb=" CD1 TYR B 125 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 TYR B 125 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR B 125 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR B 125 " 0.012 2.00e-02 2.50e+03 pdb=" CZ TYR B 125 " 0.006 2.00e-02 2.50e+03 pdb=" OH TYR B 125 " 0.007 2.00e-02 2.50e+03 ... (remaining 11639 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.55: 606 2.55 - 3.20: 65081 3.20 - 3.85: 143356 3.85 - 4.49: 209068 4.49 - 5.14: 316073 Nonbonded interactions: 734184 Sorted by model distance: nonbonded pdb=" OE1 GLU A 112 " pdb=" O HOH A 401 " model vdw 1.908 2.440 nonbonded pdb=" OE1 GLU D 337 " pdb=" O HOH D 501 " model vdw 1.929 2.440 nonbonded pdb=" OE1 GLN V 110 " pdb=" O HOH V 201 " model vdw 1.966 2.440 nonbonded pdb=" OG SER H 125 " pdb=" O HOH H 501 " model vdw 1.967 2.440 nonbonded pdb=" O14 3PE H 401 " pdb=" O HOH H 502 " model vdw 1.968 2.440 ... (remaining 734179 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' 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 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: 12.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 57.560 Check model and map are aligned: 0.770 Set scattering table: 0.460 Process input model: 162.940 Find NCS groups from input model: 2.030 Set up NCS constraints: 0.240 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 247.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 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 : 0.007 0.170 69002 Z= 0.482 Angle : 0.813 19.553 93371 Z= 0.375 Chirality : 0.843 21.320 10186 Planarity : 0.007 0.590 11642 Dihedral : 16.349 177.406 26760 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.52 % Favored : 97.47 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.09), residues: 8052 helix: 0.51 (0.08), residues: 4261 sheet: 0.13 (0.25), residues: 401 loop : 0.16 (0.11), residues: 3390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP P 73 HIS 0.009 0.001 HIS e 26 PHE 0.062 0.002 PHE D 171 TYR 0.087 0.002 TYR B 125 ARG 0.014 0.001 ARG I 43 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16104 Ramachandran restraints generated. 8052 Oldfield, 0 Emsley, 8052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16104 Ramachandran restraints generated. 8052 Oldfield, 0 Emsley, 8052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1072 residues out of total 7119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1072 time to evaluate : 6.092 Fit side-chains revert: symmetry clash REVERT: G 654 GLN cc_start: 0.7232 (mp10) cc_final: 0.6830 (mm-40) REVERT: J 4 TYR cc_start: 0.8162 (m-80) cc_final: 0.7961 (m-80) REVERT: N 311 MET cc_start: 0.8416 (tpp) cc_final: 0.8211 (tpp) REVERT: P 268 ARG cc_start: 0.7063 (tpp-160) cc_final: 0.6773 (tpt170) REVERT: T 34 SER cc_start: 0.7165 (m) cc_final: 0.6907 (m) REVERT: X 11 ASP cc_start: 0.7986 (m-30) cc_final: 0.7725 (m-30) REVERT: Z 85 GLN cc_start: 0.7838 (tt0) cc_final: 0.7545 (tt0) REVERT: g 114 ASP cc_start: 0.7917 (t70) cc_final: 0.7638 (t70) REVERT: k 72 TRP cc_start: 0.8355 (m100) cc_final: 0.8147 (m100) REVERT: q 5 GLN cc_start: 0.7841 (mm110) cc_final: 0.7312 (mp10) REVERT: q 25 ARG cc_start: 0.8012 (ttm170) cc_final: 0.7736 (ttt180) REVERT: r 29 GLU cc_start: 0.8306 (pm20) cc_final: 0.8070 (pm20) REVERT: r 63 MET cc_start: 0.8005 (mmp) cc_final: 0.7689 (mmp) outliers start: 0 outliers final: 1 residues processed: 1072 average time/residue: 1.8449 time to fit residues: 2470.9222 Evaluate side-chains 939 residues out of total 7119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 938 time to evaluate : 5.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain o residue 93 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 799 random chunks: chunk 674 optimal weight: 3.9990 chunk 605 optimal weight: 20.0000 chunk 336 optimal weight: 3.9990 chunk 206 optimal weight: 0.2980 chunk 408 optimal weight: 5.9990 chunk 323 optimal weight: 0.9980 chunk 626 optimal weight: 0.7980 chunk 242 optimal weight: 9.9990 chunk 380 optimal weight: 0.8980 chunk 466 optimal weight: 1.9990 chunk 725 optimal weight: 6.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 69 ASN C 200 ASN D 114 ASN ** D 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 74 GLN F 257 ASN G 16 GLN G 461 ASN G 546 GLN H 171 GLN ** H 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 97 GLN L 479 GLN ** L 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 82 HIS M 139 GLN N 289 ASN N 316 GLN O 252 ASN P 119 GLN P 296 HIS R 94 GLN T 35 HIS X 64 GLN c 5 GLN c 34 GLN f 30 ASN j 24 GLN j 58 GLN m 32 GLN n 61 GLN p 22 GLN q 52 ASN q 54 GLN r 8 GLN r 24 GLN r 50 ASN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.1066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.261 69002 Z= 0.412 Angle : 1.310 50.726 93371 Z= 0.841 Chirality : 0.255 6.482 10186 Planarity : 0.004 0.056 11642 Dihedral : 13.246 173.710 10640 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 0.90 % Allowed : 5.69 % Favored : 93.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.67 % 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: 1.21 (0.09), residues: 8052 helix: 1.37 (0.08), residues: 4278 sheet: 0.33 (0.26), residues: 395 loop : 0.26 (0.11), residues: 3379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 179 HIS 0.006 0.001 HIS P 134 PHE 0.027 0.001 PHE N 292 TYR 0.047 0.001 TYR B 125 ARG 0.007 0.000 ARG S 25 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16104 Ramachandran restraints generated. 8052 Oldfield, 0 Emsley, 8052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16104 Ramachandran restraints generated. 8052 Oldfield, 0 Emsley, 8052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1059 residues out of total 7119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 995 time to evaluate : 5.999 Fit side-chains revert: symmetry clash REVERT: F 77 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8198 (tp) REVERT: F 428 GLU cc_start: 0.7370 (tm-30) cc_final: 0.7135 (tp30) REVERT: G 654 GLN cc_start: 0.7395 (mp10) cc_final: 0.6853 (mm-40) REVERT: H 202 GLU cc_start: 0.7294 (OUTLIER) cc_final: 0.7023 (mp0) REVERT: J 5 ILE cc_start: 0.8578 (tp) cc_final: 0.8372 (tp) REVERT: L 507 MET cc_start: 0.7962 (OUTLIER) cc_final: 0.7735 (ttm) REVERT: N 117 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.7965 (mt-10) REVERT: P 268 ARG cc_start: 0.7305 (tpp-160) cc_final: 0.7002 (tpt170) REVERT: W 49 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8562 (mp) REVERT: Y 119 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8058 (tt) REVERT: Z 85 GLN cc_start: 0.7840 (tt0) cc_final: 0.7474 (tt0) REVERT: Z 99 LYS cc_start: 0.7998 (tttm) cc_final: 0.7731 (tttp) REVERT: c 16 LYS cc_start: 0.8396 (OUTLIER) cc_final: 0.8127 (mttm) REVERT: d 103 GLU cc_start: 0.7403 (OUTLIER) cc_final: 0.7054 (mt-10) REVERT: e 23 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.7587 (tt0) REVERT: e 53 LYS cc_start: 0.8481 (mtmt) cc_final: 0.7889 (pttt) REVERT: g 114 ASP cc_start: 0.8027 (t70) cc_final: 0.7796 (t70) REVERT: h 19 LYS cc_start: 0.8178 (OUTLIER) cc_final: 0.7952 (tptm) REVERT: k 72 TRP cc_start: 0.8318 (m100) cc_final: 0.8019 (m100) REVERT: o 35 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7577 (mp0) REVERT: o 116 GLN cc_start: 0.7692 (OUTLIER) cc_final: 0.7357 (mp10) REVERT: p 171 GLU cc_start: 0.7015 (mm-30) cc_final: 0.6460 (pp20) REVERT: q 25 ARG cc_start: 0.8033 (ttm170) cc_final: 0.7784 (ttt180) REVERT: q 107 LYS cc_start: 0.8161 (OUTLIER) cc_final: 0.7683 (mtmp) outliers start: 64 outliers final: 19 residues processed: 1017 average time/residue: 1.8021 time to fit residues: 2307.5109 Evaluate side-chains 964 residues out of total 7119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 932 time to evaluate : 5.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain F residue 77 LEU Chi-restraints excluded: chain H residue 202 GLU Chi-restraints excluded: chain I residue 11 SER Chi-restraints excluded: chain J residue 2 MET Chi-restraints excluded: chain L residue 392 LYS Chi-restraints excluded: chain L residue 411 MET Chi-restraints excluded: chain L residue 507 MET Chi-restraints excluded: chain M residue 395 LEU Chi-restraints excluded: chain N residue 117 GLU Chi-restraints excluded: chain N residue 307 SER Chi-restraints excluded: chain R residue 79 THR Chi-restraints excluded: chain S residue 58 SER Chi-restraints excluded: chain S residue 90 LEU Chi-restraints excluded: chain V residue 109 SER Chi-restraints excluded: chain W residue 49 LEU Chi-restraints excluded: chain X residue 125 SER Chi-restraints excluded: chain Y residue 119 LEU Chi-restraints excluded: chain a residue 63 SER Chi-restraints excluded: chain b residue 15 GLU Chi-restraints excluded: chain c residue 16 LYS Chi-restraints excluded: chain d residue 103 GLU Chi-restraints excluded: chain e residue 23 GLU Chi-restraints excluded: chain g residue 107 ILE Chi-restraints excluded: chain h residue 19 LYS Chi-restraints excluded: chain i residue 81 ILE Chi-restraints excluded: chain o residue 35 GLU Chi-restraints excluded: chain o residue 116 GLN Chi-restraints excluded: chain q residue 107 LYS Chi-restraints excluded: chain s residue 57 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 799 random chunks: chunk 403 optimal weight: 8.9990 chunk 225 optimal weight: 0.9980 chunk 603 optimal weight: 9.9990 chunk 494 optimal weight: 6.9990 chunk 200 optimal weight: 4.9990 chunk 726 optimal weight: 1.9990 chunk 785 optimal weight: 0.0870 chunk 647 optimal weight: 10.0000 chunk 720 optimal weight: 3.9990 chunk 247 optimal weight: 7.9990 chunk 583 optimal weight: 9.9990 overall best weight: 2.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN C 69 ASN ** D 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 74 GLN E 121 GLN F 436 GLN G 16 GLN G 461 ASN G 629 ASN ** H 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 479 GLN M 139 GLN N 235 ASN N 316 GLN O 184 GLN P 296 HIS X 64 GLN c 5 GLN c 34 GLN e 69 GLN g 36 ASN j 58 GLN l 126 GLN m 32 GLN n 123 GLN p 22 GLN r 8 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.1207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.244 69002 Z= 0.450 Angle : 1.306 50.474 93371 Z= 0.838 Chirality : 0.257 6.516 10186 Planarity : 0.004 0.056 11642 Dihedral : 12.176 174.823 10638 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.45 % Allowed : 7.06 % Favored : 91.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.67 % 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: 1.35 (0.09), residues: 8052 helix: 1.50 (0.08), residues: 4276 sheet: 0.41 (0.26), residues: 397 loop : 0.31 (0.11), residues: 3379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP N 84 HIS 0.005 0.001 HIS L 332 PHE 0.027 0.002 PHE N 292 TYR 0.040 0.002 TYR B 125 ARG 0.009 0.000 ARG r 17 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16104 Ramachandran restraints generated. 8052 Oldfield, 0 Emsley, 8052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16104 Ramachandran restraints generated. 8052 Oldfield, 0 Emsley, 8052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1048 residues out of total 7119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 945 time to evaluate : 6.009 Fit side-chains revert: symmetry clash REVERT: F 77 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8189 (tp) REVERT: H 202 GLU cc_start: 0.7313 (OUTLIER) cc_final: 0.7067 (mp0) REVERT: L 597 ILE cc_start: 0.8481 (pt) cc_final: 0.8207 (mt) REVERT: O 291 GLN cc_start: 0.8244 (OUTLIER) cc_final: 0.7544 (tm130) REVERT: P 52 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.6961 (tm-30) REVERT: P 268 ARG cc_start: 0.7293 (tpp-160) cc_final: 0.7032 (tpt170) REVERT: S 45 LYS cc_start: 0.8416 (mtpp) cc_final: 0.8146 (mttp) REVERT: T 60 PHE cc_start: 0.8249 (p90) cc_final: 0.7910 (p90) REVERT: V 21 GLU cc_start: 0.7392 (mp0) cc_final: 0.7117 (mm-30) REVERT: W 49 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8546 (mp) REVERT: Y 105 ARG cc_start: 0.6459 (OUTLIER) cc_final: 0.6219 (mmp-170) REVERT: Y 119 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.8125 (tt) REVERT: Z 85 GLN cc_start: 0.7800 (tt0) cc_final: 0.7424 (tt0) REVERT: Z 92 GLU cc_start: 0.7224 (OUTLIER) cc_final: 0.6926 (mt-10) REVERT: a 35 GLU cc_start: 0.8574 (mt-10) cc_final: 0.8370 (mt-10) REVERT: d 111 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7756 (mt-10) REVERT: e 8 ARG cc_start: 0.8285 (OUTLIER) cc_final: 0.6796 (tpt170) REVERT: e 23 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.7604 (tt0) REVERT: f 52 GLU cc_start: 0.7529 (tt0) cc_final: 0.7114 (tt0) REVERT: g 114 ASP cc_start: 0.8057 (t70) cc_final: 0.7814 (t70) REVERT: g 117 LYS cc_start: 0.8495 (OUTLIER) cc_final: 0.8154 (mmpt) REVERT: h 19 LYS cc_start: 0.8165 (OUTLIER) cc_final: 0.7944 (tptm) REVERT: k 13 MET cc_start: 0.7998 (OUTLIER) cc_final: 0.7216 (ttm) REVERT: k 72 TRP cc_start: 0.8316 (m100) cc_final: 0.8035 (m100) REVERT: o 35 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.7532 (mp0) REVERT: o 116 GLN cc_start: 0.7609 (OUTLIER) cc_final: 0.7204 (mp10) REVERT: p 171 GLU cc_start: 0.7022 (mm-30) cc_final: 0.6456 (pp20) REVERT: q 25 ARG cc_start: 0.8102 (ttm170) cc_final: 0.7785 (ttt180) REVERT: q 107 LYS cc_start: 0.8204 (OUTLIER) cc_final: 0.7724 (mtmp) REVERT: r 32 LYS cc_start: 0.8762 (OUTLIER) cc_final: 0.8483 (mtpp) REVERT: r 107 GLN cc_start: 0.8582 (OUTLIER) cc_final: 0.7411 (mp-120) outliers start: 103 outliers final: 31 residues processed: 984 average time/residue: 1.7906 time to fit residues: 2217.2267 Evaluate side-chains 969 residues out of total 7119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 919 time to evaluate : 5.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain F residue 77 LEU Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain H residue 202 GLU Chi-restraints excluded: chain I residue 11 SER Chi-restraints excluded: chain I residue 78 ILE Chi-restraints excluded: chain J residue 111 LYS Chi-restraints excluded: chain L residue 392 LYS Chi-restraints excluded: chain M residue 395 LEU Chi-restraints excluded: chain N residue 307 SER Chi-restraints excluded: chain O residue 291 GLN Chi-restraints excluded: chain P residue 52 GLU Chi-restraints excluded: chain P residue 269 LEU Chi-restraints excluded: chain R residue 7 THR Chi-restraints excluded: chain R residue 79 THR Chi-restraints excluded: chain S residue 58 SER Chi-restraints excluded: chain V residue 103 VAL Chi-restraints excluded: chain V residue 109 SER Chi-restraints excluded: chain W residue 49 LEU Chi-restraints excluded: chain X residue 13 LYS Chi-restraints excluded: chain X residue 83 GLU Chi-restraints excluded: chain X residue 125 SER Chi-restraints excluded: chain Y residue 105 ARG Chi-restraints excluded: chain Y residue 119 LEU Chi-restraints excluded: chain Z residue 92 GLU Chi-restraints excluded: chain a residue 63 SER Chi-restraints excluded: chain b residue 15 GLU Chi-restraints excluded: chain b residue 31 LEU Chi-restraints excluded: chain d residue 27 THR Chi-restraints excluded: chain d residue 111 GLU Chi-restraints excluded: chain e residue 8 ARG Chi-restraints excluded: chain e residue 23 GLU Chi-restraints excluded: chain e residue 85 LEU Chi-restraints excluded: chain e residue 92 THR Chi-restraints excluded: chain f residue 18 MET Chi-restraints excluded: chain g residue 107 ILE Chi-restraints excluded: chain g residue 117 LYS Chi-restraints excluded: chain h residue 19 LYS Chi-restraints excluded: chain j residue 71 GLU Chi-restraints excluded: chain k residue 13 MET Chi-restraints excluded: chain l residue 5 THR Chi-restraints excluded: chain m residue 21 GLU Chi-restraints excluded: chain o residue 35 GLU Chi-restraints excluded: chain o residue 116 GLN Chi-restraints excluded: chain q residue 107 LYS Chi-restraints excluded: chain q residue 122 GLN Chi-restraints excluded: chain r residue 32 LYS Chi-restraints excluded: chain r residue 107 GLN Chi-restraints excluded: chain s residue 57 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 799 random chunks: chunk 718 optimal weight: 1.9990 chunk 546 optimal weight: 10.0000 chunk 377 optimal weight: 3.9990 chunk 80 optimal weight: 5.9990 chunk 346 optimal weight: 4.9990 chunk 488 optimal weight: 9.9990 chunk 729 optimal weight: 2.9990 chunk 772 optimal weight: 0.8980 chunk 381 optimal weight: 5.9990 chunk 691 optimal weight: 0.3980 chunk 208 optimal weight: 7.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN C 69 ASN ** D 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 74 GLN E 121 GLN G 16 GLN G 461 ASN H 5 ASN ** H 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 479 GLN M 139 GLN N 235 ASN N 316 GLN P 296 HIS X 64 GLN X 105 GLN c 5 GLN c 34 GLN g 36 ASN j 58 GLN n 61 GLN p 22 GLN q 54 GLN r 8 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.1329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.245 69002 Z= 0.435 Angle : 1.295 50.498 93371 Z= 0.834 Chirality : 0.255 6.478 10186 Planarity : 0.004 0.055 11642 Dihedral : 11.720 174.601 10638 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.41 % Allowed : 7.94 % Favored : 90.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.67 % 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: 1.46 (0.09), residues: 8052 helix: 1.60 (0.08), residues: 4273 sheet: 0.44 (0.26), residues: 387 loop : 0.35 (0.11), residues: 3392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP X 85 HIS 0.006 0.001 HIS L 332 PHE 0.029 0.001 PHE N 292 TYR 0.024 0.001 TYR L 422 ARG 0.008 0.000 ARG r 17 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16104 Ramachandran restraints generated. 8052 Oldfield, 0 Emsley, 8052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16104 Ramachandran restraints generated. 8052 Oldfield, 0 Emsley, 8052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1051 residues out of total 7119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 951 time to evaluate : 6.053 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 ASP cc_start: 0.7987 (m-30) cc_final: 0.7665 (m-30) REVERT: F 77 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8184 (tp) REVERT: H 202 GLU cc_start: 0.7293 (OUTLIER) cc_final: 0.7088 (mp0) REVERT: L 203 MET cc_start: 0.8421 (tpp) cc_final: 0.8207 (mmm) REVERT: L 383 MET cc_start: 0.9085 (OUTLIER) cc_final: 0.7820 (tpp) REVERT: L 597 ILE cc_start: 0.8434 (pt) cc_final: 0.8193 (mt) REVERT: N 117 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.7979 (mt-10) REVERT: N 311 MET cc_start: 0.8404 (OUTLIER) cc_final: 0.8097 (tpp) REVERT: O 229 GLN cc_start: 0.8045 (mm110) cc_final: 0.7840 (mm110) REVERT: O 291 GLN cc_start: 0.8218 (OUTLIER) cc_final: 0.7515 (tm130) REVERT: P 52 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.6969 (tm-30) REVERT: P 268 ARG cc_start: 0.7306 (tpp-160) cc_final: 0.7020 (tpt170) REVERT: S 45 LYS cc_start: 0.8395 (mtpp) cc_final: 0.8157 (mttp) REVERT: T 60 PHE cc_start: 0.8197 (p90) cc_final: 0.7881 (p90) REVERT: W 49 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8521 (mp) REVERT: W 89 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7344 (tp30) REVERT: Z 85 GLN cc_start: 0.7804 (tt0) cc_final: 0.7404 (tt0) REVERT: Z 92 GLU cc_start: 0.7255 (OUTLIER) cc_final: 0.6975 (mt-10) REVERT: a 35 GLU cc_start: 0.8576 (mt-10) cc_final: 0.8371 (mt-10) REVERT: b 9 LYS cc_start: 0.8648 (OUTLIER) cc_final: 0.7497 (tmtp) REVERT: b 14 LYS cc_start: 0.8176 (mmtp) cc_final: 0.7852 (mmtt) REVERT: c 16 LYS cc_start: 0.8388 (OUTLIER) cc_final: 0.8144 (mttm) REVERT: d 111 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.7768 (mt-10) REVERT: e 8 ARG cc_start: 0.8271 (OUTLIER) cc_final: 0.6745 (tpt170) REVERT: e 23 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7588 (tt0) REVERT: e 53 LYS cc_start: 0.8505 (mttt) cc_final: 0.8044 (pttt) REVERT: f 52 GLU cc_start: 0.7527 (tt0) cc_final: 0.7122 (tt0) REVERT: g 114 ASP cc_start: 0.8025 (t70) cc_final: 0.7772 (t70) REVERT: g 117 LYS cc_start: 0.8479 (OUTLIER) cc_final: 0.8143 (mmpt) REVERT: h 57 GLU cc_start: 0.6640 (OUTLIER) cc_final: 0.6298 (tm-30) REVERT: k 72 TRP cc_start: 0.8277 (m100) cc_final: 0.8004 (m100) REVERT: n 61 GLN cc_start: 0.8163 (OUTLIER) cc_final: 0.7850 (tt0) REVERT: o 116 GLN cc_start: 0.7564 (OUTLIER) cc_final: 0.7204 (mp10) REVERT: o 117 ARG cc_start: 0.7024 (tmm-80) cc_final: 0.6666 (tmm160) REVERT: p 171 GLU cc_start: 0.7006 (mm-30) cc_final: 0.6407 (pp20) REVERT: q 25 ARG cc_start: 0.8076 (ttm170) cc_final: 0.7744 (ttt180) REVERT: r 32 LYS cc_start: 0.8733 (OUTLIER) cc_final: 0.8447 (mtpp) REVERT: r 107 GLN cc_start: 0.8551 (OUTLIER) cc_final: 0.7377 (mp-120) REVERT: r 108 ASP cc_start: 0.7917 (t0) cc_final: 0.7670 (t0) outliers start: 100 outliers final: 47 residues processed: 991 average time/residue: 1.7968 time to fit residues: 2238.8081 Evaluate side-chains 982 residues out of total 7119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 914 time to evaluate : 5.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 125 LYS Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain F residue 77 LEU Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 436 SER Chi-restraints excluded: chain H residue 10 ILE Chi-restraints excluded: chain H residue 202 GLU Chi-restraints excluded: chain H residue 268 MET Chi-restraints excluded: chain I residue 11 SER Chi-restraints excluded: chain I residue 78 ILE Chi-restraints excluded: chain J residue 2 MET Chi-restraints excluded: chain J residue 111 LYS Chi-restraints excluded: chain L residue 383 MET Chi-restraints excluded: chain L residue 392 LYS Chi-restraints excluded: chain M residue 395 LEU Chi-restraints excluded: chain M residue 458 LEU Chi-restraints excluded: chain N residue 117 GLU Chi-restraints excluded: chain N residue 307 SER Chi-restraints excluded: chain N residue 311 MET Chi-restraints excluded: chain O residue 291 GLN Chi-restraints excluded: chain P residue 52 GLU Chi-restraints excluded: chain P residue 269 LEU Chi-restraints excluded: chain R residue 7 THR Chi-restraints excluded: chain R residue 79 THR Chi-restraints excluded: chain S residue 90 LEU Chi-restraints excluded: chain T residue 19 LEU Chi-restraints excluded: chain T residue 32 VAL Chi-restraints excluded: chain V residue 103 VAL Chi-restraints excluded: chain V residue 109 SER Chi-restraints excluded: chain W residue 49 LEU Chi-restraints excluded: chain W residue 89 GLU Chi-restraints excluded: chain X residue 13 LYS Chi-restraints excluded: chain X residue 83 GLU Chi-restraints excluded: chain X residue 125 SER Chi-restraints excluded: chain Y residue 119 LEU Chi-restraints excluded: chain Z residue 92 GLU Chi-restraints excluded: chain Z residue 114 THR Chi-restraints excluded: chain a residue 63 SER Chi-restraints excluded: chain b residue 9 LYS Chi-restraints excluded: chain b residue 15 GLU Chi-restraints excluded: chain b residue 31 LEU Chi-restraints excluded: chain c residue 11 SER Chi-restraints excluded: chain c residue 16 LYS Chi-restraints excluded: chain d residue 27 THR Chi-restraints excluded: chain d residue 111 GLU Chi-restraints excluded: chain e residue 8 ARG Chi-restraints excluded: chain e residue 23 GLU Chi-restraints excluded: chain e residue 85 LEU Chi-restraints excluded: chain e residue 86 ILE Chi-restraints excluded: chain e residue 92 THR Chi-restraints excluded: chain f residue 18 MET Chi-restraints excluded: chain g residue 107 ILE Chi-restraints excluded: chain g residue 117 LYS Chi-restraints excluded: chain h residue 32 THR Chi-restraints excluded: chain h residue 57 GLU Chi-restraints excluded: chain j residue 71 GLU Chi-restraints excluded: chain m residue 21 GLU Chi-restraints excluded: chain m residue 23 ASP Chi-restraints excluded: chain m residue 25 SER Chi-restraints excluded: chain n residue 61 GLN Chi-restraints excluded: chain o residue 116 GLN Chi-restraints excluded: chain q residue 122 GLN Chi-restraints excluded: chain r residue 32 LYS Chi-restraints excluded: chain r residue 107 GLN Chi-restraints excluded: chain s residue 57 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 799 random chunks: chunk 643 optimal weight: 10.0000 chunk 438 optimal weight: 0.9990 chunk 11 optimal weight: 0.0770 chunk 575 optimal weight: 0.8980 chunk 318 optimal weight: 2.9990 chunk 659 optimal weight: 4.9990 chunk 533 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 394 optimal weight: 6.9990 chunk 693 optimal weight: 8.9990 chunk 194 optimal weight: 0.8980 overall best weight: 1.1742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN C 69 ASN ** D 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 74 GLN F 431 GLN F 432 GLN G 16 GLN G 313 ASN G 461 ASN ** G 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 479 GLN M 139 GLN N 47 ASN N 235 ASN N 316 GLN P 87 HIS P 119 GLN P 296 HIS W 70 ASN X 64 GLN c 5 GLN c 34 GLN d 12 GLN e 69 GLN g 36 ASN j 58 GLN m 32 GLN q 54 GLN r 8 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.1515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.246 69002 Z= 0.415 Angle : 1.283 50.537 93371 Z= 0.830 Chirality : 0.254 6.424 10186 Planarity : 0.004 0.054 11642 Dihedral : 11.271 172.801 10638 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.79 % Favored : 98.20 % Rotamer: Outliers : 1.41 % Allowed : 8.64 % Favored : 89.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.67 % 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: 1.61 (0.09), residues: 8052 helix: 1.73 (0.08), residues: 4267 sheet: 0.33 (0.26), residues: 392 loop : 0.44 (0.11), residues: 3393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP X 85 HIS 0.005 0.001 HIS N 112 PHE 0.029 0.001 PHE N 292 TYR 0.023 0.001 TYR L 422 ARG 0.008 0.000 ARG r 17 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16104 Ramachandran restraints generated. 8052 Oldfield, 0 Emsley, 8052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16104 Ramachandran restraints generated. 8052 Oldfield, 0 Emsley, 8052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1054 residues out of total 7119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 954 time to evaluate : 6.015 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 ASP cc_start: 0.7978 (m-30) cc_final: 0.7661 (m-30) REVERT: F 77 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8221 (tp) REVERT: G 475 GLN cc_start: 0.7036 (tp40) cc_final: 0.6559 (mm110) REVERT: H 234 MET cc_start: 0.9008 (mmt) cc_final: 0.8708 (mmt) REVERT: J 173 ARG cc_start: 0.7815 (OUTLIER) cc_final: 0.7162 (ptp90) REVERT: M 263 MET cc_start: 0.9096 (mmp) cc_final: 0.8895 (mmp) REVERT: N 100 MET cc_start: 0.8092 (OUTLIER) cc_final: 0.7388 (mtt) REVERT: N 117 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.7952 (mt-10) REVERT: N 320 MET cc_start: 0.7632 (OUTLIER) cc_final: 0.7420 (ttp) REVERT: O 291 GLN cc_start: 0.8182 (OUTLIER) cc_final: 0.7494 (tm130) REVERT: P 268 ARG cc_start: 0.7310 (tpp-160) cc_final: 0.7009 (tpt170) REVERT: P 333 ASP cc_start: 0.7559 (m-30) cc_final: 0.7280 (m-30) REVERT: T 34 SER cc_start: 0.7238 (m) cc_final: 0.6905 (p) REVERT: T 60 PHE cc_start: 0.8179 (p90) cc_final: 0.7895 (p90) REVERT: W 49 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8495 (mp) REVERT: W 89 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.7322 (tp30) REVERT: Z 85 GLN cc_start: 0.7804 (tt0) cc_final: 0.7365 (tt0) REVERT: Z 92 GLU cc_start: 0.7204 (OUTLIER) cc_final: 0.6772 (mt-10) REVERT: a 35 GLU cc_start: 0.8572 (mt-10) cc_final: 0.8361 (mt-10) REVERT: b 9 LYS cc_start: 0.8632 (OUTLIER) cc_final: 0.7464 (tmtp) REVERT: b 58 ASP cc_start: 0.8091 (t0) cc_final: 0.7617 (t0) REVERT: d 111 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7744 (mt-10) REVERT: e 8 ARG cc_start: 0.8269 (OUTLIER) cc_final: 0.6738 (tpt170) REVERT: e 23 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.7557 (tt0) REVERT: e 53 LYS cc_start: 0.8465 (mttt) cc_final: 0.8057 (pttt) REVERT: f 52 GLU cc_start: 0.7493 (tt0) cc_final: 0.7103 (tt0) REVERT: g 114 ASP cc_start: 0.8023 (t70) cc_final: 0.7766 (t70) REVERT: h 57 GLU cc_start: 0.6617 (OUTLIER) cc_final: 0.6286 (tm-30) REVERT: k 13 MET cc_start: 0.7913 (OUTLIER) cc_final: 0.7154 (ttm) REVERT: k 34 LYS cc_start: 0.8632 (OUTLIER) cc_final: 0.8426 (tttt) REVERT: k 72 TRP cc_start: 0.8276 (m100) cc_final: 0.8008 (m100) REVERT: m 107 ASP cc_start: 0.8495 (t70) cc_final: 0.8222 (t0) REVERT: o 35 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.7507 (mp0) REVERT: o 116 GLN cc_start: 0.7494 (OUTLIER) cc_final: 0.7116 (mp10) REVERT: o 117 ARG cc_start: 0.6966 (tmm-80) cc_final: 0.6624 (tmm160) REVERT: p 171 GLU cc_start: 0.6993 (mm-30) cc_final: 0.6440 (pp20) REVERT: q 25 ARG cc_start: 0.8071 (ttm170) cc_final: 0.7749 (ttt180) REVERT: q 107 LYS cc_start: 0.8144 (OUTLIER) cc_final: 0.7670 (mtmp) REVERT: r 32 LYS cc_start: 0.8710 (OUTLIER) cc_final: 0.8508 (mtpp) REVERT: r 108 ASP cc_start: 0.7900 (t0) cc_final: 0.7631 (t0) outliers start: 100 outliers final: 35 residues processed: 1004 average time/residue: 1.7326 time to fit residues: 2198.9116 Evaluate side-chains 988 residues out of total 7119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 933 time to evaluate : 5.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 125 LYS Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain F residue 77 LEU Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 436 SER Chi-restraints excluded: chain I residue 11 SER Chi-restraints excluded: chain I residue 78 ILE Chi-restraints excluded: chain J residue 2 MET Chi-restraints excluded: chain J residue 111 LYS Chi-restraints excluded: chain J residue 173 ARG Chi-restraints excluded: chain L residue 254 VAL Chi-restraints excluded: chain M residue 395 LEU Chi-restraints excluded: chain M residue 458 LEU Chi-restraints excluded: chain N residue 100 MET Chi-restraints excluded: chain N residue 117 GLU Chi-restraints excluded: chain N residue 307 SER Chi-restraints excluded: chain N residue 320 MET Chi-restraints excluded: chain O residue 291 GLN Chi-restraints excluded: chain R residue 79 THR Chi-restraints excluded: chain S residue 90 LEU Chi-restraints excluded: chain V residue 103 VAL Chi-restraints excluded: chain W residue 49 LEU Chi-restraints excluded: chain W residue 89 GLU Chi-restraints excluded: chain X residue 13 LYS Chi-restraints excluded: chain X residue 83 GLU Chi-restraints excluded: chain X residue 125 SER Chi-restraints excluded: chain Y residue 114 CYS Chi-restraints excluded: chain Y residue 119 LEU Chi-restraints excluded: chain Z residue 92 GLU Chi-restraints excluded: chain Z residue 96 THR Chi-restraints excluded: chain Z residue 114 THR Chi-restraints excluded: chain a residue 21 MET Chi-restraints excluded: chain a residue 63 SER Chi-restraints excluded: chain b residue 9 LYS Chi-restraints excluded: chain b residue 15 GLU Chi-restraints excluded: chain b residue 31 LEU Chi-restraints excluded: chain d residue 27 THR Chi-restraints excluded: chain d residue 111 GLU Chi-restraints excluded: chain e residue 8 ARG Chi-restraints excluded: chain e residue 23 GLU Chi-restraints excluded: chain g residue 107 ILE Chi-restraints excluded: chain h residue 36 VAL Chi-restraints excluded: chain h residue 57 GLU Chi-restraints excluded: chain j residue 71 GLU Chi-restraints excluded: chain k residue 13 MET Chi-restraints excluded: chain k residue 34 LYS Chi-restraints excluded: chain m residue 23 ASP Chi-restraints excluded: chain o residue 35 GLU Chi-restraints excluded: chain o residue 116 GLN Chi-restraints excluded: chain q residue 107 LYS Chi-restraints excluded: chain r residue 32 LYS Chi-restraints excluded: chain s residue 57 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 799 random chunks: chunk 259 optimal weight: 4.9990 chunk 695 optimal weight: 3.9990 chunk 152 optimal weight: 7.9990 chunk 453 optimal weight: 6.9990 chunk 190 optimal weight: 2.9990 chunk 773 optimal weight: 9.9990 chunk 641 optimal weight: 5.9990 chunk 357 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 255 optimal weight: 10.0000 chunk 405 optimal weight: 2.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN C 69 ASN ** D 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 74 GLN E 155 GLN F 431 GLN F 432 GLN G 16 GLN G 313 ASN G 461 ASN ** G 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 479 GLN M 139 GLN N 235 ASN N 316 GLN P 296 HIS Q 29 HIS V 72 GLN W 70 ASN X 64 GLN X 105 GLN c 5 GLN c 34 GLN d 12 GLN d 61 GLN g 36 ASN j 58 GLN m 32 GLN n 61 GLN q 52 ASN q 54 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.1307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.243 69002 Z= 0.495 Angle : 1.319 50.478 93371 Z= 0.843 Chirality : 0.258 6.561 10186 Planarity : 0.005 0.055 11642 Dihedral : 11.510 174.293 10638 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.70 % Allowed : 8.95 % Favored : 89.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.67 % 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: 1.41 (0.09), residues: 8052 helix: 1.54 (0.08), residues: 4280 sheet: 0.42 (0.26), residues: 397 loop : 0.33 (0.11), residues: 3375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP X 85 HIS 0.006 0.001 HIS N 112 PHE 0.027 0.002 PHE N 292 TYR 0.023 0.002 TYR I 118 ARG 0.010 0.000 ARG r 17 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16104 Ramachandran restraints generated. 8052 Oldfield, 0 Emsley, 8052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16104 Ramachandran restraints generated. 8052 Oldfield, 0 Emsley, 8052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1052 residues out of total 7119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 931 time to evaluate : 6.130 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 ASP cc_start: 0.7960 (m-30) cc_final: 0.7661 (m-30) REVERT: B 178 ARG cc_start: 0.8278 (OUTLIER) cc_final: 0.7645 (mtt90) REVERT: F 77 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8256 (tp) REVERT: G 475 GLN cc_start: 0.7172 (tp40) cc_final: 0.6701 (mm110) REVERT: G 613 TYR cc_start: 0.9140 (OUTLIER) cc_final: 0.8341 (p90) REVERT: H 8 MET cc_start: 0.7942 (OUTLIER) cc_final: 0.7711 (mmm) REVERT: H 204 GLU cc_start: 0.7127 (OUTLIER) cc_final: 0.6853 (tp30) REVERT: J 77 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7494 (pm20) REVERT: J 118 GLU cc_start: 0.6485 (OUTLIER) cc_final: 0.6062 (tm-30) REVERT: J 141 MET cc_start: 0.8057 (mmp) cc_final: 0.7807 (mmp) REVERT: J 173 ARG cc_start: 0.7877 (OUTLIER) cc_final: 0.7270 (ptp90) REVERT: M 304 GLN cc_start: 0.8571 (mt0) cc_final: 0.8364 (mt0) REVERT: N 100 MET cc_start: 0.8093 (OUTLIER) cc_final: 0.7368 (mtt) REVERT: N 311 MET cc_start: 0.8448 (OUTLIER) cc_final: 0.8116 (tpp) REVERT: O 60 ASP cc_start: 0.8642 (OUTLIER) cc_final: 0.8222 (m-30) REVERT: O 291 GLN cc_start: 0.8263 (OUTLIER) cc_final: 0.7579 (tm130) REVERT: P 52 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.7347 (tm-30) REVERT: P 268 ARG cc_start: 0.7300 (tpp-160) cc_final: 0.7013 (tpt170) REVERT: W 49 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8538 (mp) REVERT: Z 85 GLN cc_start: 0.7808 (tt0) cc_final: 0.7396 (tt0) REVERT: Z 92 GLU cc_start: 0.7277 (OUTLIER) cc_final: 0.6969 (mt-10) REVERT: a 35 GLU cc_start: 0.8584 (mt-10) cc_final: 0.8353 (mt-10) REVERT: b 9 LYS cc_start: 0.8680 (OUTLIER) cc_final: 0.7515 (tmtp) REVERT: b 14 LYS cc_start: 0.8192 (mmtp) cc_final: 0.7843 (mmtt) REVERT: d 111 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7775 (mt-10) REVERT: e 8 ARG cc_start: 0.8319 (OUTLIER) cc_final: 0.6767 (tpt170) REVERT: e 23 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.7580 (tt0) REVERT: e 53 LYS cc_start: 0.8505 (mttt) cc_final: 0.8039 (pttt) REVERT: f 52 GLU cc_start: 0.7555 (tt0) cc_final: 0.7153 (tt0) REVERT: g 114 ASP cc_start: 0.8043 (t70) cc_final: 0.7784 (t70) REVERT: g 117 LYS cc_start: 0.8499 (OUTLIER) cc_final: 0.8187 (mmpt) REVERT: h 57 GLU cc_start: 0.6635 (OUTLIER) cc_final: 0.6305 (tm-30) REVERT: k 13 MET cc_start: 0.7932 (OUTLIER) cc_final: 0.7239 (ttm) REVERT: k 72 TRP cc_start: 0.8317 (m100) cc_final: 0.8080 (m100) REVERT: n 61 GLN cc_start: 0.8185 (OUTLIER) cc_final: 0.7804 (tm130) REVERT: p 171 GLU cc_start: 0.7015 (mm-30) cc_final: 0.6552 (pp20) REVERT: q 25 ARG cc_start: 0.8089 (ttm170) cc_final: 0.7749 (ttt180) REVERT: q 107 LYS cc_start: 0.8195 (OUTLIER) cc_final: 0.7720 (mtmp) REVERT: r 32 LYS cc_start: 0.8768 (OUTLIER) cc_final: 0.8468 (mtpp) REVERT: r 107 GLN cc_start: 0.8581 (OUTLIER) cc_final: 0.7426 (mp10) REVERT: r 108 ASP cc_start: 0.7976 (t0) cc_final: 0.7707 (t0) outliers start: 121 outliers final: 49 residues processed: 983 average time/residue: 1.7674 time to fit residues: 2197.9540 Evaluate side-chains 989 residues out of total 7119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 914 time to evaluate : 5.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 178 ARG Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain F residue 77 LEU Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 436 SER Chi-restraints excluded: chain G residue 535 GLN Chi-restraints excluded: chain G residue 613 TYR Chi-restraints excluded: chain H residue 8 MET Chi-restraints excluded: chain H residue 10 ILE Chi-restraints excluded: chain H residue 204 GLU Chi-restraints excluded: chain H residue 268 MET Chi-restraints excluded: chain I residue 11 SER Chi-restraints excluded: chain J residue 2 MET Chi-restraints excluded: chain J residue 77 GLU Chi-restraints excluded: chain J residue 111 LYS Chi-restraints excluded: chain J residue 118 GLU Chi-restraints excluded: chain J residue 173 ARG Chi-restraints excluded: chain L residue 254 VAL Chi-restraints excluded: chain L residue 392 LYS Chi-restraints excluded: chain M residue 144 ASN Chi-restraints excluded: chain M residue 395 LEU Chi-restraints excluded: chain M residue 458 LEU Chi-restraints excluded: chain N residue 100 MET Chi-restraints excluded: chain N residue 307 SER Chi-restraints excluded: chain N residue 311 MET Chi-restraints excluded: chain N residue 320 MET Chi-restraints excluded: chain O residue 60 ASP Chi-restraints excluded: chain O residue 291 GLN Chi-restraints excluded: chain P residue 52 GLU Chi-restraints excluded: chain P residue 269 LEU Chi-restraints excluded: chain R residue 7 THR Chi-restraints excluded: chain R residue 79 THR Chi-restraints excluded: chain S residue 90 LEU Chi-restraints excluded: chain V residue 103 VAL Chi-restraints excluded: chain V residue 109 SER Chi-restraints excluded: chain W residue 49 LEU Chi-restraints excluded: chain X residue 11 ASP Chi-restraints excluded: chain X residue 13 LYS Chi-restraints excluded: chain X residue 83 GLU Chi-restraints excluded: chain X residue 125 SER Chi-restraints excluded: chain Y residue 119 LEU Chi-restraints excluded: chain Z residue 92 GLU Chi-restraints excluded: chain Z residue 96 THR Chi-restraints excluded: chain Z residue 114 THR Chi-restraints excluded: chain Z residue 131 GLU Chi-restraints excluded: chain a residue 63 SER Chi-restraints excluded: chain b residue 9 LYS Chi-restraints excluded: chain b residue 15 GLU Chi-restraints excluded: chain b residue 31 LEU Chi-restraints excluded: chain c residue 11 SER Chi-restraints excluded: chain d residue 27 THR Chi-restraints excluded: chain d residue 111 GLU Chi-restraints excluded: chain e residue 8 ARG Chi-restraints excluded: chain e residue 23 GLU Chi-restraints excluded: chain e residue 85 LEU Chi-restraints excluded: chain e residue 86 ILE Chi-restraints excluded: chain e residue 92 THR Chi-restraints excluded: chain f residue 18 MET Chi-restraints excluded: chain g residue 107 ILE Chi-restraints excluded: chain g residue 117 LYS Chi-restraints excluded: chain h residue 36 VAL Chi-restraints excluded: chain h residue 57 GLU Chi-restraints excluded: chain j residue 71 GLU Chi-restraints excluded: chain k residue 13 MET Chi-restraints excluded: chain k residue 34 LYS Chi-restraints excluded: chain m residue 23 ASP Chi-restraints excluded: chain m residue 25 SER Chi-restraints excluded: chain n residue 61 GLN Chi-restraints excluded: chain o residue 27 ASP Chi-restraints excluded: chain q residue 107 LYS Chi-restraints excluded: chain q residue 122 GLN Chi-restraints excluded: chain r residue 32 LYS Chi-restraints excluded: chain r residue 107 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 799 random chunks: chunk 745 optimal weight: 0.4980 chunk 87 optimal weight: 4.9990 chunk 440 optimal weight: 0.0010 chunk 564 optimal weight: 0.0370 chunk 437 optimal weight: 0.6980 chunk 650 optimal weight: 2.9990 chunk 431 optimal weight: 0.1980 chunk 770 optimal weight: 8.9990 chunk 481 optimal weight: 1.9990 chunk 469 optimal weight: 4.9990 chunk 355 optimal weight: 7.9990 overall best weight: 0.2864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN C 69 ASN ** D 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 74 GLN F 432 GLN F 436 GLN G 16 GLN G 313 ASN G 461 ASN G 475 GLN L 479 GLN M 139 GLN M 366 ASN N 235 ASN N 316 GLN P 296 HIS V 72 GLN X 64 GLN c 5 GLN c 34 GLN d 12 GLN d 61 GLN j 24 GLN j 58 GLN q 52 ASN q 54 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.249 69002 Z= 0.408 Angle : 1.279 50.561 93371 Z= 0.828 Chirality : 0.252 6.354 10186 Planarity : 0.004 0.053 11642 Dihedral : 10.781 169.913 10638 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.56 % Favored : 98.42 % Rotamer: Outliers : 1.07 % Allowed : 9.76 % Favored : 89.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.67 % 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: 1.67 (0.09), residues: 8052 helix: 1.79 (0.08), residues: 4255 sheet: 0.36 (0.26), residues: 396 loop : 0.46 (0.11), residues: 3401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP X 85 HIS 0.005 0.001 HIS D 348 PHE 0.032 0.001 PHE N 292 TYR 0.025 0.001 TYR L 422 ARG 0.009 0.000 ARG r 17 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16104 Ramachandran restraints generated. 8052 Oldfield, 0 Emsley, 8052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16104 Ramachandran restraints generated. 8052 Oldfield, 0 Emsley, 8052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1067 residues out of total 7119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 991 time to evaluate : 6.124 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 ASP cc_start: 0.7947 (m-30) cc_final: 0.7628 (m-30) REVERT: B 178 ARG cc_start: 0.8250 (OUTLIER) cc_final: 0.7656 (mtt90) REVERT: F 77 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8221 (tp) REVERT: G 475 GLN cc_start: 0.7000 (tp-100) cc_final: 0.6631 (mm110) REVERT: J 141 MET cc_start: 0.8061 (mmp) cc_final: 0.7780 (mmp) REVERT: J 170 GLU cc_start: 0.8176 (mm-30) cc_final: 0.7975 (mm-30) REVERT: J 173 ARG cc_start: 0.7823 (OUTLIER) cc_final: 0.7171 (ptp90) REVERT: N 117 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7878 (mt-10) REVERT: O 229 GLN cc_start: 0.7989 (mm110) cc_final: 0.7774 (mm110) REVERT: O 291 GLN cc_start: 0.8131 (OUTLIER) cc_final: 0.7458 (tm130) REVERT: P 52 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.7362 (tm-30) REVERT: P 268 ARG cc_start: 0.7329 (tpp-160) cc_final: 0.7072 (tpt170) REVERT: P 333 ASP cc_start: 0.7504 (m-30) cc_final: 0.7294 (m-30) REVERT: T 29 LYS cc_start: 0.7368 (mtpp) cc_final: 0.7027 (mtpt) REVERT: T 34 SER cc_start: 0.7263 (m) cc_final: 0.6914 (p) REVERT: T 52 MET cc_start: 0.8384 (mtm) cc_final: 0.8078 (mtm) REVERT: T 60 PHE cc_start: 0.8253 (p90) cc_final: 0.7919 (p90) REVERT: U 69 LYS cc_start: 0.8936 (OUTLIER) cc_final: 0.8617 (mttm) REVERT: V 21 GLU cc_start: 0.7402 (mp0) cc_final: 0.7149 (mm-30) REVERT: W 49 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8388 (mp) REVERT: W 89 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7342 (tp30) REVERT: X 125 SER cc_start: 0.8844 (p) cc_final: 0.8568 (t) REVERT: Z 52 LYS cc_start: 0.8454 (mmmm) cc_final: 0.8193 (mmmt) REVERT: Z 85 GLN cc_start: 0.7793 (tt0) cc_final: 0.7354 (tt0) REVERT: Z 92 GLU cc_start: 0.7182 (OUTLIER) cc_final: 0.6788 (mt-10) REVERT: a 35 GLU cc_start: 0.8578 (mt-10) cc_final: 0.8362 (mt-10) REVERT: b 9 LYS cc_start: 0.8619 (OUTLIER) cc_final: 0.7458 (tmtp) REVERT: b 14 LYS cc_start: 0.8173 (mmtp) cc_final: 0.7876 (mmtt) REVERT: b 58 ASP cc_start: 0.8064 (t0) cc_final: 0.7725 (t0) REVERT: d 95 LYS cc_start: 0.8436 (ttmm) cc_final: 0.8048 (ttpt) REVERT: e 53 LYS cc_start: 0.8424 (mttt) cc_final: 0.8015 (pttt) REVERT: f 52 GLU cc_start: 0.7510 (tt0) cc_final: 0.7130 (tt0) REVERT: g 114 ASP cc_start: 0.7998 (t70) cc_final: 0.7736 (t70) REVERT: j 32 MET cc_start: 0.8754 (ttp) cc_final: 0.8516 (ttp) REVERT: k 72 TRP cc_start: 0.8229 (m100) cc_final: 0.7984 (m100) REVERT: m 107 ASP cc_start: 0.8447 (t70) cc_final: 0.8198 (t0) REVERT: o 116 GLN cc_start: 0.7501 (OUTLIER) cc_final: 0.7132 (mp10) REVERT: o 117 ARG cc_start: 0.6900 (tmm-80) cc_final: 0.6562 (tmm160) REVERT: p 171 GLU cc_start: 0.6990 (mm-30) cc_final: 0.6497 (pp20) REVERT: q 25 ARG cc_start: 0.8038 (ttm170) cc_final: 0.7733 (ttt180) REVERT: q 107 LYS cc_start: 0.8098 (OUTLIER) cc_final: 0.7578 (mtmp) REVERT: r 108 ASP cc_start: 0.7822 (t0) cc_final: 0.7598 (t0) REVERT: s 59 SER cc_start: 0.8531 (t) cc_final: 0.8252 (p) REVERT: s 63 MET cc_start: 0.8119 (mmm) cc_final: 0.7864 (mmp) outliers start: 76 outliers final: 22 residues processed: 1027 average time/residue: 1.7387 time to fit residues: 2262.6814 Evaluate side-chains 981 residues out of total 7119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 946 time to evaluate : 6.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 178 ARG Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain F residue 77 LEU Chi-restraints excluded: chain G residue 436 SER Chi-restraints excluded: chain I residue 78 ILE Chi-restraints excluded: chain J residue 2 MET Chi-restraints excluded: chain J residue 173 ARG Chi-restraints excluded: chain L residue 392 LYS Chi-restraints excluded: chain N residue 117 GLU Chi-restraints excluded: chain O residue 291 GLN Chi-restraints excluded: chain P residue 52 GLU Chi-restraints excluded: chain U residue 69 LYS Chi-restraints excluded: chain V residue 103 VAL Chi-restraints excluded: chain V residue 109 SER Chi-restraints excluded: chain W residue 49 LEU Chi-restraints excluded: chain W residue 89 GLU Chi-restraints excluded: chain X residue 83 GLU Chi-restraints excluded: chain Y residue 114 CYS Chi-restraints excluded: chain Y residue 119 LEU Chi-restraints excluded: chain Z residue 13 VAL Chi-restraints excluded: chain Z residue 92 GLU Chi-restraints excluded: chain Z residue 114 THR Chi-restraints excluded: chain a residue 21 MET Chi-restraints excluded: chain b residue 9 LYS Chi-restraints excluded: chain b residue 15 GLU Chi-restraints excluded: chain b residue 31 LEU Chi-restraints excluded: chain d residue 85 VAL Chi-restraints excluded: chain g residue 107 ILE Chi-restraints excluded: chain j residue 71 GLU Chi-restraints excluded: chain o residue 27 ASP Chi-restraints excluded: chain o residue 116 GLN Chi-restraints excluded: chain p residue 16 THR Chi-restraints excluded: chain q residue 107 LYS Chi-restraints excluded: chain s residue 53 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 799 random chunks: chunk 476 optimal weight: 0.7980 chunk 307 optimal weight: 0.8980 chunk 459 optimal weight: 0.5980 chunk 231 optimal weight: 1.9990 chunk 151 optimal weight: 6.9990 chunk 149 optimal weight: 1.9990 chunk 489 optimal weight: 4.9990 chunk 524 optimal weight: 20.0000 chunk 380 optimal weight: 5.9990 chunk 71 optimal weight: 0.8980 chunk 605 optimal weight: 8.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN C 69 ASN ** D 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 74 GLN E 155 GLN F 431 GLN F 432 GLN F 436 GLN G 16 GLN G 313 ASN G 461 ASN ** H 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 479 GLN M 139 GLN M 304 GLN M 366 ASN N 235 ASN N 316 GLN O 252 ASN P 119 GLN P 296 HIS V 72 GLN W 70 ASN c 5 GLN c 34 GLN d 12 GLN g 36 ASN j 6 HIS n 61 GLN q 52 ASN q 54 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.245 69002 Z= 0.412 Angle : 1.281 50.555 93371 Z= 0.828 Chirality : 0.254 6.407 10186 Planarity : 0.004 0.053 11642 Dihedral : 10.640 172.423 10638 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.64 % Favored : 98.35 % Rotamer: Outliers : 0.98 % Allowed : 10.40 % Favored : 88.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.67 % 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: 1.76 (0.09), residues: 8052 helix: 1.85 (0.08), residues: 4271 sheet: 0.41 (0.26), residues: 397 loop : 0.50 (0.11), residues: 3384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP X 85 HIS 0.005 0.001 HIS N 112 PHE 0.029 0.001 PHE N 292 TYR 0.023 0.001 TYR L 422 ARG 0.009 0.000 ARG r 17 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16104 Ramachandran restraints generated. 8052 Oldfield, 0 Emsley, 8052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16104 Ramachandran restraints generated. 8052 Oldfield, 0 Emsley, 8052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1016 residues out of total 7119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 946 time to evaluate : 6.089 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 ASP cc_start: 0.7933 (m-30) cc_final: 0.7625 (m-30) REVERT: B 109 GLU cc_start: 0.8159 (mt-10) cc_final: 0.7932 (mt-10) REVERT: B 178 ARG cc_start: 0.8273 (OUTLIER) cc_final: 0.7669 (mtt90) REVERT: C 73 LYS cc_start: 0.8904 (mmtt) cc_final: 0.8656 (mptt) REVERT: F 77 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8214 (tp) REVERT: G 475 GLN cc_start: 0.7000 (tp-100) cc_final: 0.6722 (mm110) REVERT: J 173 ARG cc_start: 0.7850 (OUTLIER) cc_final: 0.7219 (ptp90) REVERT: N 100 MET cc_start: 0.7941 (OUTLIER) cc_final: 0.7161 (mtt) REVERT: O 291 GLN cc_start: 0.8157 (OUTLIER) cc_final: 0.7483 (tm130) REVERT: P 52 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.7291 (tm-30) REVERT: P 268 ARG cc_start: 0.7303 (tpp-160) cc_final: 0.7050 (tpt170) REVERT: P 333 ASP cc_start: 0.7511 (m-30) cc_final: 0.7296 (m-30) REVERT: T 34 SER cc_start: 0.7263 (m) cc_final: 0.6943 (p) REVERT: T 52 MET cc_start: 0.8417 (mtm) cc_final: 0.8179 (mtm) REVERT: T 60 PHE cc_start: 0.8255 (p90) cc_final: 0.7910 (p90) REVERT: V 21 GLU cc_start: 0.7439 (mp0) cc_final: 0.7180 (mm-30) REVERT: W 49 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8477 (mp) REVERT: Z 52 LYS cc_start: 0.8442 (mmmm) cc_final: 0.8183 (mmmt) REVERT: Z 85 GLN cc_start: 0.7817 (tt0) cc_final: 0.7360 (tt0) REVERT: Z 92 GLU cc_start: 0.7204 (OUTLIER) cc_final: 0.6809 (mt-10) REVERT: a 35 GLU cc_start: 0.8573 (mt-10) cc_final: 0.8365 (mt-10) REVERT: b 9 LYS cc_start: 0.8638 (OUTLIER) cc_final: 0.7474 (tmtp) REVERT: b 14 LYS cc_start: 0.8171 (mmtp) cc_final: 0.7862 (mmtt) REVERT: b 58 ASP cc_start: 0.8093 (t0) cc_final: 0.7783 (t0) REVERT: d 103 GLU cc_start: 0.7371 (OUTLIER) cc_final: 0.7032 (mt-10) REVERT: e 8 ARG cc_start: 0.8293 (OUTLIER) cc_final: 0.6674 (tpt170) REVERT: e 53 LYS cc_start: 0.8433 (mttt) cc_final: 0.8097 (pttt) REVERT: e 57 ILE cc_start: 0.8680 (OUTLIER) cc_final: 0.8470 (mp) REVERT: f 52 GLU cc_start: 0.7515 (tt0) cc_final: 0.7148 (tt0) REVERT: g 114 ASP cc_start: 0.8031 (t70) cc_final: 0.7771 (t70) REVERT: g 117 LYS cc_start: 0.8469 (OUTLIER) cc_final: 0.8136 (mmpt) REVERT: j 32 MET cc_start: 0.8779 (ttp) cc_final: 0.8545 (ttp) REVERT: k 13 MET cc_start: 0.7878 (OUTLIER) cc_final: 0.7126 (ttm) REVERT: k 72 TRP cc_start: 0.8226 (m100) cc_final: 0.7995 (m100) REVERT: m 107 ASP cc_start: 0.8490 (t70) cc_final: 0.8215 (t0) REVERT: m 113 LYS cc_start: 0.8147 (ttpp) cc_final: 0.7764 (tttp) REVERT: o 116 GLN cc_start: 0.7415 (OUTLIER) cc_final: 0.6982 (mp10) REVERT: o 117 ARG cc_start: 0.6863 (tmm-80) cc_final: 0.6526 (tmm160) REVERT: p 171 GLU cc_start: 0.6991 (mm-30) cc_final: 0.6493 (pp20) REVERT: q 25 ARG cc_start: 0.8075 (ttm170) cc_final: 0.7748 (ttt180) REVERT: r 108 ASP cc_start: 0.7859 (t0) cc_final: 0.7628 (t0) REVERT: s 59 SER cc_start: 0.8562 (t) cc_final: 0.8299 (p) REVERT: s 63 MET cc_start: 0.8135 (mmm) cc_final: 0.7866 (mmp) outliers start: 70 outliers final: 30 residues processed: 980 average time/residue: 1.7559 time to fit residues: 2174.8009 Evaluate side-chains 970 residues out of total 7119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 925 time to evaluate : 5.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 178 ARG Chi-restraints excluded: chain D residue 37 ASP Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain F residue 77 LEU Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 436 SER Chi-restraints excluded: chain H residue 156 MET Chi-restraints excluded: chain I residue 78 ILE Chi-restraints excluded: chain J residue 2 MET Chi-restraints excluded: chain J residue 173 ARG Chi-restraints excluded: chain L residue 392 LYS Chi-restraints excluded: chain N residue 100 MET Chi-restraints excluded: chain O residue 291 GLN Chi-restraints excluded: chain P residue 52 GLU Chi-restraints excluded: chain R residue 3 ARG Chi-restraints excluded: chain R residue 7 THR Chi-restraints excluded: chain V residue 103 VAL Chi-restraints excluded: chain V residue 109 SER Chi-restraints excluded: chain W residue 49 LEU Chi-restraints excluded: chain W residue 96 VAL Chi-restraints excluded: chain X residue 83 GLU Chi-restraints excluded: chain Y residue 114 CYS Chi-restraints excluded: chain Y residue 119 LEU Chi-restraints excluded: chain Z residue 13 VAL Chi-restraints excluded: chain Z residue 92 GLU Chi-restraints excluded: chain Z residue 96 THR Chi-restraints excluded: chain Z residue 114 THR Chi-restraints excluded: chain a residue 21 MET Chi-restraints excluded: chain b residue 9 LYS Chi-restraints excluded: chain b residue 15 GLU Chi-restraints excluded: chain b residue 31 LEU Chi-restraints excluded: chain d residue 85 VAL Chi-restraints excluded: chain d residue 103 GLU Chi-restraints excluded: chain e residue 8 ARG Chi-restraints excluded: chain e residue 57 ILE Chi-restraints excluded: chain e residue 85 LEU Chi-restraints excluded: chain e residue 92 THR Chi-restraints excluded: chain g residue 107 ILE Chi-restraints excluded: chain g residue 117 LYS Chi-restraints excluded: chain j residue 71 GLU Chi-restraints excluded: chain k residue 13 MET Chi-restraints excluded: chain m residue 25 SER Chi-restraints excluded: chain o residue 116 GLN Chi-restraints excluded: chain p residue 16 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 799 random chunks: chunk 700 optimal weight: 8.9990 chunk 737 optimal weight: 0.9990 chunk 673 optimal weight: 3.9990 chunk 717 optimal weight: 5.9990 chunk 431 optimal weight: 6.9990 chunk 312 optimal weight: 7.9990 chunk 563 optimal weight: 6.9990 chunk 220 optimal weight: 7.9990 chunk 648 optimal weight: 0.4980 chunk 678 optimal weight: 4.9990 chunk 715 optimal weight: 0.8980 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN C 69 ASN ** D 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 74 GLN F 432 GLN G 16 GLN G 461 ASN ** H 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 479 GLN M 139 GLN N 235 ASN N 316 GLN P 296 HIS T 35 HIS V 72 GLN W 70 ASN X 64 GLN c 34 GLN d 12 GLN g 36 ASN j 6 HIS n 61 GLN n 123 GLN p 22 GLN q 52 ASN q 54 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.1574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.244 69002 Z= 0.442 Angle : 1.299 50.506 93371 Z= 0.835 Chirality : 0.256 6.480 10186 Planarity : 0.004 0.053 11642 Dihedral : 10.814 175.763 10638 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.85 % Favored : 98.14 % Rotamer: Outliers : 1.12 % Allowed : 10.44 % Favored : 88.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.67 % 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: 1.66 (0.09), residues: 8052 helix: 1.76 (0.08), residues: 4278 sheet: 0.39 (0.26), residues: 397 loop : 0.48 (0.11), residues: 3377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP X 85 HIS 0.006 0.001 HIS L 332 PHE 0.026 0.002 PHE N 292 TYR 0.020 0.001 TYR L 422 ARG 0.009 0.000 ARG r 17 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16104 Ramachandran restraints generated. 8052 Oldfield, 0 Emsley, 8052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16104 Ramachandran restraints generated. 8052 Oldfield, 0 Emsley, 8052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1003 residues out of total 7119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 923 time to evaluate : 6.105 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 ASP cc_start: 0.7917 (m-30) cc_final: 0.7631 (m-30) REVERT: B 171 LYS cc_start: 0.8583 (mtmm) cc_final: 0.8156 (mttm) REVERT: B 178 ARG cc_start: 0.8280 (OUTLIER) cc_final: 0.7654 (mtt90) REVERT: C 73 LYS cc_start: 0.8951 (mmtt) cc_final: 0.8690 (mptt) REVERT: F 77 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8268 (tp) REVERT: G 475 GLN cc_start: 0.7096 (tp-100) cc_final: 0.6803 (mm110) REVERT: G 613 TYR cc_start: 0.9083 (OUTLIER) cc_final: 0.8235 (p90) REVERT: J 173 ARG cc_start: 0.7855 (OUTLIER) cc_final: 0.7251 (ptp90) REVERT: N 100 MET cc_start: 0.7964 (OUTLIER) cc_final: 0.7174 (mtt) REVERT: O 291 GLN cc_start: 0.8226 (OUTLIER) cc_final: 0.7544 (tm130) REVERT: P 52 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.7334 (tm-30) REVERT: P 268 ARG cc_start: 0.7274 (tpp-160) cc_final: 0.7053 (tpt170) REVERT: P 333 ASP cc_start: 0.7507 (m-30) cc_final: 0.7303 (m-30) REVERT: T 29 LYS cc_start: 0.7479 (mtpp) cc_final: 0.6697 (mmtt) REVERT: T 60 PHE cc_start: 0.8248 (p90) cc_final: 0.7918 (p90) REVERT: W 49 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8504 (mp) REVERT: W 89 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7359 (tp30) REVERT: Z 85 GLN cc_start: 0.7808 (tt0) cc_final: 0.7373 (tt0) REVERT: Z 92 GLU cc_start: 0.7215 (OUTLIER) cc_final: 0.6802 (mt-10) REVERT: b 9 LYS cc_start: 0.8654 (OUTLIER) cc_final: 0.7497 (tmtp) REVERT: b 58 ASP cc_start: 0.8181 (t0) cc_final: 0.7806 (t0) REVERT: d 103 GLU cc_start: 0.7398 (OUTLIER) cc_final: 0.7041 (mt-10) REVERT: e 8 ARG cc_start: 0.8362 (OUTLIER) cc_final: 0.6760 (tpt170) REVERT: e 23 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7574 (tt0) REVERT: e 53 LYS cc_start: 0.8468 (mttt) cc_final: 0.8079 (pttt) REVERT: f 52 GLU cc_start: 0.7534 (tt0) cc_final: 0.7164 (tt0) REVERT: g 114 ASP cc_start: 0.8032 (t70) cc_final: 0.7760 (t70) REVERT: g 117 LYS cc_start: 0.8467 (OUTLIER) cc_final: 0.8144 (mmpt) REVERT: k 13 MET cc_start: 0.7893 (OUTLIER) cc_final: 0.7219 (ttm) REVERT: o 117 ARG cc_start: 0.6898 (tmm-80) cc_final: 0.6537 (tmm160) REVERT: p 171 GLU cc_start: 0.7007 (mm-30) cc_final: 0.6504 (pp20) REVERT: q 25 ARG cc_start: 0.8088 (ttm170) cc_final: 0.7762 (ttt180) REVERT: r 108 ASP cc_start: 0.7916 (t0) cc_final: 0.7684 (t0) outliers start: 80 outliers final: 37 residues processed: 964 average time/residue: 1.7624 time to fit residues: 2142.5336 Evaluate side-chains 965 residues out of total 7119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 912 time to evaluate : 5.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 178 ARG Chi-restraints excluded: chain D residue 37 ASP Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain F residue 77 LEU Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 436 SER Chi-restraints excluded: chain G residue 613 TYR Chi-restraints excluded: chain I residue 78 ILE Chi-restraints excluded: chain J residue 2 MET Chi-restraints excluded: chain J residue 173 ARG Chi-restraints excluded: chain L residue 392 LYS Chi-restraints excluded: chain M residue 144 ASN Chi-restraints excluded: chain M residue 458 LEU Chi-restraints excluded: chain N residue 100 MET Chi-restraints excluded: chain N residue 320 MET Chi-restraints excluded: chain O residue 291 GLN Chi-restraints excluded: chain P residue 52 GLU Chi-restraints excluded: chain R residue 3 ARG Chi-restraints excluded: chain R residue 7 THR Chi-restraints excluded: chain V residue 103 VAL Chi-restraints excluded: chain V residue 109 SER Chi-restraints excluded: chain W residue 49 LEU Chi-restraints excluded: chain W residue 89 GLU Chi-restraints excluded: chain W residue 96 VAL Chi-restraints excluded: chain X residue 83 GLU Chi-restraints excluded: chain X residue 105 GLN Chi-restraints excluded: chain X residue 125 SER Chi-restraints excluded: chain Y residue 114 CYS Chi-restraints excluded: chain Y residue 119 LEU Chi-restraints excluded: chain Z residue 13 VAL Chi-restraints excluded: chain Z residue 92 GLU Chi-restraints excluded: chain Z residue 96 THR Chi-restraints excluded: chain Z residue 114 THR Chi-restraints excluded: chain b residue 9 LYS Chi-restraints excluded: chain b residue 15 GLU Chi-restraints excluded: chain b residue 31 LEU Chi-restraints excluded: chain c residue 11 SER Chi-restraints excluded: chain d residue 20 SER Chi-restraints excluded: chain d residue 85 VAL Chi-restraints excluded: chain d residue 103 GLU Chi-restraints excluded: chain e residue 8 ARG Chi-restraints excluded: chain e residue 23 GLU Chi-restraints excluded: chain e residue 85 LEU Chi-restraints excluded: chain e residue 92 THR Chi-restraints excluded: chain g residue 107 ILE Chi-restraints excluded: chain g residue 117 LYS Chi-restraints excluded: chain j residue 71 GLU Chi-restraints excluded: chain k residue 13 MET Chi-restraints excluded: chain m residue 25 SER Chi-restraints excluded: chain o residue 27 ASP Chi-restraints excluded: chain q residue 122 GLN Chi-restraints excluded: chain s residue 53 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 799 random chunks: chunk 471 optimal weight: 1.9990 chunk 758 optimal weight: 1.9990 chunk 463 optimal weight: 5.9990 chunk 359 optimal weight: 2.9990 chunk 527 optimal weight: 4.9990 chunk 796 optimal weight: 3.9990 chunk 732 optimal weight: 3.9990 chunk 633 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 489 optimal weight: 1.9990 chunk 388 optimal weight: 7.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN C 69 ASN ** D 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 74 GLN F 432 GLN G 16 GLN G 461 ASN ** H 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 479 GLN M 139 GLN N 235 ASN N 316 GLN P 296 HIS V 72 GLN c 34 GLN d 12 GLN d 61 GLN g 36 ASN j 6 HIS j 58 GLN n 61 GLN n 123 GLN p 22 GLN q 52 ASN q 54 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.245 69002 Z= 0.434 Angle : 1.295 50.515 93371 Z= 0.834 Chirality : 0.255 6.458 10186 Planarity : 0.004 0.053 11642 Dihedral : 10.746 175.315 10638 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.75 % Favored : 98.24 % Rotamer: Outliers : 1.05 % Allowed : 10.54 % Favored : 88.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.67 % 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: 1.63 (0.09), residues: 8052 helix: 1.73 (0.08), residues: 4272 sheet: 0.32 (0.26), residues: 392 loop : 0.47 (0.11), residues: 3388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP X 85 HIS 0.005 0.001 HIS L 332 PHE 0.027 0.001 PHE N 292 TYR 0.020 0.001 TYR L 422 ARG 0.009 0.000 ARG r 17 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16104 Ramachandran restraints generated. 8052 Oldfield, 0 Emsley, 8052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16104 Ramachandran restraints generated. 8052 Oldfield, 0 Emsley, 8052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 993 residues out of total 7119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 918 time to evaluate : 6.118 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 ASP cc_start: 0.7902 (m-30) cc_final: 0.7622 (m-30) REVERT: B 178 ARG cc_start: 0.8270 (OUTLIER) cc_final: 0.7637 (mtt90) REVERT: C 73 LYS cc_start: 0.8945 (mmtt) cc_final: 0.8686 (mptt) REVERT: D 164 MET cc_start: 0.7915 (ptt) cc_final: 0.7632 (ptt) REVERT: F 77 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8257 (tp) REVERT: G 475 GLN cc_start: 0.7099 (tp-100) cc_final: 0.6809 (mm110) REVERT: G 613 TYR cc_start: 0.9085 (OUTLIER) cc_final: 0.8243 (p90) REVERT: J 118 GLU cc_start: 0.6369 (OUTLIER) cc_final: 0.5904 (tm-30) REVERT: J 173 ARG cc_start: 0.7842 (OUTLIER) cc_final: 0.7246 (ptp90) REVERT: N 100 MET cc_start: 0.7961 (OUTLIER) cc_final: 0.7179 (mtt) REVERT: O 60 ASP cc_start: 0.8616 (OUTLIER) cc_final: 0.8211 (m-30) REVERT: O 291 GLN cc_start: 0.8208 (OUTLIER) cc_final: 0.7524 (tm130) REVERT: P 52 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.7279 (tm-30) REVERT: P 268 ARG cc_start: 0.7268 (tpp-160) cc_final: 0.7047 (tpt170) REVERT: P 333 ASP cc_start: 0.7492 (m-30) cc_final: 0.7283 (m-30) REVERT: T 29 LYS cc_start: 0.7445 (mtpp) cc_final: 0.6671 (mmtm) REVERT: T 52 MET cc_start: 0.8311 (mtm) cc_final: 0.8096 (mtm) REVERT: T 60 PHE cc_start: 0.8231 (p90) cc_final: 0.7876 (p90) REVERT: W 49 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8493 (mp) REVERT: W 89 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7362 (tp30) REVERT: Z 85 GLN cc_start: 0.7809 (tt0) cc_final: 0.7346 (tt0) REVERT: Z 92 GLU cc_start: 0.7222 (OUTLIER) cc_final: 0.6821 (mt-10) REVERT: Z 98 MET cc_start: 0.7887 (OUTLIER) cc_final: 0.7137 (mpt) REVERT: b 9 LYS cc_start: 0.8660 (OUTLIER) cc_final: 0.7527 (tmtp) REVERT: b 58 ASP cc_start: 0.8157 (t0) cc_final: 0.7808 (t0) REVERT: d 95 LYS cc_start: 0.8463 (ttmm) cc_final: 0.8080 (ttpt) REVERT: d 103 GLU cc_start: 0.7351 (OUTLIER) cc_final: 0.7004 (mt-10) REVERT: e 8 ARG cc_start: 0.8351 (OUTLIER) cc_final: 0.6733 (tpt170) REVERT: e 23 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.7588 (tt0) REVERT: e 53 LYS cc_start: 0.8470 (mttt) cc_final: 0.8089 (pttt) REVERT: f 52 GLU cc_start: 0.7519 (tt0) cc_final: 0.7158 (tt0) REVERT: g 114 ASP cc_start: 0.8035 (t70) cc_final: 0.7766 (t70) REVERT: g 117 LYS cc_start: 0.8450 (OUTLIER) cc_final: 0.8149 (mmpt) REVERT: h 57 GLU cc_start: 0.6599 (OUTLIER) cc_final: 0.6282 (tm-30) REVERT: k 13 MET cc_start: 0.7866 (OUTLIER) cc_final: 0.7166 (ttm) REVERT: m 113 LYS cc_start: 0.8150 (ttpp) cc_final: 0.7756 (tttp) REVERT: n 61 GLN cc_start: 0.8118 (OUTLIER) cc_final: 0.7692 (tm130) REVERT: o 117 ARG cc_start: 0.6962 (tmm-80) cc_final: 0.6601 (tmm160) REVERT: p 171 GLU cc_start: 0.7016 (mm-30) cc_final: 0.6512 (pp20) REVERT: q 25 ARG cc_start: 0.8073 (ttm170) cc_final: 0.7737 (ttt180) REVERT: r 32 LYS cc_start: 0.8715 (OUTLIER) cc_final: 0.8500 (mtpp) REVERT: r 108 ASP cc_start: 0.7933 (t0) cc_final: 0.7705 (t0) outliers start: 75 outliers final: 39 residues processed: 960 average time/residue: 1.8056 time to fit residues: 2183.7209 Evaluate side-chains 966 residues out of total 7119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 905 time to evaluate : 6.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 178 ARG Chi-restraints excluded: chain D residue 37 ASP Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain F residue 77 LEU Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 436 SER Chi-restraints excluded: chain G residue 535 GLN Chi-restraints excluded: chain G residue 613 TYR Chi-restraints excluded: chain H residue 231 ILE Chi-restraints excluded: chain I residue 11 SER Chi-restraints excluded: chain I residue 78 ILE Chi-restraints excluded: chain J residue 2 MET Chi-restraints excluded: chain J residue 118 GLU Chi-restraints excluded: chain J residue 173 ARG Chi-restraints excluded: chain L residue 392 LYS Chi-restraints excluded: chain M residue 144 ASN Chi-restraints excluded: chain M residue 458 LEU Chi-restraints excluded: chain N residue 100 MET Chi-restraints excluded: chain O residue 60 ASP Chi-restraints excluded: chain O residue 291 GLN Chi-restraints excluded: chain P residue 52 GLU Chi-restraints excluded: chain R residue 3 ARG Chi-restraints excluded: chain R residue 7 THR Chi-restraints excluded: chain V residue 103 VAL Chi-restraints excluded: chain V residue 109 SER Chi-restraints excluded: chain W residue 49 LEU Chi-restraints excluded: chain W residue 89 GLU Chi-restraints excluded: chain W residue 96 VAL Chi-restraints excluded: chain X residue 83 GLU Chi-restraints excluded: chain X residue 105 GLN Chi-restraints excluded: chain X residue 125 SER Chi-restraints excluded: chain Y residue 114 CYS Chi-restraints excluded: chain Y residue 119 LEU Chi-restraints excluded: chain Z residue 13 VAL Chi-restraints excluded: chain Z residue 92 GLU Chi-restraints excluded: chain Z residue 96 THR Chi-restraints excluded: chain Z residue 98 MET Chi-restraints excluded: chain Z residue 114 THR Chi-restraints excluded: chain b residue 9 LYS Chi-restraints excluded: chain b residue 15 GLU Chi-restraints excluded: chain b residue 31 LEU Chi-restraints excluded: chain c residue 11 SER Chi-restraints excluded: chain d residue 20 SER Chi-restraints excluded: chain d residue 85 VAL Chi-restraints excluded: chain d residue 103 GLU Chi-restraints excluded: chain e residue 8 ARG Chi-restraints excluded: chain e residue 23 GLU Chi-restraints excluded: chain e residue 85 LEU Chi-restraints excluded: chain e residue 92 THR Chi-restraints excluded: chain g residue 107 ILE Chi-restraints excluded: chain g residue 117 LYS Chi-restraints excluded: chain h residue 57 GLU Chi-restraints excluded: chain j residue 71 GLU Chi-restraints excluded: chain k residue 13 MET Chi-restraints excluded: chain m residue 25 SER Chi-restraints excluded: chain n residue 61 GLN Chi-restraints excluded: chain q residue 122 GLN Chi-restraints excluded: chain r residue 32 LYS Chi-restraints excluded: chain s residue 53 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 799 random chunks: chunk 503 optimal weight: 9.9990 chunk 675 optimal weight: 1.9990 chunk 194 optimal weight: 2.9990 chunk 584 optimal weight: 10.0000 chunk 93 optimal weight: 0.8980 chunk 176 optimal weight: 7.9990 chunk 634 optimal weight: 5.9990 chunk 265 optimal weight: 0.0970 chunk 651 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 116 optimal weight: 5.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN C 69 ASN ** D 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 74 GLN F 432 GLN G 16 GLN G 461 ASN H 248 ASN H 317 GLN L 479 GLN M 139 GLN N 235 ASN N 316 GLN O 229 GLN P 296 HIS V 72 GLN c 34 GLN d 12 GLN d 61 GLN d 117 HIS g 36 ASN j 6 HIS j 58 GLN n 61 GLN n 123 GLN p 22 GLN q 52 ASN q 54 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.094726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.079982 restraints weight = 74102.427| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 1.12 r_work: 0.2939 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.2847 rms_B_bonded: 2.60 restraints_weight: 0.2500 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8844 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.245 69002 Z= 0.435 Angle : 1.321 59.199 93371 Z= 0.849 Chirality : 0.255 6.450 10186 Planarity : 0.004 0.053 11642 Dihedral : 10.745 175.302 10638 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.79 % Favored : 98.20 % Rotamer: Outliers : 1.12 % Allowed : 10.49 % Favored : 88.39 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 3.67 % 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: 1.63 (0.09), residues: 8052 helix: 1.73 (0.08), residues: 4272 sheet: 0.32 (0.26), residues: 392 loop : 0.47 (0.11), residues: 3388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP X 85 HIS 0.005 0.001 HIS L 332 PHE 0.028 0.001 PHE N 292 TYR 0.020 0.001 TYR L 422 ARG 0.008 0.000 ARG r 17 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 30796.28 seconds wall clock time: 533 minutes 46.69 seconds (32026.69 seconds total)