Starting phenix.real_space_refine on Thu Mar 14 21:31:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r4d_14297/03_2024/7r4d_14297_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r4d_14297/03_2024/7r4d_14297.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r4d_14297/03_2024/7r4d_14297_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r4d_14297/03_2024/7r4d_14297_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r4d_14297/03_2024/7r4d_14297_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r4d_14297/03_2024/7r4d_14297.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r4d_14297/03_2024/7r4d_14297.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r4d_14297/03_2024/7r4d_14297_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r4d_14297/03_2024/7r4d_14297_updated.pdb" } resolution = 2.3 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= 0.010 sd= 1.090 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 32 5.49 5 Mg 1 5.21 5 S 465 5.16 5 Cl 1 4.86 5 C 42923 2.51 5 N 10976 2.21 5 O 13575 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 112": "OE1" <-> "OE2" Residue "B ARG 71": "NH1" <-> "NH2" Residue "B GLU 109": "OE1" <-> "OE2" 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 GLU 31": "OE1" <-> "OE2" Residue "C PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 147": "OD1" <-> "OD2" Residue "C ARG 149": "NH1" <-> "NH2" Residue "C GLU 173": "OE1" <-> "OE2" Residue "C GLU 179": "OE1" <-> "OE2" Residue "C GLU 186": "OE1" <-> "OE2" Residue "C ASP 198": "OD1" <-> "OD2" Residue "D ARG 2": "NH1" <-> "NH2" Residue "D PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 71": "OE1" <-> "OE2" Residue "D TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 123": "OE1" <-> "OE2" Residue "D PHE 171": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 ARG 233": "NH1" <-> "NH2" Residue "D GLU 248": "OE1" <-> "OE2" Residue "D GLU 303": "OE1" <-> "OE2" Residue "D GLU 343": "OE1" <-> "OE2" Residue "D ASP 422": "OD1" <-> "OD2" Residue "D GLU 427": "OE1" <-> "OE2" Residue "E ASP 11": "OD1" <-> "OD2" Residue "E GLU 14": "OE1" <-> "OE2" Residue "E GLU 18": "OE1" <-> "OE2" Residue "E GLU 26": "OE1" <-> "OE2" Residue "E ASP 134": "OD1" <-> "OD2" Residue "E ASP 158": "OD1" <-> "OD2" Residue "E TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 163": "OD1" <-> "OD2" Residue "E ASP 168": "OD1" <-> "OD2" Residue "E GLU 171": "OE1" <-> "OE2" Residue "E ASP 174": "OD1" <-> "OD2" Residue "E ARG 190": "NH1" <-> "NH2" Residue "E GLU 204": "OE1" <-> "OE2" Residue "F PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 18": "OE1" <-> "OE2" Residue "F ARG 32": "NH1" <-> "NH2" Residue "F ASP 87": "OD1" <-> "OD2" Residue "F GLU 109": "OE1" <-> "OE2" Residue "F ARG 112": "NH1" <-> "NH2" Residue "F ARG 132": "NH1" <-> "NH2" Residue "F TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 139": "NH1" <-> "NH2" Residue "F GLU 155": "OE1" <-> "OE2" Residue "F GLU 158": "OE1" <-> "OE2" Residue "F GLU 189": "OE1" <-> "OE2" Residue "F GLU 226": "OE1" <-> "OE2" Residue "F ARG 249": "NH1" <-> "NH2" Residue "F PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 269": "OE1" <-> "OE2" Residue "F GLU 270": "OE1" <-> "OE2" Residue "F GLU 278": "OE1" <-> "OE2" Residue "F GLU 281": "OE1" <-> "OE2" Residue "F ASP 318": "OD1" <-> "OD2" Residue "F ARG 349": "NH1" <-> "NH2" Residue "F GLU 352": "OE1" <-> "OE2" Residue "F GLU 367": "OE1" <-> "OE2" Residue "F ASP 370": "OD1" <-> "OD2" Residue "F GLU 394": "OE1" <-> "OE2" Residue "F PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 427": "OE1" <-> "OE2" Residue "F ARG 429": "NH1" <-> "NH2" Residue "G PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 14": "OD1" <-> "OD2" Residue "G GLU 31": "OE1" <-> "OE2" Residue "G ARG 39": "NH1" <-> "NH2" Residue "G ARG 53": "NH1" <-> "NH2" Residue "G GLU 58": "OE1" <-> "OE2" Residue "G GLU 60": "OE1" <-> "OE2" Residue "G GLU 84": "OE1" <-> "OE2" Residue "G GLU 165": "OE1" <-> "OE2" Residue "G ARG 218": "NH1" <-> "NH2" Residue "G ASP 232": "OD1" <-> "OD2" Residue "G ARG 243": "NH1" <-> "NH2" Residue "G ARG 253": "NH1" <-> "NH2" Residue "G GLU 261": "OE1" <-> "OE2" Residue "G ARG 285": "NH1" <-> "NH2" Residue "G ARG 302": "NH1" <-> "NH2" Residue "G ASP 339": "OD1" <-> "OD2" Residue "G ASP 341": "OD1" <-> "OD2" Residue "G GLU 347": "OE1" <-> "OE2" Residue "G GLU 372": "OE1" <-> "OE2" Residue "G GLU 373": "OE1" <-> "OE2" Residue "G ARG 385": "NH1" <-> "NH2" Residue "G ARG 418": "NH1" <-> "NH2" Residue "G GLU 445": "OE1" <-> "OE2" Residue "G PHE 523": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 536": "OD1" <-> "OD2" Residue "G ASP 540": "OD1" <-> "OD2" Residue "G GLU 625": "OE1" <-> "OE2" Residue "G GLU 637": "OE1" <-> "OE2" Residue "G ASP 659": "OD1" <-> "OD2" Residue "H GLU 24": "OE1" <-> "OE2" Residue "H ARG 25": "NH1" <-> "NH2" Residue "H ARG 34": "NH1" <-> "NH2" Residue "H TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 62": "NH1" <-> "NH2" Residue "H GLU 192": "OE1" <-> "OE2" Residue "H GLU 202": "OE1" <-> "OE2" Residue "H GLU 204": "OE1" <-> "OE2" Residue "H PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 253": "OE1" <-> "OE2" Residue "I ARG 8": "NH1" <-> "NH2" Residue "I ASP 13": "OD1" <-> "OD2" Residue "I GLU 74": "OE1" <-> "OE2" Residue "I ARG 108": "NH1" <-> "NH2" Residue "I ASP 129": "OD1" <-> "OD2" Residue "I GLU 146": "OE1" <-> "OE2" Residue "J TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 100": "OE1" <-> "OE2" Residue "J ASP 110": "OD1" <-> "OD2" Residue "J ASP 129": "OD1" <-> "OD2" Residue "J ASP 132": "OD1" <-> "OD2" Residue "J PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 170": "OE1" <-> "OE2" Residue "J ARG 173": "NH1" <-> "NH2" Residue "K TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 145": "OE1" <-> "OE2" Residue "L ARG 161": "NH1" <-> "NH2" 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 ASP 352": "OD1" <-> "OD2" Residue "L GLU 353": "OE1" <-> "OE2" Residue "L PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 466": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 503": "OE1" <-> "OE2" Residue "L TYR 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 588": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 606": "OE1" <-> "OE2" Residue "M GLU 87": "OE1" <-> "OE2" Residue "M PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 123": "OE1" <-> "OE2" Residue "M GLU 141": "OE1" <-> "OE2" Residue "M ARG 142": "NH1" <-> "NH2" Residue "M TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 255": "OD1" <-> "OD2" Residue "M PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 346": "NH1" <-> "NH2" Residue "M TYR 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 432": "NH1" <-> "NH2" Residue "M TYR 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 54": "OE1" <-> "OE2" Residue "N PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 117": "OE1" <-> "OE2" Residue "N ARG 295": "NH1" <-> "NH2" Residue "O ARG 104": "NH1" <-> "NH2" Residue "O ASP 110": "OD1" <-> "OD2" Residue "O GLU 113": "OE1" <-> "OE2" Residue "O ARG 126": "NH1" <-> "NH2" Residue "O TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 131": "OD1" <-> "OD2" Residue "O PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 136": "OE1" <-> "OE2" Residue "O ASP 150": "OD1" <-> "OD2" Residue "O GLU 162": "OE1" <-> "OE2" Residue "O GLU 203": "OE1" <-> "OE2" Residue "O GLU 216": "OE1" <-> "OE2" Residue "O GLU 219": "OE1" <-> "OE2" Residue "O GLU 236": "OE1" <-> "OE2" Residue "O ASP 237": "OD1" <-> "OD2" Residue "O ASP 253": "OD1" <-> "OD2" Residue "O PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 302": "NH1" <-> "NH2" Residue "O ARG 305": "NH1" <-> "NH2" Residue "P ARG 40": "NH1" <-> "NH2" Residue "P ARG 50": "NH1" <-> "NH2" Residue "P GLU 52": "OE1" <-> "OE2" Residue "P ASP 79": "OD1" <-> "OD2" Residue "P ARG 82": "NH1" <-> "NH2" Residue "P GLU 86": "OE1" <-> "OE2" Residue "P ARG 97": "NH1" <-> "NH2" Residue "P TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 147": "NH1" <-> "NH2" Residue "P GLU 155": "OE1" <-> "OE2" Residue "P ARG 157": "NH1" <-> "NH2" Residue "P GLU 158": "OE1" <-> "OE2" Residue "P GLU 162": "OE1" <-> "OE2" Residue "P PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 175": "OE1" <-> "OE2" Residue "P ARG 235": "NH1" <-> "NH2" Residue "P PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 251": "NH1" <-> "NH2" Residue "P ASP 282": "OD1" <-> "OD2" Residue "P ASP 302": "OD1" <-> "OD2" Residue "P GLU 306": "OE1" <-> "OE2" Residue "Q GLU 27": "OE1" <-> "OE2" Residue "Q GLU 58": "OE1" <-> "OE2" Residue "Q GLU 66": "OE1" <-> "OE2" Residue "Q GLU 97": "OE1" <-> "OE2" Residue "Q ASP 104": "OD1" <-> "OD2" Residue "Q GLU 106": "OE1" <-> "OE2" Residue "R ASP 19": "OD1" <-> "OD2" Residue "R TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 31": "NH1" <-> "NH2" Residue "S GLU 17": "OE1" <-> "OE2" Residue "S ASP 34": "OD1" <-> "OD2" Residue "S PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 13": "OD1" <-> "OD2" Residue "T TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 23": "OD1" <-> "OD2" Residue "T ASP 26": "OD1" <-> "OD2" Residue "T GLU 55": "OE1" <-> "OE2" Residue "U TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 49": "OE1" <-> "OE2" Residue "U GLU 55": "OE1" <-> "OE2" Residue "U GLU 68": "OE1" <-> "OE2" Residue "U GLU 75": "OE1" <-> "OE2" Residue "U GLU 88": "OE1" <-> "OE2" Residue "V ARG 22": "NH1" <-> "NH2" Residue "V GLU 68": "OE1" <-> "OE2" Residue "V GLU 78": "OE1" <-> "OE2" Residue "V GLU 86": "OE1" <-> "OE2" Residue "V GLU 100": "OE1" <-> "OE2" Residue "V GLU 105": "OE1" <-> "OE2" Residue "W ARG 30": "NH1" <-> "NH2" Residue "W TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 53": "OD1" <-> "OD2" Residue "W ASP 61": "OD1" <-> "OD2" Residue "W GLU 91": "OE1" <-> "OE2" Residue "W PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 109": "OE1" <-> "OE2" Residue "X GLU 5": "OE1" <-> "OE2" Residue "X ASP 11": "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 GLU 57": "OE1" <-> "OE2" Residue "X ARG 97": "NH1" <-> "NH2" Residue "X ARG 118": "NH1" <-> "NH2" Residue "X ASP 120": "OD1" <-> "OD2" 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 "X ASP 156": "OD1" <-> "OD2" Residue "Y TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 57": "NH1" <-> "NH2" Residue "Y ASP 84": "OD1" <-> "OD2" Residue "Y ARG 103": "NH1" <-> "NH2" Residue "Y TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 82": "NH1" <-> "NH2" Residue "Z GLU 89": "OE1" <-> "OE2" Residue "Z GLU 93": "OE1" <-> "OE2" Residue "Z GLU 123": "OE1" <-> "OE2" Residue "Z GLU 132": "OE1" <-> "OE2" Residue "a GLU 35": "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 ARG 3": "NH1" <-> "NH2" Residue "b ARG 57": "NH1" <-> "NH2" Residue "b ASP 64": "OD1" <-> "OD2" Residue "c GLU 6": "OE1" <-> "OE2" Residue "c PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 44": "NH1" <-> "NH2" Residue "d PHE 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 51": "NH1" <-> "NH2" Residue "d ARG 86": "NH1" <-> "NH2" Residue "d GLU 114": "OE1" <-> "OE2" Residue "e ASP 4": "OD1" <-> "OD2" Residue "e ARG 8": "NH1" <-> "NH2" Residue "e GLU 36": "OE1" <-> "OE2" Residue "e GLU 38": "OE1" <-> "OE2" Residue "e ARG 50": "NH1" <-> "NH2" Residue "f ARG 28": "NH1" <-> "NH2" Residue "f ASP 31": "OD1" <-> "OD2" Residue "f GLU 32": "OE1" <-> "OE2" Residue "f ARG 46": "NH1" <-> "NH2" Residue "f GLU 47": "OE1" <-> "OE2" Residue "f GLU 52": "OE1" <-> "OE2" Residue "f GLU 53": "OE1" <-> "OE2" Residue "g ASP 50": "OD1" <-> "OD2" Residue "g GLU 94": "OE1" <-> "OE2" Residue "g TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 122": "OE1" <-> "OE2" Residue "h PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ARG 20": "NH1" <-> "NH2" Residue "h GLU 49": "OE1" <-> "OE2" Residue "h GLU 51": "OE1" <-> "OE2" Residue "h GLU 65": "OE1" <-> "OE2" Residue "h ARG 77": "NH1" <-> "NH2" Residue "h ASP 81": "OD1" <-> "OD2" Residue "h GLU 84": "OE1" <-> "OE2" Residue "h GLU 99": "OE1" <-> "OE2" Residue "h GLU 102": "OE1" <-> "OE2" Residue "h ARG 112": "NH1" <-> "NH2" Residue "h ASP 129": "OD1" <-> "OD2" 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 114": "OE1" <-> "OE2" Residue "i ASP 124": "OD1" <-> "OD2" Residue "j PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ASP 43": "OD1" <-> "OD2" Residue "j GLU 63": "OE1" <-> "OE2" Residue "j ASP 70": "OD1" <-> "OD2" Residue "k TYR 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k GLU 24": "OE1" <-> "OE2" Residue "k GLU 29": "OE1" <-> "OE2" Residue "k GLU 33": "OE1" <-> "OE2" Residue "k ARG 38": "NH1" <-> "NH2" Residue "k ARG 41": "NH1" <-> "NH2" Residue "k ASP 42": "OD1" <-> "OD2" Residue "k TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l GLU 18": "OE1" <-> "OE2" Residue "l ARG 30": "NH1" <-> "NH2" Residue "l GLU 57": "OE1" <-> "OE2" Residue "l ASP 63": "OD1" <-> "OD2" Residue "l GLU 120": "OE1" <-> "OE2" Residue "l GLU 141": "OE1" <-> "OE2" Residue "l ARG 142": "NH1" <-> "NH2" Residue "l TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l GLU 157": "OE1" <-> "OE2" Residue "m ASP 18": "OD1" <-> "OD2" Residue "m ASP 23": "OD1" <-> "OD2" Residue "m ARG 29": "NH1" <-> "NH2" Residue "m GLU 34": "OE1" <-> "OE2" Residue "m ARG 39": "NH1" <-> "NH2" Residue "m GLU 45": "OE1" <-> "OE2" Residue "m ARG 55": "NH1" <-> "NH2" Residue "m ARG 71": "NH1" <-> "NH2" Residue "m ASP 107": "OD1" <-> "OD2" Residue "m GLU 112": "OE1" <-> "OE2" Residue "m GLU 117": "OE1" <-> "OE2" Residue "n ARG 21": "NH1" <-> "NH2" Residue "n ARG 37": "NH1" <-> "NH2" Residue "n ASP 48": "OD1" <-> "OD2" Residue "n ARG 64": "NH1" <-> "NH2" Residue "n GLU 67": "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 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n GLU 122": "OE1" <-> "OE2" Residue "n GLU 130": "OE1" <-> "OE2" Residue "n ARG 149": "NH1" <-> "NH2" Residue "o ARG 6": "NH1" <-> "NH2" Residue "o ASP 17": "OD1" <-> "OD2" Residue "o GLU 35": "OE1" <-> "OE2" Residue "o ARG 36": "NH1" <-> "NH2" Residue "o GLU 37": "OE1" <-> "OE2" Residue "o GLU 44": "OE1" <-> "OE2" Residue "o ASP 93": "OD1" <-> "OD2" 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 ASP 120": "OD1" <-> "OD2" Residue "p TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p ASP 41": "OD1" <-> "OD2" Residue "p GLU 52": "OE1" <-> "OE2" Residue "p ASP 72": "OD1" <-> "OD2" Residue "p GLU 78": "OE1" <-> "OE2" Residue "p GLU 100": "OE1" <-> "OE2" Residue "p GLU 116": "OE1" <-> "OE2" Residue "p GLU 127": "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 PHE 28": "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 78": "OD1" <-> "OD2" Residue "q GLU 85": "OE1" <-> "OE2" Residue "q ARG 88": "NH1" <-> "NH2" Residue "q ASP 95": "OD1" <-> "OD2" Residue "q PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q GLU 136": "OE1" <-> "OE2" Residue "r ARG 59": "NH1" <-> "NH2" Residue "r GLU 109": "OE1" <-> "OE2" Residue "s ASP 34": "OD1" <-> "OD2" Time to flip residues: 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 68004 Number of models: 1 Model: "" Number of chains: 115 Chain: "A" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 799 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain breaks: 1 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: 1230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1230 Classifications: {'peptide': 154} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 143} Chain: "C" Number of atoms: 1714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1714 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 16, 'TRANS': 189} Chain: "D" Number of atoms: 3362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 3362 Classifications: {'peptide': 416} Link IDs: {'PTRANS': 26, 'TRANS': 389} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'2MR:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "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: 3301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3301 Classifications: {'peptide': 429} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 407} 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: 2440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2440 Classifications: {'peptide': 309} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 286} Chain breaks: 1 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: 730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 730 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 1, 'TRANS': 94} 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: 4695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 592, 4695 Classifications: {'peptide': 592} Link IDs: {'PTRANS': 27, 'TRANS': 564} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "M" Number of atoms: 3654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3654 Classifications: {'peptide': 459} Link IDs: {'PCIS': 3, 'PTRANS': 17, 'TRANS': 438} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "N" Number of atoms: 2733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2733 Classifications: {'peptide': 347} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 325} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "O" Number of atoms: 2589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2589 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 15, 'TRANS': 304} Chain: "P" Number of atoms: 2305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2305 Classifications: {'peptide': 290} Link IDs: {'PTRANS': 15, 'TRANS': 274} Chain breaks: 3 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: 720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 720 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 3, 'TRANS': 90} Chain: "S" Number of atoms: 669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 669 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 4, 'TRANS': 78} 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: 681 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 681 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 3, '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: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1152 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 7, 'TRANS': 133} Chain: "a" Number of atoms: 561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 561 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 3, 'TRANS': 65} 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: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 444 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 2, 'TRANS': 48} Chain: "g" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 813 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 8, 'TRANS': 88} 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: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 884 Classifications: {'peptide': 103} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 90} 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: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 638 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} 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: 908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 908 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain breaks: 1 Chain: "n" Number of atoms: 1487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1487 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 15, 'TRANS': 155} Chain: "o" Number of atoms: 1043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 1043 Classifications: {'peptide': 121} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 113} 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: 364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 364 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 3, 'TRANS': 39} Chain: "A" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 77 Unusual residues: {'3PE': 1, 'LMT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 43 Unusual residues: {'PC1': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 19 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: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 120 Unusual residues: {'3PE': 2, 'LMT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'3PE:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "I" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'SF4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" 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: 233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 233 Unusual residues: {'3PE': 2, 'CDL': 1, 'LMT': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 39 Chain: "M" Number of atoms: 135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 135 Unusual residues: {'3PE': 1, 'LMT': 1, 'PC1': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "N" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 93 Unusual residues: {'3PE': 1, 'I49': 1, 'LMT': 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: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 80 Unusual residues: {' MG': 1, '3PE': 1, 'GTP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "P" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NDP': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'EHZ': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 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: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 68 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 32 Chain: "Y" Number of atoms: 139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 139 Unusual residues: {'3PE': 3, 'LMT': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 49 Chain: "d" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 65 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 35 Chain: "f" 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: 137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 137 Unusual residues: {'CDL': 1, 'LMT': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 33 Chain: "j" 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: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'MYR': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MYR:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "r" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 76 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 24 Chain: "A" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "B" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 58 Classifications: {'water': 58} Link IDs: {None: 57} Chain: "C" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 102 Classifications: {'water': 102} Link IDs: {None: 101} Chain: "D" Number of atoms: 157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 157 Classifications: {'water': 157} Link IDs: {None: 156} Chain: "E" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 29 Classifications: {'water': 29} Link IDs: {None: 28} Chain: "F" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 70 Classifications: {'water': 70} Link IDs: {None: 69} Chain: "G" Number of atoms: 227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 227 Classifications: {'water': 227} Link IDs: {None: 226} Chain: "H" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 46 Classifications: {'water': 46} Link IDs: {None: 45} Chain: "I" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 104 Classifications: {'water': 104} Link IDs: {None: 103} 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: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "L" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 65 Classifications: {'water': 65} Link IDs: {None: 64} Chain: "M" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 71 Classifications: {'water': 71} Link IDs: {None: 70} Chain: "N" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 46 Classifications: {'water': 46} Link IDs: {None: 45} Chain: "O" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "P" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 47 Classifications: {'water': 47} Link IDs: {None: 46} Chain: "Q" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 74 Classifications: {'water': 74} Link IDs: {None: 73} Chain: "R" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 47 Classifications: {'water': 47} Link IDs: {None: 46} Chain: "S" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "U" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 23 Classifications: {'water': 23} Link IDs: {None: 22} Chain: "V" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "W" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 28 Classifications: {'water': 28} Link IDs: {None: 27} 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: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 21 Classifications: {'water': 21} Link IDs: {None: 20} Chain: "a" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Chain: "b" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "c" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} 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: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "f" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "g" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "h" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 29 Classifications: {'water': 29} Link IDs: {None: 28} Chain: "i" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "j" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "k" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "l" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 30 Classifications: {'water': 30} Link IDs: {None: 29} Chain: "m" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "n" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 31 Classifications: {'water': 31} Link IDs: {None: 30} Chain: "o" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "p" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 37 Classifications: {'water': 37} Link IDs: {None: 36} Chain: "q" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 40 Classifications: {'water': 40} Link IDs: {None: 39} Chain: "r" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "s" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1535 SG CYS B 119 96.337 93.764 206.378 1.00 15.36 S ATOM 1765 SG CYS B 149 93.984 91.375 211.127 1.00 14.31 S ATOM 1031 SG CYS B 54 90.611 90.210 205.657 1.00 16.79 S ATOM 1037 SG CYS B 55 90.510 96.093 208.335 1.00 16.51 S ATOM 7909 SG CYS E 103 112.741 45.352 262.696 1.00 25.71 S ATOM 7943 SG CYS E 108 110.834 42.791 264.622 1.00 26.18 S ATOM 8223 SG CYS E 144 114.722 41.862 259.294 1.00 24.33 S ATOM 8246 SG CYS E 148 113.374 39.191 260.415 1.00 27.01 S ATOM 11455 SG CYS F 362 117.735 51.517 238.902 1.00 16.31 S ATOM 11475 SG CYS F 365 114.858 51.063 243.726 1.00 17.51 S ATOM 11799 SG CYS F 405 119.383 46.463 242.925 1.00 18.42 S ATOM 11436 SG CYS F 359 121.403 52.323 244.281 1.00 18.63 S ATOM 12887 SG CYS G 114 114.851 70.092 229.398 1.00 15.10 S ATOM 12826 SG CYS G 105 108.985 72.682 231.114 1.00 14.36 S ATOM 12847 SG CYS G 108 114.666 75.070 233.250 1.00 14.77 S ATOM 13219 SG CYS G 156 123.019 63.776 234.321 1.00 15.63 S ATOM 13196 SG CYS G 153 120.316 66.184 239.963 1.00 15.49 S ATOM 13243 SG CYS G 159 126.499 66.993 238.437 1.00 17.39 S ATOM 13573 SG CYS G 203 121.983 69.842 234.651 1.00 16.20 S ATOM 12332 SG CYS G 41 123.199 56.979 232.240 1.00 15.51 S ATOM 12418 SG CYS G 52 119.387 57.470 231.119 1.00 15.58 S ATOM 12443 SG CYS G 55 120.746 53.022 227.876 1.00 16.42 S ATOM 12544 SG CYS G 69 124.024 53.487 229.140 1.00 16.48 S ATOM 20734 SG CYS I 119 96.870 85.527 217.223 1.00 13.67 S ATOM 20708 SG CYS I 116 97.399 92.123 217.934 1.00 13.63 S ATOM 20755 SG CYS I 122 98.566 87.746 222.845 1.00 13.45 S ATOM 20482 SG CYS I 87 102.595 88.220 217.508 1.00 13.00 S ATOM 20784 SG CYS I 126 101.033 84.508 230.259 1.00 14.21 S ATOM 20413 SG CYS I 77 106.042 88.621 231.208 1.00 15.02 S ATOM 20455 SG CYS I 83 104.347 86.951 225.212 1.00 13.86 S ATOM 20432 SG CYS I 80 106.384 82.225 228.807 1.00 14.42 S ATOM 40712 SG CYS R 59 102.491 80.219 245.428 1.00 18.57 S ATOM 40890 SG CYS R 84 105.660 80.703 243.360 1.00 18.76 S ATOM 40912 SG CYS R 87 103.402 83.435 244.142 1.00 17.79 S Time building chain proxies: 27.41, per 1000 atoms: 0.40 Number of scatterers: 68004 At special positions: 0 Unit cell: (184.943, 201.025, 295.324, 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 465 16.00 P 32 15.00 Mg 1 11.99 O 13575 8.00 N 10976 7.00 C 42923 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS X 45 " - pdb=" SG CYS X 55 " distance=2.04 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 o 68 " - pdb=" SG CYS o 79 " distance=2.04 Simple disulfide: pdb=" SG CYS p 112 " - pdb=" SG CYS p 124 " distance=2.04 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=5, symmetry=0 Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 22.26 Conformation dependent library (CDL) restraints added in 9.3 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E 301 " pdb="FE1 FES E 301 " - pdb=" SG CYS E 103 " pdb="FE2 FES E 301 " - pdb=" SG CYS E 144 " pdb="FE2 FES E 301 " - pdb=" SG CYS E 148 " pdb="FE1 FES E 301 " - pdb=" SG CYS E 108 " pdb=" FES G 803 " pdb="FE1 FES G 803 " - pdb=" SG CYS G 52 " pdb="FE2 FES G 803 " - pdb=" SG CYS G 69 " pdb="FE2 FES G 803 " - pdb=" SG CYS G 55 " pdb="FE1 FES G 803 " - pdb=" SG CYS G 41 " pdb=" SF4 B 201 " pdb="FE2 SF4 B 201 " - pdb=" SG CYS B 149 " pdb="FE1 SF4 B 201 " - pdb=" SG CYS B 119 " pdb="FE4 SF4 B 201 " - pdb=" SG CYS B 55 " pdb="FE3 SF4 B 201 " - pdb=" SG CYS B 54 " pdb=" SF4 F 502 " pdb="FE4 SF4 F 502 " - pdb=" SG CYS F 359 " pdb="FE3 SF4 F 502 " - pdb=" SG CYS F 405 " pdb="FE2 SF4 F 502 " - pdb=" SG CYS F 365 " 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="FE2 SF4 G 801 " - pdb=" SG CYS G 105 " pdb="FE1 SF4 G 801 " - pdb=" SG CYS G 114 " pdb="FE4 SF4 G 801 " - pdb=" SG CYS G 108 " pdb=" SF4 G 802 " pdb="FE2 SF4 G 802 " - pdb=" SG CYS G 153 " pdb="FE3 SF4 G 802 " - pdb=" SG CYS G 159 " pdb="FE4 SF4 G 802 " - pdb=" SG CYS G 203 " pdb="FE1 SF4 G 802 " - pdb=" SG CYS G 156 " pdb=" SF4 I 201 " pdb="FE2 SF4 I 201 " - pdb=" SG CYS I 116 " pdb="FE4 SF4 I 201 " - pdb=" SG CYS I 87 " pdb="FE1 SF4 I 201 " - pdb=" SG CYS I 119 " pdb="FE3 SF4 I 201 " - pdb=" SG CYS I 122 " pdb=" SF4 I 202 " pdb="FE2 SF4 I 202 " - pdb=" SG CYS I 77 " pdb="FE1 SF4 I 202 " - pdb=" SG CYS I 126 " pdb="FE4 SF4 I 202 " - pdb=" SG CYS I 80 " pdb="FE3 SF4 I 202 " - pdb=" SG CYS I 83 " 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 15862 Ramachandran restraints generated. 7931 Oldfield, 0 Emsley, 7931 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15140 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 354 helices and 29 sheets defined 54.5% alpha, 4.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.64 Creating SS restraints... Processing helix chain 'A' and resid 3 through 22 Processing helix chain 'A' and resid 53 through 80 removed outlier: 3.512A pdb=" N LEU A 71 " --> pdb=" O LEU A 67 " (cutoff:3.500A) Proline residue: A 74 - end of helix removed outlier: 5.447A pdb=" N TRP A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 4.436A 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 28 through 42 Processing helix chain 'B' and resid 54 through 63 removed outlier: 3.847A pdb=" N GLU B 58 " --> pdb=" O CYS B 54 " (cutoff:3.500A) 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 106 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: 4.771A pdb=" N ILE C 58 " --> pdb=" O ASP C 55 " (cutoff:3.500A) Proline residue: C 59 - end of helix Processing helix chain 'C' and resid 125 through 138 removed outlier: 3.895A pdb=" N TRP C 129 " --> pdb=" O ALA C 126 " (cutoff:3.500A) removed outlier: 3.838A 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: 3.874A pdb=" N GLN D 13 " --> pdb=" O GLU D 9 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N TYR D 14 " --> pdb=" O TRP D 10 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 93 removed outlier: 3.814A pdb=" N GLU D 92 " --> pdb=" O GLU D 88 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N TYR D 93 " --> pdb=" O LYS D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 105 Proline residue: D 101 - end of helix removed outlier: 3.905A pdb=" N ASP D 104 " --> pdb=" O LEU D 100 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ARG D 105 " --> pdb=" O PRO D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 126 Processing helix chain 'D' and resid 132 through 161 removed outlier: 3.725A pdb=" N ILE D 161 " --> pdb=" O HIS D 157 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 185 removed outlier: 3.744A pdb=" N GLU D 173 " --> pdb=" O TRP D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 229 removed outlier: 4.013A pdb=" N ASN D 217 " --> pdb=" O GLU D 213 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N SER D 219 " --> pdb=" O SER D 215 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N LEU D 220 " --> pdb=" O LYS D 216 " (cutoff:3.500A) removed outlier: 3.565A 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: 4.847A 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 316 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 406 removed outlier: 3.563A pdb=" N LEU D 402 " --> pdb=" O HIS D 398 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N ASP D 403 " --> pdb=" O LEU D 399 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N LYS D 404 " --> pdb=" O ALA D 400 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 421 removed outlier: 3.906A pdb=" N VAL D 415 " --> pdb=" O LEU D 411 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA D 416 " --> pdb=" O ALA D 412 " (cutoff:3.500A) Processing helix chain 'D' and resid 425 through 429 Processing helix chain 'E' and resid 25 through 37 removed outlier: 3.551A pdb=" N ASN E 37 " --> pdb=" O ALA E 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 58 removed outlier: 4.597A pdb=" N LEU E 48 " --> pdb=" O ALA E 45 " (cutoff:3.500A) Proline residue: E 49 - end of helix removed outlier: 3.616A pdb=" N GLN E 57 " --> pdb=" O ALA E 54 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 73 Processing helix chain 'E' and resid 77 through 86 Processing helix chain 'E' and resid 106 through 110 Processing helix chain 'E' and resid 113 through 124 Processing helix chain 'E' and resid 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 39 Processing helix chain 'F' and resid 45 through 51 Processing helix chain 'F' and resid 53 through 63 Processing helix chain 'F' and resid 75 through 82 removed outlier: 3.630A pdb=" N PHE F 81 " --> pdb=" O LEU F 77 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N MET F 82 " --> pdb=" O LYS F 78 " (cutoff:3.500A) Processing helix chain 'F' and resid 106 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 229 Processing helix chain 'F' and resid 231 through 237 Processing helix chain 'F' and resid 239 through 244 Processing helix chain 'F' and resid 276 through 283 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 312 No H-bonds generated for 'chain 'F' and resid 309 through 312' 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: 4.290A pdb=" N ASP F 370 " --> pdb=" O ARG F 366 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG F 381 " --> pdb=" O ALA F 377 " (cutoff:3.500A) Processing helix chain 'F' and resid 386 through 399 removed outlier: 3.557A pdb=" N ASP F 390 " --> pdb=" O ALA F 387 " (cutoff:3.500A) Processing helix chain 'F' and resid 406 through 435 Proline residue: F 414 - end of helix removed outlier: 3.705A 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: 3.969A 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 105 through 107 No H-bonds generated for 'chain 'G' and resid 105 through 107' 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: 3.576A 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: 5.093A pdb=" N TYR G 271 " --> pdb=" O THR G 267 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ASP G 272 " --> pdb=" O ARG G 268 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N GLY G 273 " --> pdb=" O PHE G 269 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N LEU G 274 " --> pdb=" O ALA G 270 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N LYS G 275 " --> pdb=" O TYR G 271 " (cutoff:3.500A) Processing helix chain 'G' and resid 296 through 309 Processing helix chain 'G' and resid 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: 3.667A 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 480 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 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 692 Processing helix chain 'H' and resid 3 through 32 Proline residue: H 12 - end of helix removed outlier: 3.777A 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 56 Processing helix chain 'H' and resid 68 through 86 removed outlier: 3.524A pdb=" N ALA H 74 " --> pdb=" O MET H 70 " (cutoff:3.500A) Proline residue: H 75 - end of helix removed outlier: 4.163A pdb=" N TRP H 86 " --> pdb=" O ALA H 82 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 123 removed outlier: 3.709A pdb=" N LEU H 111 " --> pdb=" O ALA H 107 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA H 112 " --> pdb=" O MET H 108 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N VAL H 113 " --> pdb=" O SER H 109 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N TYR H 114 " --> pdb=" O SER H 110 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N SER H 115 " --> pdb=" O LEU H 111 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ILE H 116 " --> pdb=" O ALA H 112 " (cutoff:3.500A) Processing helix chain 'H' and resid 126 through 157 removed outlier: 3.909A pdb=" N THR H 145 " --> pdb=" O SER H 141 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N MET H 156 " --> pdb=" O SER H 152 " (cutoff:3.500A) Processing helix chain 'H' and resid 162 through 168 removed outlier: 3.939A pdb=" N ILE H 166 " --> pdb=" O LEU H 162 " (cutoff:3.500A) removed outlier: 3.579A 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 200 through 206 Processing helix chain 'H' and resid 218 through 242 Processing helix chain 'H' and resid 252 through 274 Processing helix chain 'H' and resid 282 through 290 Processing helix chain 'H' and resid 293 through 311 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 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: 5.791A pdb=" N ALA I 163 " --> pdb=" O ASP I 159 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N GLU I 164 " --> pdb=" O LYS I 160 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA I 167 " --> pdb=" O ALA I 163 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N LEU I 174 " --> pdb=" O GLN I 170 " (cutoff:3.500A) removed outlier: 5.875A 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: 3.778A pdb=" N PHE J 47 " --> pdb=" O ILE J 43 " (cutoff:3.500A) Processing helix chain 'J' and resid 50 through 58 Processing helix chain 'J' and resid 64 through 75 Processing helix chain 'J' and resid 87 through 110 Processing helix chain 'J' and resid 124 through 127 removed outlier: 3.543A pdb=" N ILE J 127 " --> pdb=" O ASP J 124 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 124 through 127' Processing helix chain 'J' and resid 138 through 147 removed outlier: 4.068A pdb=" N LEU J 146 " --> pdb=" O GLY J 142 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N TYR J 147 " --> pdb=" O ILE J 143 " (cutoff:3.500A) Processing helix chain 'J' and resid 151 through 173 Processing helix chain 'K' and resid 3 through 20 removed outlier: 3.779A pdb=" N ASN K 7 " --> pdb=" O MET K 3 " (cutoff:3.500A) Processing helix chain 'K' and resid 26 through 51 Processing helix chain 'K' and resid 55 through 85 removed outlier: 3.592A pdb=" N MET K 58 " --> pdb=" O LEU K 55 " (cutoff:3.500A) Proline residue: K 60 - end of helix removed outlier: 3.558A pdb=" N PHE K 66 " --> pdb=" O LEU K 63 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA K 67 " --> pdb=" O LEU K 64 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TYR K 85 " --> pdb=" O SER K 82 " (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 'L' and resid 3 through 23 removed outlier: 3.811A pdb=" N LEU L 12 " --> pdb=" O SER L 8 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU L 15 " --> pdb=" O THR L 11 " (cutoff:3.500A) Proline residue: L 18 - end of helix removed outlier: 3.582A pdb=" N MET L 22 " --> pdb=" O PRO L 18 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N SER L 23 " --> pdb=" O ILE L 19 " (cutoff:3.500A) Processing helix chain 'L' and resid 29 through 57 Proline residue: L 33 - end of helix removed outlier: 3.565A pdb=" N PHE L 44 " --> pdb=" O SER L 41 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE L 49 " --> pdb=" O THR L 46 " (cutoff:3.500A) Proline residue: L 50 - end of helix removed outlier: 3.645A 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: 3.835A pdb=" N TRP L 106 " --> pdb=" O GLU L 102 " (cutoff:3.500A) Processing helix chain 'L' and resid 114 through 133 Processing helix chain 'L' and resid 137 through 155 Processing helix chain 'L' and resid 162 through 193 removed outlier: 4.152A 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 223 Processing helix chain 'L' and resid 231 through 238 removed outlier: 4.113A pdb=" N MET L 237 " --> pdb=" O LEU L 233 " (cutoff:3.500A) removed outlier: 5.204A 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 269 removed outlier: 4.311A pdb=" N GLY L 256 " --> pdb=" O MET L 252 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ILE L 257 " --> pdb=" O VAL L 253 " (cutoff:3.500A) Proline residue: L 265 - end of helix removed outlier: 4.542A pdb=" N ASN L 269 " --> pdb=" O PRO L 265 " (cutoff:3.500A) Processing helix chain 'L' and resid 271 through 293 Processing helix chain 'L' and resid 298 through 318 Processing helix chain 'L' and resid 322 through 349 removed outlier: 3.793A pdb=" N PHE L 334 " --> pdb=" O CYS L 330 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N PHE L 335 " --> pdb=" O THR L 331 " (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 380 Processing helix chain 'L' and resid 387 through 400 removed outlier: 3.752A pdb=" N LYS L 392 " --> pdb=" O PHE L 389 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N ASP L 393 " --> pdb=" O TYR L 390 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU L 397 " --> pdb=" O LEU L 394 " (cutoff:3.500A) Processing helix chain 'L' and resid 406 through 431 removed outlier: 3.634A pdb=" N ALA L 420 " --> pdb=" O THR L 416 " (cutoff:3.500A) Processing helix chain 'L' and resid 448 through 469 removed outlier: 6.053A pdb=" N GLY L 465 " --> pdb=" O SER L 461 " (cutoff:3.500A) removed outlier: 5.096A 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: 3.534A pdb=" N THR L 508 " --> pdb=" O ILE L 504 " (cutoff:3.500A) removed outlier: 4.405A 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 544 Proline residue: L 530 - end of helix removed outlier: 3.709A pdb=" N MET L 533 " --> pdb=" O PRO L 530 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N HIS L 534 " --> pdb=" O THR L 531 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU L 536 " --> pdb=" O MET L 533 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N ALA L 537 " --> pdb=" O HIS L 534 " (cutoff:3.500A) Proline residue: L 538 - end of helix removed outlier: 3.569A pdb=" N LEU L 542 " --> pdb=" O TYR L 539 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N SER L 543 " --> pdb=" O MET L 540 " (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: 4.104A pdb=" N MET M 12 " --> pdb=" O THR M 8 " (cutoff:3.500A) Proline residue: M 13 - end of helix Processing helix chain 'M' and resid 20 through 42 removed outlier: 3.958A pdb=" N ILE M 23 " --> pdb=" O ASN M 20 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N TRP M 24 " --> pdb=" O ASN M 21 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASN M 26 " --> pdb=" O ILE M 23 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N SER M 27 " --> pdb=" O TRP M 24 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR M 28 " --> pdb=" O VAL M 25 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N HIS M 30 " --> pdb=" O SER M 27 " (cutoff:3.500A) Processing helix chain 'M' and resid 60 through 80 Proline residue: M 64 - end of helix Proline residue: M 74 - end of helix Processing helix chain 'M' and resid 89 through 111 Processing helix chain 'M' and resid 115 through 136 removed outlier: 4.522A pdb=" N LEU M 126 " --> pdb=" O PHE M 122 " (cutoff:3.500A) removed outlier: 4.374A 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: 3.536A pdb=" N ASN M 144 " --> pdb=" O GLU M 141 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TYR M 148 " --> pdb=" O ALA M 145 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N TYR M 152 " --> pdb=" O PHE M 149 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU M 154 " --> pdb=" O PHE M 151 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER M 157 " --> pdb=" O LEU M 154 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N LEU M 158 " --> pdb=" O ALA M 155 " (cutoff:3.500A) Proline residue: M 159 - end of helix removed outlier: 3.555A pdb=" N VAL M 171 " --> pdb=" O GLN M 168 " (cutoff:3.500A) Processing helix chain 'M' and resid 176 through 182 removed outlier: 3.836A pdb=" N TYR M 181 " --> pdb=" O LEU M 177 " (cutoff:3.500A) Processing helix chain 'M' and resid 190 through 206 removed outlier: 4.865A pdb=" N ALA M 202 " --> pdb=" O ALA M 198 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N PHE M 203 " --> pdb=" O CYS M 199 " (cutoff:3.500A) Processing helix chain 'M' and resid 214 through 222 removed outlier: 3.710A 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 250 removed outlier: 4.138A pdb=" N GLY M 239 " --> pdb=" O LEU M 235 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLY M 240 " --> pdb=" O LEU M 236 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N LEU M 248 " --> pdb=" O LEU M 244 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N ILE M 249 " --> pdb=" O ARG M 245 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU M 250 " --> pdb=" O ILE M 246 " (cutoff:3.500A) Processing helix chain 'M' and resid 253 through 257 removed outlier: 3.549A pdb=" N MET M 257 " --> pdb=" O THR M 254 " (cutoff:3.500A) Processing helix chain 'M' and resid 259 through 278 removed outlier: 3.934A pdb=" N ILE M 270 " --> pdb=" O LEU M 266 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU M 277 " --> pdb=" O SER M 273 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ARG M 278 " --> pdb=" O SER M 274 " (cutoff:3.500A) Processing helix chain 'M' and resid 282 through 303 removed outlier: 3.730A pdb=" N LEU M 296 " --> pdb=" O SER M 292 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL M 297 " --> pdb=" O HIS M 293 " (cutoff:3.500A) Processing helix chain 'M' and resid 306 through 337 removed outlier: 3.732A pdb=" N ARG M 336 " --> pdb=" O SER M 332 " (cutoff:3.500A) Processing helix chain 'M' and resid 348 through 351 No H-bonds generated for 'chain 'M' and resid 348 through 351' Processing helix chain 'M' and resid 353 through 366 Processing helix chain 'M' and resid 373 through 388 removed outlier: 3.598A pdb=" N SER M 387 " --> pdb=" O MET M 383 " (cutoff:3.500A) Processing helix chain 'M' and resid 390 through 415 removed outlier: 3.507A pdb=" N MET M 396 " --> pdb=" O ILE M 393 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL M 398 " --> pdb=" O LEU M 395 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU M 408 " --> pdb=" O LEU M 405 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N MET M 413 " --> pdb=" O MET M 410 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR M 414 " --> pdb=" O LEU M 411 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLN M 415 " --> pdb=" O ILE M 412 " (cutoff:3.500A) Processing helix chain 'M' and resid 431 through 448 Proline residue: M 443 - end of helix removed outlier: 3.976A 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: 3.744A pdb=" N GLU N 117 " --> pdb=" O PHE N 113 " (cutoff:3.500A) Processing helix chain 'N' and resid 124 through 131 Processing helix chain 'N' and resid 133 through 148 removed outlier: 4.397A pdb=" N ALA N 137 " --> pdb=" O TRP N 133 " (cutoff:3.500A) Proline residue: N 138 - end of helix removed outlier: 3.673A pdb=" N GLN N 144 " --> pdb=" O SER N 140 " (cutoff:3.500A) Proline residue: N 147 - end of helix Processing helix chain 'N' and resid 151 through 171 removed outlier: 3.671A pdb=" N LEU N 170 " --> pdb=" O GLY N 166 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ASN N 171 " --> pdb=" O TRP N 167 " (cutoff:3.500A) Processing helix chain 'N' and resid 175 through 192 Processing helix chain 'N' and resid 198 through 222 removed outlier: 3.610A pdb=" N ASN N 222 " --> pdb=" O MET N 218 " (cutoff:3.500A) Processing helix chain 'N' and resid 227 through 235 removed outlier: 3.737A pdb=" N HIS N 232 " --> pdb=" O LEU N 228 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N THR N 233 " --> pdb=" O SER N 229 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N TRP N 234 " --> pdb=" O LEU N 230 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N ASN N 235 " --> pdb=" O SER N 231 " (cutoff:3.500A) Processing helix chain 'N' and resid 238 through 251 Processing helix chain 'N' and resid 258 through 273 Proline residue: N 262 - end of helix removed outlier: 3.550A pdb=" N MET N 265 " --> pdb=" O PRO N 262 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET N 270 " --> pdb=" O ILE N 267 " (cutoff:3.500A) Processing helix chain 'N' and resid 277 through 300 removed outlier: 3.643A pdb=" N LEU N 287 " --> pdb=" O ALA N 283 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N LEU N 288 " --> pdb=" O ILE N 284 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ASN N 289 " --> pdb=" O THR N 285 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU N 296 " --> pdb=" O PHE N 292 " (cutoff:3.500A) Processing helix chain 'N' and resid 309 through 316 Processing helix chain 'N' and resid 326 through 334 Processing helix chain 'N' and resid 337 through 346 Proline residue: N 341 - end of helix Processing helix chain 'O' and resid 5 through 9 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: 3.628A pdb=" N GLU O 136 " --> pdb=" O VAL O 133 " (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: 3.980A 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 Processing helix chain 'O' and resid 247 through 249 No H-bonds generated for 'chain 'O' and resid 247 through 249' Processing helix chain 'O' and resid 253 through 263 Processing helix chain 'O' and resid 266 through 269 No H-bonds generated for 'chain 'O' and resid 266 through 269' Processing helix chain 'O' and resid 271 through 274 removed outlier: 3.704A 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 310 through 312 No H-bonds generated for 'chain 'O' and resid 310 through 312' 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 41 removed outlier: 4.144A pdb=" N TYR P 33 " --> pdb=" O PHE P 29 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N MET P 41 " --> pdb=" O HIS P 37 " (cutoff:3.500A) Processing helix chain 'P' and resid 53 through 62 removed outlier: 5.038A 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 124 Processing helix chain 'P' and resid 144 through 159 Processing helix chain 'P' and resid 179 through 183 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 281 through 287 Processing helix chain 'P' and resid 300 through 303 Processing helix chain 'P' and resid 310 through 318 removed outlier: 5.043A pdb=" N ILE P 315 " --> pdb=" O GLU P 311 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N GLU P 316 " --> pdb=" O LEU P 312 " (cutoff:3.500A) Processing helix chain 'Q' and resid 20 through 22 No H-bonds generated for 'chain 'Q' and resid 20 through 22' Processing helix chain 'Q' and resid 27 through 31 removed outlier: 4.182A 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 119 through 122 Processing helix chain 'R' and resid 23 through 28 Processing helix chain 'R' and resid 40 through 46 removed outlier: 3.601A 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: 5.010A pdb=" N GLY S 31 " --> pdb=" O GLY S 28 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ARG S 39 " --> pdb=" O ILE S 36 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N TYR S 40 " --> pdb=" O GLU S 37 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N VAL S 41 " --> pdb=" O LYS S 38 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS S 45 " --> pdb=" O GLU S 42 " (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 95 Processing helix chain 'T' and resid 10 through 21 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: 4.477A pdb=" N LYS T 69 " --> pdb=" O ILE T 65 " (cutoff:3.500A) Processing helix chain 'T' and resid 73 through 80 Processing helix chain 'U' and resid 8 through 21 Processing helix chain 'U' and resid 44A through 58 Processing helix chain 'U' and resid 64 through 69 removed outlier: 4.441A 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: 4.093A pdb=" N HIS V 36 " --> pdb=" O ASP V 32 " (cutoff:3.500A) Processing helix chain 'V' and resid 42 through 58 Processing helix chain 'V' and resid 64 through 71 Processing helix chain 'V' and resid 76 through 96 removed outlier: 3.714A pdb=" N GLN V 95 " --> pdb=" O ARG V 91 " (cutoff:3.500A) Processing helix chain 'W' and resid 25 through 49 removed outlier: 3.521A pdb=" N ARG W 31 " --> pdb=" O GLU W 27 " (cutoff:3.500A) Proline residue: W 44 - end of helix Processing helix chain 'W' and resid 56 through 70 removed outlier: 4.310A 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: 4.382A 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 21 through 34 removed outlier: 4.846A pdb=" N HIS X 29 " --> pdb=" O LYS X 25 " (cutoff:3.500A) removed outlier: 5.693A 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 76 removed outlier: 4.229A pdb=" N LEU X 56 " --> pdb=" O ARG X 53 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N GLU X 57 " --> pdb=" O ARG X 54 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU X 67 " --> pdb=" O GLN X 64 " (cutoff:3.500A) 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 113 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 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 Processing helix chain 'Z' and resid 121 through 125 Processing helix chain 'Z' and resid 130 through 142 removed outlier: 5.986A pdb=" N PHE Z 140 " --> pdb=" O ALA Z 136 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N ILE Z 141 " --> pdb=" O THR Z 137 " (cutoff:3.500A) Processing helix chain 'a' and resid 2 through 31 Proline residue: a 7 - end of helix removed outlier: 3.502A pdb=" N VAL a 11 " --> pdb=" O GLY a 8 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ILE a 18 " --> pdb=" O CYS a 15 " (cutoff:3.500A) Proline residue: a 19 - end of helix removed outlier: 3.594A pdb=" N THR a 23 " --> pdb=" O GLY a 20 " (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 38 through 47 removed outlier: 4.078A pdb=" N LEU b 42 " --> pdb=" O THR b 38 " (cutoff:3.500A) Processing helix chain 'b' and resid 78 through 82 Processing helix chain 'c' and resid 14 through 46 Processing helix chain 'd' and resid 16 through 20 Processing helix chain 'd' and resid 29 through 48 Processing helix chain 'd' and resid 58 through 96 removed outlier: 3.618A pdb=" N TYR d 74 " --> pdb=" O PHE d 70 " (cutoff:3.500A) Processing helix chain 'e' and resid 5 through 9 Processing helix chain 'e' and resid 15 through 17 No H-bonds generated for 'chain 'e' and resid 15 through 17' Processing helix chain 'e' and resid 25 through 27 No H-bonds generated for 'chain 'e' and resid 25 through 27' Processing helix chain 'e' and resid 33 through 43 Processing helix chain 'e' and resid 48 through 54 removed outlier: 4.030A 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 88 Processing helix chain 'f' and resid 11 through 33 removed outlier: 4.751A pdb=" N VAL f 16 " --> pdb=" O HIS f 13 " (cutoff:3.500A) Proline residue: f 17 - end of helix removed outlier: 3.530A pdb=" N PHE f 22 " --> pdb=" O GLY f 19 " (cutoff:3.500A) 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 66 Processing helix chain 'g' and resid 69 through 79 Processing helix chain 'g' and resid 83 through 102 removed outlier: 3.930A pdb=" N GLN g 86 " --> pdb=" O TYR g 83 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N GLU g 87 " --> pdb=" O ARG g 84 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA g 89 " --> pdb=" O GLN g 86 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL g 97 " --> pdb=" O GLU g 94 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LYS g 98 " --> pdb=" O ARG g 95 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG g 100 " --> pdb=" O VAL g 97 " (cutoff:3.500A) removed outlier: 3.644A 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: 4.103A 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: 3.759A 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 79 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 60 through 73 Processing helix chain 'i' and resid 75 through 87 Processing helix chain 'j' and resid 19 through 48 removed outlier: 7.176A pdb=" N ASP j 45 " --> pdb=" O TRP j 41 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ALA j 46 " --> pdb=" O HIS j 42 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N VAL j 47 " --> pdb=" O ASP j 43 " (cutoff:3.500A) Processing helix chain 'j' and resid 56 through 58 No H-bonds generated for 'chain 'j' and resid 56 through 58' Processing helix chain 'k' and resid 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: 3.864A pdb=" N ARG k 38 " --> pdb=" O LYS k 34 " (cutoff:3.500A) Processing helix chain 'k' and resid 46 through 52 removed outlier: 4.980A 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 17 through 26 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 21 No H-bonds generated for 'chain 'm' and resid 19 through 21' Processing helix chain 'm' and resid 26 through 50 removed outlier: 3.862A pdb=" N GLN m 49 " --> pdb=" O GLU m 45 " (cutoff:3.500A) Processing helix chain 'm' and resid 62 through 72 Processing helix chain 'm' and resid 95 through 117 Processing helix chain 'n' and resid 11 through 30 Processing helix chain 'n' and resid 33 through 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: 3.630A pdb=" N MET n 113 " --> pdb=" O SER n 109 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N TYR n 114 " --> pdb=" O GLU n 110 " (cutoff:3.500A) Proline residue: n 115 - end of helix removed outlier: 4.828A pdb=" N GLU n 133 " --> pdb=" O ARG n 129 " (cutoff:3.500A) removed outlier: 5.250A 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 8 Processing helix chain 'o' and resid 12 through 14 No H-bonds generated for 'chain 'o' and resid 12 through 14' Processing helix chain 'o' and resid 42 through 47 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 72 Processing helix chain 'o' and resid 80 through 120 removed outlier: 3.679A pdb=" N GLU o 118 " --> pdb=" O ARG o 114 " (cutoff:3.500A) Processing helix chain 'p' and resid 28 through 39 Processing helix chain 'p' and resid 41 through 57 removed outlier: 3.592A 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: 3.584A pdb=" N GLU p 86 " --> pdb=" O LEU p 82 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N GLU p 118 " --> pdb=" O GLN p 114 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N SER p 119 " --> pdb=" O ARG p 115 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N HIS p 120 " --> pdb=" O GLU p 116 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N ARG p 121 " --> pdb=" O GLY p 117 " (cutoff:3.500A) removed outlier: 6.469A 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 16 removed outlier: 3.673A pdb=" N VAL q 14 " --> pdb=" O GLY q 10 " (cutoff:3.500A) Processing helix chain 'q' and resid 20 through 30 Processing helix chain 'q' and resid 79 through 81 No H-bonds generated for 'chain 'q' and resid 79 through 81' Processing helix chain 'q' and resid 84 through 90 removed outlier: 4.463A 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 19 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: 4.774A 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 47 through 51 removed outlier: 6.326A pdb=" N VAL B 85 " --> pdb=" O MET B 48 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N PHE B 50 " --> pdb=" O VAL B 85 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ILE B 87 " --> pdb=" O PHE B 50 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N TYR B 112 " --> pdb=" O MET B 86 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N VAL B 88 " --> pdb=" O TYR B 112 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N VAL B 114 " --> pdb=" O VAL B 88 " (cutoff:3.500A) removed outlier: 6.317A 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: 6.758A pdb=" N ASN C 95 " --> pdb=" O ALA C 76 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N LEU C 78 " --> pdb=" O VAL C 93 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N VAL C 93 " --> pdb=" O LEU C 78 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ALA C 80 " --> pdb=" O GLU C 91 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N GLU C 91 " --> pdb=" O ALA C 80 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N LEU C 48 " --> pdb=" O ARG C 104 " (cutoff:3.500A) removed outlier: 4.772A 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 49 removed outlier: 6.510A pdb=" N SER D 69 " --> pdb=" O VAL D 73 " (cutoff:3.500A) removed outlier: 5.481A 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: 6.397A pdb=" N TYR E 98 " --> pdb=" O THR E 138 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N ILE E 140 " --> pdb=" O TYR E 98 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ILE E 100 " --> pdb=" O ILE E 140 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N VAL E 142 " --> pdb=" O ILE E 100 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N VAL E 102 " --> pdb=" O VAL E 142 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'F' and resid 220 through 224 removed outlier: 6.841A pdb=" N TYR F 92 " --> pdb=" O THR F 221 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N ALA F 223 " --> pdb=" O TYR F 92 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N VAL F 94 " --> pdb=" O ALA F 223 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ALA F 133 " --> pdb=" O LEU F 93 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N VAL F 95 " --> pdb=" O ALA F 133 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N TYR F 135 " --> pdb=" O VAL F 95 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ALA F 97 " --> pdb=" O TYR F 135 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N TYR F 137 " --> pdb=" O ALA F 97 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ASP F 174 " --> pdb=" O ALA F 134 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N ILE F 136 " --> pdb=" O ASP F 174 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N PHE F 176 " --> pdb=" O ILE F 136 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N ILE F 138 " --> pdb=" O PHE F 176 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N VAL F 178 " --> pdb=" O ILE F 138 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'F' and resid 266 through 271 Processing sheet with id= I, first strand: chain 'G' and resid 9 through 13 Processing sheet with id= J, first strand: chain 'G' and resid 146 through 148 Processing sheet with id= K, first strand: chain 'G' and resid 173 through 175 Processing sheet with id= L, first strand: chain 'G' and resid 223 through 228 removed outlier: 6.345A pdb=" N ARG G 243 " --> pdb=" O VAL G 247 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N VAL G 247 " --> pdb=" O ARG G 243 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'G' and resid 283 through 285 Processing sheet with id= N, first strand: chain 'G' and resid 343 through 345 removed outlier: 8.400A pdb=" N CYS G 344 " --> pdb=" O VAL G 315 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N ALA G 317 " --> pdb=" O CYS G 344 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N MET G 521 " --> pdb=" O ALA G 316 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N ILE G 318 " --> pdb=" O MET G 521 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N PHE G 523 " --> pdb=" O ILE G 318 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N PHE G 542 " --> pdb=" O LEU G 522 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N LEU G 524 " --> pdb=" O PHE G 542 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N VAL G 544 " --> pdb=" O LEU G 524 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N VAL G 559 " --> pdb=" O TYR G 545 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N GLY G 547 " --> pdb=" O VAL G 559 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N LEU G 561 " --> pdb=" O GLY G 547 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'G' and resid 490 through 493 removed outlier: 8.125A pdb=" N ASN G 491 " --> pdb=" O PRO G 449 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N VAL G 451 " --> pdb=" O ASN G 491 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N LEU G 493 " --> pdb=" O VAL G 451 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N LEU G 453 " --> pdb=" O LEU G 493 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N VAL G 376 " --> pdb=" O MET G 450 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N ILE G 452 " --> pdb=" O VAL G 376 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N LEU G 378 " --> pdb=" O ILE G 452 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N GLY G 454 " --> pdb=" O LEU G 378 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N VAL G 380 " --> pdb=" O GLY G 454 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N LYS G 405 " --> pdb=" O VAL G 377 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N LEU G 379 " --> pdb=" O LYS G 405 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ALA G 407 " --> pdb=" O LEU G 379 " (cutoff:3.500A) removed outlier: 6.466A 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: 6.066A pdb=" N GLU I 97 " --> pdb=" O THR I 106 " (cutoff:3.500A) removed outlier: 5.349A 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: 7.006A pdb=" N LEU L 78 " --> pdb=" O ASN L 65 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'O' and resid 122 through 125 removed outlier: 6.510A pdb=" N VAL O 168 " --> pdb=" O THR O 26 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N ASP O 28 " --> pdb=" O VAL O 168 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N VAL O 170 " --> pdb=" O ASP O 28 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N GLU O 219 " --> pdb=" O VAL O 169 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N TYR O 171 " --> pdb=" O GLU O 219 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N LEU O 221 " --> pdb=" O TYR O 171 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N ASP O 173 " --> pdb=" O LEU O 221 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N TYR O 223 " --> pdb=" O ASP O 173 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'P' and resid 227 through 230 removed outlier: 6.538A pdb=" N ILE P 165 " --> pdb=" O PHE P 228 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N PHE P 230 " --> pdb=" O ILE P 165 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N LYS P 167 " --> pdb=" O PHE P 230 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE P 132 " --> pdb=" O ASN P 93 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N GLN P 44 " --> pdb=" O ALA P 21 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N VAL P 23 " --> pdb=" O GLN P 44 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ILE P 46 " --> pdb=" O VAL P 23 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'Q' and resid 102 through 105 Processing sheet with id= Y, first strand: chain 'Q' and resid 64 through 66 Processing sheet with id= Z, first strand: chain 'R' and resid 50 through 52 Processing sheet with id= AA, first strand: chain 'R' and resid 56 through 59 Processing sheet with id= AB, first strand: chain 'S' and resid 51 through 56 removed outlier: 6.610A pdb=" N ARG S 67 " --> pdb=" O ARG S 16 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ILE S 18 " --> pdb=" O TRP S 65 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N TRP S 65 " --> pdb=" O ILE S 18 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N ILE S 20 " --> pdb=" O LYS S 63 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N LYS S 63 " --> pdb=" O ILE S 20 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'q' and resid 60 through 63 removed outlier: 6.744A pdb=" N GLU q 50 " --> pdb=" O LEU q 38 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N LEU q 38 " --> pdb=" O GLU q 50 " (cutoff:3.500A) 2909 hydrogen bonds defined for protein. 7821 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 22.61 Time building geometry restraints manager: 24.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.40: 27351 1.40 - 1.63: 39805 1.63 - 1.86: 817 1.86 - 2.09: 0 2.09 - 2.31: 81 Bond restraints: 68054 Sorted by residual: bond pdb=" C5 GTP O1202 " pdb=" N7 GTP O1202 " ideal model delta sigma weight residual 1.350 1.521 -0.171 2.00e-02 2.50e+03 7.33e+01 bond pdb=" C6 GTP O1202 " pdb=" O6 GTP O1202 " ideal model delta sigma weight residual 1.230 1.395 -0.165 2.00e-02 2.50e+03 6.78e+01 bond pdb=" C SAC i 1 " pdb=" O SAC i 1 " ideal model delta sigma weight residual 1.231 1.364 -0.133 2.00e-02 2.50e+03 4.45e+01 bond pdb=" C2 GTP O1202 " pdb=" N2 GTP O1202 " ideal model delta sigma weight residual 1.330 1.451 -0.121 2.00e-02 2.50e+03 3.68e+01 bond pdb=" C1B LMT L 705 " pdb=" O5B LMT L 705 " ideal model delta sigma weight residual 1.393 1.514 -0.121 2.00e-02 2.50e+03 3.64e+01 ... (remaining 68049 not shown) Histogram of bond angle deviations from ideal: 72.74 - 85.05: 76 85.05 - 97.36: 1 97.36 - 109.66: 8563 109.66 - 121.97: 71655 121.97 - 134.28: 11788 Bond angle restraints: 92083 Sorted by residual: angle pdb=" C51 CDL X1701 " pdb=" CB5 CDL X1701 " pdb=" OB6 CDL X1701 " ideal model delta sigma weight residual 111.33 121.45 -10.12 1.32e+00 5.72e-01 5.86e+01 angle pdb=" C51 CDL h1001 " pdb=" CB5 CDL h1001 " pdb=" OB6 CDL h1001 " ideal model delta sigma weight residual 111.33 121.38 -10.05 1.32e+00 5.72e-01 5.78e+01 angle pdb=" O 2MR D 85 " pdb=" C 2MR D 85 " pdb=" N GLY D 86 " ideal model delta sigma weight residual 123.00 110.99 12.01 1.60e+00 3.91e-01 5.63e+01 angle pdb=" C11 CDL d 201 " pdb=" CA5 CDL d 201 " pdb=" OA6 CDL d 201 " ideal model delta sigma weight residual 111.33 120.87 -9.54 1.32e+00 5.72e-01 5.21e+01 angle pdb=" C11 CDL X1701 " pdb=" CA5 CDL X1701 " pdb=" OA6 CDL X1701 " ideal model delta sigma weight residual 111.33 120.56 -9.23 1.32e+00 5.72e-01 4.87e+01 ... (remaining 92078 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.23: 40398 35.23 - 70.47: 941 70.47 - 105.70: 196 105.70 - 140.94: 54 140.94 - 176.17: 5 Dihedral angle restraints: 41594 sinusoidal: 18118 harmonic: 23476 Sorted by residual: dihedral pdb=" O5' GTP O1202 " pdb=" O3A GTP O1202 " pdb=" PA GTP O1202 " pdb=" PB GTP O1202 " ideal model delta sinusoidal sigma weight residual -85.88 90.29 -176.17 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 84.72 172.87 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" O2G GTP O1202 " pdb=" O3B GTP O1202 " pdb=" PG GTP O1202 " pdb=" PB GTP O1202 " ideal model delta sinusoidal sigma weight residual 177.30 10.97 166.33 1 2.00e+01 2.50e-03 4.73e+01 ... (remaining 41591 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.293: 10069 4.293 - 8.586: 0 8.586 - 12.879: 0 12.879 - 17.172: 0 17.172 - 21.465: 16 Chirality restraints: 10085 Sorted by residual: chirality pdb="FE3 SF4 I 201 " pdb=" S1 SF4 I 201 " pdb=" S2 SF4 I 201 " pdb=" S4 SF4 I 201 " both_signs ideal model delta sigma weight residual False -10.55 10.91 -21.46 2.00e-01 2.50e+01 1.15e+04 chirality pdb="FE1 SF4 I 201 " pdb=" S2 SF4 I 201 " pdb=" S3 SF4 I 201 " pdb=" S4 SF4 I 201 " both_signs ideal model delta sigma weight residual False -10.55 10.88 -21.44 2.00e-01 2.50e+01 1.15e+04 chirality pdb="FE1 SF4 G 802 " pdb=" S2 SF4 G 802 " pdb=" S3 SF4 G 802 " pdb=" S4 SF4 G 802 " both_signs ideal model delta sigma weight residual False -10.55 10.86 -21.41 2.00e-01 2.50e+01 1.15e+04 ... (remaining 10082 not shown) Planarity restraints: 11467 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C08 I49 N 503 " 0.070 2.00e-02 2.50e+03 5.45e-01 5.95e+03 pdb=" C14 I49 N 503 " 0.106 2.00e-02 2.50e+03 pdb=" C15 I49 N 503 " 0.023 2.00e-02 2.50e+03 pdb=" N01 I49 N 503 " 0.491 2.00e-02 2.50e+03 pdb=" N02 I49 N 503 " 0.600 2.00e-02 2.50e+03 pdb=" N03 I49 N 503 " -0.709 2.00e-02 2.50e+03 pdb=" N04 I49 N 503 " -1.029 2.00e-02 2.50e+03 pdb=" N05 I49 N 503 " 0.448 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA 2MR D 85 " 0.082 2.00e-02 2.50e+03 1.52e-01 2.32e+02 pdb=" C 2MR D 85 " -0.264 2.00e-02 2.50e+03 pdb=" O 2MR D 85 " 0.088 2.00e-02 2.50e+03 pdb=" N GLY D 86 " 0.093 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE K 53 " 0.025 2.00e-02 2.50e+03 3.85e-02 2.60e+01 pdb=" CG PHE K 53 " -0.084 2.00e-02 2.50e+03 pdb=" CD1 PHE K 53 " 0.045 2.00e-02 2.50e+03 pdb=" CD2 PHE K 53 " 0.019 2.00e-02 2.50e+03 pdb=" CE1 PHE K 53 " -0.017 2.00e-02 2.50e+03 pdb=" CE2 PHE K 53 " 0.007 2.00e-02 2.50e+03 pdb=" CZ PHE K 53 " 0.005 2.00e-02 2.50e+03 ... (remaining 11464 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.52: 583 2.52 - 3.17: 61229 3.17 - 3.83: 146543 3.83 - 4.48: 212590 4.48 - 5.14: 321241 Nonbonded interactions: 742186 Sorted by model distance: nonbonded pdb=" OG SER J 25 " pdb=" OE1 GLU J 77 " model vdw 1.863 2.440 nonbonded pdb=" OH TYR O 83 " pdb=" O2' GTP O1202 " model vdw 1.885 2.440 nonbonded pdb=" OD2 ASP q 78 " pdb=" OG SER q 80 " model vdw 1.887 2.440 nonbonded pdb=" O HOH A 407 " pdb=" O HOH A 408 " model vdw 1.901 2.440 nonbonded pdb=" OE1 GLU M 335 " pdb=" O HOH M1401 " model vdw 1.919 2.440 ... (remaining 742181 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: 0.010 Normalize map: mean=0, sd=1: 11.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 58.350 Check model and map are aligned: 0.830 Set scattering table: 0.510 Process input model: 163.990 Find NCS groups from input model: 2.110 Set up NCS constraints: 0.290 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:11.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 249.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.171 68054 Z= 0.495 Angle : 0.842 16.627 92083 Z= 0.398 Chirality : 0.852 21.465 10085 Planarity : 0.007 0.545 11467 Dihedral : 16.835 176.171 26436 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.08 % Favored : 97.91 % Rotamer: Outliers : 0.03 % Allowed : 0.16 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.61 (0.09), residues: 7931 helix: 0.66 (0.08), residues: 4284 sheet: 0.15 (0.25), residues: 367 loop : 0.29 (0.11), residues: 3280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP P 73 HIS 0.015 0.002 HIS D 150 PHE 0.084 0.003 PHE K 53 TYR 0.083 0.002 TYR B 125 ARG 0.018 0.001 ARG d 120 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15862 Ramachandran restraints generated. 7931 Oldfield, 0 Emsley, 7931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15862 Ramachandran restraints generated. 7931 Oldfield, 0 Emsley, 7931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1118 residues out of total 7028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1116 time to evaluate : 6.395 Fit side-chains REVERT: F 249 ARG cc_start: 0.8022 (mtm110) cc_final: 0.7804 (mtm110) REVERT: L 581 LYS cc_start: 0.8688 (mmtp) cc_final: 0.8447 (mmmm) REVERT: S 63 LYS cc_start: 0.8858 (ttmm) cc_final: 0.8510 (mttm) REVERT: V 70 ARG cc_start: 0.8196 (mmm-85) cc_final: 0.7985 (mmm-85) REVERT: Y 60 PHE cc_start: 0.7468 (t80) cc_final: 0.7152 (t80) REVERT: Y 98 LEU cc_start: 0.7943 (mt) cc_final: 0.7696 (mt) REVERT: e 58 GLU cc_start: 0.8489 (mp0) cc_final: 0.8240 (mp0) REVERT: o 11 ASP cc_start: 0.7565 (t0) cc_final: 0.7269 (t70) outliers start: 2 outliers final: 3 residues processed: 1117 average time/residue: 1.8834 time to fit residues: 2620.0601 Evaluate side-chains 967 residues out of total 7028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 964 time to evaluate : 6.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 28 ASP Chi-restraints excluded: chain T residue 44 SER Chi-restraints excluded: chain k residue 85 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 785 random chunks: chunk 662 optimal weight: 3.9990 chunk 594 optimal weight: 0.9990 chunk 330 optimal weight: 2.9990 chunk 203 optimal weight: 9.9990 chunk 401 optimal weight: 0.9980 chunk 317 optimal weight: 0.7980 chunk 615 optimal weight: 2.9990 chunk 238 optimal weight: 2.9990 chunk 374 optimal weight: 0.8980 chunk 457 optimal weight: 0.9980 chunk 712 optimal weight: 4.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 211 GLN D 114 ASN E 214 GLN G 16 GLN ** G 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 124 ASN H 287 HIS J 46 ASN K 52 HIS L 479 GLN L 605 HIS M 138 ASN M 293 HIS N 222 ASN P 87 HIS P 102 GLN S 75 ASN W 45 ASN X 64 GLN Y 128 GLN Z 24 ASN a 58 ASN c 5 GLN c 34 GLN e 69 GLN f 30 ASN g 86 GLN k 90 GLN m 32 GLN m 116 GLN n 72 HIS o 116 GLN p 120 HIS Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.1253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.271 68054 Z= 0.426 Angle : 1.321 50.728 92083 Z= 0.845 Chirality : 0.261 6.661 10085 Planarity : 0.004 0.051 11467 Dihedral : 13.299 172.642 10520 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 0.70 % Allowed : 5.39 % Favored : 93.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 7931 helix: 1.53 (0.08), residues: 4295 sheet: 0.24 (0.25), residues: 360 loop : 0.44 (0.11), residues: 3276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP L 144 HIS 0.010 0.001 HIS G 101 PHE 0.027 0.001 PHE N 292 TYR 0.035 0.001 TYR B 125 ARG 0.012 0.000 ARG p 14 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15862 Ramachandran restraints generated. 7931 Oldfield, 0 Emsley, 7931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15862 Ramachandran restraints generated. 7931 Oldfield, 0 Emsley, 7931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1079 residues out of total 7028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 1030 time to evaluate : 6.525 Fit side-chains revert: symmetry clash REVERT: B 48 MET cc_start: 0.7808 (tmt) cc_final: 0.7551 (tmt) REVERT: F 249 ARG cc_start: 0.8015 (mtm110) cc_final: 0.7785 (mtm110) REVERT: H 126 LYS cc_start: 0.7414 (mmtt) cc_final: 0.6998 (mmmt) REVERT: L 581 LYS cc_start: 0.8668 (mmtp) cc_final: 0.8434 (mmmm) REVERT: P 322 ARG cc_start: 0.7983 (OUTLIER) cc_final: 0.7191 (mtm-85) REVERT: V 70 ARG cc_start: 0.8093 (mmm-85) cc_final: 0.7882 (mmm-85) REVERT: Y 60 PHE cc_start: 0.7415 (t80) cc_final: 0.7140 (t80) REVERT: Z 85 GLN cc_start: 0.7879 (OUTLIER) cc_final: 0.7671 (tt0) REVERT: f 53 GLU cc_start: 0.7143 (OUTLIER) cc_final: 0.6707 (mp0) REVERT: q 51 ASP cc_start: 0.8576 (t0) cc_final: 0.8375 (t0) outliers start: 49 outliers final: 12 residues processed: 1043 average time/residue: 1.8007 time to fit residues: 2357.7531 Evaluate side-chains 983 residues out of total 7028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 968 time to evaluate : 6.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain G residue 486 ASP Chi-restraints excluded: chain H residue 121 TRP Chi-restraints excluded: chain H residue 194 ASN Chi-restraints excluded: chain H residue 234 MET Chi-restraints excluded: chain P residue 312 LEU Chi-restraints excluded: chain P residue 322 ARG Chi-restraints excluded: chain Z residue 85 GLN Chi-restraints excluded: chain c residue 11 SER Chi-restraints excluded: chain e residue 83 GLU Chi-restraints excluded: chain f residue 53 GLU Chi-restraints excluded: chain h residue 6 LYS Chi-restraints excluded: chain j residue 45 ASP Chi-restraints excluded: chain q residue 8 LYS Chi-restraints excluded: chain q residue 142 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 785 random chunks: chunk 396 optimal weight: 3.9990 chunk 221 optimal weight: 10.0000 chunk 593 optimal weight: 1.9990 chunk 485 optimal weight: 4.9990 chunk 196 optimal weight: 9.9990 chunk 714 optimal weight: 2.9990 chunk 771 optimal weight: 1.9990 chunk 636 optimal weight: 9.9990 chunk 708 optimal weight: 4.9990 chunk 243 optimal weight: 10.0000 chunk 572 optimal weight: 7.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 GLN F 432 GLN F 435 GLN ** G 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 479 GLN L 541 ASN L 605 HIS M 138 ASN Q 9 GLN W 45 ASN Y 128 GLN Z 24 ASN a 68 ASN c 34 GLN d 61 GLN e 69 GLN f 30 ASN k 32 GLN l 147 ASN m 116 GLN o 116 GLN q 5 GLN r 24 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.1411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.244 68054 Z= 0.518 Angle : 1.340 50.320 92083 Z= 0.853 Chirality : 0.263 6.674 10085 Planarity : 0.005 0.054 11467 Dihedral : 11.805 173.189 10515 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.31 % Allowed : 6.45 % Favored : 92.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 1.43 (0.09), residues: 7931 helix: 1.49 (0.08), residues: 4312 sheet: 0.31 (0.26), residues: 348 loop : 0.43 (0.11), residues: 3271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP n 71 HIS 0.010 0.001 HIS G 101 PHE 0.027 0.002 PHE N 292 TYR 0.029 0.002 TYR B 125 ARG 0.012 0.001 ARG X 98 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15862 Ramachandran restraints generated. 7931 Oldfield, 0 Emsley, 7931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15862 Ramachandran restraints generated. 7931 Oldfield, 0 Emsley, 7931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1076 residues out of total 7028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 984 time to evaluate : 6.283 Fit side-chains REVERT: B 48 MET cc_start: 0.7876 (tmt) cc_final: 0.7661 (tmt) REVERT: B 165 LYS cc_start: 0.8989 (OUTLIER) cc_final: 0.8084 (mmtp) REVERT: B 175 ILE cc_start: 0.9231 (OUTLIER) cc_final: 0.8743 (mt) REVERT: B 176 TRP cc_start: 0.8616 (t-100) cc_final: 0.8202 (t60) REVERT: D 75 LYS cc_start: 0.8748 (OUTLIER) cc_final: 0.8543 (ttpt) REVERT: D 407 LYS cc_start: 0.8562 (OUTLIER) cc_final: 0.7888 (mptt) REVERT: D 410 MET cc_start: 0.8700 (OUTLIER) cc_final: 0.7693 (mmt) REVERT: F 249 ARG cc_start: 0.8043 (mtm110) cc_final: 0.7751 (mtm110) REVERT: G 444 GLN cc_start: 0.7778 (OUTLIER) cc_final: 0.7340 (tp40) REVERT: G 447 LYS cc_start: 0.8520 (OUTLIER) cc_final: 0.8149 (mptp) REVERT: K 70 GLU cc_start: 0.7559 (OUTLIER) cc_final: 0.7321 (tt0) REVERT: L 581 LYS cc_start: 0.8671 (mmtp) cc_final: 0.8424 (mmmm) REVERT: S 90 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8762 (mm) REVERT: V 70 ARG cc_start: 0.8160 (mmm-85) cc_final: 0.7935 (mmm-85) REVERT: Y 60 PHE cc_start: 0.7420 (t80) cc_final: 0.7219 (t80) REVERT: b 9 LYS cc_start: 0.8574 (OUTLIER) cc_final: 0.8320 (tttm) REVERT: f 53 GLU cc_start: 0.7169 (OUTLIER) cc_final: 0.6729 (mp0) REVERT: n 58 LYS cc_start: 0.7734 (OUTLIER) cc_final: 0.7457 (tmtt) REVERT: o 45 MET cc_start: 0.8751 (mtm) cc_final: 0.8458 (mtm) REVERT: r 101 LYS cc_start: 0.8160 (OUTLIER) cc_final: 0.7890 (mtmm) outliers start: 92 outliers final: 30 residues processed: 1023 average time/residue: 1.8252 time to fit residues: 2331.4383 Evaluate side-chains 1010 residues out of total 7028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 967 time to evaluate : 6.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 165 LYS Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 75 LYS Chi-restraints excluded: chain D residue 407 LYS Chi-restraints excluded: chain D residue 410 MET Chi-restraints excluded: chain D residue 420 THR Chi-restraints excluded: chain F residue 314 THR Chi-restraints excluded: chain G residue 309 SER Chi-restraints excluded: chain G residue 444 GLN Chi-restraints excluded: chain G residue 447 LYS Chi-restraints excluded: chain G residue 486 ASP Chi-restraints excluded: chain H residue 121 TRP Chi-restraints excluded: chain H residue 194 ASN Chi-restraints excluded: chain H residue 205 SER Chi-restraints excluded: chain H residue 234 MET Chi-restraints excluded: chain H residue 289 LEU Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 70 GLU Chi-restraints excluded: chain L residue 393 ASP Chi-restraints excluded: chain P residue 312 LEU Chi-restraints excluded: chain S residue 90 LEU Chi-restraints excluded: chain W residue 120 SER Chi-restraints excluded: chain X residue 130 VAL Chi-restraints excluded: chain Y residue 119 LEU Chi-restraints excluded: chain b residue 9 LYS Chi-restraints excluded: chain c residue 11 SER Chi-restraints excluded: chain e residue 83 GLU Chi-restraints excluded: chain f residue 53 GLU Chi-restraints excluded: chain g residue 116 SER Chi-restraints excluded: chain h residue 6 LYS Chi-restraints excluded: chain j residue 45 ASP Chi-restraints excluded: chain n residue 58 LYS Chi-restraints excluded: chain o residue 80 LYS Chi-restraints excluded: chain p residue 24 SER Chi-restraints excluded: chain p residue 38 LEU Chi-restraints excluded: chain q residue 142 THR Chi-restraints excluded: chain r residue 68 VAL Chi-restraints excluded: chain r residue 101 LYS Chi-restraints excluded: chain s residue 59 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 785 random chunks: chunk 705 optimal weight: 0.8980 chunk 536 optimal weight: 8.9990 chunk 370 optimal weight: 8.9990 chunk 79 optimal weight: 0.6980 chunk 340 optimal weight: 9.9990 chunk 479 optimal weight: 1.9990 chunk 716 optimal weight: 0.6980 chunk 758 optimal weight: 0.5980 chunk 374 optimal weight: 1.9990 chunk 679 optimal weight: 0.1980 chunk 204 optimal weight: 6.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 GLN C 211 GLN F 432 GLN F 435 GLN G 475 GLN H 5 ASN L 479 GLN L 605 HIS M 138 ASN Q 9 GLN W 45 ASN X 15 GLN X 64 GLN Y 128 GLN Z 24 ASN a 58 ASN c 34 GLN d 61 GLN f 30 ASN k 32 GLN l 147 ASN m 32 GLN m 116 GLN q 5 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.247 68054 Z= 0.432 Angle : 1.292 50.534 92083 Z= 0.835 Chirality : 0.255 6.412 10085 Planarity : 0.004 0.051 11467 Dihedral : 10.693 171.773 10515 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.07 % Allowed : 7.50 % Favored : 91.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 1.72 (0.09), residues: 7931 helix: 1.79 (0.08), residues: 4280 sheet: 0.31 (0.26), residues: 360 loop : 0.51 (0.11), residues: 3291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP L 144 HIS 0.006 0.001 HIS G 101 PHE 0.029 0.001 PHE N 292 TYR 0.022 0.001 TYR L 422 ARG 0.011 0.000 ARG o 114 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15862 Ramachandran restraints generated. 7931 Oldfield, 0 Emsley, 7931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15862 Ramachandran restraints generated. 7931 Oldfield, 0 Emsley, 7931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1092 residues out of total 7028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 1017 time to evaluate : 6.812 Fit side-chains revert: symmetry clash REVERT: B 48 MET cc_start: 0.7873 (tmt) cc_final: 0.7654 (tmt) REVERT: B 59 MET cc_start: 0.7929 (OUTLIER) cc_final: 0.6957 (tpt) REVERT: B 175 ILE cc_start: 0.9210 (OUTLIER) cc_final: 0.8690 (mt) REVERT: B 176 TRP cc_start: 0.8578 (t-100) cc_final: 0.8208 (t60) REVERT: F 249 ARG cc_start: 0.8047 (mtm110) cc_final: 0.7759 (mtm110) REVERT: G 613 TYR cc_start: 0.9279 (OUTLIER) cc_final: 0.8682 (p90) REVERT: H 234 MET cc_start: 0.7948 (OUTLIER) cc_final: 0.7546 (mmt) REVERT: J 111 LYS cc_start: 0.7036 (mmtt) cc_final: 0.6460 (mtpp) REVERT: K 70 GLU cc_start: 0.7500 (OUTLIER) cc_final: 0.7249 (tt0) REVERT: L 404 THR cc_start: 0.8171 (p) cc_final: 0.7957 (p) REVERT: S 90 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8665 (mm) REVERT: V 70 ARG cc_start: 0.8067 (mmm-85) cc_final: 0.7761 (mmm-85) REVERT: Y 119 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8287 (mt) REVERT: f 53 GLU cc_start: 0.7076 (OUTLIER) cc_final: 0.6591 (mp0) REVERT: o 45 MET cc_start: 0.8704 (mtm) cc_final: 0.8457 (mtm) outliers start: 75 outliers final: 19 residues processed: 1048 average time/residue: 1.8361 time to fit residues: 2413.5794 Evaluate side-chains 1004 residues out of total 7028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 977 time to evaluate : 6.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain B residue 59 MET Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain G residue 444 GLN Chi-restraints excluded: chain G residue 613 TYR Chi-restraints excluded: chain H residue 121 TRP Chi-restraints excluded: chain H residue 234 MET Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 70 GLU Chi-restraints excluded: chain L residue 393 ASP Chi-restraints excluded: chain M residue 130 LEU Chi-restraints excluded: chain P residue 312 LEU Chi-restraints excluded: chain S residue 90 LEU Chi-restraints excluded: chain Y residue 119 LEU Chi-restraints excluded: chain a residue 69 ILE Chi-restraints excluded: chain c residue 11 SER Chi-restraints excluded: chain f residue 53 GLU Chi-restraints excluded: chain g residue 60 VAL Chi-restraints excluded: chain g residue 116 SER Chi-restraints excluded: chain h residue 6 LYS Chi-restraints excluded: chain k residue 85 TYR Chi-restraints excluded: chain o residue 80 LYS Chi-restraints excluded: chain p residue 24 SER Chi-restraints excluded: chain p residue 38 LEU Chi-restraints excluded: chain q residue 142 THR Chi-restraints excluded: chain r residue 68 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 785 random chunks: chunk 631 optimal weight: 7.9990 chunk 430 optimal weight: 4.9990 chunk 11 optimal weight: 7.9990 chunk 564 optimal weight: 5.9990 chunk 313 optimal weight: 5.9990 chunk 647 optimal weight: 4.9990 chunk 524 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 387 optimal weight: 0.4980 chunk 681 optimal weight: 5.9990 chunk 191 optimal weight: 3.9990 overall best weight: 3.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 ASN C 69 ASN C 211 GLN E 74 GLN F 432 GLN H 194 ASN K 83 ASN L 479 GLN L 605 HIS W 45 ASN Y 128 GLN Z 24 ASN a 58 ASN c 34 GLN d 61 GLN e 69 GLN f 30 ASN k 32 GLN l 147 ASN m 116 GLN q 5 GLN q 52 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.244 68054 Z= 0.512 Angle : 1.327 50.445 92083 Z= 0.849 Chirality : 0.261 6.648 10085 Planarity : 0.005 0.053 11467 Dihedral : 10.786 179.405 10515 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.44 % Allowed : 7.95 % Favored : 90.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 1.58 (0.09), residues: 7931 helix: 1.63 (0.08), residues: 4309 sheet: 0.38 (0.26), residues: 354 loop : 0.47 (0.11), residues: 3268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP n 71 HIS 0.008 0.001 HIS C 160 PHE 0.027 0.002 PHE N 292 TYR 0.025 0.002 TYR I 118 ARG 0.009 0.001 ARG X 98 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15862 Ramachandran restraints generated. 7931 Oldfield, 0 Emsley, 7931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15862 Ramachandran restraints generated. 7931 Oldfield, 0 Emsley, 7931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1076 residues out of total 7028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 975 time to evaluate : 6.318 Fit side-chains revert: symmetry clash REVERT: B 48 MET cc_start: 0.7963 (tmt) cc_final: 0.7702 (tmt) REVERT: B 59 MET cc_start: 0.7995 (OUTLIER) cc_final: 0.7072 (tpt) REVERT: B 165 LYS cc_start: 0.8980 (OUTLIER) cc_final: 0.8159 (mmtp) REVERT: B 175 ILE cc_start: 0.9221 (OUTLIER) cc_final: 0.8736 (mt) REVERT: B 176 TRP cc_start: 0.8641 (t-100) cc_final: 0.8249 (t60) REVERT: D 410 MET cc_start: 0.8702 (OUTLIER) cc_final: 0.7679 (mmt) REVERT: F 249 ARG cc_start: 0.8063 (mtm110) cc_final: 0.7762 (mtm110) REVERT: G 444 GLN cc_start: 0.7768 (OUTLIER) cc_final: 0.7280 (tp40) REVERT: G 447 LYS cc_start: 0.8522 (OUTLIER) cc_final: 0.8172 (mptp) REVERT: G 613 TYR cc_start: 0.9360 (OUTLIER) cc_final: 0.8705 (p90) REVERT: J 111 LYS cc_start: 0.7113 (mmtt) cc_final: 0.6508 (mtpp) REVERT: M 168 GLN cc_start: 0.8935 (OUTLIER) cc_final: 0.8600 (tt0) REVERT: N 322 LYS cc_start: 0.7859 (mttm) cc_final: 0.7602 (mmtp) REVERT: S 90 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8738 (mm) REVERT: V 70 ARG cc_start: 0.8127 (mmm-85) cc_final: 0.7886 (mmm-85) REVERT: W 68 LYS cc_start: 0.8711 (OUTLIER) cc_final: 0.8446 (tmtp) REVERT: Y 119 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8330 (mt) REVERT: f 53 GLU cc_start: 0.7149 (OUTLIER) cc_final: 0.6654 (mp0) REVERT: o 45 MET cc_start: 0.8764 (mtm) cc_final: 0.8422 (mtm) REVERT: r 101 LYS cc_start: 0.8178 (OUTLIER) cc_final: 0.7899 (mtmm) outliers start: 101 outliers final: 36 residues processed: 1017 average time/residue: 1.8122 time to fit residues: 2310.1228 Evaluate side-chains 1011 residues out of total 7028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 962 time to evaluate : 6.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 59 MET Chi-restraints excluded: chain B residue 165 LYS Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 410 MET Chi-restraints excluded: chain D residue 420 THR Chi-restraints excluded: chain E residue 114 ASP Chi-restraints excluded: chain E residue 192 SER Chi-restraints excluded: chain G residue 444 GLN Chi-restraints excluded: chain G residue 447 LYS Chi-restraints excluded: chain G residue 486 ASP Chi-restraints excluded: chain G residue 613 TYR Chi-restraints excluded: chain H residue 121 TRP Chi-restraints excluded: chain H residue 194 ASN Chi-restraints excluded: chain H residue 205 SER Chi-restraints excluded: chain H residue 234 MET Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 133 SER Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain L residue 21 MET Chi-restraints excluded: chain L residue 28 LYS Chi-restraints excluded: chain L residue 393 ASP Chi-restraints excluded: chain L residue 566 ILE Chi-restraints excluded: chain M residue 130 LEU Chi-restraints excluded: chain M residue 168 GLN Chi-restraints excluded: chain P residue 312 LEU Chi-restraints excluded: chain S residue 90 LEU Chi-restraints excluded: chain T residue 34 SER Chi-restraints excluded: chain W residue 68 LYS Chi-restraints excluded: chain W residue 120 SER Chi-restraints excluded: chain X residue 130 VAL Chi-restraints excluded: chain Y residue 114 CYS Chi-restraints excluded: chain Y residue 119 LEU Chi-restraints excluded: chain Z residue 25 LEU Chi-restraints excluded: chain c residue 11 SER Chi-restraints excluded: chain d residue 92 SER Chi-restraints excluded: chain f residue 53 GLU Chi-restraints excluded: chain j residue 45 ASP Chi-restraints excluded: chain k residue 87 LEU Chi-restraints excluded: chain l residue 151 GLU Chi-restraints excluded: chain o residue 80 LYS Chi-restraints excluded: chain p residue 24 SER Chi-restraints excluded: chain p residue 38 LEU Chi-restraints excluded: chain q residue 142 THR Chi-restraints excluded: chain r residue 68 VAL Chi-restraints excluded: chain r residue 101 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 785 random chunks: chunk 255 optimal weight: 0.8980 chunk 683 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 chunk 445 optimal weight: 6.9990 chunk 187 optimal weight: 4.9990 chunk 759 optimal weight: 9.9990 chunk 630 optimal weight: 5.9990 chunk 351 optimal weight: 0.8980 chunk 63 optimal weight: 5.9990 chunk 251 optimal weight: 1.9990 chunk 398 optimal weight: 2.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 ASN C 69 ASN F 432 GLN F 435 GLN H 194 ASN L 479 GLN L 605 HIS Q 9 GLN W 45 ASN X 15 GLN X 64 GLN Y 128 GLN Y 133 GLN Z 24 ASN c 34 GLN f 30 ASN k 32 GLN l 147 ASN m 32 GLN m 116 GLN q 52 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.1701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.246 68054 Z= 0.462 Angle : 1.309 50.546 92083 Z= 0.842 Chirality : 0.258 6.541 10085 Planarity : 0.004 0.073 11467 Dihedral : 10.521 175.909 10515 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.27 % Allowed : 8.45 % Favored : 90.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 1.60 (0.09), residues: 7931 helix: 1.67 (0.08), residues: 4298 sheet: 0.34 (0.26), residues: 358 loop : 0.46 (0.11), residues: 3275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP X 85 HIS 0.008 0.001 HIS G 101 PHE 0.028 0.002 PHE N 292 TYR 0.022 0.001 TYR I 118 ARG 0.015 0.000 ARG p 14 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15862 Ramachandran restraints generated. 7931 Oldfield, 0 Emsley, 7931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15862 Ramachandran restraints generated. 7931 Oldfield, 0 Emsley, 7931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1065 residues out of total 7028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 976 time to evaluate : 6.353 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 48 MET cc_start: 0.7939 (tmt) cc_final: 0.7698 (tmt) REVERT: B 59 MET cc_start: 0.7965 (OUTLIER) cc_final: 0.6981 (tpt) REVERT: B 125 TYR cc_start: 0.9479 (OUTLIER) cc_final: 0.8943 (t80) REVERT: B 165 LYS cc_start: 0.8969 (OUTLIER) cc_final: 0.8030 (mmtp) REVERT: B 175 ILE cc_start: 0.9217 (OUTLIER) cc_final: 0.8737 (mt) REVERT: B 176 TRP cc_start: 0.8639 (t-100) cc_final: 0.8239 (t60) REVERT: D 410 MET cc_start: 0.8693 (OUTLIER) cc_final: 0.7673 (mmt) REVERT: F 249 ARG cc_start: 0.8050 (mtm110) cc_final: 0.7719 (mtm110) REVERT: G 613 TYR cc_start: 0.9348 (OUTLIER) cc_final: 0.8788 (p90) REVERT: J 111 LYS cc_start: 0.7095 (mmtt) cc_final: 0.6488 (mtpp) REVERT: K 70 GLU cc_start: 0.7537 (OUTLIER) cc_final: 0.7324 (tt0) REVERT: M 168 GLN cc_start: 0.8909 (OUTLIER) cc_final: 0.8591 (tt0) REVERT: N 322 LYS cc_start: 0.7859 (mttm) cc_final: 0.7606 (mmtp) REVERT: P 322 ARG cc_start: 0.8131 (OUTLIER) cc_final: 0.7417 (mtm180) REVERT: S 90 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8732 (mm) REVERT: U 37 MET cc_start: 0.7703 (OUTLIER) cc_final: 0.6234 (mmt) REVERT: W 68 LYS cc_start: 0.8713 (OUTLIER) cc_final: 0.8471 (tmtp) REVERT: Y 60 PHE cc_start: 0.7351 (t80) cc_final: 0.7122 (t80) REVERT: Y 119 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8343 (mt) REVERT: Y 130 GLU cc_start: 0.8904 (OUTLIER) cc_final: 0.7607 (mt-10) REVERT: f 53 GLU cc_start: 0.7126 (OUTLIER) cc_final: 0.6622 (mp0) REVERT: o 45 MET cc_start: 0.8759 (mtm) cc_final: 0.8477 (mtm) REVERT: r 101 LYS cc_start: 0.8173 (OUTLIER) cc_final: 0.7909 (mtmm) outliers start: 89 outliers final: 41 residues processed: 1016 average time/residue: 1.8105 time to fit residues: 2314.7632 Evaluate side-chains 1021 residues out of total 7028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 964 time to evaluate : 6.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 59 MET Chi-restraints excluded: chain B residue 125 TYR Chi-restraints excluded: chain B residue 165 LYS Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 410 MET Chi-restraints excluded: chain D residue 420 THR Chi-restraints excluded: chain E residue 114 ASP Chi-restraints excluded: chain F residue 314 THR Chi-restraints excluded: chain G residue 444 GLN Chi-restraints excluded: chain G residue 613 TYR Chi-restraints excluded: chain H residue 121 TRP Chi-restraints excluded: chain H residue 194 ASN Chi-restraints excluded: chain H residue 205 SER Chi-restraints excluded: chain H residue 234 MET Chi-restraints excluded: chain H residue 289 LEU Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 133 SER Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 70 GLU Chi-restraints excluded: chain L residue 21 MET Chi-restraints excluded: chain L residue 28 LYS Chi-restraints excluded: chain L residue 393 ASP Chi-restraints excluded: chain L residue 544 MET Chi-restraints excluded: chain L residue 566 ILE Chi-restraints excluded: chain M residue 113 MET Chi-restraints excluded: chain M residue 130 LEU Chi-restraints excluded: chain M residue 168 GLN Chi-restraints excluded: chain P residue 312 LEU Chi-restraints excluded: chain P residue 322 ARG Chi-restraints excluded: chain S residue 90 LEU Chi-restraints excluded: chain T residue 34 SER Chi-restraints excluded: chain U residue 37 MET Chi-restraints excluded: chain W residue 68 LYS Chi-restraints excluded: chain W residue 96 VAL Chi-restraints excluded: chain X residue 130 VAL Chi-restraints excluded: chain Y residue 114 CYS Chi-restraints excluded: chain Y residue 119 LEU Chi-restraints excluded: chain Y residue 130 GLU Chi-restraints excluded: chain Z residue 13 VAL Chi-restraints excluded: chain a residue 69 ILE Chi-restraints excluded: chain c residue 11 SER Chi-restraints excluded: chain d residue 92 SER Chi-restraints excluded: chain f residue 14 VAL Chi-restraints excluded: chain f residue 53 GLU Chi-restraints excluded: chain g residue 70 LEU Chi-restraints excluded: chain j residue 43 ASP Chi-restraints excluded: chain j residue 45 ASP Chi-restraints excluded: chain o residue 80 LYS Chi-restraints excluded: chain o residue 118 GLU Chi-restraints excluded: chain p residue 24 SER Chi-restraints excluded: chain p residue 38 LEU Chi-restraints excluded: chain q residue 142 THR Chi-restraints excluded: chain r residue 68 VAL Chi-restraints excluded: chain r residue 101 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 785 random chunks: chunk 732 optimal weight: 8.9990 chunk 85 optimal weight: 10.0000 chunk 432 optimal weight: 2.9990 chunk 554 optimal weight: 7.9990 chunk 429 optimal weight: 4.9990 chunk 639 optimal weight: 6.9990 chunk 424 optimal weight: 1.9990 chunk 756 optimal weight: 7.9990 chunk 473 optimal weight: 7.9990 chunk 461 optimal weight: 8.9990 chunk 349 optimal weight: 5.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 83 ASN C 69 ASN F 257 ASN F 432 GLN G 16 GLN ** G 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 5 ASN H 194 ASN L 479 GLN L 605 HIS N 268 GLN Q 9 GLN W 45 ASN X 15 GLN X 64 GLN Y 128 GLN Z 24 ASN a 58 ASN c 34 GLN f 30 ASN k 32 GLN l 147 ASN m 32 GLN m 116 GLN q 5 GLN q 52 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.244 68054 Z= 0.588 Angle : 1.356 50.549 92083 Z= 0.860 Chirality : 0.264 6.780 10085 Planarity : 0.005 0.063 11467 Dihedral : 10.863 173.876 10515 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.44 % Allowed : 8.52 % Favored : 90.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 7931 helix: 1.44 (0.08), residues: 4310 sheet: 0.36 (0.26), residues: 348 loop : 0.38 (0.11), residues: 3273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP n 71 HIS 0.009 0.001 HIS M 30 PHE 0.029 0.002 PHE M 122 TYR 0.029 0.002 TYR I 118 ARG 0.015 0.001 ARG p 14 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15862 Ramachandran restraints generated. 7931 Oldfield, 0 Emsley, 7931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15862 Ramachandran restraints generated. 7931 Oldfield, 0 Emsley, 7931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1059 residues out of total 7028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 958 time to evaluate : 6.344 Fit side-chains revert: symmetry clash REVERT: B 32 LYS cc_start: 0.8429 (OUTLIER) cc_final: 0.8102 (mmpt) REVERT: B 48 MET cc_start: 0.7930 (tmt) cc_final: 0.7667 (tmt) REVERT: B 59 MET cc_start: 0.8031 (OUTLIER) cc_final: 0.7061 (tpt) REVERT: B 165 LYS cc_start: 0.8998 (OUTLIER) cc_final: 0.8348 (mmtp) REVERT: B 175 ILE cc_start: 0.9231 (OUTLIER) cc_final: 0.8771 (mt) REVERT: B 176 TRP cc_start: 0.8657 (t-100) cc_final: 0.8250 (t60) REVERT: D 407 LYS cc_start: 0.8546 (OUTLIER) cc_final: 0.7795 (mptt) REVERT: D 410 MET cc_start: 0.8702 (OUTLIER) cc_final: 0.7682 (mmt) REVERT: F 249 ARG cc_start: 0.8039 (mtm110) cc_final: 0.7716 (mtm110) REVERT: G 444 GLN cc_start: 0.7779 (OUTLIER) cc_final: 0.7287 (tp40) REVERT: G 447 LYS cc_start: 0.8539 (OUTLIER) cc_final: 0.8174 (mptp) REVERT: G 613 TYR cc_start: 0.9383 (OUTLIER) cc_final: 0.8744 (p90) REVERT: K 70 GLU cc_start: 0.7554 (OUTLIER) cc_final: 0.7343 (tt0) REVERT: N 117 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.7291 (mt-10) REVERT: N 322 LYS cc_start: 0.7915 (mttm) cc_final: 0.7659 (mmtp) REVERT: P 322 ARG cc_start: 0.8195 (OUTLIER) cc_final: 0.7344 (mtm180) REVERT: S 90 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8805 (mm) REVERT: U 37 MET cc_start: 0.7730 (OUTLIER) cc_final: 0.6312 (mmt) REVERT: W 68 LYS cc_start: 0.8730 (OUTLIER) cc_final: 0.8484 (tmtp) REVERT: Y 60 PHE cc_start: 0.7350 (t80) cc_final: 0.7058 (t80) REVERT: Y 130 GLU cc_start: 0.8932 (OUTLIER) cc_final: 0.7617 (mt-10) REVERT: f 53 GLU cc_start: 0.7187 (OUTLIER) cc_final: 0.6719 (mp0) REVERT: o 45 MET cc_start: 0.8773 (mtm) cc_final: 0.8490 (mtm) REVERT: q 4 LEU cc_start: 0.8117 (OUTLIER) cc_final: 0.7916 (mm) REVERT: r 101 LYS cc_start: 0.8146 (OUTLIER) cc_final: 0.7881 (mtmm) outliers start: 101 outliers final: 47 residues processed: 1004 average time/residue: 1.8232 time to fit residues: 2290.7785 Evaluate side-chains 1015 residues out of total 7028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 949 time to evaluate : 6.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 59 MET Chi-restraints excluded: chain B residue 165 LYS Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 407 LYS Chi-restraints excluded: chain D residue 410 MET Chi-restraints excluded: chain D residue 420 THR Chi-restraints excluded: chain E residue 114 ASP Chi-restraints excluded: chain E residue 192 SER Chi-restraints excluded: chain F residue 314 THR Chi-restraints excluded: chain G residue 444 GLN Chi-restraints excluded: chain G residue 447 LYS Chi-restraints excluded: chain G residue 613 TYR Chi-restraints excluded: chain H residue 121 TRP Chi-restraints excluded: chain H residue 194 ASN Chi-restraints excluded: chain H residue 205 SER Chi-restraints excluded: chain H residue 234 MET Chi-restraints excluded: chain H residue 289 LEU Chi-restraints excluded: chain I residue 122 CYS Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 133 SER Chi-restraints excluded: chain K residue 70 GLU Chi-restraints excluded: chain L residue 21 MET Chi-restraints excluded: chain L residue 28 LYS Chi-restraints excluded: chain L residue 393 ASP Chi-restraints excluded: chain L residue 566 ILE Chi-restraints excluded: chain L residue 568 LEU Chi-restraints excluded: chain M residue 113 MET Chi-restraints excluded: chain M residue 130 LEU Chi-restraints excluded: chain N residue 117 GLU Chi-restraints excluded: chain P residue 312 LEU Chi-restraints excluded: chain P residue 322 ARG Chi-restraints excluded: chain P residue 338 LYS Chi-restraints excluded: chain S residue 90 LEU Chi-restraints excluded: chain T residue 34 SER Chi-restraints excluded: chain U residue 37 MET Chi-restraints excluded: chain W residue 68 LYS Chi-restraints excluded: chain W residue 120 SER Chi-restraints excluded: chain X residue 130 VAL Chi-restraints excluded: chain Y residue 114 CYS Chi-restraints excluded: chain Y residue 119 LEU Chi-restraints excluded: chain Y residue 130 GLU Chi-restraints excluded: chain Z residue 13 VAL Chi-restraints excluded: chain Z residue 25 LEU Chi-restraints excluded: chain a residue 69 ILE Chi-restraints excluded: chain c residue 11 SER Chi-restraints excluded: chain d residue 20 SER Chi-restraints excluded: chain d residue 92 SER Chi-restraints excluded: chain f residue 53 GLU Chi-restraints excluded: chain g residue 60 VAL Chi-restraints excluded: chain j residue 45 ASP Chi-restraints excluded: chain k residue 87 LEU Chi-restraints excluded: chain l residue 151 GLU Chi-restraints excluded: chain o residue 80 LYS Chi-restraints excluded: chain o residue 118 GLU Chi-restraints excluded: chain p residue 24 SER Chi-restraints excluded: chain p residue 38 LEU Chi-restraints excluded: chain q residue 4 LEU Chi-restraints excluded: chain q residue 142 THR Chi-restraints excluded: chain r residue 68 VAL Chi-restraints excluded: chain r residue 101 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 785 random chunks: chunk 468 optimal weight: 7.9990 chunk 302 optimal weight: 0.8980 chunk 451 optimal weight: 0.7980 chunk 227 optimal weight: 1.9990 chunk 148 optimal weight: 4.9990 chunk 146 optimal weight: 0.5980 chunk 481 optimal weight: 0.9990 chunk 515 optimal weight: 6.9990 chunk 374 optimal weight: 0.6980 chunk 70 optimal weight: 0.7980 chunk 594 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 ASN C 69 ASN F 257 ASN F 432 GLN F 435 GLN G 461 ASN G 535 GLN H 194 ASN K 83 ASN L 479 GLN L 605 HIS S 75 ASN W 45 ASN X 64 GLN Y 128 GLN Z 24 ASN a 58 ASN c 34 GLN f 30 ASN k 32 GLN l 147 ASN m 32 GLN m 116 GLN q 52 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.247 68054 Z= 0.436 Angle : 1.297 50.565 92083 Z= 0.838 Chirality : 0.255 6.439 10085 Planarity : 0.004 0.060 11467 Dihedral : 10.207 172.381 10515 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.01 % Allowed : 9.18 % Favored : 89.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 7931 helix: 1.76 (0.08), residues: 4274 sheet: 0.28 (0.26), residues: 357 loop : 0.46 (0.11), residues: 3300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP L 144 HIS 0.006 0.001 HIS G 101 PHE 0.029 0.001 PHE N 292 TYR 0.022 0.001 TYR L 422 ARG 0.014 0.000 ARG p 14 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15862 Ramachandran restraints generated. 7931 Oldfield, 0 Emsley, 7931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15862 Ramachandran restraints generated. 7931 Oldfield, 0 Emsley, 7931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1044 residues out of total 7028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 973 time to evaluate : 6.599 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 48 MET cc_start: 0.7928 (tmt) cc_final: 0.7669 (tmt) REVERT: B 165 LYS cc_start: 0.8936 (OUTLIER) cc_final: 0.8688 (mttp) REVERT: B 175 ILE cc_start: 0.9217 (OUTLIER) cc_final: 0.8708 (mt) REVERT: B 176 TRP cc_start: 0.8621 (t-100) cc_final: 0.8242 (t60) REVERT: D 323 ILE cc_start: 0.9323 (OUTLIER) cc_final: 0.8862 (pp) REVERT: D 407 LYS cc_start: 0.8547 (OUTLIER) cc_final: 0.7799 (mptt) REVERT: D 410 MET cc_start: 0.8703 (OUTLIER) cc_final: 0.7625 (mmt) REVERT: F 249 ARG cc_start: 0.8007 (mtm110) cc_final: 0.7699 (mtm110) REVERT: G 613 TYR cc_start: 0.9332 (OUTLIER) cc_final: 0.8778 (p90) REVERT: H 234 MET cc_start: 0.7981 (OUTLIER) cc_final: 0.7634 (mmt) REVERT: J 111 LYS cc_start: 0.7075 (mmtt) cc_final: 0.6467 (mtpp) REVERT: M 168 GLN cc_start: 0.8874 (OUTLIER) cc_final: 0.8583 (tt0) REVERT: N 117 GLU cc_start: 0.7700 (OUTLIER) cc_final: 0.7162 (mt-10) REVERT: S 90 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8707 (mm) REVERT: Y 60 PHE cc_start: 0.7297 (t80) cc_final: 0.7057 (t80) REVERT: Y 119 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8353 (mt) REVERT: Y 130 GLU cc_start: 0.8865 (OUTLIER) cc_final: 0.7574 (mt-10) REVERT: o 45 MET cc_start: 0.8707 (mtm) cc_final: 0.8480 (mtm) REVERT: q 4 LEU cc_start: 0.8033 (OUTLIER) cc_final: 0.7833 (mm) REVERT: r 101 LYS cc_start: 0.8172 (OUTLIER) cc_final: 0.7913 (mtmm) outliers start: 71 outliers final: 31 residues processed: 1003 average time/residue: 1.8258 time to fit residues: 2295.7090 Evaluate side-chains 1003 residues out of total 7028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 958 time to evaluate : 6.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 165 LYS Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 323 ILE Chi-restraints excluded: chain D residue 407 LYS Chi-restraints excluded: chain D residue 410 MET Chi-restraints excluded: chain D residue 420 THR Chi-restraints excluded: chain E residue 114 ASP Chi-restraints excluded: chain F residue 362 CYS Chi-restraints excluded: chain G residue 444 GLN Chi-restraints excluded: chain G residue 613 TYR Chi-restraints excluded: chain H residue 121 TRP Chi-restraints excluded: chain H residue 234 MET Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 133 SER Chi-restraints excluded: chain L residue 21 MET Chi-restraints excluded: chain L residue 28 LYS Chi-restraints excluded: chain L residue 393 ASP Chi-restraints excluded: chain L residue 566 ILE Chi-restraints excluded: chain L residue 568 LEU Chi-restraints excluded: chain M residue 113 MET Chi-restraints excluded: chain M residue 130 LEU Chi-restraints excluded: chain M residue 168 GLN Chi-restraints excluded: chain N residue 117 GLU Chi-restraints excluded: chain N residue 320 MET Chi-restraints excluded: chain P residue 312 LEU Chi-restraints excluded: chain S residue 75 ASN Chi-restraints excluded: chain S residue 90 LEU Chi-restraints excluded: chain Y residue 114 CYS Chi-restraints excluded: chain Y residue 119 LEU Chi-restraints excluded: chain Y residue 130 GLU Chi-restraints excluded: chain a residue 12 MET Chi-restraints excluded: chain c residue 11 SER Chi-restraints excluded: chain d residue 92 SER Chi-restraints excluded: chain f residue 14 VAL Chi-restraints excluded: chain g residue 60 VAL Chi-restraints excluded: chain n residue 158 LYS Chi-restraints excluded: chain o residue 80 LYS Chi-restraints excluded: chain p residue 24 SER Chi-restraints excluded: chain p residue 38 LEU Chi-restraints excluded: chain q residue 4 LEU Chi-restraints excluded: chain q residue 142 THR Chi-restraints excluded: chain r residue 101 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 785 random chunks: chunk 688 optimal weight: 0.0980 chunk 724 optimal weight: 7.9990 chunk 661 optimal weight: 2.9990 chunk 705 optimal weight: 1.9990 chunk 424 optimal weight: 0.0570 chunk 307 optimal weight: 3.9990 chunk 553 optimal weight: 0.9980 chunk 216 optimal weight: 6.9990 chunk 637 optimal weight: 2.9990 chunk 666 optimal weight: 0.9980 chunk 702 optimal weight: 10.0000 overall best weight: 0.8300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 83 ASN C 211 GLN F 432 GLN F 435 GLN F 436 GLN G 16 GLN G 237 ASN G 535 GLN H 194 ASN K 83 ASN L 479 GLN Q 9 GLN S 75 ASN W 45 ASN X 15 GLN Y 128 GLN Y 133 GLN Z 24 ASN c 34 GLN e 69 GLN f 30 ASN k 32 GLN l 147 ASN m 116 GLN q 5 GLN q 52 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.247 68054 Z= 0.436 Angle : 1.295 50.547 92083 Z= 0.836 Chirality : 0.256 6.439 10085 Planarity : 0.004 0.073 11467 Dihedral : 9.871 171.218 10515 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 0.88 % Allowed : 9.38 % Favored : 89.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 1.79 (0.09), residues: 7931 helix: 1.85 (0.08), residues: 4272 sheet: 0.32 (0.26), residues: 355 loop : 0.54 (0.11), residues: 3304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP L 144 HIS 0.006 0.001 HIS G 101 PHE 0.028 0.001 PHE N 292 TYR 0.027 0.001 TYR k 85 ARG 0.017 0.000 ARG p 14 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15862 Ramachandran restraints generated. 7931 Oldfield, 0 Emsley, 7931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15862 Ramachandran restraints generated. 7931 Oldfield, 0 Emsley, 7931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1027 residues out of total 7028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 965 time to evaluate : 6.315 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 48 MET cc_start: 0.7932 (tmt) cc_final: 0.7670 (tmt) REVERT: B 175 ILE cc_start: 0.9209 (OUTLIER) cc_final: 0.8702 (mt) REVERT: B 176 TRP cc_start: 0.8618 (t-100) cc_final: 0.8216 (t60) REVERT: D 323 ILE cc_start: 0.9326 (OUTLIER) cc_final: 0.8819 (pp) REVERT: F 249 ARG cc_start: 0.8032 (mtm110) cc_final: 0.7708 (mtm110) REVERT: G 613 TYR cc_start: 0.9308 (OUTLIER) cc_final: 0.8656 (p90) REVERT: H 234 MET cc_start: 0.7965 (OUTLIER) cc_final: 0.7676 (mmt) REVERT: J 111 LYS cc_start: 0.7054 (mmtt) cc_final: 0.6459 (mtpp) REVERT: K 70 GLU cc_start: 0.7533 (OUTLIER) cc_final: 0.7328 (tt0) REVERT: M 168 GLN cc_start: 0.8851 (OUTLIER) cc_final: 0.8570 (tt0) REVERT: S 90 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8698 (mm) REVERT: W 68 LYS cc_start: 0.8685 (OUTLIER) cc_final: 0.8417 (tmtp) REVERT: Y 60 PHE cc_start: 0.7330 (t80) cc_final: 0.7105 (t80) REVERT: Y 119 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.8317 (mt) REVERT: o 45 MET cc_start: 0.8720 (mtm) cc_final: 0.8508 (mtm) REVERT: q 4 LEU cc_start: 0.8045 (OUTLIER) cc_final: 0.7844 (mm) REVERT: r 101 LYS cc_start: 0.8163 (OUTLIER) cc_final: 0.7908 (mtmm) outliers start: 62 outliers final: 30 residues processed: 996 average time/residue: 1.8583 time to fit residues: 2317.8387 Evaluate side-chains 996 residues out of total 7028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 955 time to evaluate : 6.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 323 ILE Chi-restraints excluded: chain D residue 420 THR Chi-restraints excluded: chain E residue 114 ASP Chi-restraints excluded: chain G residue 444 GLN Chi-restraints excluded: chain G residue 613 TYR Chi-restraints excluded: chain H residue 121 TRP Chi-restraints excluded: chain H residue 194 ASN Chi-restraints excluded: chain H residue 234 MET Chi-restraints excluded: chain J residue 133 SER Chi-restraints excluded: chain K residue 70 GLU Chi-restraints excluded: chain L residue 21 MET Chi-restraints excluded: chain L residue 28 LYS Chi-restraints excluded: chain L residue 393 ASP Chi-restraints excluded: chain L residue 568 LEU Chi-restraints excluded: chain M residue 113 MET Chi-restraints excluded: chain M residue 130 LEU Chi-restraints excluded: chain M residue 168 GLN Chi-restraints excluded: chain N residue 320 MET Chi-restraints excluded: chain P residue 312 LEU Chi-restraints excluded: chain S residue 75 ASN Chi-restraints excluded: chain S residue 90 LEU Chi-restraints excluded: chain W residue 68 LYS Chi-restraints excluded: chain X residue 130 VAL 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 c residue 11 SER Chi-restraints excluded: chain d residue 92 SER Chi-restraints excluded: chain f residue 14 VAL Chi-restraints excluded: chain g residue 70 LEU Chi-restraints excluded: chain n residue 158 LYS Chi-restraints excluded: chain o residue 80 LYS Chi-restraints excluded: chain p residue 24 SER Chi-restraints excluded: chain p residue 38 LEU Chi-restraints excluded: chain q residue 4 LEU Chi-restraints excluded: chain q residue 142 THR Chi-restraints excluded: chain r residue 101 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 785 random chunks: chunk 462 optimal weight: 1.9990 chunk 745 optimal weight: 1.9990 chunk 455 optimal weight: 0.7980 chunk 353 optimal weight: 0.9980 chunk 518 optimal weight: 5.9990 chunk 782 optimal weight: 10.0000 chunk 719 optimal weight: 0.0970 chunk 622 optimal weight: 4.9990 chunk 64 optimal weight: 6.9990 chunk 481 optimal weight: 1.9990 chunk 381 optimal weight: 0.7980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 ASN F 432 GLN F 435 GLN G 16 GLN ** G 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 535 GLN G 643 GLN H 194 ASN H 317 GLN L 479 GLN M 144 ASN Q 9 GLN W 45 ASN X 15 GLN Y 128 GLN Z 24 ASN Z 85 GLN a 58 ASN e 69 GLN f 30 ASN k 32 GLN ** l 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 147 ASN m 32 GLN m 116 GLN q 5 GLN q 52 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.246 68054 Z= 0.443 Angle : 1.329 59.192 92083 Z= 0.858 Chirality : 0.256 6.441 10085 Planarity : 0.004 0.125 11467 Dihedral : 9.870 171.223 10515 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 0.78 % Allowed : 9.68 % Favored : 89.54 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 3.57 % 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: 1.79 (0.09), residues: 7931 helix: 1.85 (0.08), residues: 4272 sheet: 0.29 (0.26), residues: 355 loop : 0.54 (0.11), residues: 3304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP L 144 HIS 0.006 0.001 HIS G 101 PHE 0.028 0.001 PHE N 292 TYR 0.021 0.001 TYR L 422 ARG 0.017 0.000 ARG p 14 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15862 Ramachandran restraints generated. 7931 Oldfield, 0 Emsley, 7931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15862 Ramachandran restraints generated. 7931 Oldfield, 0 Emsley, 7931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1011 residues out of total 7028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 956 time to evaluate : 6.252 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 48 MET cc_start: 0.7934 (tmt) cc_final: 0.7674 (tmt) REVERT: B 175 ILE cc_start: 0.9210 (OUTLIER) cc_final: 0.8703 (mt) REVERT: B 176 TRP cc_start: 0.8618 (t-100) cc_final: 0.8219 (t60) REVERT: F 249 ARG cc_start: 0.8032 (mtm110) cc_final: 0.7708 (mtm110) REVERT: G 447 LYS cc_start: 0.8519 (OUTLIER) cc_final: 0.8194 (mptp) REVERT: G 613 TYR cc_start: 0.9308 (OUTLIER) cc_final: 0.8657 (p90) REVERT: H 234 MET cc_start: 0.7966 (OUTLIER) cc_final: 0.7679 (mmt) REVERT: J 111 LYS cc_start: 0.7053 (mmtt) cc_final: 0.6463 (mtpp) REVERT: K 70 GLU cc_start: 0.7531 (OUTLIER) cc_final: 0.7327 (tt0) REVERT: M 168 GLN cc_start: 0.8852 (OUTLIER) cc_final: 0.8570 (tt0) REVERT: S 90 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8698 (mm) REVERT: W 68 LYS cc_start: 0.8685 (OUTLIER) cc_final: 0.8418 (tmtp) REVERT: Y 60 PHE cc_start: 0.7329 (t80) cc_final: 0.7112 (t80) REVERT: Y 119 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.8317 (mt) REVERT: o 45 MET cc_start: 0.8721 (mtm) cc_final: 0.8508 (mtm) REVERT: r 101 LYS cc_start: 0.8165 (OUTLIER) cc_final: 0.7910 (mtmm) outliers start: 55 outliers final: 31 residues processed: 984 average time/residue: 1.8325 time to fit residues: 2257.6507 Evaluate side-chains 995 residues out of total 7028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 954 time to evaluate : 6.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 420 THR Chi-restraints excluded: chain E residue 114 ASP Chi-restraints excluded: chain F residue 362 CYS Chi-restraints excluded: chain G residue 444 GLN Chi-restraints excluded: chain G residue 447 LYS Chi-restraints excluded: chain G residue 613 TYR Chi-restraints excluded: chain H residue 121 TRP Chi-restraints excluded: chain H residue 234 MET Chi-restraints excluded: chain K residue 70 GLU Chi-restraints excluded: chain L residue 21 MET Chi-restraints excluded: chain L residue 28 LYS Chi-restraints excluded: chain L residue 393 ASP Chi-restraints excluded: chain L residue 568 LEU Chi-restraints excluded: chain M residue 113 MET Chi-restraints excluded: chain M residue 130 LEU Chi-restraints excluded: chain M residue 168 GLN Chi-restraints excluded: chain N residue 320 MET Chi-restraints excluded: chain O residue 135 LEU Chi-restraints excluded: chain P residue 312 LEU Chi-restraints excluded: chain S residue 90 LEU Chi-restraints excluded: chain W residue 68 LYS Chi-restraints excluded: chain X residue 130 VAL 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 c residue 11 SER Chi-restraints excluded: chain d residue 92 SER Chi-restraints excluded: chain f residue 14 VAL Chi-restraints excluded: chain g residue 70 LEU Chi-restraints excluded: chain k residue 85 TYR Chi-restraints excluded: chain n residue 158 LYS Chi-restraints excluded: chain o residue 80 LYS Chi-restraints excluded: chain p residue 24 SER Chi-restraints excluded: chain p residue 38 LEU Chi-restraints excluded: chain q residue 142 THR Chi-restraints excluded: chain r residue 101 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 785 random chunks: chunk 494 optimal weight: 1.9990 chunk 663 optimal weight: 0.5980 chunk 190 optimal weight: 9.9990 chunk 574 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 173 optimal weight: 6.9990 chunk 623 optimal weight: 4.9990 chunk 261 optimal weight: 8.9990 chunk 640 optimal weight: 4.9990 chunk 78 optimal weight: 0.6980 chunk 114 optimal weight: 0.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 ASN F 432 GLN F 435 GLN G 16 GLN ** G 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 535 GLN G 643 GLN ** H 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 479 GLN M 144 ASN Q 9 GLN W 45 ASN X 15 GLN Y 128 GLN Z 24 ASN a 58 ASN f 30 ASN k 32 GLN ** l 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 147 ASN m 116 GLN q 5 GLN q 52 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.099946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.078350 restraints weight = 62662.685| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 1.11 r_work: 0.2808 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.2707 rms_B_bonded: 2.41 restraints_weight: 0.2500 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8916 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.246 68054 Z= 0.443 Angle : 1.329 59.192 92083 Z= 0.858 Chirality : 0.256 6.441 10085 Planarity : 0.004 0.125 11467 Dihedral : 9.870 171.223 10515 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 0.64 % Allowed : 9.83 % Favored : 89.53 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 3.57 % 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: 1.79 (0.09), residues: 7931 helix: 1.85 (0.08), residues: 4272 sheet: 0.29 (0.26), residues: 355 loop : 0.54 (0.11), residues: 3304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP L 144 HIS 0.006 0.001 HIS G 101 PHE 0.028 0.001 PHE N 292 TYR 0.021 0.001 TYR L 422 ARG 0.017 0.000 ARG p 14 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 32574.16 seconds wall clock time: 563 minutes 51.44 seconds (33831.44 seconds total)