Starting phenix.real_space_refine on Fri Jun 28 13:15:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r46_14277/06_2024/7r46_14277_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r46_14277/06_2024/7r46_14277.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r46_14277/06_2024/7r46_14277_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r46_14277/06_2024/7r46_14277_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r46_14277/06_2024/7r46_14277_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r46_14277/06_2024/7r46_14277.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r46_14277/06_2024/7r46_14277.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r46_14277/06_2024/7r46_14277_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r46_14277/06_2024/7r46_14277_updated.pdb" } resolution = 2.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.008 sd= 1.048 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 37 5.49 5 Mg 1 5.21 5 S 466 5.16 5 Cl 1 4.86 5 C 43137 2.51 5 N 11038 2.21 5 O 12903 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 105": "OE1" <-> "OE2" Residue "B GLU 27": "OE1" <-> "OE2" Residue "B ARG 71": "NH1" <-> "NH2" Residue "B ARG 111": "NH1" <-> "NH2" Residue "B TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 170": "OE1" <-> "OE2" Residue "C ARG 8": "NH1" <-> "NH2" Residue "C ARG 12": "NH1" <-> "NH2" Residue "C GLU 27": "OE1" <-> "OE2" Residue "C GLU 31": "OE1" <-> "OE2" Residue "C GLU 49": "OE1" <-> "OE2" Residue "C PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 149": "NH1" <-> "NH2" Residue "C ASP 154": "OD1" <-> "OD2" Residue "C PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 173": "OE1" <-> "OE2" Residue "C ASP 178": "OD1" <-> "OD2" Residue "C GLU 179": "OE1" <-> "OE2" Residue "D ARG 2": "NH1" <-> "NH2" Residue "D GLU 12": "OE1" <-> "OE2" Residue "D TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 123": "OE1" <-> "OE2" Residue "D PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 179": "OE1" <-> "OE2" Residue "D ARG 221": "NH1" <-> "NH2" Residue "D ARG 233": "NH1" <-> "NH2" Residue "D ASP 241": "OD1" <-> "OD2" Residue "D GLU 248": "OE1" <-> "OE2" Residue "D GLU 303": "OE1" <-> "OE2" Residue "D GLU 343": "OE1" <-> "OE2" Residue "D GLU 427": "OE1" <-> "OE2" Residue "D ASP 429": "OD1" <-> "OD2" Residue "E GLU 18": "OE1" <-> "OE2" Residue "E PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 32": "OE1" <-> "OE2" Residue "E ASP 158": "OD1" <-> "OD2" Residue "E ASP 168": "OD1" <-> "OD2" Residue "E ASP 174": "OD1" <-> "OD2" Residue "E ARG 190": "NH1" <-> "NH2" Residue "F PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 32": "NH1" <-> "NH2" Residue "F GLU 59": "OE1" <-> "OE2" Residue "F PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 109": "OE1" <-> "OE2" Residue "F ARG 112": "NH1" <-> "NH2" Residue "F ARG 132": "NH1" <-> "NH2" Residue "F ARG 139": "NH1" <-> "NH2" Residue "F GLU 158": "OE1" <-> "OE2" Residue "F GLU 189": "OE1" <-> "OE2" Residue "F GLU 194": "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 ARG 349": "NH1" <-> "NH2" Residue "F GLU 352": "OE1" <-> "OE2" Residue "F GLU 367": "OE1" <-> "OE2" Residue "F GLU 394": "OE1" <-> "OE2" Residue "F PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 425": "OE1" <-> "OE2" Residue "F ARG 429": "NH1" <-> "NH2" Residue "F PHE 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 14": "OD1" <-> "OD2" Residue "G GLU 21": "OE1" <-> "OE2" Residue "G GLU 31": "OE1" <-> "OE2" Residue "G ARG 39": "NH1" <-> "NH2" Residue "G GLU 44": "OE1" <-> "OE2" 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 ASP 180": "OD1" <-> "OD2" Residue "G ARG 218": "NH1" <-> "NH2" Residue "G ARG 243": "NH1" <-> "NH2" Residue "G ARG 253": "NH1" <-> "NH2" Residue "G GLU 261": "OE1" <-> "OE2" Residue "G TYR 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 285": "NH1" <-> "NH2" Residue "G ARG 302": "NH1" <-> "NH2" Residue "G ASP 339": "OD1" <-> "OD2" Residue "G ARG 385": "NH1" <-> "NH2" Residue "G ARG 418": "NH1" <-> "NH2" Residue "G GLU 512": "OE1" <-> "OE2" Residue "G PHE 523": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 617": "OD1" <-> "OD2" Residue "G GLU 625": "OE1" <-> "OE2" Residue "G GLU 637": "OE1" <-> "OE2" Residue "G ASP 675": "OD1" <-> "OD2" Residue "G GLU 693": "OE1" <-> "OE2" Residue "H ARG 25": "NH1" <-> "NH2" Residue "H ARG 34": "NH1" <-> "NH2" Residue "H ARG 62": "NH1" <-> "NH2" Residue "H TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 143": "OE1" <-> "OE2" Residue "H GLU 170": "OE1" <-> "OE2" Residue "H TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 8": "NH1" <-> "NH2" Residue "I ASP 19": "OD1" <-> "OD2" Residue "I TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 108": "NH1" <-> "NH2" Residue "I ASP 129": "OD1" <-> "OD2" Residue "I GLU 164": "OE1" <-> "OE2" Residue "J TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 GLU 100": "OE1" <-> "OE2" Residue "J TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 110": "OD1" <-> "OD2" Residue "J GLU 118": "OE1" <-> "OE2" Residue "J GLU 138": "OE1" <-> "OE2" Residue "J GLU 170": "OE1" <-> "OE2" Residue "J ARG 173": "NH1" <-> "NH2" Residue "L TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 161": "NH1" <-> "NH2" Residue "L ASP 197": "OD1" <-> "OD2" Residue "L ASP 208": "OD1" <-> "OD2" Residue "L GLU 238": "OE1" <-> "OE2" Residue "L ARG 262": "NH1" <-> "NH2" Residue "L GLU 268": "OE1" <-> "OE2" Residue "L ASP 297": "OD1" <-> "OD2" Residue "L ASP 352": "OD1" <-> "OD2" Residue "L GLU 353": "OE1" <-> "OE2" Residue "L TYR 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 445": "OE1" <-> "OE2" Residue "L GLU 503": "OE1" <-> "OE2" Residue "L TYR 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 588": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 141": "OE1" <-> "OE2" Residue "M ARG 142": "NH1" <-> "NH2" Residue "M TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 222": "OE1" <-> "OE2" Residue "M ASP 255": "OD1" <-> "OD2" Residue "M PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 335": "OE1" <-> "OE2" Residue "M ARG 346": "NH1" <-> "NH2" Residue "M GLU 378": "OE1" <-> "OE2" Residue "M TYR 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 432": "NH1" <-> "NH2" Residue "M TYR 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 295": "NH1" <-> "NH2" Residue "N PHE 325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 104": "NH1" <-> "NH2" Residue "O GLU 113": "OE1" <-> "OE2" Residue "O ARG 126": "NH1" <-> "NH2" Residue "O ASP 131": "OD1" <-> "OD2" Residue "O GLU 162": "OE1" <-> "OE2" Residue "O ASP 173": "OD1" <-> "OD2" 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 253": "OD1" <-> "OD2" Residue "O GLU 295": "OE1" <-> "OE2" Residue "O PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 302": "NH1" <-> "NH2" Residue "O ARG 305": "NH1" <-> "NH2" Residue "O TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 40": "NH1" <-> "NH2" Residue "P ARG 50": "NH1" <-> "NH2" Residue "P ASP 72": "OD1" <-> "OD2" 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 GLU 98": "OE1" <-> "OE2" Residue "P PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 175": "OE1" <-> "OE2" Residue "P ARG 235": "NH1" <-> "NH2" Residue "P TYR 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 251": "NH1" <-> "NH2" Residue "Q ASP 14": "OD1" <-> "OD2" Residue "Q PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 "R GLU 78": "OE1" <-> "OE2" Residue "S GLU 37": "OE1" <-> "OE2" Residue "S GLU 42": "OE1" <-> "OE2" Residue "S ASP 59": "OD1" <-> "OD2" Residue "S TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 9": "OE1" <-> "OE2" Residue "T GLU 49": "OE1" <-> "OE2" Residue "T GLU 55": "OE1" <-> "OE2" Residue "T ASP 82": "OD1" <-> "OD2" Residue "U TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 49": "OE1" <-> "OE2" Residue "U GLU 55": "OE1" <-> "OE2" Residue "U GLU 61": "OE1" <-> "OE2" Residue "U GLU 68": "OE1" <-> "OE2" Residue "U GLU 75": "OE1" <-> "OE2" Residue "V GLU 17": "OE1" <-> "OE2" Residue "V ARG 22": "NH1" <-> "NH2" Residue "V ASP 63": "OD1" <-> "OD2" Residue "V GLU 68": "OE1" <-> "OE2" Residue "V GLU 84": "OE1" <-> "OE2" Residue "V GLU 86": "OE1" <-> "OE2" Residue "V GLU 100": "OE1" <-> "OE2" Residue "V GLU 104": "OE1" <-> "OE2" Residue "V GLU 105": "OE1" <-> "OE2" Residue "W ASP 24": "OD1" <-> "OD2" Residue "W GLU 27": "OE1" <-> "OE2" Residue "W ARG 30": "NH1" <-> "NH2" Residue "W TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 65": "OE1" <-> "OE2" Residue "W GLU 89": "OE1" <-> "OE2" Residue "W PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 109": "OE1" <-> "OE2" Residue "X ASP 11": "OD1" <-> "OD2" 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 ASP 112": "OD1" <-> "OD2" Residue "X ARG 118": "NH1" <-> "NH2" Residue "X ARG 134": "NH1" <-> "NH2" Residue "X GLU 138": "OE1" <-> "OE2" Residue "X ARG 144": "NH1" <-> "NH2" Residue "X ARG 146": "NH1" <-> "NH2" Residue "X GLU 154": "OE1" <-> "OE2" Residue "Y TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 57": "NH1" <-> "NH2" Residue "Y ASP 85": "OD1" <-> "OD2" Residue "Y ARG 103": "NH1" <-> "NH2" Residue "Y GLU 137": "OE1" <-> "OE2" Residue "Z TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 82": "NH1" <-> "NH2" Residue "Z ASP 100": "OD1" <-> "OD2" Residue "Z GLU 108": "OE1" <-> "OE2" Residue "a GLU 4": "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 "b GLU 2": "OE1" <-> "OE2" Residue "b ARG 3": "NH1" <-> "NH2" Residue "b ARG 57": "NH1" <-> "NH2" Residue "c PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ASP 38": "OD1" <-> "OD2" Residue "c GLU 41": "OE1" <-> "OE2" Residue "c ARG 44": "NH1" <-> "NH2" Residue "d PHE 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 45": "OD1" <-> "OD2" Residue "d ARG 51": "NH1" <-> "NH2" Residue "d ARG 86": "NH1" <-> "NH2" Residue "d GLU 99": "OE1" <-> "OE2" Residue "d GLU 111": "OE1" <-> "OE2" Residue "d GLU 114": "OE1" <-> "OE2" Residue "d GLU 115": "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 "e GLU 64": "OE1" <-> "OE2" Residue "e GLU 83": "OE1" <-> "OE2" Residue "f TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ARG 28": "NH1" <-> "NH2" Residue "f GLU 32": "OE1" <-> "OE2" Residue "f PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ARG 46": "NH1" <-> "NH2" Residue "g GLU 35": "OE1" <-> "OE2" Residue "g ASP 43": "OD1" <-> "OD2" Residue "g ASP 50": "OD1" <-> "OD2" Residue "g GLU 87": "OE1" <-> "OE2" Residue "g GLU 94": "OE1" <-> "OE2" 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 57": "OE1" <-> "OE2" Residue "h TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 62": "OE1" <-> "OE2" Residue "h ARG 77": "NH1" <-> "NH2" Residue "h GLU 84": "OE1" <-> "OE2" Residue "h TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 99": "OE1" <-> "OE2" Residue "h GLU 102": "OE1" <-> "OE2" Residue "h ARG 112": "NH1" <-> "NH2" Residue "i GLU 6": "OE1" <-> "OE2" Residue "i ARG 18": "NH1" <-> "NH2" Residue "i GLU 26": "OE1" <-> "OE2" Residue "i TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i GLU 111": "OE1" <-> "OE2" Residue "i GLU 114": "OE1" <-> "OE2" Residue "j GLU 8": "OE1" <-> "OE2" Residue "j PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ASP 55": "OD1" <-> "OD2" Residue "j ASP 70": "OD1" <-> "OD2" Residue "k GLU 14": "OE1" <-> "OE2" Residue "k GLU 24": "OE1" <-> "OE2" Residue "k GLU 29": "OE1" <-> "OE2" Residue "k ARG 38": "NH1" <-> "NH2" Residue "k ARG 41": "NH1" <-> "NH2" Residue "k ASP 42": "OD1" <-> "OD2" Residue "k GLU 84": "OE1" <-> "OE2" Residue "k TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k GLU 88": "OE1" <-> "OE2" Residue "l ASP 7": "OD1" <-> "OD2" Residue "l GLU 19": "OE1" <-> "OE2" Residue "l ARG 30": "NH1" <-> "NH2" Residue "l GLU 32": "OE1" <-> "OE2" Residue "l GLU 120": "OE1" <-> "OE2" Residue "l GLU 141": "OE1" <-> "OE2" Residue "l ARG 142": "NH1" <-> "NH2" Residue "l ASP 145": "OD1" <-> "OD2" Residue "l GLU 149": "OE1" <-> "OE2" Residue "l TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l GLU 157": "OE1" <-> "OE2" Residue "m TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m GLU 27": "OE1" <-> "OE2" Residue "m ARG 39": "NH1" <-> "NH2" 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 ASP 121": "OD1" <-> "OD2" Residue "n ARG 21": "NH1" <-> "NH2" Residue "n ARG 37": "NH1" <-> "NH2" Residue "n ARG 64": "NH1" <-> "NH2" Residue "n GLU 65": "OE1" <-> "OE2" Residue "n GLU 67": "OE1" <-> "OE2" Residue "n GLU 68": "OE1" <-> "OE2" Residue "n GLU 69": "OE1" <-> "OE2" Residue "n GLU 83": "OE1" <-> "OE2" Residue "n GLU 91": "OE1" <-> "OE2" Residue "n ARG 92": "NH1" <-> "NH2" Residue "n TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n GLU 130": "OE1" <-> "OE2" Residue "n ARG 149": "NH1" <-> "NH2" Residue "o ARG 6": "NH1" <-> "NH2" Residue "o ASP 11": "OD1" <-> "OD2" Residue "o ASP 27": "OD1" <-> "OD2" Residue "o GLU 35": "OE1" <-> "OE2" Residue "o ARG 36": "NH1" <-> "NH2" Residue "o GLU 44": "OE1" <-> "OE2" Residue "o ASP 87": "OD1" <-> "OD2" Residue "o ASP 93": "OD1" <-> "OD2" Residue "o ARG 97": "NH1" <-> "NH2" Residue "o GLU 102": "OE1" <-> "OE2" 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 PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p ASP 37": "OD1" <-> "OD2" Residue "p ASP 41": "OD1" <-> "OD2" Residue "p GLU 52": "OE1" <-> "OE2" Residue "p TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p GLU 107": "OE1" <-> "OE2" Residue "p GLU 116": "OE1" <-> "OE2" Residue "p GLU 118": "OE1" <-> "OE2" Residue "p GLU 129": "OE1" <-> "OE2" Residue "p TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p GLU 171": "OE1" <-> "OE2" Residue "q GLU 2": "OE1" <-> "OE2" Residue "q ARG 21": "NH1" <-> "NH2" Residue "q PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ARG 29": "NH1" <-> "NH2" Residue "q GLU 67": "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 GLU 136": "OE1" <-> "OE2" Residue "q TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r GLU 29": "OE1" <-> "OE2" Residue "r ARG 59": "NH1" <-> "NH2" Residue "r GLU 104": "OE1" <-> "OE2" Residue "s ASP 57": "OD1" <-> "OD2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 67614 Number of models: 1 Model: "" Number of chains: 113 Chain: "A" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 814 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 4, 'TRANS': 96} 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: 1241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1241 Classifications: {'peptide': 155} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 144} Chain: "C" Number of atoms: 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: 3395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 3395 Classifications: {'peptide': 421} Link IDs: {'PTRANS': 26, 'TRANS': 394} Chain breaks: 1 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: 3310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3310 Classifications: {'peptide': 430} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 408} 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: 2462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2462 Classifications: {'peptide': 312} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 289} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 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: 739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 739 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 1, 'TRANS': 95} 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: 4784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4784 Classifications: {'peptide': 606} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 27, 'TRANS': 578} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'FME:plan-2': 1, 'PHE:plan': 1, 'ASN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "M" Number of atoms: 3654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3654 Classifications: {'peptide': 459} Link IDs: {'PCIS': 3, 'PTRANS': 17, 'TRANS': 438} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "N" Number of atoms: 2733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2733 Classifications: {'peptide': 347} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 325} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "O" Number of atoms: 2589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2589 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 15, 'TRANS': 304} Chain: "P" Number of atoms: 2298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2298 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 15, 'TRANS': 273} 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: 663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 663 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 4, 'TRANS': 77} Chain: "T" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 612 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "U" Number of atoms: 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: 1050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1050 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 7, 'TRANS': 118} 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: 1209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1209 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 11, 'TRANS': 133} 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: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 75 Unusual residues: {'3PE': 1, 'LMT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 Chain: "B" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 79 Unusual residues: {'3PE': 1, 'PC1': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 34 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: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 41 Unusual residues: {'3PE': 1, 'I49': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'3PE:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "I" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 98 Unusual residues: {'3PE': 2, 'SF4': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 20 Chain: "K" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 50 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'CDL:plan-3': 1, 'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 8 Chain: "L" Number of atoms: 222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 222 Unusual residues: {'3PE': 3, 'CDL': 1, 'LMT': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 66 Chain: "M" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 70 Unusual residues: {'LMT': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 154 Unusual residues: {'3PE': 2, 'LMT': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 18 Chain: "O" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "P" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NDP': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'EHZ': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 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: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 72 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 28 Chain: "Y" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 116 Unusual residues: {'3PE': 2, 'LMT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 21 Chain: "Z" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 26 Chain: "d" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 103 Unusual residues: {'3PE': 1, 'CDL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 48 Chain: "g" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "h" Number of atoms: 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: "q" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 61 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 39 Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 42 Classifications: {'water': 42} Link IDs: {None: 41} Chain: "C" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 61 Classifications: {'water': 61} Link IDs: {None: 60} Chain: "D" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 96 Classifications: {'water': 96} Link IDs: {None: 95} Chain: "E" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "F" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 44 Classifications: {'water': 44} Link IDs: {None: 43} Chain: "G" Number of atoms: 139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 139 Classifications: {'water': 139} Link IDs: {None: 138} Chain: "H" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 30 Classifications: {'water': 30} Link IDs: {None: 29} Chain: "I" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 76 Classifications: {'water': 76} Link IDs: {None: 75} Chain: "J" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "K" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 25 Classifications: {'water': 25} Link IDs: {None: 24} Chain: "M" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 26 Classifications: {'water': 26} Link IDs: {None: 25} Chain: "N" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "O" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "P" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 25 Classifications: {'water': 25} Link IDs: {None: 24} Chain: "Q" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 51 Classifications: {'water': 51} Link IDs: {None: 50} Chain: "R" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "U" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "V" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "W" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "X" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} 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: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "a" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "b" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "d" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "e" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "f" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "g" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "h" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "i" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "j" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "k" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "l" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "m" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "n" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "o" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "p" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "q" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 21 Classifications: {'water': 21} Link IDs: {None: 20} Chain: "r" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "s" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1561 SG CYS B 119 95.897 93.957 203.956 1.00 29.46 S ATOM 1791 SG CYS B 149 93.650 91.698 208.762 1.00 27.19 S ATOM 1057 SG CYS B 54 90.150 90.426 203.416 1.00 32.68 S ATOM 1063 SG CYS B 55 90.050 96.219 206.007 1.00 32.66 S ATOM 7968 SG CYS E 103 113.303 45.933 260.171 1.00 47.53 S ATOM 8002 SG CYS E 108 111.645 43.310 262.144 1.00 47.86 S ATOM 8282 SG CYS E 144 115.276 42.459 256.762 1.00 45.50 S ATOM 8305 SG CYS E 148 113.968 39.704 258.008 1.00 48.94 S ATOM 11514 SG CYS F 362 117.918 52.003 236.321 1.00 31.28 S ATOM 11534 SG CYS F 365 115.122 51.568 241.282 1.00 32.72 S ATOM 11858 SG CYS F 405 119.582 47.005 240.472 1.00 35.11 S ATOM 11495 SG CYS F 359 121.617 52.749 241.687 1.00 34.60 S ATOM 12955 SG CYS G 114 114.767 70.449 226.749 1.00 28.01 S ATOM 12894 SG CYS G 105 109.015 73.083 228.788 1.00 27.39 S ATOM 12915 SG CYS G 108 114.739 75.402 230.712 1.00 28.24 S ATOM 13287 SG CYS G 156 122.879 64.214 231.583 1.00 29.09 S ATOM 13264 SG CYS G 153 120.558 66.635 237.247 1.00 29.04 S ATOM 13311 SG CYS G 159 126.631 67.426 235.677 1.00 32.19 S ATOM 13641 SG CYS G 203 122.102 70.195 231.872 1.00 29.90 S ATOM 12400 SG CYS G 41 123.301 57.389 229.534 1.00 28.92 S ATOM 12486 SG CYS G 52 119.452 57.904 228.605 1.00 29.55 S ATOM 12511 SG CYS G 55 120.784 53.363 225.342 1.00 30.60 S ATOM 12612 SG CYS G 69 124.063 53.990 226.404 1.00 32.28 S ATOM 20824 SG CYS I 119 96.654 85.819 214.914 1.00 24.94 S ATOM 20798 SG CYS I 116 97.195 92.422 215.607 1.00 25.56 S ATOM 20845 SG CYS I 122 98.393 88.089 220.356 1.00 25.46 S ATOM 20572 SG CYS I 87 102.339 88.547 215.022 1.00 24.53 S ATOM 20874 SG CYS I 126 100.975 84.798 227.785 1.00 27.18 S ATOM 20503 SG CYS I 77 106.018 89.009 228.678 1.00 27.98 S ATOM 20545 SG CYS I 83 104.258 87.261 222.835 1.00 26.04 S ATOM 20522 SG CYS I 80 106.431 82.605 226.431 1.00 26.64 S ATOM 40893 SG CYS R 59 102.861 80.646 243.044 1.00 34.02 S ATOM 41071 SG CYS R 84 105.886 81.141 240.883 1.00 33.92 S ATOM 41093 SG CYS R 87 103.622 83.914 241.680 1.00 32.97 S Time building chain proxies: 32.03, per 1000 atoms: 0.47 Number of scatterers: 67614 At special positions: 0 Unit cell: (185.674, 201.025, 291.669, 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 466 16.00 P 37 15.00 Mg 1 11.99 O 12903 8.00 N 11038 7.00 C 43137 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=2.04 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=2.03 Simple disulfide: pdb=" SG CYS p 112 " - pdb=" SG CYS p 124 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 22.75 Conformation dependent library (CDL) restraints added in 8.8 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E 301 " pdb="FE1 FES E 301 " - pdb=" SG CYS E 108 " pdb="FE1 FES E 301 " - pdb=" SG CYS E 103 " pdb="FE2 FES E 301 " - pdb=" SG CYS E 144 " pdb="FE2 FES E 301 " - pdb=" SG CYS E 148 " pdb=" FES G 803 " pdb="FE1 FES G 803 " - pdb=" SG CYS G 52 " pdb="FE2 FES G 803 " - pdb=" SG CYS G 69 " pdb="FE1 FES G 803 " - pdb=" SG CYS G 41 " pdb="FE2 FES G 803 " - pdb=" SG CYS G 55 " pdb=" SF4 B1002 " pdb="FE2 SF4 B1002 " - pdb=" SG CYS B 149 " pdb="FE1 SF4 B1002 " - pdb=" SG CYS B 119 " pdb="FE4 SF4 B1002 " - pdb=" SG CYS B 55 " pdb="FE3 SF4 B1002 " - pdb=" SG CYS B 54 " pdb=" SF4 F 502 " pdb="FE2 SF4 F 502 " - pdb=" SG CYS F 365 " pdb="FE4 SF4 F 502 " - pdb=" SG CYS F 359 " pdb="FE3 SF4 F 502 " - pdb=" SG CYS F 405 " pdb="FE1 SF4 F 502 " - pdb=" SG CYS F 362 " pdb=" SF4 G 801 " pdb="FE3 SF4 G 801 " - pdb=" NE2 HIS G 101 " pdb="FE1 SF4 G 801 " - pdb=" SG CYS G 114 " pdb="FE4 SF4 G 801 " - pdb=" SG CYS G 108 " pdb="FE2 SF4 G 801 " - pdb=" SG CYS G 105 " pdb=" SF4 G 802 " pdb="FE1 SF4 G 802 " - pdb=" SG CYS G 156 " 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=" SF4 I 202 " pdb="FE2 SF4 I 202 " - pdb=" SG CYS I 116 " pdb="FE4 SF4 I 202 " - pdb=" SG CYS I 87 " pdb="FE3 SF4 I 202 " - pdb=" SG CYS I 122 " pdb="FE1 SF4 I 202 " - pdb=" SG CYS I 119 " pdb=" SF4 I 203 " pdb="FE3 SF4 I 203 " - pdb=" SG CYS I 83 " pdb="FE1 SF4 I 203 " - pdb=" SG CYS I 126 " pdb="FE2 SF4 I 203 " - pdb=" SG CYS I 77 " pdb="FE4 SF4 I 203 " - pdb=" SG CYS I 80 " Number of angles added : 81 Zn2+ tetrahedral coordination pdb=" ZN R 201 " pdb="ZN ZN R 201 " - pdb=" NE2 HIS R 68 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 84 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 87 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 59 " Number of angles added : 3 15962 Ramachandran restraints generated. 7981 Oldfield, 0 Emsley, 7981 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15224 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 352 helices and 29 sheets defined 54.0% alpha, 4.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.07 Creating SS restraints... Processing helix chain 'A' and resid 3 through 27 Proline residue: A 25 - end of helix Processing helix chain 'A' and resid 53 through 80 Proline residue: A 74 - end of helix removed outlier: 5.423A pdb=" N TRP A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N GLN A 80 " --> pdb=" O PRO A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 107 Processing helix chain 'B' and resid 26 through 42 Processing helix chain 'B' and resid 54 through 63 Processing helix chain 'B' and resid 69 through 72 Processing helix chain 'B' and resid 80 through 82 No H-bonds generated for 'chain 'B' and resid 80 through 82' Processing helix chain 'B' and resid 94 through 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 168 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: 4.717A pdb=" N ILE C 58 " --> pdb=" O ASP C 55 " (cutoff:3.500A) Proline residue: C 59 - end of helix removed outlier: 3.596A pdb=" N THR C 62 " --> pdb=" O PRO C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 138 removed outlier: 3.858A pdb=" N TRP C 129 " --> pdb=" O ALA C 126 " (cutoff:3.500A) removed outlier: 3.710A 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: 3.935A pdb=" N GLN D 13 " --> pdb=" O GLU D 9 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N TYR D 14 " --> pdb=" O TRP D 10 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 93 removed outlier: 3.886A pdb=" N GLU D 92 " --> pdb=" O GLU D 88 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N TYR D 93 " --> pdb=" O LYS D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 104 Processing helix chain 'D' and resid 111 through 126 Processing helix chain 'D' and resid 132 through 161 removed outlier: 3.709A pdb=" N ILE D 161 " --> pdb=" O HIS D 157 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 185 removed outlier: 3.924A pdb=" N GLU D 173 " --> pdb=" O TRP D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 229 removed outlier: 3.709A pdb=" N ASN D 217 " --> pdb=" O GLU D 213 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N SER D 219 " --> pdb=" O SER D 215 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N LEU D 220 " --> pdb=" O LYS D 216 " (cutoff:3.500A) removed outlier: 3.698A 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: 4.530A 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 removed outlier: 3.507A pdb=" N ASN D 316 " --> pdb=" O SER D 312 " (cutoff:3.500A) 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 351 Processing helix chain 'D' and resid 394 through 405 removed outlier: 3.545A pdb=" N LEU D 402 " --> pdb=" O HIS D 398 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N ASP D 403 " --> pdb=" O LEU D 399 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N LYS D 404 " --> pdb=" O ALA D 400 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 421 removed outlier: 4.070A pdb=" N VAL D 415 " --> pdb=" O LEU D 411 " (cutoff:3.500A) removed outlier: 3.853A 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: 3.574A pdb=" N ASN E 37 " --> pdb=" O ALA E 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 58 removed outlier: 4.595A pdb=" N LEU E 48 " --> pdb=" O ALA E 45 " (cutoff:3.500A) Proline residue: E 49 - end of helix Processing helix chain 'E' and resid 63 through 73 Processing helix chain 'E' and resid 77 through 86 removed outlier: 3.579A pdb=" N VAL E 83 " --> pdb=" O ARG E 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 110 Processing helix chain 'E' and resid 113 through 124 Processing helix chain 'E' and resid 148 through 150 No H-bonds generated for 'chain 'E' and resid 148 through 150' Processing helix chain 'E' and resid 166 through 178 Processing helix chain 'F' and resid 17 through 19 No H-bonds generated for 'chain 'F' and resid 17 through 19' Processing helix chain 'F' and resid 33 through 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 81 removed outlier: 3.726A pdb=" N PHE F 81 " --> pdb=" O LEU F 77 " (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 313 Processing helix chain 'F' and resid 319 through 324 Processing helix chain 'F' and resid 343 through 357 Processing helix chain 'F' and resid 363 through 381 removed outlier: 4.298A pdb=" N ASP F 370 " --> pdb=" O ARG F 366 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ARG F 378 " --> pdb=" O LYS F 374 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG F 381 " --> pdb=" O ALA F 377 " (cutoff:3.500A) Processing helix chain 'F' and resid 386 through 399 removed outlier: 3.687A pdb=" N ASP F 390 " --> pdb=" O ALA F 387 " (cutoff:3.500A) Processing helix chain 'F' and resid 407 through 436 Proline residue: F 414 - end of helix removed outlier: 3.562A 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: 3.923A 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: 3.572A 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: 5.154A pdb=" N TYR G 271 " --> pdb=" O THR G 267 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ASP G 272 " --> pdb=" O ARG G 268 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N GLY G 273 " --> pdb=" O PHE G 269 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N LEU G 274 " --> pdb=" O ALA G 270 " (cutoff:3.500A) removed outlier: 4.276A 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: 3.569A 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 368 through 372 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 removed outlier: 3.710A pdb=" N GLN G 444 " --> pdb=" O GLN G 441 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU G 445 " --> pdb=" O VAL G 442 " (cutoff:3.500A) Processing helix chain 'G' and resid 457 through 459 No H-bonds generated for 'chain 'G' and resid 457 through 459' Processing helix chain 'G' and resid 463 through 479 Processing helix chain 'G' and resid 499 through 505 Processing helix chain 'G' and resid 512 through 516 Processing helix chain 'G' and resid 534 through 536 No H-bonds generated for 'chain 'G' and resid 534 through 536' Processing helix chain 'G' and resid 554 through 556 No H-bonds generated for 'chain 'G' and resid 554 through 556' Processing helix chain 'G' and resid 596 through 606 Processing helix chain 'G' and resid 616 through 626 Processing helix chain 'G' and resid 628 through 631 removed outlier: 3.569A pdb=" N VAL G 631 " --> pdb=" O PRO G 628 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 628 through 631' Processing helix chain 'G' and resid 642 through 649 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: 3.566A pdb=" N THR H 21 " --> pdb=" O VAL H 17 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LEU H 22 " --> pdb=" O ALA H 18 " (cutoff:3.500A) Processing helix chain 'H' and resid 42 through 44 No H-bonds generated for 'chain 'H' and resid 42 through 44' Processing helix chain 'H' and resid 47 through 57 Processing helix chain 'H' and resid 68 through 86 removed outlier: 3.605A pdb=" N ALA H 74 " --> pdb=" O MET H 70 " (cutoff:3.500A) Proline residue: H 75 - end of helix removed outlier: 4.255A pdb=" N TRP H 86 " --> pdb=" O ALA H 82 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 111 removed outlier: 3.606A pdb=" N LEU H 111 " --> pdb=" O ALA H 107 " (cutoff:3.500A) Processing helix chain 'H' and resid 113 through 123 Processing helix chain 'H' and resid 126 through 157 removed outlier: 4.067A pdb=" N THR H 145 " --> pdb=" O SER H 141 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N MET H 156 " --> pdb=" O SER H 152 " (cutoff:3.500A) Processing helix chain 'H' and resid 162 through 168 removed outlier: 3.980A pdb=" N ILE H 166 " --> pdb=" O LEU H 162 " (cutoff:3.500A) removed outlier: 3.596A 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 203 No H-bonds generated for 'chain 'H' and resid 200 through 203' Processing helix chain 'H' and resid 220 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 310 Proline residue: H 308 - end of helix Processing helix chain 'I' and resid 14 through 26 Processing helix chain 'I' and resid 28 through 41 removed outlier: 3.544A pdb=" N THR I 37 " --> pdb=" O GLY I 33 " (cutoff:3.500A) Processing helix chain 'I' and resid 82 through 86 Processing helix chain 'I' and resid 121 through 125 Processing helix chain 'I' and resid 145 through 147 No H-bonds generated for 'chain 'I' and resid 145 through 147' Processing helix chain 'I' and resid 151 through 175 removed outlier: 5.537A pdb=" N ALA I 163 " --> pdb=" O ASP I 159 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N GLU I 164 " --> pdb=" O LYS I 160 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N LEU I 174 " --> pdb=" O GLN I 170 " (cutoff:3.500A) removed outlier: 5.940A 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: 3.705A pdb=" N PHE J 47 " --> pdb=" O ILE J 43 " (cutoff:3.500A) Processing helix chain 'J' and resid 50 through 58 removed outlier: 3.548A pdb=" N PHE J 57 " --> pdb=" O GLY J 53 " (cutoff:3.500A) 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: 3.605A pdb=" N ILE J 127 " --> pdb=" O ASP J 124 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 124 through 127' Processing helix chain 'J' and resid 138 through 146 removed outlier: 4.033A pdb=" N LEU J 146 " --> pdb=" O GLY J 142 " (cutoff:3.500A) Processing helix chain 'J' and resid 151 through 173 Processing helix chain 'K' and resid 3 through 20 removed outlier: 4.035A 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: 3.665A pdb=" N MET K 58 " --> pdb=" O LEU K 55 " (cutoff:3.500A) Proline residue: K 60 - end of helix removed outlier: 3.504A pdb=" N LEU K 63 " --> pdb=" O PRO K 60 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE K 66 " --> pdb=" O LEU K 63 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA K 67 " --> pdb=" O LEU K 64 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N CYS K 69 " --> pdb=" O PHE K 66 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL K 79 " --> pdb=" O SER K 76 " (cutoff:3.500A) removed outlier: 3.513A 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: 3.867A pdb=" N LEU L 12 " --> pdb=" O SER L 8 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU L 15 " --> pdb=" O THR L 11 " (cutoff:3.500A) Proline residue: L 18 - end of helix removed outlier: 4.271A pdb=" N SER L 23 " --> pdb=" O ILE L 19 " (cutoff:3.500A) Processing helix chain 'L' and resid 29 through 57 removed outlier: 3.934A pdb=" N TYR L 32 " --> pdb=" O PRO L 29 " (cutoff:3.500A) Proline residue: L 33 - end of helix removed outlier: 3.503A pdb=" N ALA L 43 " --> pdb=" O ILE L 40 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHE L 44 " --> pdb=" O SER L 41 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR L 46 " --> pdb=" O ALA L 43 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE L 49 " --> pdb=" O THR L 46 " (cutoff:3.500A) Proline residue: L 50 - end of helix removed outlier: 3.876A 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: 3.782A pdb=" N TRP L 106 " --> pdb=" O GLU L 102 " (cutoff:3.500A) Processing helix chain 'L' and resid 114 through 133 removed outlier: 3.566A pdb=" N MET L 128 " --> pdb=" O PHE L 124 " (cutoff:3.500A) Processing helix chain 'L' and resid 137 through 155 removed outlier: 3.620A pdb=" N GLY L 148 " --> pdb=" O TRP L 144 " (cutoff:3.500A) Processing helix chain 'L' and resid 162 through 193 removed outlier: 4.283A pdb=" N GLY L 181 " --> pdb=" O ILE L 177 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N PHE L 182 " --> pdb=" O GLY L 178 " (cutoff:3.500A) Processing helix chain 'L' and resid 198 through 204 Processing helix chain 'L' and resid 210 through 223 Processing helix chain 'L' and resid 231 through 238 removed outlier: 4.150A pdb=" N MET L 237 " --> pdb=" O LEU L 233 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N GLU L 238 " --> pdb=" O PRO L 234 " (cutoff:3.500A) Processing helix chain 'L' and resid 241 through 249 Processing helix chain 'L' and resid 252 through 262 removed outlier: 4.032A pdb=" N GLY L 256 " --> pdb=" O VAL L 253 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE L 257 " --> pdb=" O VAL L 254 " (cutoff:3.500A) Processing helix chain 'L' and resid 264 through 269 removed outlier: 4.460A pdb=" N ASN L 269 " --> pdb=" O PRO L 265 " (cutoff:3.500A) Processing helix chain 'L' and resid 271 through 293 removed outlier: 3.534A pdb=" N ALA L 289 " --> pdb=" O THR L 285 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU L 293 " --> pdb=" O ALA L 289 " (cutoff:3.500A) Processing helix chain 'L' and resid 298 through 318 Processing helix chain 'L' and resid 322 through 349 removed outlier: 3.921A pdb=" N PHE L 334 " --> pdb=" O CYS L 330 " (cutoff:3.500A) removed outlier: 3.799A 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 389 through 400 removed outlier: 5.010A pdb=" N LEU L 394 " --> pdb=" O TYR L 390 " (cutoff:3.500A) Processing helix chain 'L' and resid 406 through 430 removed outlier: 3.624A pdb=" N ALA L 420 " --> pdb=" O THR L 416 " (cutoff:3.500A) Processing helix chain 'L' and resid 448 through 469 removed outlier: 3.559A pdb=" N LEU L 457 " --> pdb=" O SER L 453 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N GLY L 465 " --> pdb=" O SER L 461 " (cutoff:3.500A) removed outlier: 5.114A 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: 3.763A pdb=" N THR L 508 " --> pdb=" O ILE L 504 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N LYS L 509 " --> pdb=" O SER L 505 " (cutoff:3.500A) Processing helix chain 'L' and resid 518 through 524 Processing helix chain 'L' and resid 526 through 547 Proline residue: L 530 - end of helix removed outlier: 3.601A pdb=" N MET L 533 " --> pdb=" O PRO L 530 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N HIS L 534 " --> pdb=" O THR L 531 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU L 536 " --> pdb=" O MET L 533 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N ALA L 537 " --> pdb=" O HIS L 534 " (cutoff:3.500A) Proline residue: L 538 - end of helix removed outlier: 3.518A pdb=" N LEU L 542 " --> pdb=" O TYR L 539 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER L 545 " --> pdb=" O LEU L 542 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLN L 546 " --> pdb=" O SER L 543 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LYS L 547 " --> pdb=" O MET L 544 " (cutoff:3.500A) Processing helix chain 'L' and resid 557 through 560 No H-bonds generated for 'chain 'L' and resid 557 through 560' Processing helix chain 'L' and resid 563 through 578 Processing helix chain 'L' and resid 584 through 600 Processing helix chain 'M' and resid 5 through 16 removed outlier: 4.376A pdb=" N MET M 12 " --> pdb=" O THR M 8 " (cutoff:3.500A) Proline residue: M 13 - end of helix Processing helix chain 'M' and resid 23 through 42 removed outlier: 4.030A pdb=" N LEU M 39 " --> pdb=" O SER M 35 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N LEU M 40 " --> pdb=" O PHE M 36 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N LEU M 41 " --> pdb=" O THR M 37 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N MET M 42 " --> pdb=" O SER M 38 " (cutoff:3.500A) Processing helix chain 'M' and resid 60 through 80 Proline residue: M 64 - end of helix removed outlier: 3.577A pdb=" N LEU M 73 " --> pdb=" O THR M 69 " (cutoff:3.500A) Proline residue: M 74 - end of helix Processing helix chain 'M' and resid 89 through 109 Processing helix chain 'M' and resid 115 through 136 removed outlier: 4.646A pdb=" N LEU M 126 " --> pdb=" O PHE M 122 " (cutoff:3.500A) removed outlier: 4.400A 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: 3.637A pdb=" N LEU M 143 " --> pdb=" O THR M 140 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA M 145 " --> pdb=" O ARG M 142 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N TYR M 152 " --> pdb=" O PHE M 149 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU M 154 " --> pdb=" O PHE M 151 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA M 155 " --> pdb=" O TYR M 152 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N LEU M 158 " --> pdb=" O ALA M 155 " (cutoff:3.500A) Proline residue: M 159 - end of helix removed outlier: 3.920A pdb=" N VAL M 171 " --> pdb=" O GLN M 168 " (cutoff:3.500A) Processing helix chain 'M' and resid 176 through 182 removed outlier: 3.800A pdb=" N TYR M 181 " --> pdb=" O LEU M 177 " (cutoff:3.500A) Processing helix chain 'M' and resid 190 through 206 removed outlier: 4.600A pdb=" N ALA M 202 " --> pdb=" O ALA M 198 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N PHE M 203 " --> pdb=" O CYS M 199 " (cutoff:3.500A) Processing helix chain 'M' and resid 214 through 222 removed outlier: 3.793A 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: 4.351A pdb=" N GLY M 239 " --> pdb=" O LEU M 235 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLY M 240 " --> pdb=" O LEU M 236 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N LEU M 248 " --> pdb=" O LEU M 244 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N ILE M 249 " --> pdb=" O ARG M 245 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LEU M 250 " --> pdb=" O ILE M 246 " (cutoff:3.500A) Processing helix chain 'M' and resid 253 through 257 removed outlier: 3.688A pdb=" N MET M 257 " --> pdb=" O THR M 254 " (cutoff:3.500A) Processing helix chain 'M' and resid 259 through 278 removed outlier: 3.988A pdb=" N ILE M 270 " --> pdb=" O LEU M 266 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU M 277 " --> pdb=" O SER M 273 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ARG M 278 " --> pdb=" O SER M 274 " (cutoff:3.500A) Processing helix chain 'M' and resid 282 through 303 removed outlier: 3.854A pdb=" N LEU M 296 " --> pdb=" O SER M 292 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL M 297 " --> pdb=" O HIS M 293 " (cutoff:3.500A) Processing helix chain 'M' and resid 306 through 337 removed outlier: 3.620A pdb=" N ARG M 336 " --> pdb=" O SER M 332 " (cutoff:3.500A) Processing helix chain 'M' and resid 348 through 350 No H-bonds generated for 'chain 'M' and resid 348 through 350' Processing helix chain 'M' and resid 353 through 366 Processing helix chain 'M' and resid 373 through 388 Processing helix chain 'M' and resid 390 through 415 removed outlier: 3.512A pdb=" N MET M 396 " --> pdb=" O ILE M 393 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE M 402 " --> pdb=" O ASN M 399 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N THR M 403 " --> pdb=" O MET M 400 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N TYR M 406 " --> pdb=" O THR M 403 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER M 407 " --> pdb=" O ALA M 404 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU M 408 " --> pdb=" O LEU M 405 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TYR M 409 " --> pdb=" O TYR M 406 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N MET M 413 " --> pdb=" O MET M 410 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N THR M 414 " --> pdb=" O LEU M 411 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLN M 415 " --> pdb=" O ILE M 412 " (cutoff:3.500A) Processing helix chain 'M' and resid 431 through 448 removed outlier: 3.621A pdb=" N HIS M 440 " --> pdb=" O LEU M 436 " (cutoff:3.500A) Proline residue: M 443 - end of helix removed outlier: 4.084A 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: 3.768A 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: 4.507A pdb=" N ALA N 137 " --> pdb=" O GLN N 134 " (cutoff:3.500A) Proline residue: N 138 - end of helix removed outlier: 3.792A pdb=" N TYR N 143 " --> pdb=" O SER N 140 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE N 145 " --> pdb=" O LEU N 142 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N PHE N 146 " --> pdb=" O TYR N 143 " (cutoff:3.500A) Proline residue: N 147 - end of helix Processing helix chain 'N' and resid 151 through 171 removed outlier: 3.527A pdb=" N LEU N 170 " --> pdb=" O GLY N 166 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ASN N 171 " --> pdb=" O TRP N 167 " (cutoff:3.500A) Processing helix chain 'N' and resid 175 through 194 removed outlier: 3.506A pdb=" N TRP N 189 " --> pdb=" O ALA N 185 " (cutoff:3.500A) Processing helix chain 'N' and resid 198 through 222 Processing helix chain 'N' and resid 227 through 235 removed outlier: 3.757A pdb=" N HIS N 232 " --> pdb=" O LEU N 228 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N THR N 233 " --> pdb=" O SER N 229 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N TRP N 234 " --> pdb=" O LEU N 230 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N ASN N 235 " --> pdb=" O SER N 231 " (cutoff:3.500A) Processing helix chain 'N' and resid 238 through 251 Processing helix chain 'N' and resid 258 through 272 Proline residue: N 262 - end of helix removed outlier: 3.576A pdb=" N MET N 265 " --> pdb=" O PRO N 262 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE N 267 " --> pdb=" O TRP N 264 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N THR N 271 " --> pdb=" O GLN N 268 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS N 272 " --> pdb=" O GLU N 269 " (cutoff:3.500A) Processing helix chain 'N' and resid 277 through 300 removed outlier: 3.672A pdb=" N LEU N 287 " --> pdb=" O ALA N 283 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N LEU N 288 " --> pdb=" O ILE N 284 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ASN N 289 " --> pdb=" O THR N 285 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU N 296 " --> pdb=" O PHE N 292 " (cutoff:3.500A) Processing helix chain 'N' and resid 309 through 316 Processing helix chain 'N' and resid 326 through 332 Processing helix chain 'N' and resid 337 through 346 Proline residue: N 341 - end of helix Processing helix chain 'O' and resid 5 through 10 Processing helix chain 'O' and resid 14 through 17 No H-bonds generated for 'chain 'O' and resid 14 through 17' Processing helix chain 'O' and resid 35 through 46 Processing helix chain 'O' and resid 60 through 62 No H-bonds generated for 'chain 'O' and resid 60 through 62' Processing helix chain 'O' and resid 71 through 74 Processing helix chain 'O' and resid 79 through 84 Processing helix chain 'O' and resid 92 through 118 Processing helix chain 'O' and resid 131 through 140 removed outlier: 3.549A pdb=" N PHE O 134 " --> pdb=" O ASP O 131 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG O 140 " --> pdb=" O ALA O 137 " (cutoff:3.500A) Processing helix chain 'O' and resid 146 through 162 removed outlier: 3.960A pdb=" N CYS O 161 " --> pdb=" O LYS O 157 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N GLU O 162 " --> pdb=" O VAL O 158 " (cutoff:3.500A) Processing helix chain 'O' and resid 176 through 186 removed outlier: 3.503A pdb=" N LYS O 186 " --> pdb=" O ARG O 182 " (cutoff:3.500A) 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: 4.158A pdb=" N GLU O 216 " --> pdb=" O PRO O 212 " (cutoff:3.500A) Processing helix chain 'O' and resid 225 through 228 No H-bonds generated for 'chain 'O' and resid 225 through 228' Processing helix chain 'O' and resid 231 through 240 Processing helix chain 'O' and resid 248 through 250 No H-bonds generated for 'chain 'O' and resid 248 through 250' Processing helix chain 'O' and resid 253 through 263 Processing helix chain 'O' and resid 266 through 269 No H-bonds generated for 'chain 'O' and resid 266 through 269' Processing helix chain 'O' and resid 286 through 298 Processing helix chain 'O' and resid 310 through 312 No H-bonds generated for 'chain 'O' and resid 310 through 312' Processing helix chain 'P' and resid 3 through 5 No H-bonds generated for 'chain 'P' and resid 3 through 5' Processing helix chain 'P' and resid 29 through 40 removed outlier: 4.015A pdb=" N TYR P 33 " --> pdb=" O PHE P 29 " (cutoff:3.500A) Processing helix chain 'P' and resid 53 through 62 removed outlier: 3.536A pdb=" N MET P 57 " --> pdb=" O TYR P 54 " (cutoff:3.500A) removed outlier: 4.835A 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 removed outlier: 3.604A pdb=" N ALA P 84 " --> pdb=" O SER P 80 " (cutoff:3.500A) Processing helix chain 'P' and resid 106 through 110 Processing helix chain 'P' and resid 112 through 124 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 310 through 321 removed outlier: 4.778A pdb=" N ILE P 315 " --> pdb=" O GLU P 311 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N GLU P 316 " --> pdb=" O LEU P 312 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N ARG P 320 " --> pdb=" O GLU P 316 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N HIS P 321 " --> pdb=" O VAL P 317 " (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 28 through 31 No H-bonds generated for 'chain 'Q' and resid 28 through 31' Processing helix chain 'Q' and resid 50 through 52 No H-bonds generated for 'chain 'Q' and resid 50 through 52' Processing helix chain 'Q' and resid 89 through 99 Processing helix chain 'Q' and resid 118 through 122 Processing helix chain 'R' and resid 23 through 28 Processing helix chain 'R' and resid 40 through 46 removed outlier: 3.581A 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: 4.765A pdb=" N GLY S 31 " --> pdb=" O GLY S 28 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ARG S 39 " --> pdb=" O ILE S 36 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N TYR S 40 " --> pdb=" O GLU S 37 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N VAL S 41 " --> pdb=" O LYS S 38 " (cutoff:3.500A) Processing helix chain 'S' and resid 83 through 94 Processing helix chain 'T' and resid 8 through 21 removed outlier: 3.529A pdb=" N LEU T 21 " --> pdb=" O TYR T 17 " (cutoff:3.500A) Processing helix chain 'T' and resid 44A through 58 Processing helix chain 'T' and resid 64 through 67 No H-bonds generated for 'chain 'T' and resid 64 through 67' Processing helix chain 'T' and resid 73 through 81 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: 5.026A pdb=" N LYS U 69 " --> pdb=" O ILE U 65 " (cutoff:3.500A) Processing helix chain 'U' and resid 73 through 84 Processing helix chain 'V' and resid 19 through 36 removed outlier: 4.075A pdb=" N HIS V 36 " --> pdb=" O ASP V 32 " (cutoff:3.500A) Processing helix chain 'V' and resid 42 through 60 Processing helix chain 'V' and resid 64 through 71 Processing helix chain 'V' and resid 76 through 96 removed outlier: 3.780A pdb=" N GLN V 95 " --> pdb=" O ARG V 91 " (cutoff:3.500A) Processing helix chain 'W' and resid 25 through 49 Proline residue: W 44 - end of helix Processing helix chain 'W' and resid 56 through 70 removed outlier: 4.298A 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: 4.372A pdb=" N PHE W 106 " --> pdb=" O HIS W 102 " (cutoff:3.500A) Processing helix chain 'W' and resid 118 through 124 Processing helix chain 'X' and resid 9 through 12 Processing helix chain 'X' and resid 21 through 34 removed outlier: 4.788A pdb=" N HIS X 29 " --> pdb=" O LYS X 25 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N HIS X 30 " --> pdb=" O ALA X 26 " (cutoff:3.500A) Processing helix chain 'X' and resid 36 through 49 Processing helix chain 'X' and resid 52 through 54 No H-bonds generated for 'chain 'X' and resid 52 through 54' Processing helix chain 'X' and resid 56 through 76 Processing helix chain 'X' and resid 78 through 90 removed outlier: 3.503A pdb=" N CYS X 87 " --> pdb=" O GLU X 83 " (cutoff:3.500A) Processing helix chain 'X' and resid 97 through 114 removed outlier: 4.285A pdb=" N ARG X 100 " --> pdb=" O ARG X 97 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N LYS X 101 " --> pdb=" O ARG X 98 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU X 108 " --> pdb=" O GLN X 105 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL X 110 " --> pdb=" O ASP X 107 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LYS X 113 " --> pdb=" O VAL X 110 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LEU X 114 " --> pdb=" O LEU X 111 " (cutoff:3.500A) 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 104 Processing helix chain 'Y' and resid 107 through 130 Processing helix chain 'Z' and resid 32 through 97 Proline residue: Z 73 - end of helix removed outlier: 3.594A pdb=" N ALA Z 95 " --> pdb=" O LEU Z 91 " (cutoff:3.500A) Processing helix chain 'Z' and resid 121 through 127 removed outlier: 5.532A pdb=" N LEU Z 127 " --> pdb=" O GLU Z 123 " (cutoff:3.500A) Processing helix chain 'Z' and resid 130 through 142 removed outlier: 5.831A pdb=" N PHE Z 140 " --> pdb=" O ALA Z 136 " (cutoff:3.500A) removed outlier: 5.166A 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: 3.758A pdb=" N ILE a 18 " --> pdb=" O CYS a 15 " (cutoff:3.500A) Proline residue: a 19 - end of helix removed outlier: 3.832A pdb=" N THR a 23 " --> pdb=" O GLY a 20 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE a 26 " --> pdb=" O THR a 23 " (cutoff:3.500A) Processing helix chain 'a' and resid 42 through 55 Processing helix chain 'b' and resid 3 through 14 removed outlier: 3.906A pdb=" N ASN b 10 " --> pdb=" O ALA b 6 " (cutoff:3.500A) 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: 3.997A 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 45 Processing helix chain 'd' and resid 16 through 20 Processing helix chain 'd' and resid 29 through 48 Processing helix chain 'd' and resid 58 through 96 removed outlier: 3.780A 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 47 through 54 removed outlier: 4.095A 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: 5.140A pdb=" N VAL f 16 " --> pdb=" O HIS f 13 " (cutoff:3.500A) Proline residue: f 17 - end of helix removed outlier: 3.528A 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 65 Processing helix chain 'g' and resid 69 through 79 Processing helix chain 'g' and resid 83 through 103 removed outlier: 3.672A pdb=" N GLN g 86 " --> pdb=" O TYR g 83 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N GLU g 87 " --> pdb=" O ARG g 84 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N TRP g 88 " --> pdb=" O MET g 85 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA g 89 " --> pdb=" O GLN g 86 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS g 98 " --> pdb=" O ARG g 95 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N TYR g 99 " --> pdb=" O LEU g 96 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG g 100 " --> pdb=" O VAL g 97 " (cutoff:3.500A) removed outlier: 3.864A 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: 3.802A 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: 3.635A 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 removed outlier: 3.573A pdb=" N GLU i 16 " --> pdb=" O GLN i 12 " (cutoff:3.500A) Processing helix chain 'i' and resid 61 through 73 removed outlier: 3.648A pdb=" N HIS i 66 " --> pdb=" O LYS i 62 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N PHE i 69 " --> pdb=" O ARG i 65 " (cutoff:3.500A) Processing helix chain 'i' and resid 75 through 87 Processing helix chain 'j' and resid 19 through 48 removed outlier: 7.758A pdb=" N ASP j 45 " --> pdb=" O TRP j 41 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ALA j 46 " --> pdb=" O HIS j 42 " (cutoff:3.500A) removed outlier: 4.022A 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: 3.662A pdb=" N ARG k 38 " --> pdb=" O LYS k 34 " (cutoff:3.500A) Processing helix chain 'k' and resid 45 through 52 removed outlier: 5.027A 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 removed outlier: 3.610A pdb=" N SER k 89 " --> pdb=" O TYR k 85 " (cutoff:3.500A) 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 22 No H-bonds generated for 'chain 'm' and resid 19 through 22' Processing helix chain 'm' and resid 27 through 50 removed outlier: 3.838A pdb=" N GLN m 49 " --> pdb=" O GLU m 45 " (cutoff:3.500A) Processing helix chain 'm' and resid 62 through 70 Processing helix chain 'm' and resid 73 through 78 Proline residue: m 77 - end of helix No H-bonds generated for 'chain 'm' and resid 73 through 78' Processing helix chain 'm' and resid 83 through 93 Processing helix chain 'm' and resid 95 through 116 Processing helix chain 'n' and resid 11 through 30 Processing helix chain 'n' and resid 33 through 50 removed outlier: 4.204A pdb=" N HIS n 50 " --> pdb=" O ARG n 46 " (cutoff:3.500A) 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: 3.829A pdb=" N MET n 113 " --> pdb=" O SER n 109 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N TYR n 114 " --> pdb=" O GLU n 110 " (cutoff:3.500A) Proline residue: n 115 - end of helix removed outlier: 4.589A pdb=" N GLU n 133 " --> pdb=" O ARG n 129 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N ARG n 134 " --> pdb=" O GLU n 130 " (cutoff:3.500A) Processing helix chain 'n' and resid 167 through 170 No H-bonds generated for 'chain 'n' and resid 167 through 170' Processing helix chain 'o' and resid 3 through 8 Processing helix chain 'o' and resid 42 through 48 Processing helix chain 'o' and resid 52 through 54 No H-bonds generated for 'chain 'o' and resid 52 through 54' Processing helix chain 'o' and resid 59 through 71 Processing helix chain 'o' and resid 80 through 119 removed outlier: 3.776A 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 Processing helix chain 'p' and resid 73 through 75 No H-bonds generated for 'chain 'p' and resid 73 through 75' Processing helix chain 'p' and resid 81 through 115 removed outlier: 3.805A pdb=" N GLU p 86 " --> pdb=" O LEU p 82 " (cutoff:3.500A) Processing helix chain 'p' and resid 117 through 123 removed outlier: 4.878A pdb=" N ARG p 121 " --> 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 171 Processing helix chain 'q' and resid 2 through 17 removed outlier: 3.685A pdb=" N VAL q 14 " --> pdb=" O GLY q 10 " (cutoff:3.500A) Processing helix chain 'q' and resid 20 through 29 Processing helix chain 'q' and resid 79 through 81 No H-bonds generated for 'chain 'q' and resid 79 through 81' Processing helix chain 'q' and resid 84 through 90 removed outlier: 4.360A 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 44 No H-bonds generated for 'chain 's' and resid 42 through 44' Processing helix chain 's' and resid 50 through 60 removed outlier: 3.538A pdb=" N SER s 59 " --> pdb=" O ASN s 55 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N LYS s 60 " --> pdb=" O LEU s 56 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.490A pdb=" N VAL B 85 " --> pdb=" O MET B 48 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N PHE B 50 " --> pdb=" O VAL B 85 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ILE B 87 " --> pdb=" O PHE B 50 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N TYR B 112 " --> pdb=" O MET B 86 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N VAL B 88 " --> pdb=" O TYR B 112 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N VAL B 114 " --> pdb=" O VAL B 88 " (cutoff:3.500A) removed outlier: 6.358A 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: 6.784A pdb=" N ASN C 95 " --> pdb=" O ALA C 76 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N LEU C 78 " --> pdb=" O VAL C 93 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N VAL C 93 " --> pdb=" O LEU C 78 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ALA C 80 " --> pdb=" O GLU C 91 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N GLU C 91 " --> pdb=" O ALA C 80 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N LEU C 48 " --> pdb=" O ARG C 104 " (cutoff:3.500A) removed outlier: 4.895A 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 removed outlier: 3.544A pdb=" N ARG C 182 " --> pdb=" O ASP C 177 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 47 through 49 removed outlier: 3.564A pdb=" N MET D 66 " --> pdb=" O LEU D 49 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N SER D 69 " --> pdb=" O VAL D 73 " (cutoff:3.500A) removed outlier: 5.662A 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: 6.525A pdb=" N TYR E 98 " --> pdb=" O THR E 138 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N ILE E 140 " --> pdb=" O TYR E 98 " (cutoff:3.500A) removed outlier: 6.449A 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: 6.055A 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: 7.017A pdb=" N TYR F 92 " --> pdb=" O THR F 221 " (cutoff:3.500A) removed outlier: 8.136A pdb=" N ALA F 223 " --> pdb=" O TYR F 92 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N VAL F 94 " --> pdb=" O ALA F 223 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ALA F 133 " --> pdb=" O LEU F 93 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N VAL F 95 " --> pdb=" O ALA F 133 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N TYR F 135 " --> pdb=" O VAL F 95 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N ALA F 97 " --> pdb=" O TYR F 135 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N TYR F 137 " --> pdb=" O ALA F 97 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ASP F 174 " --> pdb=" O ALA F 134 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N ILE F 136 " --> pdb=" O ASP F 174 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N PHE F 176 " --> pdb=" O ILE F 136 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N ILE F 138 " --> pdb=" O PHE F 176 " (cutoff:3.500A) removed outlier: 6.241A 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: 6.310A pdb=" N ARG G 243 " --> pdb=" O VAL G 247 " (cutoff:3.500A) removed outlier: 5.460A 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: 8.560A pdb=" N CYS G 344 " --> pdb=" O VAL G 315 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ALA G 317 " --> pdb=" O CYS G 344 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N MET G 521 " --> pdb=" O ALA G 316 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N ILE G 318 " --> pdb=" O MET G 521 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N PHE G 523 " --> pdb=" O ILE G 318 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N PHE G 542 " --> pdb=" O LEU G 522 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N LEU G 524 " --> pdb=" O PHE G 542 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N VAL G 544 " --> pdb=" O LEU G 524 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N VAL G 559 " --> pdb=" O TYR G 545 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N GLY G 547 " --> pdb=" O VAL G 559 " (cutoff:3.500A) removed outlier: 6.081A 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 405 through 409 Processing sheet with id= P, first strand: chain 'G' and resid 572 through 574 Processing sheet with id= Q, first strand: chain 'I' and resid 65 through 67 Processing sheet with id= R, first strand: chain 'I' and resid 92 through 98 removed outlier: 6.040A pdb=" N GLU I 97 " --> pdb=" O THR I 106 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N THR I 106 " --> pdb=" O GLU I 97 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'J' and resid 112 through 115 Processing sheet with id= T, first strand: chain 'L' and resid 69 through 71 Processing sheet with id= U, first strand: chain 'L' and resid 61 through 67 removed outlier: 6.985A pdb=" N LEU L 78 " --> pdb=" O ASN L 65 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'O' and resid 219 through 223 removed outlier: 6.059A pdb=" N VAL O 122 " --> pdb=" O ILE O 25 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N VAL O 27 " --> pdb=" O VAL O 122 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LEU O 124 " --> pdb=" O VAL O 27 " (cutoff:3.500A) removed outlier: 8.613A pdb=" N GLY O 29 " --> pdb=" O LEU O 124 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N LYS O 49 " --> pdb=" O VAL O 123 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N GLU O 125 " --> pdb=" O LYS O 49 " (cutoff:3.500A) removed outlier: 8.188A pdb=" N PHE O 51 " --> pdb=" O GLU O 125 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'P' and resid 227 through 230 removed outlier: 6.650A pdb=" N ILE P 165 " --> pdb=" O PHE P 228 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N PHE P 230 " --> pdb=" O ILE P 165 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N LYS P 167 " --> pdb=" O PHE P 230 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N GLN P 44 " --> pdb=" O ALA P 21 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N VAL P 23 " --> pdb=" O GLN P 44 " (cutoff:3.500A) removed outlier: 6.623A 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: 3.521A pdb=" N LEU S 22 " --> pdb=" O ARG S 55 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ARG S 67 " --> pdb=" O ARG S 16 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ILE S 18 " --> pdb=" O TRP S 65 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N TRP S 65 " --> pdb=" O ILE S 18 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ILE S 20 " --> pdb=" O LYS S 63 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LYS S 63 " --> pdb=" O ILE S 20 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLN S 72 " --> pdb=" O TYR S 68 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'q' and resid 60 through 63 removed outlier: 3.549A pdb=" N GLY q 40 " --> pdb=" O TYR q 48 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N GLU q 50 " --> pdb=" O LEU q 38 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N LEU q 38 " --> pdb=" O GLU q 50 " (cutoff:3.500A) 2883 hydrogen bonds defined for protein. 7818 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: 25.03 Time building geometry restraints manager: 25.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.40: 27545 1.40 - 1.63: 39959 1.63 - 1.85: 830 1.85 - 2.08: 0 2.08 - 2.31: 81 Bond restraints: 68415 Sorted by residual: bond pdb=" C5 GTP O 401 " pdb=" N7 GTP O 401 " ideal model delta sigma weight residual 1.350 1.521 -0.171 2.00e-02 2.50e+03 7.27e+01 bond pdb=" C6 GTP O 401 " pdb=" O6 GTP O 401 " ideal model delta sigma weight residual 1.230 1.397 -0.167 2.00e-02 2.50e+03 7.00e+01 bond pdb=" C SAC i 1 " pdb=" O SAC i 1 " ideal model delta sigma weight residual 1.231 1.361 -0.130 2.00e-02 2.50e+03 4.25e+01 bond pdb=" CB7 CDL X1701 " pdb=" OB8 CDL X1701 " ideal model delta sigma weight residual 1.334 1.402 -0.068 1.10e-02 8.26e+03 3.81e+01 bond pdb=" C 2MR D 85 " pdb=" O 2MR D 85 " ideal model delta sigma weight residual 1.231 1.352 -0.121 2.00e-02 2.50e+03 3.63e+01 ... (remaining 68410 not shown) Histogram of bond angle deviations from ideal: 72.64 - 84.92: 76 84.92 - 97.21: 1 97.21 - 109.49: 7446 109.49 - 121.78: 71809 121.78 - 134.07: 13240 Bond angle restraints: 92572 Sorted by residual: angle pdb=" O SAC i 1 " pdb=" C SAC i 1 " pdb=" N GLY i 2 " ideal model delta sigma weight residual 123.00 99.94 23.06 1.60e+00 3.91e-01 2.08e+02 angle pdb=" C51 CDL h1001 " pdb=" CB5 CDL h1001 " pdb=" OB6 CDL h1001 " ideal model delta sigma weight residual 111.33 121.17 -9.84 1.32e+00 5.72e-01 5.54e+01 angle pdb=" C11 CDL X1701 " pdb=" CA5 CDL X1701 " pdb=" OA6 CDL X1701 " ideal model delta sigma weight residual 111.33 120.40 -9.07 1.32e+00 5.72e-01 4.70e+01 angle pdb=" C51 CDL X1701 " pdb=" CB5 CDL X1701 " pdb=" OB6 CDL X1701 " ideal model delta sigma weight residual 111.33 120.25 -8.92 1.32e+00 5.72e-01 4.55e+01 angle pdb=" C11 CDL q 201 " pdb=" CA5 CDL q 201 " pdb=" OA6 CDL q 201 " ideal model delta sigma weight residual 111.33 120.24 -8.91 1.32e+00 5.72e-01 4.55e+01 ... (remaining 92567 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.27: 40575 35.27 - 70.54: 991 70.54 - 105.82: 152 105.82 - 141.09: 46 141.09 - 176.36: 4 Dihedral angle restraints: 41768 sinusoidal: 18160 harmonic: 23608 Sorted by residual: dihedral pdb=" C10 FMN F 501 " pdb=" C1' FMN F 501 " pdb=" N10 FMN F 501 " pdb=" C2' FMN F 501 " ideal model delta sinusoidal sigma weight residual 257.59 81.23 176.36 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O3A GTP O 401 " pdb=" O3B GTP O 401 " pdb=" PB GTP O 401 " pdb=" PG GTP O 401 " ideal model delta sinusoidal sigma weight residual -56.21 117.51 -173.71 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" O2G GTP O 401 " pdb=" O3B GTP O 401 " pdb=" PG GTP O 401 " pdb=" PB GTP O 401 " ideal model delta sinusoidal sigma weight residual 177.30 11.80 165.50 1 2.00e+01 2.50e-03 4.72e+01 ... (remaining 41765 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.270: 10105 4.270 - 8.540: 0 8.540 - 12.810: 0 12.810 - 17.081: 0 17.081 - 21.351: 16 Chirality restraints: 10121 Sorted by residual: chirality pdb="FE1 SF4 I 202 " pdb=" S2 SF4 I 202 " pdb=" S3 SF4 I 202 " pdb=" S4 SF4 I 202 " both_signs ideal model delta sigma weight residual False -10.55 10.80 -21.35 2.00e-01 2.50e+01 1.14e+04 chirality pdb="FE2 SF4 G 801 " pdb=" S1 SF4 G 801 " pdb=" S3 SF4 G 801 " pdb=" S4 SF4 G 801 " both_signs ideal model delta sigma weight residual False 10.55 -10.75 21.31 2.00e-01 2.50e+01 1.13e+04 chirality pdb="FE3 SF4 I 202 " pdb=" S1 SF4 I 202 " pdb=" S2 SF4 I 202 " pdb=" S4 SF4 I 202 " both_signs ideal model delta sigma weight residual False -10.55 10.74 -21.30 2.00e-01 2.50e+01 1.13e+04 ... (remaining 10118 not shown) Planarity restraints: 11537 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C08 I49 H 602 " 0.439 2.00e-02 2.50e+03 4.32e-01 3.73e+03 pdb=" C14 I49 H 602 " -0.220 2.00e-02 2.50e+03 pdb=" C15 I49 H 602 " -0.096 2.00e-02 2.50e+03 pdb=" N01 I49 H 602 " -0.156 2.00e-02 2.50e+03 pdb=" N02 I49 H 602 " -0.808 2.00e-02 2.50e+03 pdb=" N03 I49 H 602 " 0.208 2.00e-02 2.50e+03 pdb=" N04 I49 H 602 " 0.718 2.00e-02 2.50e+03 pdb=" N05 I49 H 602 " -0.085 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SAC i 1 " 0.115 2.00e-02 2.50e+03 1.98e-01 3.91e+02 pdb=" C SAC i 1 " -0.342 2.00e-02 2.50e+03 pdb=" O SAC i 1 " 0.108 2.00e-02 2.50e+03 pdb=" N GLY i 2 " 0.119 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 125 " 0.039 2.00e-02 2.50e+03 3.24e-02 2.10e+01 pdb=" CG TYR B 125 " -0.078 2.00e-02 2.50e+03 pdb=" CD1 TYR B 125 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TYR B 125 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR B 125 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR B 125 " 0.014 2.00e-02 2.50e+03 pdb=" CZ TYR B 125 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR B 125 " 0.004 2.00e-02 2.50e+03 ... (remaining 11534 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.60: 820 2.60 - 3.23: 69070 3.23 - 3.87: 143526 3.87 - 4.50: 204468 4.50 - 5.14: 308031 Nonbonded interactions: 725915 Sorted by model distance: nonbonded pdb=" OD1 ASP G 232 " pdb=" O HOH G 901 " model vdw 1.964 2.440 nonbonded pdb=" OH TYR O 83 " pdb=" O3' GTP O 401 " model vdw 1.967 2.440 nonbonded pdb=" O THR G 366 " pdb=" OG1 THR G 367 " model vdw 1.975 2.440 nonbonded pdb=" O PRO P 48 " pdb=" O HOH P 601 " model vdw 1.981 2.440 nonbonded pdb=" O HOH m 205 " pdb=" O HOH m 206 " model vdw 1.982 2.440 ... (remaining 725910 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'T' selection = (chain 'U' and (resid 7 through 82 or resid 101)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 13.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.060 Extract box with map and model: 55.690 Check model and map are aligned: 0.430 Set scattering table: 0.470 Process input model: 170.710 Find NCS groups from input model: 2.090 Set up NCS constraints: 0.300 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:12.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 256.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 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 68415 Z= 0.490 Angle : 0.809 23.060 92572 Z= 0.375 Chirality : 0.846 21.351 10121 Planarity : 0.006 0.432 11537 Dihedral : 16.850 176.359 26526 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.91 % Favored : 97.07 % Rotamer: Outliers : 0.01 % Allowed : 0.13 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.56 % 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: 0.30 (0.09), residues: 7981 helix: 0.46 (0.08), residues: 4270 sheet: -0.05 (0.26), residues: 376 loop : 0.09 (0.11), residues: 3335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP H 121 HIS 0.010 0.001 HIS D 150 PHE 0.073 0.002 PHE K 53 TYR 0.078 0.002 TYR B 125 ARG 0.015 0.000 ARG G 394 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15962 Ramachandran restraints generated. 7981 Oldfield, 0 Emsley, 7981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15962 Ramachandran restraints generated. 7981 Oldfield, 0 Emsley, 7981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1098 residues out of total 7064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1097 time to evaluate : 5.801 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 341 ASP cc_start: 0.7980 (m-30) cc_final: 0.7758 (m-30) REVERT: H 108 MET cc_start: 0.8545 (mmp) cc_final: 0.8276 (mmp) REVERT: J 114 GLU cc_start: 0.7384 (tt0) cc_final: 0.7177 (tt0) REVERT: L 593 ILE cc_start: 0.8356 (mt) cc_final: 0.8001 (mp) REVERT: P 209 ASP cc_start: 0.7975 (m-30) cc_final: 0.7752 (m-30) REVERT: Z 5 LYS cc_start: 0.7503 (ttpt) cc_final: 0.7259 (ttpp) REVERT: e 81 GLN cc_start: 0.8613 (tp40) cc_final: 0.8238 (mm-40) REVERT: l 53 ARG cc_start: 0.7497 (mtp85) cc_final: 0.7206 (mtp-110) REVERT: o 117 ARG cc_start: 0.7218 (ttp-110) cc_final: 0.6904 (ttp-170) REVERT: q 5 GLN cc_start: 0.6835 (mp10) cc_final: 0.6594 (mp10) REVERT: q 52 ASN cc_start: 0.8817 (m110) cc_final: 0.8498 (m-40) REVERT: q 53 LYS cc_start: 0.8221 (mmpt) cc_final: 0.7880 (mmmt) REVERT: r 69 MET cc_start: 0.8223 (tmm) cc_final: 0.7847 (tmt) REVERT: s 41 LEU cc_start: 0.9034 (mt) cc_final: 0.8820 (mp) outliers start: 1 outliers final: 1 residues processed: 1097 average time/residue: 1.7807 time to fit residues: 2463.2606 Evaluate side-chains 934 residues out of total 7064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 933 time to evaluate : 5.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain q residue 7 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 667 optimal weight: 7.9990 chunk 599 optimal weight: 10.0000 chunk 332 optimal weight: 1.9990 chunk 204 optimal weight: 9.9990 chunk 404 optimal weight: 1.9990 chunk 320 optimal weight: 3.9990 chunk 619 optimal weight: 6.9990 chunk 239 optimal weight: 5.9990 chunk 376 optimal weight: 2.9990 chunk 461 optimal weight: 0.9990 chunk 718 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 59 HIS F 431 GLN G 444 GLN H 124 ASN M 169 ASN N 316 GLN ** O 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 119 GLN S 72 GLN V 95 GLN W 126 HIS X 142 HIS Y 18 HIS Z 85 GLN Z 90 ASN b 70 GLN g 86 GLN h 143 ASN ** m 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 116 GLN n 159 GLN q 12 GLN q 72 ASN r 24 GLN s 40 ASN s 44 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.1073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.262 68415 Z= 0.485 Angle : 1.325 50.545 92572 Z= 0.847 Chirality : 0.258 6.541 10121 Planarity : 0.005 0.050 11537 Dihedral : 13.606 175.936 10535 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.83 % Favored : 98.16 % Rotamer: Outliers : 1.19 % Allowed : 6.13 % Favored : 92.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.09), residues: 7981 helix: 1.22 (0.08), residues: 4272 sheet: -0.01 (0.25), residues: 383 loop : 0.16 (0.11), residues: 3326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP X 85 HIS 0.006 0.001 HIS N 112 PHE 0.027 0.002 PHE M 122 TYR 0.042 0.002 TYR B 125 ARG 0.007 0.000 ARG F 339 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15962 Ramachandran restraints generated. 7981 Oldfield, 0 Emsley, 7981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15962 Ramachandran restraints generated. 7981 Oldfield, 0 Emsley, 7981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1069 residues out of total 7064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 985 time to evaluate : 5.967 Fit side-chains REVERT: D 411 LEU cc_start: 0.8764 (tp) cc_final: 0.8537 (tm) REVERT: E 153 MET cc_start: 0.9128 (OUTLIER) cc_final: 0.8910 (ppp) REVERT: F 428 GLU cc_start: 0.7209 (OUTLIER) cc_final: 0.6542 (tp30) REVERT: F 432 GLN cc_start: 0.7721 (OUTLIER) cc_final: 0.7048 (mp10) REVERT: G 287 GLU cc_start: 0.7303 (OUTLIER) cc_final: 0.6890 (pm20) REVERT: G 288 LYS cc_start: 0.8530 (mmmt) cc_final: 0.8277 (mtmp) REVERT: G 341 ASP cc_start: 0.7968 (m-30) cc_final: 0.7748 (m-30) REVERT: H 108 MET cc_start: 0.8555 (mmp) cc_final: 0.8230 (mmp) REVERT: J 114 GLU cc_start: 0.7295 (tt0) cc_final: 0.7053 (tt0) REVERT: L 593 ILE cc_start: 0.8273 (mt) cc_final: 0.7812 (mp) REVERT: M 114 GLU cc_start: 0.8095 (OUTLIER) cc_final: 0.7312 (mm-30) REVERT: O 237 ASP cc_start: 0.7951 (OUTLIER) cc_final: 0.7734 (m-30) REVERT: P 209 ASP cc_start: 0.7991 (m-30) cc_final: 0.7784 (m-30) REVERT: Q 44 ASN cc_start: 0.9019 (OUTLIER) cc_final: 0.8817 (t0) REVERT: Q 106 GLU cc_start: 0.7812 (mt-10) cc_final: 0.7595 (mt-10) REVERT: S 74 LYS cc_start: 0.8126 (mmtp) cc_final: 0.7756 (mmtt) REVERT: U 37 MET cc_start: 0.8240 (OUTLIER) cc_final: 0.7202 (mmm) REVERT: V 70 ARG cc_start: 0.8168 (OUTLIER) cc_final: 0.7745 (mtp85) REVERT: W 117 ASP cc_start: 0.8532 (OUTLIER) cc_final: 0.8223 (p0) REVERT: X 161 ARG cc_start: 0.8224 (OUTLIER) cc_final: 0.7728 (mtt180) REVERT: Y 88 ASN cc_start: 0.8245 (m-40) cc_final: 0.7906 (m110) REVERT: Z 5 LYS cc_start: 0.7494 (ttpt) cc_final: 0.7238 (ttpp) REVERT: c 40 LEU cc_start: 0.8336 (OUTLIER) cc_final: 0.7806 (tm) REVERT: e 56 LYS cc_start: 0.8264 (mtmm) cc_final: 0.8047 (mttp) REVERT: e 76 HIS cc_start: 0.7790 (t70) cc_final: 0.7538 (t-90) REVERT: e 81 GLN cc_start: 0.8649 (tp40) cc_final: 0.8394 (mm-40) REVERT: n 54 LYS cc_start: 0.7883 (OUTLIER) cc_final: 0.7639 (ptpt) REVERT: o 117 ARG cc_start: 0.7399 (ttp-110) cc_final: 0.7046 (ttp-170) REVERT: q 52 ASN cc_start: 0.8773 (m110) cc_final: 0.8485 (m-40) REVERT: q 53 LYS cc_start: 0.8321 (mmpt) cc_final: 0.7974 (mmmt) REVERT: s 41 LEU cc_start: 0.9053 (mt) cc_final: 0.8837 (mp) outliers start: 84 outliers final: 25 residues processed: 1014 average time/residue: 1.7706 time to fit residues: 2272.0858 Evaluate side-chains 982 residues out of total 7064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 944 time to evaluate : 5.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain E residue 153 MET Chi-restraints excluded: chain F residue 428 GLU Chi-restraints excluded: chain F residue 432 GLN Chi-restraints excluded: chain G residue 287 GLU Chi-restraints excluded: chain G residue 436 SER Chi-restraints excluded: chain H residue 121 TRP Chi-restraints excluded: chain H residue 200 LEU Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain L residue 596 LEU Chi-restraints excluded: chain M residue 114 GLU Chi-restraints excluded: chain M residue 138 ASN Chi-restraints excluded: chain N residue 229 SER Chi-restraints excluded: chain O residue 176 VAL Chi-restraints excluded: chain O residue 237 ASP Chi-restraints excluded: chain P residue 279 THR Chi-restraints excluded: chain Q residue 44 ASN Chi-restraints excluded: chain Q residue 102 SER Chi-restraints excluded: chain Q residue 115 SER Chi-restraints excluded: chain U residue 37 MET Chi-restraints excluded: chain V residue 70 ARG Chi-restraints excluded: chain W residue 27 GLU Chi-restraints excluded: chain W residue 117 ASP Chi-restraints excluded: chain X residue 161 ARG Chi-restraints excluded: chain Y residue 73 SER Chi-restraints excluded: chain Y residue 128 GLN Chi-restraints excluded: chain Z residue 31 SER Chi-restraints excluded: chain Z residue 97 VAL Chi-restraints excluded: chain c residue 40 LEU Chi-restraints excluded: chain c residue 48 LEU Chi-restraints excluded: chain d residue 95 LYS Chi-restraints excluded: chain e residue 17 MET Chi-restraints excluded: chain e residue 80 ARG Chi-restraints excluded: chain i residue 16 GLU Chi-restraints excluded: chain m residue 85 THR Chi-restraints excluded: chain n residue 54 LYS Chi-restraints excluded: chain p residue 20 SER Chi-restraints excluded: chain r residue 101 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 399 optimal weight: 6.9990 chunk 222 optimal weight: 5.9990 chunk 597 optimal weight: 2.9990 chunk 489 optimal weight: 7.9990 chunk 198 optimal weight: 10.0000 chunk 719 optimal weight: 5.9990 chunk 777 optimal weight: 0.0770 chunk 640 optimal weight: 10.0000 chunk 713 optimal weight: 10.0000 chunk 245 optimal weight: 2.9990 chunk 577 optimal weight: 10.0000 overall best weight: 3.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 316 GLN O 190 HIS P 119 GLN S 72 GLN V 95 GLN X 102 GLN Z 85 GLN b 51 ASN g 86 GLN h 143 ASN ** m 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 159 GLN o 109 GLN q 12 GLN q 72 ASN s 40 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.1142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.244 68415 Z= 0.527 Angle : 1.332 50.523 92572 Z= 0.849 Chirality : 0.259 6.566 10121 Planarity : 0.005 0.049 11537 Dihedral : 12.408 176.028 10533 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.38 % Favored : 97.61 % Rotamer: Outliers : 1.60 % Allowed : 7.98 % Favored : 90.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.56 % 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: 1.07 (0.09), residues: 7981 helix: 1.30 (0.08), residues: 4278 sheet: -0.00 (0.25), residues: 379 loop : 0.15 (0.11), residues: 3324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP N 84 HIS 0.007 0.001 HIS C 160 PHE 0.026 0.002 PHE M 122 TYR 0.029 0.002 TYR B 125 ARG 0.010 0.000 ARG X 46 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15962 Ramachandran restraints generated. 7981 Oldfield, 0 Emsley, 7981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15962 Ramachandran restraints generated. 7981 Oldfield, 0 Emsley, 7981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1063 residues out of total 7064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 950 time to evaluate : 5.886 Fit side-chains REVERT: D 74 ARG cc_start: 0.8254 (mmt90) cc_final: 0.7838 (mpt180) REVERT: D 107 ASP cc_start: 0.8292 (t0) cc_final: 0.8068 (t0) REVERT: D 411 LEU cc_start: 0.8761 (tp) cc_final: 0.8534 (tm) REVERT: F 249 ARG cc_start: 0.8840 (mtm110) cc_final: 0.8602 (mtt90) REVERT: F 432 GLN cc_start: 0.7782 (OUTLIER) cc_final: 0.6856 (mp10) REVERT: G 287 GLU cc_start: 0.7300 (OUTLIER) cc_final: 0.6886 (pm20) REVERT: G 288 LYS cc_start: 0.8528 (mmmt) cc_final: 0.8305 (mtmp) REVERT: G 341 ASP cc_start: 0.7962 (m-30) cc_final: 0.7741 (m-30) REVERT: H 108 MET cc_start: 0.8554 (mmp) cc_final: 0.8232 (mmp) REVERT: I 29 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.7579 (pm20) REVERT: J 87 LYS cc_start: 0.7114 (mttm) cc_final: 0.6880 (mmtp) REVERT: J 114 GLU cc_start: 0.7274 (tt0) cc_final: 0.7056 (tt0) REVERT: L 366 MET cc_start: 0.9021 (mtp) cc_final: 0.8600 (mtp) REVERT: L 547 LYS cc_start: 0.7797 (OUTLIER) cc_final: 0.7574 (tttp) REVERT: T 19 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8406 (mm) REVERT: U 37 MET cc_start: 0.8167 (OUTLIER) cc_final: 0.6959 (mmm) REVERT: V 70 ARG cc_start: 0.8156 (OUTLIER) cc_final: 0.7761 (mtp85) REVERT: W 117 ASP cc_start: 0.8534 (OUTLIER) cc_final: 0.8224 (p0) REVERT: X 11 ASP cc_start: 0.7820 (OUTLIER) cc_final: 0.7378 (m-30) REVERT: X 161 ARG cc_start: 0.8236 (OUTLIER) cc_final: 0.7745 (mtt180) REVERT: Y 88 ASN cc_start: 0.8179 (m-40) cc_final: 0.7885 (m110) REVERT: Y 128 GLN cc_start: 0.8037 (OUTLIER) cc_final: 0.7591 (tm-30) REVERT: Z 5 LYS cc_start: 0.7557 (ttpt) cc_final: 0.7272 (ttpp) REVERT: a 67 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7423 (pm20) REVERT: c 40 LEU cc_start: 0.8343 (OUTLIER) cc_final: 0.7795 (tm) REVERT: e 56 LYS cc_start: 0.8277 (mtmm) cc_final: 0.8069 (mttp) REVERT: e 76 HIS cc_start: 0.7864 (t70) cc_final: 0.7581 (t-90) REVERT: e 81 GLN cc_start: 0.8700 (tp40) cc_final: 0.8337 (mm-40) REVERT: n 54 LYS cc_start: 0.7985 (OUTLIER) cc_final: 0.7735 (ptpt) REVERT: o 117 ARG cc_start: 0.7381 (ttp-110) cc_final: 0.7101 (ttp-170) REVERT: q 52 ASN cc_start: 0.8805 (m110) cc_final: 0.8511 (m-40) REVERT: q 53 LYS cc_start: 0.8383 (mmpt) cc_final: 0.8000 (mmmt) REVERT: q 67 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.7315 (tt0) outliers start: 113 outliers final: 42 residues processed: 988 average time/residue: 1.7448 time to fit residues: 2180.8883 Evaluate side-chains 981 residues out of total 7064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 924 time to evaluate : 5.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain C residue 211 GLN Chi-restraints excluded: chain D residue 420 THR Chi-restraints excluded: chain F residue 432 GLN Chi-restraints excluded: chain G residue 287 GLU Chi-restraints excluded: chain G residue 436 SER Chi-restraints excluded: chain G residue 540 ASP Chi-restraints excluded: chain H residue 201 THR Chi-restraints excluded: chain I residue 29 GLU Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain L residue 214 ILE Chi-restraints excluded: chain L residue 544 MET Chi-restraints excluded: chain L residue 547 LYS Chi-restraints excluded: chain L residue 596 LEU Chi-restraints excluded: chain M residue 138 ASN Chi-restraints excluded: chain N residue 229 SER Chi-restraints excluded: chain N residue 237 THR Chi-restraints excluded: chain O residue 44 GLU Chi-restraints excluded: chain O residue 176 VAL Chi-restraints excluded: chain P residue 279 THR Chi-restraints excluded: chain Q residue 66 GLU Chi-restraints excluded: chain Q residue 102 SER Chi-restraints excluded: chain Q residue 110 VAL Chi-restraints excluded: chain Q residue 115 SER Chi-restraints excluded: chain R residue 80 LYS Chi-restraints excluded: chain S residue 34 ASP Chi-restraints excluded: chain T residue 19 LEU Chi-restraints excluded: chain T residue 51 ILE Chi-restraints excluded: chain U residue 37 MET Chi-restraints excluded: chain V residue 70 ARG Chi-restraints excluded: chain W residue 27 GLU Chi-restraints excluded: chain W residue 117 ASP Chi-restraints excluded: chain X residue 11 ASP Chi-restraints excluded: chain X residue 22 SER Chi-restraints excluded: chain X residue 143 SER Chi-restraints excluded: chain X residue 161 ARG Chi-restraints excluded: chain Y residue 73 SER Chi-restraints excluded: chain Y residue 128 GLN Chi-restraints excluded: chain Z residue 31 SER Chi-restraints excluded: chain Z residue 97 VAL Chi-restraints excluded: chain a residue 67 GLU Chi-restraints excluded: chain b residue 81 LYS Chi-restraints excluded: chain c residue 15 LEU Chi-restraints excluded: chain c residue 40 LEU Chi-restraints excluded: chain c residue 48 LEU Chi-restraints excluded: chain e residue 17 MET Chi-restraints excluded: chain g residue 122 GLU Chi-restraints excluded: chain i residue 16 GLU Chi-restraints excluded: chain l residue 5 THR Chi-restraints excluded: chain m residue 85 THR Chi-restraints excluded: chain n residue 54 LYS Chi-restraints excluded: chain p residue 20 SER Chi-restraints excluded: chain q residue 7 LEU Chi-restraints excluded: chain q residue 20 LEU Chi-restraints excluded: chain q residue 67 GLU Chi-restraints excluded: chain q residue 96 ASP Chi-restraints excluded: chain r residue 101 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 710 optimal weight: 0.9990 chunk 541 optimal weight: 0.4980 chunk 373 optimal weight: 0.9980 chunk 79 optimal weight: 2.9990 chunk 343 optimal weight: 4.9990 chunk 483 optimal weight: 3.9990 chunk 722 optimal weight: 5.9990 chunk 764 optimal weight: 1.9990 chunk 377 optimal weight: 0.9990 chunk 684 optimal weight: 2.9990 chunk 206 optimal weight: 0.7980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 431 GLN N 316 GLN P 119 GLN S 72 GLN V 95 GLN X 102 GLN Z 85 GLN b 70 GLN g 86 GLN ** m 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 159 GLN o 109 GLN p 160 GLN q 12 GLN q 72 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.1517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.247 68415 Z= 0.438 Angle : 1.291 50.541 92572 Z= 0.834 Chirality : 0.255 6.408 10121 Planarity : 0.004 0.050 11537 Dihedral : 11.376 173.673 10533 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.64 % Favored : 98.35 % Rotamer: Outliers : 1.22 % Allowed : 9.12 % Favored : 89.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.56 % 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: 1.40 (0.09), residues: 7981 helix: 1.61 (0.08), residues: 4283 sheet: -0.05 (0.25), residues: 377 loop : 0.28 (0.11), residues: 3321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP X 85 HIS 0.006 0.001 HIS N 112 PHE 0.028 0.001 PHE N 292 TYR 0.028 0.001 TYR A 30 ARG 0.006 0.000 ARG r 102 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15962 Ramachandran restraints generated. 7981 Oldfield, 0 Emsley, 7981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15962 Ramachandran restraints generated. 7981 Oldfield, 0 Emsley, 7981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1089 residues out of total 7064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 1003 time to evaluate : 5.944 Fit side-chains revert: symmetry clash REVERT: D 411 LEU cc_start: 0.8716 (tp) cc_final: 0.8509 (tm) REVERT: F 432 GLN cc_start: 0.7772 (OUTLIER) cc_final: 0.6575 (mp10) REVERT: G 122 MET cc_start: 0.9111 (mmt) cc_final: 0.8589 (mmt) REVERT: G 287 GLU cc_start: 0.7186 (OUTLIER) cc_final: 0.6813 (pm20) REVERT: G 341 ASP cc_start: 0.7905 (m-30) cc_final: 0.7693 (m-30) REVERT: H 108 MET cc_start: 0.8567 (mmp) cc_final: 0.8287 (mmp) REVERT: I 29 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7394 (pm20) REVERT: J 87 LYS cc_start: 0.7145 (mttm) cc_final: 0.6908 (mmtp) REVERT: J 114 GLU cc_start: 0.7131 (tt0) cc_final: 0.6848 (tt0) REVERT: L 14 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8627 (tt) REVERT: L 128 MET cc_start: 0.8665 (tpt) cc_final: 0.8154 (tpt) REVERT: L 366 MET cc_start: 0.8887 (mtp) cc_final: 0.8635 (mtp) REVERT: L 593 ILE cc_start: 0.8247 (OUTLIER) cc_final: 0.7940 (mt) REVERT: M 114 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7158 (mm-30) REVERT: N 117 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7153 (mm-30) REVERT: O 188 ASN cc_start: 0.8125 (t0) cc_final: 0.7815 (t0) REVERT: S 74 LYS cc_start: 0.8109 (OUTLIER) cc_final: 0.7811 (mmtt) REVERT: V 70 ARG cc_start: 0.8107 (OUTLIER) cc_final: 0.7669 (mtp85) REVERT: W 117 ASP cc_start: 0.8430 (OUTLIER) cc_final: 0.8081 (p0) REVERT: X 161 ARG cc_start: 0.8232 (OUTLIER) cc_final: 0.7748 (mtt180) REVERT: Y 128 GLN cc_start: 0.8008 (pp30) cc_final: 0.7626 (tm-30) REVERT: Z 5 LYS cc_start: 0.7540 (ttpt) cc_final: 0.7326 (ttpp) REVERT: Z 134 LEU cc_start: 0.8881 (tp) cc_final: 0.8652 (tm) REVERT: c 40 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.7772 (tm) REVERT: e 76 HIS cc_start: 0.7796 (t70) cc_final: 0.7524 (t-90) REVERT: e 81 GLN cc_start: 0.8657 (tp40) cc_final: 0.8389 (mm-40) REVERT: m 21 GLU cc_start: 0.7341 (mm-30) cc_final: 0.7078 (mm-30) REVERT: o 38 MET cc_start: 0.8899 (tpt) cc_final: 0.8692 (tpt) REVERT: o 117 ARG cc_start: 0.7359 (ttp-110) cc_final: 0.7071 (ttp-170) REVERT: q 32 ASP cc_start: 0.8301 (OUTLIER) cc_final: 0.8090 (t70) REVERT: q 52 ASN cc_start: 0.8688 (m110) cc_final: 0.8446 (m-40) REVERT: q 53 LYS cc_start: 0.8353 (mmpt) cc_final: 0.7952 (mmmt) REVERT: q 122 GLN cc_start: 0.8455 (mt0) cc_final: 0.8242 (mp10) outliers start: 86 outliers final: 22 residues processed: 1038 average time/residue: 1.7044 time to fit residues: 2250.4993 Evaluate side-chains 978 residues out of total 7064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 943 time to evaluate : 5.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain C residue 211 GLN Chi-restraints excluded: chain D residue 420 THR Chi-restraints excluded: chain F residue 432 GLN Chi-restraints excluded: chain G residue 287 GLU Chi-restraints excluded: chain G residue 436 SER Chi-restraints excluded: chain H residue 121 TRP Chi-restraints excluded: chain I residue 29 GLU Chi-restraints excluded: chain L residue 14 LEU Chi-restraints excluded: chain L residue 214 ILE Chi-restraints excluded: chain L residue 500 LEU Chi-restraints excluded: chain L residue 593 ILE Chi-restraints excluded: chain L residue 596 LEU Chi-restraints excluded: chain M residue 114 GLU Chi-restraints excluded: chain N residue 117 GLU Chi-restraints excluded: chain N residue 223 SER Chi-restraints excluded: chain P residue 279 THR Chi-restraints excluded: chain Q residue 102 SER Chi-restraints excluded: chain R residue 80 LYS Chi-restraints excluded: chain S residue 74 LYS Chi-restraints excluded: chain V residue 70 ARG Chi-restraints excluded: chain W residue 27 GLU Chi-restraints excluded: chain W residue 117 ASP Chi-restraints excluded: chain X residue 161 ARG Chi-restraints excluded: chain b residue 81 LYS Chi-restraints excluded: chain c residue 40 LEU Chi-restraints excluded: chain c residue 48 LEU Chi-restraints excluded: chain e residue 80 ARG Chi-restraints excluded: chain g residue 122 GLU Chi-restraints excluded: chain l residue 5 THR Chi-restraints excluded: chain m residue 85 THR Chi-restraints excluded: chain n residue 133 GLU Chi-restraints excluded: chain q residue 32 ASP Chi-restraints excluded: chain q residue 96 ASP Chi-restraints excluded: chain r residue 101 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1477, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1379, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1260, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 58.1326 > 50: distance: 32 - 63: 13.688 distance: 41 - 71: 17.935 distance: 49 - 80: 3.349 distance: 53 - 63: 10.744 distance: 54 - 86: 5.718 distance: 63 - 64: 27.391 distance: 64 - 65: 30.467 distance: 64 - 67: 26.376 distance: 65 - 66: 34.241 distance: 65 - 71: 35.126 distance: 67 - 68: 3.192 distance: 67 - 69: 20.293 distance: 68 - 70: 31.079 distance: 71 - 72: 26.386 distance: 72 - 73: 31.203 distance: 72 - 75: 12.116 distance: 73 - 74: 35.202 distance: 73 - 80: 16.966 distance: 75 - 76: 30.411 distance: 76 - 77: 20.690 distance: 77 - 78: 14.384 distance: 77 - 79: 13.220 distance: 80 - 81: 9.538 distance: 81 - 82: 14.419 distance: 81 - 84: 9.558 distance: 82 - 83: 12.491 distance: 82 - 86: 13.260 distance: 84 - 85: 16.357 distance: 85 - 169: 9.170 distance: 86 - 87: 16.874 distance: 87 - 88: 14.140 distance: 87 - 90: 3.882 distance: 88 - 89: 10.790 distance: 88 - 91: 23.136 distance: 91 - 92: 13.466 distance: 92 - 93: 23.151 distance: 92 - 95: 13.407 distance: 93 - 94: 30.178 distance: 93 - 101: 22.443 distance: 95 - 96: 34.224 distance: 96 - 97: 39.263 distance: 96 - 98: 39.692 distance: 97 - 99: 43.578 distance: 98 - 100: 36.180 distance: 99 - 100: 37.114 distance: 101 - 102: 20.507 distance: 102 - 103: 29.288 distance: 103 - 104: 30.406 distance: 103 - 105: 38.385 distance: 105 - 106: 56.060 distance: 106 - 107: 30.714 distance: 106 - 109: 28.153 distance: 107 - 108: 32.151 distance: 107 - 113: 38.454 distance: 109 - 110: 37.754 distance: 109 - 111: 12.263 distance: 110 - 112: 33.744 distance: 113 - 114: 53.642 distance: 114 - 115: 49.258 distance: 115 - 116: 43.601 distance: 115 - 117: 44.125 distance: 116 - 142: 24.694 distance: 117 - 118: 27.132 distance: 118 - 119: 13.790 distance: 118 - 121: 16.791 distance: 119 - 120: 9.991 distance: 119 - 123: 12.596 distance: 120 - 147: 6.683 distance: 121 - 122: 20.453 distance: 123 - 124: 17.441 distance: 124 - 125: 12.742 distance: 124 - 127: 7.225 distance: 125 - 126: 9.341 distance: 125 - 131: 11.369 distance: 127 - 128: 18.838 distance: 127 - 129: 15.974 distance: 128 - 130: 14.770