Starting phenix.real_space_refine on Thu Feb 15 20:14:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qso_14140/02_2024/7qso_14140_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qso_14140/02_2024/7qso_14140.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qso_14140/02_2024/7qso_14140_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qso_14140/02_2024/7qso_14140_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qso_14140/02_2024/7qso_14140_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qso_14140/02_2024/7qso_14140.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qso_14140/02_2024/7qso_14140.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qso_14140/02_2024/7qso_14140_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qso_14140/02_2024/7qso_14140_updated.pdb" } resolution = 3.02 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= -0.001 sd= 0.958 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: 9 Type Number sf(0) Gaussians K 1 8.98 5 Fe 28 7.16 5 Zn 1 6.06 5 P 41 5.49 5 Mg 1 5.21 5 S 461 5.16 5 C 42768 2.51 5 N 10949 2.21 5 O 11863 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 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 68": "OE1" <-> "OE2" Residue "B ARG 71": "NH1" <-> "NH2" Residue "B PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 77": "NH1" <-> "NH2" Residue "B GLU 109": "OE1" <-> "OE2" Residue "B ARG 111": "NH1" <-> "NH2" Residue "B GLU 154": "OE1" <-> "OE2" Residue "B GLU 170": "OE1" <-> "OE2" Residue "C ARG 8": "NH1" <-> "NH2" Residue "C ARG 12": "NH1" <-> "NH2" Residue "C GLU 31": "OE1" <-> "OE2" Residue "C PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 149": "NH1" <-> "NH2" Residue "C GLU 173": "OE1" <-> "OE2" Residue "C GLU 179": "OE1" <-> "OE2" Residue "C GLU 186": "OE1" <-> "OE2" Residue "C GLU 193": "OE1" <-> "OE2" Residue "D PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 123": "OE1" <-> "OE2" Residue "D PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 179": "OE1" <-> "OE2" Residue "D ARG 221": "NH1" <-> "NH2" Residue "D ARG 233": "NH1" <-> "NH2" Residue "D TYR 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 337": "OE1" <-> "OE2" Residue "D GLU 343": "OE1" <-> "OE2" Residue "D PHE 425": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 427": "OE1" <-> "OE2" Residue "E PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 22": "OD1" <-> "OD2" Residue "E GLU 82": "OE1" <-> "OE2" Residue "E ASP 134": "OD1" <-> "OD2" Residue "E ASP 168": "OD1" <-> "OD2" Residue "E GLU 171": "OE1" <-> "OE2" Residue "E ARG 190": "NH1" <-> "NH2" Residue "F ARG 32": "NH1" <-> "NH2" 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 TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 158": "OE1" <-> "OE2" Residue "F PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 278": "OE1" <-> "OE2" Residue "F GLU 313": "OE1" <-> "OE2" Residue "F ARG 349": "NH1" <-> "NH2" 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 PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 60": "OE1" <-> "OE2" Residue "G PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 170": "OD1" <-> "OD2" Residue "G ARG 218": "NH1" <-> "NH2" Residue "G GLU 226": "OE1" <-> "OE2" Residue "G ARG 243": "NH1" <-> "NH2" Residue "G GLU 246": "OE1" <-> "OE2" Residue "G ARG 253": "NH1" <-> "NH2" Residue "G ASP 265": "OD1" <-> "OD2" Residue "G GLU 281": "OE1" <-> "OE2" Residue "G ARG 285": "NH1" <-> "NH2" Residue "G GLU 287": "OE1" <-> "OE2" Residue "G ASP 298": "OD1" <-> "OD2" Residue "G ARG 302": "NH1" <-> "NH2" Residue "G ARG 385": "NH1" <-> "NH2" Residue "G ASP 403": "OD1" <-> "OD2" Residue "G ARG 418": "NH1" <-> "NH2" Residue "G PHE 523": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 577": "OE1" <-> "OE2" Residue "G GLU 624": "OE1" <-> "OE2" Residue "G GLU 637": "OE1" <-> "OE2" Residue "G GLU 693": "OE1" <-> "OE2" Residue "H ARG 25": "NH1" <-> "NH2" Residue "H ARG 34": "NH1" <-> "NH2" Residue "H PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 59": "OE1" <-> "OE2" Residue "H ARG 62": "NH1" <-> "NH2" Residue "H TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 8": "NH1" <-> "NH2" Residue "I GLU 9": "OE1" <-> "OE2" Residue "I GLU 95": "OE1" <-> "OE2" Residue "I ARG 108": "NH1" <-> "NH2" Residue "I GLU 152": "OE1" <-> "OE2" Residue "I TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 129": "OD1" <-> "OD2" Residue "J ASP 132": "OD1" <-> "OD2" Residue "J ARG 173": "NH1" <-> "NH2" Residue "L PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 102": "OE1" <-> "OE2" Residue "L TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 161": "NH1" <-> "NH2" Residue "L ASP 179": "OD1" <-> "OD2" Residue "L GLU 238": "OE1" <-> "OE2" Residue "L ARG 262": "NH1" <-> "NH2" Residue "L TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 268": "OE1" <-> "OE2" Residue "L TYR 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 352": "OD1" <-> "OD2" Residue "L PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 456": "NH1" <-> "NH2" Residue "L TYR 466": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 513": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 91": "NH1" <-> "NH2" Residue "M GLU 114": "OE1" <-> "OE2" Residue "M PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 123": "OE1" <-> "OE2" Residue "M ARG 142": "NH1" <-> "NH2" Residue "M TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 222": "OE1" <-> "OE2" Residue "M TYR 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 255": "OD1" <-> "OD2" Residue "M PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 "N GLU 34": "OE1" <-> "OE2" Residue "N GLU 54": "OE1" <-> "OE2" Residue "N PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 295": "NH1" <-> "NH2" Residue "N PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 12": "OE1" <-> "OE2" Residue "O GLU 44": "OE1" <-> "OE2" Residue "O GLU 53": "OE1" <-> "OE2" Residue "O ASP 60": "OD1" <-> "OD2" Residue "O TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 104": "NH1" <-> "NH2" Residue "O GLU 113": "OE1" <-> "OE2" Residue "O ARG 126": "NH1" <-> "NH2" Residue "O PHE 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 162": "OE1" <-> "OE2" Residue "O GLU 213": "OE1" <-> "OE2" Residue "O GLU 216": "OE1" <-> "OE2" Residue "O GLU 219": "OE1" <-> "OE2" Residue "O ASP 230": "OD1" <-> "OD2" Residue "O PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 281": "OE1" <-> "OE2" Residue "O PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 302": "NH1" <-> "NH2" Residue "O ARG 305": "NH1" <-> "NH2" Residue "P PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 40": "NH1" <-> "NH2" Residue "P ARG 50": "NH1" <-> "NH2" Residue "P TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 82": "NH1" <-> "NH2" Residue "P GLU 86": "OE1" <-> "OE2" Residue "P ARG 97": "NH1" <-> "NH2" Residue "P PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 107": "OE1" <-> "OE2" Residue "P GLU 123": "OE1" <-> "OE2" Residue "P ARG 147": "NH1" <-> "NH2" Residue "P ARG 157": "NH1" <-> "NH2" Residue "P PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 162": "OE1" <-> "OE2" Residue "P GLU 170": "OE1" <-> "OE2" Residue "P GLU 175": "OE1" <-> "OE2" Residue "P TYR 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 235": "NH1" <-> "NH2" Residue "P TYR 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 240": "OD1" <-> "OD2" Residue "P PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 251": "NH1" <-> "NH2" Residue "P PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 285": "OE1" <-> "OE2" Residue "P ASP 302": "OD1" <-> "OD2" Residue "Q GLU 27": "OE1" <-> "OE2" Residue "Q PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 90": "OE1" <-> "OE2" Residue "Q TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 106": "OE1" <-> "OE2" Residue "R TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 31": "NH1" <-> "NH2" Residue "S GLU 17": "OE1" <-> "OE2" Residue "S ASP 34": "OD1" <-> "OD2" Residue "S GLU 42": "OE1" <-> "OE2" Residue "S ASP 49": "OD1" <-> "OD2" Residue "S PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 13": "OD1" <-> "OD2" Residue "T ASP 39": "OD1" <-> "OD2" Residue "T ASP 64": "OD1" <-> "OD2" Residue "T GLU 68": "OE1" <-> "OE2" Residue "U GLU 9": "OE1" <-> "OE2" Residue "U ASP 13": "OD1" <-> "OD2" Residue "U TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 23": "OD1" <-> "OD2" Residue "U GLU 28": "OE1" <-> "OE2" Residue "U ASP 43": "OD1" <-> "OD2" Residue "U ASP 46": "OD1" <-> "OD2" Residue "U ASP 56": "OD1" <-> "OD2" Residue "U GLU 57": "OE1" <-> "OE2" Residue "U ASP 66": "OD1" <-> "OD2" Residue "U GLU 68": "OE1" <-> "OE2" Residue "V GLU 17": "OE1" <-> "OE2" Residue "V ARG 22": "NH1" <-> "NH2" Residue "V GLU 53": "OE1" <-> "OE2" Residue "V GLU 68": "OE1" <-> "OE2" Residue "V GLU 69": "OE1" <-> "OE2" Residue "V GLU 77": "OE1" <-> "OE2" Residue "V GLU 84": "OE1" <-> "OE2" Residue "W ARG 30": "NH1" <-> "NH2" Residue "W GLU 65": "OE1" <-> "OE2" Residue "W GLU 91": "OE1" <-> "OE2" Residue "W PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 117": "OD1" <-> "OD2" Residue "X GLU 41": "OE1" <-> "OE2" Residue "X GLU 49": "OE1" <-> "OE2" Residue "X GLU 57": "OE1" <-> "OE2" Residue "X PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 79": "OE1" <-> "OE2" Residue "X ARG 97": "NH1" <-> "NH2" Residue "X ARG 118": "NH1" <-> "NH2" Residue "X ARG 134": "NH1" <-> "NH2" Residue "X GLU 138": "OE1" <-> "OE2" Residue "X TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 144": "NH1" <-> "NH2" Residue "X ARG 146": "NH1" <-> "NH2" Residue "X GLU 148": "OE1" <-> "OE2" Residue "Y GLU 137": "OE1" <-> "OE2" Residue "Z GLU 56": "OE1" <-> "OE2" Residue "Z GLU 63": "OE1" <-> "OE2" Residue "Z ASP 64": "OD1" <-> "OD2" Residue "Z ARG 82": "NH1" <-> "NH2" Residue "Z GLU 108": "OE1" <-> "OE2" Residue "Z PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 131": "OE1" <-> "OE2" Residue "Z TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ARG 59": "NH1" <-> "NH2" Residue "b GLU 15": "OE1" <-> "OE2" Residue "b ARG 57": "NH1" <-> "NH2" Residue "b ASP 58": "OD1" <-> "OD2" Residue "b GLU 78": "OE1" <-> "OE2" Residue "c GLU 6": "OE1" <-> "OE2" Residue "c GLU 37": "OE1" <-> "OE2" Residue "c GLU 41": "OE1" <-> "OE2" Residue "c ARG 44": "NH1" <-> "NH2" Residue "d GLU 17": "OE1" <-> "OE2" Residue "d ASP 45": "OD1" <-> "OD2" Residue "d ARG 51": "NH1" <-> "NH2" Residue "d TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 86": "NH1" <-> "NH2" Residue "e ARG 8": "NH1" <-> "NH2" Residue "e GLU 23": "OE1" <-> "OE2" Residue "e GLU 36": "OE1" <-> "OE2" Residue "e GLU 38": "OE1" <-> "OE2" Residue "e ARG 50": "NH1" <-> "NH2" Residue "e GLU 58": "OE1" <-> "OE2" Residue "e TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ARG 28": "NH1" <-> "NH2" Residue "f ASP 31": "OD1" <-> "OD2" Residue "f ARG 46": "NH1" <-> "NH2" Residue "g GLU 39": "OE1" <-> "OE2" Residue "g ASP 50": "OD1" <-> "OD2" Residue "g GLU 94": "OE1" <-> "OE2" Residue "g GLU 109": "OE1" <-> "OE2" Residue "h PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ARG 20": "NH1" <-> "NH2" Residue "h GLU 49": "OE1" <-> "OE2" Residue "h ARG 77": "NH1" <-> "NH2" Residue "h GLU 84": "OE1" <-> "OE2" Residue "h GLU 88": "OE1" <-> "OE2" Residue "h ARG 112": "NH1" <-> "NH2" Residue "h ASP 142": "OD1" <-> "OD2" Residue "i ARG 18": "NH1" <-> "NH2" Residue "i GLU 26": "OE1" <-> "OE2" Residue "i PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i GLU 111": "OE1" <-> "OE2" Residue "i ASP 124": "OD1" <-> "OD2" Residue "j ASP 55": "OD1" <-> "OD2" Residue "k ASP 17": "OD1" <-> "OD2" Residue "k GLU 24": "OE1" <-> "OE2" Residue "k ARG 38": "NH1" <-> "NH2" Residue "k ARG 41": "NH1" <-> "NH2" Residue "k TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k GLU 84": "OE1" <-> "OE2" Residue "k GLU 88": "OE1" <-> "OE2" Residue "l TYR 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ARG 30": "NH1" <-> "NH2" Residue "l GLU 32": "OE1" <-> "OE2" Residue "l TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ASP 40": "OD1" <-> "OD2" Residue "l ASP 59": "OD1" <-> "OD2" Residue "l ASP 63": "OD1" <-> "OD2" Residue "l TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ARG 142": "NH1" <-> "NH2" Residue "l GLU 157": "OE1" <-> "OE2" Residue "m TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m ARG 39": "NH1" <-> "NH2" Residue "m TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m ARG 55": "NH1" <-> "NH2" Residue "m GLU 60": "OE1" <-> "OE2" Residue "m ARG 71": "NH1" <-> "NH2" Residue "m TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m ASP 107": "OD1" <-> "OD2" Residue "m GLU 112": "OE1" <-> "OE2" Residue "m GLU 117": "OE1" <-> "OE2" Residue "m ASP 121": "OD1" <-> "OD2" Residue "n ARG 21": "NH1" <-> "NH2" Residue "n ARG 24": "NH1" <-> "NH2" Residue "n GLU 27": "OE1" <-> "OE2" Residue "n ARG 33": "NH1" <-> "NH2" Residue "n ASP 48": "OD1" <-> "OD2" Residue "n ASP 55": "OD1" <-> "OD2" Residue "n ARG 64": "NH1" <-> "NH2" Residue "n TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n GLU 83": "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 TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n GLU 122": "OE1" <-> "OE2" Residue "n GLU 130": "OE1" <-> "OE2" Residue "n GLU 133": "OE1" <-> "OE2" Residue "n ARG 149": "NH1" <-> "NH2" Residue "o ARG 6": "NH1" <-> "NH2" Residue "o ASP 27": "OD1" <-> "OD2" Residue "o GLU 32": "OE1" <-> "OE2" Residue "o GLU 35": "OE1" <-> "OE2" Residue "o ARG 36": "NH1" <-> "NH2" Residue "o GLU 37": "OE1" <-> "OE2" Residue "o GLU 44": "OE1" <-> "OE2" Residue "o PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o GLU 90": "OE1" <-> "OE2" Residue "o ARG 97": "NH1" <-> "NH2" Residue "o ARG 103": "NH1" <-> "NH2" Residue "o GLU 104": "OE1" <-> "OE2" Residue "o ARG 105": "NH1" <-> "NH2" Residue "o ARG 106": "NH1" <-> "NH2" Residue "o ARG 114": "NH1" <-> "NH2" Residue "o GLU 115": "OE1" <-> "OE2" Residue "o GLU 118": "OE1" <-> "OE2" Residue "p ASP 5": "OD1" <-> "OD2" Residue "p TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p ARG 15": "NH1" <-> "NH2" Residue "p PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p ASP 37": "OD1" <-> "OD2" Residue "p GLU 66": "OE1" <-> "OE2" Residue "p PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p GLU 88": "OE1" <-> "OE2" Residue "p GLU 100": "OE1" <-> "OE2" Residue "p GLU 116": "OE1" <-> "OE2" Residue "p GLU 127": "OE1" <-> "OE2" Residue "p GLU 129": "OE1" <-> "OE2" Residue "p TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q GLU 67": "OE1" <-> "OE2" Residue "q GLU 85": "OE1" <-> "OE2" Residue "q ARG 88": "NH1" <-> "NH2" Residue "r GLU 29": "OE1" <-> "OE2" Residue "r TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r ARG 59": "NH1" <-> "NH2" Residue "r GLU 61": "OE1" <-> "OE2" Residue "r GLU 90": "OE1" <-> "OE2" Residue "r GLU 104": "OE1" <-> "OE2" Residue "r GLU 109": "OE1" <-> "OE2" Residue "s PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s ASP 57": "OD1" <-> "OD2" Residue "s PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 66113 Number of models: 1 Model: "" Number of chains: 68 Chain: "A" Number of atoms: 864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 864 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} 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: 1260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1260 Classifications: {'peptide': 158} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 147} Chain: "C" Number of atoms: 1743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1743 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 16, 'TRANS': 193} Chain: "D" Number of atoms: 3110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3110 Classifications: {'peptide': 388} Link IDs: {'PTRANS': 21, 'TRANS': 366} 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: 1659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1659 Classifications: {'peptide': 214} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 192} Chain: "F" Number of atoms: 3324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3324 Classifications: {'peptide': 432} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 410} Chain: "G" Number of atoms: 5360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 700, 5360 Classifications: {'peptide': 700} Link IDs: {'PTRANS': 33, 'TRANS': 666} Chain: "H" Number of atoms: 2509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2509 Classifications: {'peptide': 318} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 295} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "I" Number of atoms: 1414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1414 Classifications: {'peptide': 176} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 165} Chain: "J" Number of atoms: 1226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1226 Classifications: {'peptide': 161} Link IDs: {'PTRANS': 2, 'TRANS': 158} 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: "K" Number of atoms: 647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 647 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 1, 'TRANS': 84} 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: 4334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 547, 4334 Classifications: {'peptide': 547} Link IDs: {'PTRANS': 26, 'TRANS': 520} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "M" Number of atoms: 3654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3654 Classifications: {'peptide': 459} Link IDs: {'PCIS': 3, 'PTRANS': 17, 'TRANS': 438} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "N" Number of atoms: 2733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2733 Classifications: {'peptide': 347} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 325} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "O" Number of atoms: 2589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2589 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 15, 'TRANS': 304} Chain: "P" Number of atoms: 2560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2560 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 20, 'TRANS': 299} Chain breaks: 2 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: 740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 740 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "S" Number of atoms: 701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 701 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 4, 'TRANS': 82} Chain: "T" 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: "U" Number of atoms: 707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 707 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 5, 'TRANS': 82} Chain: "V" Number of atoms: 919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 919 Classifications: {'peptide': 113} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 104} Chain: "W" Number of atoms: 977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 977 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} 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: 248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 248 Classifications: {'peptide': 33} Link IDs: {'PTRANS': 2, 'TRANS': 30} Chain breaks: 1 Chain: "Z" Number of atoms: 1157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1157 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 7, 'TRANS': 134} Chain: "a" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 569 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "b" Number of atoms: 651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 651 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 11, 'TRANS': 71} Chain: "c" Number of atoms: 405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 405 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 3, 'TRANS': 44} Chain: "d" Number of atoms: 1000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 1000 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 9, 'TRANS': 110} Chain: "e" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 829 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 5, 'TRANS': 93} Chain: "f" Number of atoms: 492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 492 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 2, 'TRANS': 54} Chain: "g" Number of atoms: 750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 750 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 6, 'TRANS': 83} Chain: "h" Number of atoms: 1186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1186 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 10, 'TRANS': 132} Chain: "i" Number of atoms: 1097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1097 Classifications: {'peptide': 127} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 113} 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: 592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 592 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 7, 'TRANS': 62} Chain: "k" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 653 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 3, 'TRANS': 77} Chain: "l" Number of atoms: 1314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1314 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 20, 'TRANS': 135} Chain: "m" Number of atoms: 1061 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1061 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 8, 'TRANS': 118} Chain: "n" Number of atoms: 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: 1035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 1035 Classifications: {'peptide': 120} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 112} Chain: "p" Number of atoms: 1455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1455 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 10, 'TRANS': 162} 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: 785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 785 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 11, 'TRANS': 84} 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: 380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 380 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 4, 'TRANS': 40} Chain: "A" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 124 Unusual residues: {'3PE': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 29 Chain: "B" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 109 Unusual residues: {'PC1': 2, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 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: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'3PE': 1, 'CHD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 18 Chain: "I" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 100 Unusual residues: {'3PE': 2, 'SF4': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 18 Chain: "J" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 Chain: "L" Number of atoms: 181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 181 Unusual residues: {'3PE': 2, 'CDL': 1, 'CHD': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 50 Chain: "M" Number of atoms: 147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 147 Unusual residues: {'3PE': 1, 'PC1': 1, 'U10': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 21 Chain: "N" Number of atoms: 157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 157 Unusual residues: {'3PE': 2, 'CDL': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 45 Chain: "O" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "P" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NDP': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'EHZ': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "U" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'EHZ': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "X" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 79 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 21 Chain: "Y" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 39 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "d" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 98 Unusual residues: {'CDL': 1, 'PC1': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 56 Chain: "h" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 109 Unusual residues: {'3PE': 1, 'CDL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 42 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: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 17 Chain: "r" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 109 Unusual residues: {'3PE': 1, 'CDL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 42 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1630 SG CYS B 119 97.106 95.351 209.476 1.00 27.84 S ATOM 1860 SG CYS B 149 94.720 92.950 214.063 1.00 26.31 S ATOM 1126 SG CYS B 54 91.599 91.696 208.410 1.00 31.24 S ATOM 1132 SG CYS B 55 91.159 97.431 211.276 1.00 31.02 S ATOM 7785 SG CYS E 103 112.899 46.876 266.067 1.00 42.49 S ATOM 7819 SG CYS E 108 111.094 44.239 267.833 1.00 43.58 S ATOM 8099 SG CYS E 144 115.202 43.430 262.751 1.00 41.79 S ATOM 8122 SG CYS E 148 113.747 40.709 263.718 1.00 46.25 S ATOM 11340 SG CYS F 362 118.476 53.342 242.444 1.00 29.21 S ATOM 11360 SG CYS F 365 115.438 52.578 247.209 1.00 29.19 S ATOM 11684 SG CYS F 405 119.973 48.363 246.559 1.00 32.00 S ATOM 11321 SG CYS F 359 121.949 53.998 248.058 1.00 31.34 S ATOM 12791 SG CYS G 114 115.547 71.874 233.084 1.00 26.41 S ATOM 12730 SG CYS G 105 109.661 74.339 234.625 1.00 24.44 S ATOM 12751 SG CYS G 108 115.189 76.875 236.921 1.00 26.36 S ATOM 13123 SG CYS G 156 123.515 65.882 238.052 1.00 27.36 S ATOM 13100 SG CYS G 153 120.636 68.040 243.621 1.00 26.91 S ATOM 13147 SG CYS G 159 126.917 68.946 242.476 1.00 29.63 S ATOM 13477 SG CYS G 203 122.577 71.697 238.453 1.00 27.35 S ATOM 12236 SG CYS G 41 124.155 58.995 235.970 1.00 27.84 S ATOM 12322 SG CYS G 52 120.345 59.402 234.847 1.00 27.73 S ATOM 12347 SG CYS G 55 121.852 54.879 231.690 1.00 29.26 S ATOM 12448 SG CYS G 69 125.014 55.456 232.970 1.00 29.72 S ATOM 20783 SG CYS I 119 97.449 87.004 220.337 1.00 24.56 S ATOM 20757 SG CYS I 116 97.868 93.565 221.133 1.00 25.48 S ATOM 20804 SG CYS I 122 99.122 89.242 226.047 1.00 23.62 S ATOM 20531 SG CYS I 87 103.131 89.952 220.953 1.00 24.20 S ATOM 20833 SG CYS I 126 101.310 86.035 233.378 1.00 23.66 S ATOM 20462 SG CYS I 77 106.138 90.305 234.625 1.00 26.51 S ATOM 20504 SG CYS I 83 104.944 88.555 228.625 1.00 23.77 S ATOM 20481 SG CYS I 80 106.758 83.914 232.406 1.00 25.52 S ATOM 40461 SG CYS R 59 102.378 81.706 248.831 1.00 30.20 S ATOM 40639 SG CYS R 84 105.553 82.315 246.757 1.00 31.83 S ATOM 40661 SG CYS R 87 103.285 84.879 247.544 1.00 29.40 S Time building chain proxies: 26.22, per 1000 atoms: 0.40 Number of scatterers: 66113 At special positions: 0 Unit cell: (185.901, 200.893, 298.341, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) Zn 1 29.99 Fe 28 26.01 K 1 19.00 S 461 16.00 P 41 15.00 Mg 1 11.99 O 11863 8.00 N 10949 7.00 C 42768 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS X 45 " - pdb=" SG CYS X 55 " distance=2.03 Simple disulfide: pdb=" SG CYS X 77 " - pdb=" SG CYS X 109 " distance=2.03 Simple disulfide: pdb=" SG CYS X 87 " - pdb=" SG CYS X 99 " distance=2.03 Simple disulfide: pdb=" SG CYS e 32 " - pdb=" SG CYS e 65 " distance=2.03 Simple disulfide: pdb=" SG CYS e 42 " - pdb=" SG CYS e 55 " distance=2.04 Simple disulfide: pdb=" SG CYS o 68 " - pdb=" SG CYS o 79 " distance=2.03 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: 25.77 Conformation dependent library (CDL) restraints added in 8.6 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 148 " pdb="FE2 FES E 301 " - pdb=" SG CYS E 144 " pdb=" FES G 803 " pdb="FE2 FES G 803 " - pdb=" SG CYS G 55 " pdb="FE2 FES G 803 " - pdb=" SG CYS G 69 " pdb="FE1 FES G 803 " - pdb=" SG CYS G 52 " pdb="FE1 FES G 803 " - pdb=" SG CYS G 41 " pdb=" SF4 B 302 " pdb="FE2 SF4 B 302 " - pdb=" SG CYS B 149 " pdb="FE1 SF4 B 302 " - pdb=" SG CYS B 119 " pdb="FE4 SF4 B 302 " - pdb=" SG CYS B 55 " pdb="FE3 SF4 B 302 " - pdb=" SG CYS B 54 " pdb=" SF4 F 502 " pdb="FE3 SF4 F 502 " - pdb=" SG CYS F 405 " pdb="FE4 SF4 F 502 " - pdb=" SG CYS F 359 " pdb="FE2 SF4 F 502 " - pdb=" SG CYS F 365 " pdb="FE1 SF4 F 502 " - pdb=" SG CYS F 362 " pdb=" SF4 G 801 " pdb="FE3 SF4 G 801 " - pdb=" NE2 HIS G 101 " pdb="FE4 SF4 G 801 " - pdb=" SG CYS G 108 " pdb="FE1 SF4 G 801 " - pdb=" SG CYS G 114 " pdb="FE2 SF4 G 801 " - pdb=" SG CYS G 105 " pdb=" SF4 G 802 " pdb="FE1 SF4 G 802 " - pdb=" SG CYS G 156 " pdb="FE2 SF4 G 802 " - pdb=" SG CYS G 153 " pdb="FE4 SF4 G 802 " - pdb=" SG CYS G 203 " pdb="FE3 SF4 G 802 " - pdb=" SG CYS G 159 " 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="FE1 SF4 I 202 " - pdb=" SG CYS I 119 " pdb="FE3 SF4 I 202 " - pdb=" SG CYS I 122 " pdb=" SF4 I 203 " pdb="FE4 SF4 I 203 " - pdb=" SG CYS I 80 " pdb="FE1 SF4 I 203 " - pdb=" SG CYS I 126 " pdb="FE3 SF4 I 203 " - pdb=" SG CYS I 83 " pdb="FE2 SF4 I 203 " - pdb=" SG CYS I 77 " Number of angles added : 81 Zn2+ tetrahedral coordination pdb=" ZN R 201 " pdb="ZN ZN R 201 " - pdb=" NE2 HIS R 68 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 87 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 84 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 59 " Number of angles added : 3 15806 Ramachandran restraints generated. 7903 Oldfield, 0 Emsley, 7903 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15060 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 342 helices and 28 sheets defined 52.6% alpha, 4.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.19 Creating SS restraints... Processing helix chain 'A' and resid 3 through 26 Proline residue: A 25 - end of helix Processing helix chain 'A' and resid 53 through 80 removed outlier: 3.650A pdb=" N ALA A 59 " --> pdb=" O PHE A 55 " (cutoff:3.500A) Proline residue: A 74 - end of helix removed outlier: 5.351A pdb=" N TRP A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N GLN A 80 " --> pdb=" O PRO A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 108 Processing helix chain 'B' and resid 26 through 43 Processing helix chain 'B' and resid 54 through 63 Processing helix chain 'B' and resid 69 through 72 Processing helix chain 'B' and resid 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 178 removed outlier: 3.603A pdb=" N ARG B 178 " --> pdb=" O ARG B 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 32 Processing helix chain 'C' and resid 54 through 66 removed outlier: 3.825A pdb=" N VAL C 57 " --> pdb=" O PRO C 54 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N ILE C 58 " --> pdb=" O ASP C 55 " (cutoff:3.500A) Proline residue: C 59 - end of helix removed outlier: 3.729A pdb=" N THR C 62 " --> pdb=" O PRO C 59 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASP C 66 " --> pdb=" O PHE C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 138 removed outlier: 3.910A pdb=" N TRP C 129 " --> pdb=" O ALA C 126 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLU C 131 " --> pdb=" O ASN C 128 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N MET C 137 " --> pdb=" O ILE C 134 " (cutoff:3.500A) removed outlier: 3.687A 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 87 through 93 removed outlier: 3.867A pdb=" N GLU D 92 " --> pdb=" O GLU D 88 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N TYR D 93 " --> pdb=" O LYS D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 104 removed outlier: 3.516A pdb=" N LEU D 100 " --> pdb=" O TYR D 96 " (cutoff:3.500A) Proline residue: D 101 - end of helix removed outlier: 3.705A pdb=" N ASP D 104 " --> pdb=" O LEU D 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 96 through 104' Processing helix chain 'D' and resid 111 through 126 Processing helix chain 'D' and resid 132 through 160 Processing helix chain 'D' and resid 165 through 185 removed outlier: 3.559A pdb=" N GLU D 172 " --> pdb=" O PHE D 168 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLU D 173 " --> pdb=" O TRP D 169 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N PHE D 180 " --> pdb=" O LYS D 176 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 216 Processing helix chain 'D' and resid 218 through 228 Processing helix chain 'D' and resid 233 through 239 Processing helix chain 'D' and resid 247 through 253 Processing helix chain 'D' and resid 257 through 263 removed outlier: 4.300A pdb=" N GLY D 262 " --> pdb=" O MET D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 272 No H-bonds generated for 'chain 'D' and resid 269 through 272' Processing helix chain 'D' and resid 278 through 280 No H-bonds generated for 'chain 'D' and resid 278 through 280' Processing helix chain 'D' and resid 293 through 317 Processing helix chain 'D' and resid 335 through 338 No H-bonds generated for 'chain 'D' and resid 335 through 338' Processing helix chain 'D' and resid 342 through 351 Processing helix chain 'D' and resid 394 through 400 Processing helix chain 'D' and resid 402 through 406 Processing helix chain 'D' and resid 411 through 421 removed outlier: 3.992A pdb=" N VAL D 415 " --> pdb=" O LEU D 411 " (cutoff:3.500A) removed outlier: 3.909A 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: 3.681A pdb=" N LYS E 29 " --> pdb=" O PRO E 25 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASN E 37 " --> pdb=" O ALA E 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 58 removed outlier: 4.452A pdb=" N LEU E 48 " --> pdb=" O ALA E 45 " (cutoff:3.500A) Proline residue: E 49 - end of helix removed outlier: 3.519A pdb=" N ASP E 52 " --> pdb=" O PRO E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 72 Processing helix chain 'E' and resid 77 through 86 removed outlier: 3.673A 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 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 79 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 removed outlier: 3.537A pdb=" N ASN F 148 " --> pdb=" O ASN F 144 " (cutoff:3.500A) 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 282 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: 4.306A pdb=" N ASP F 370 " --> pdb=" O ARG F 366 " (cutoff:3.500A) Processing helix chain 'F' and resid 386 through 399 removed outlier: 3.659A pdb=" N ILE F 389 " --> pdb=" O PRO F 386 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASP F 390 " --> pdb=" O ALA F 387 " (cutoff:3.500A) Processing helix chain 'F' and resid 407 through 421 Proline residue: F 414 - end of helix Processing helix chain 'F' and resid 423 through 438 Processing helix chain 'G' and resid 26 through 33 removed outlier: 3.525A pdb=" N LYS G 32 " --> pdb=" O GLN G 28 " (cutoff:3.500A) removed outlier: 4.031A 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: 3.715A 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 269 Processing helix chain 'G' and resid 271 through 275 Processing helix chain 'G' and resid 296 through 309 removed outlier: 3.744A pdb=" N SER G 309 " --> pdb=" O GLY G 305 " (cutoff:3.500A) Processing helix chain 'G' and resid 312 through 314 No H-bonds generated for 'chain 'G' and resid 312 through 314' Processing helix chain 'G' and resid 325 through 336 Processing helix chain 'G' and resid 355 through 357 No H-bonds generated for 'chain 'G' and resid 355 through 357' Processing helix chain 'G' and resid 359 through 362 Processing helix chain 'G' and resid 369 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: 3.664A pdb=" N LEU G 443 " --> pdb=" O SER G 440 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU G 445 " --> pdb=" O VAL G 442 " (cutoff:3.500A) Processing helix chain 'G' and resid 455 through 459 removed outlier: 3.575A pdb=" N GLN G 459 " --> pdb=" O SER G 455 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 455 through 459' Processing helix chain 'G' and resid 463 through 479 Processing helix chain 'G' and resid 499 through 505 Processing helix chain 'G' and resid 512 through 516 Processing helix chain 'G' and resid 554 through 556 No H-bonds generated for 'chain 'G' and resid 554 through 556' Processing helix chain 'G' and resid 566 through 568 No H-bonds generated for 'chain 'G' and resid 566 through 568' Processing helix chain 'G' and resid 596 through 607 Processing helix chain 'G' and resid 616 through 626 Processing helix chain 'G' and resid 628 through 630 No H-bonds generated for 'chain 'G' and resid 628 through 630' Processing helix chain 'G' and resid 642 through 650 Processing helix chain 'G' and resid 668 through 670 No H-bonds generated for 'chain 'G' and resid 668 through 670' Processing helix chain 'G' and resid 676 through 680 Processing helix chain 'G' and resid 682 through 693 Processing helix chain 'H' and resid 3 through 32 removed outlier: 3.525A pdb=" N LEU H 9 " --> pdb=" O ASN H 5 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE H 11 " --> pdb=" O LEU H 7 " (cutoff:3.500A) Proline residue: H 12 - end of helix removed outlier: 3.596A pdb=" N THR H 21 " --> pdb=" O VAL H 17 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LEU H 22 " --> pdb=" O ALA H 18 " (cutoff:3.500A) Processing helix chain 'H' and resid 42 through 44 No H-bonds generated for 'chain 'H' and resid 42 through 44' Processing helix chain 'H' and resid 47 through 56 Processing helix chain 'H' and resid 68 through 86 Proline residue: H 75 - end of helix removed outlier: 4.302A pdb=" N TRP H 86 " --> pdb=" O ALA H 82 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 121 removed outlier: 3.630A pdb=" N LEU H 111 " --> pdb=" O ALA H 107 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA H 112 " --> pdb=" O MET H 108 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N VAL H 113 " --> pdb=" O SER H 109 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N TYR H 114 " --> pdb=" O SER H 110 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N SER H 115 " --> pdb=" O LEU H 111 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ILE H 116 " --> pdb=" O ALA H 112 " (cutoff:3.500A) Processing helix chain 'H' and resid 126 through 157 removed outlier: 3.556A pdb=" N VAL H 144 " --> pdb=" O ILE H 140 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N THR H 145 " --> pdb=" O SER H 141 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N MET H 156 " --> pdb=" O SER H 152 " (cutoff:3.500A) Processing helix chain 'H' and resid 162 through 168 removed outlier: 4.042A pdb=" N ILE H 166 " --> pdb=" O LEU H 162 " (cutoff:3.500A) removed outlier: 3.780A 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 193 removed outlier: 3.664A pdb=" N MET H 184 " --> pdb=" O PRO H 180 " (cutoff:3.500A) 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 211 through 213 No H-bonds generated for 'chain 'H' and resid 211 through 213' Processing helix chain 'H' and resid 217 through 242 Processing helix chain 'H' and resid 252 through 274 removed outlier: 3.673A pdb=" N LEU H 271 " --> pdb=" O THR H 267 " (cutoff:3.500A) Processing helix chain 'H' and resid 282 through 290 removed outlier: 3.634A pdb=" N LEU H 289 " --> pdb=" O LEU H 285 " (cutoff:3.500A) Processing helix chain 'H' and resid 293 through 310 Proline residue: H 308 - end of helix Processing helix chain 'I' and resid 14 through 26 Processing helix chain 'I' and resid 28 through 42 removed outlier: 3.694A pdb=" N PHE I 42 " --> pdb=" O LEU I 38 " (cutoff:3.500A) Processing helix chain 'I' and resid 82 through 86 Processing helix chain 'I' and resid 121 through 125 Processing helix chain 'I' and resid 144 through 147 Processing helix chain 'I' and resid 151 through 172 removed outlier: 5.647A pdb=" N ALA I 163 " --> pdb=" O ASP I 159 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLU I 164 " --> pdb=" O LYS I 160 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA I 167 " --> pdb=" O ALA I 163 " (cutoff:3.500A) Processing helix chain 'J' and resid 5 through 22 Processing helix chain 'J' and resid 28 through 47 removed outlier: 3.548A pdb=" N LEU J 33 " --> pdb=" O GLY J 29 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N PHE J 47 " --> pdb=" O ILE J 43 " (cutoff:3.500A) Processing helix chain 'J' and resid 50 through 59 Processing helix chain 'J' and resid 64 through 75 Processing helix chain 'J' and resid 104 through 108 Processing helix chain 'J' and resid 124 through 127 Processing helix chain 'J' and resid 138 through 146 removed outlier: 3.905A pdb=" N LEU J 146 " --> pdb=" O GLY J 142 " (cutoff:3.500A) Processing helix chain 'J' and resid 151 through 172 Processing helix chain 'K' and resid 3 through 21 Processing helix chain 'K' and resid 26 through 50 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 59 through 85 removed outlier: 3.684A pdb=" N THR K 84 " --> pdb=" O MET K 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 3 through 23 removed outlier: 3.599A pdb=" N LEU L 9 " --> pdb=" O SER L 5 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N THR L 11 " --> pdb=" O LEU L 7 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N LEU L 12 " --> pdb=" O SER L 8 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR L 16 " --> pdb=" O LEU L 12 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N MET L 17 " --> pdb=" O LEU L 13 " (cutoff:3.500A) Proline residue: L 18 - end of helix removed outlier: 3.643A pdb=" N SER L 23 " --> pdb=" O ILE L 19 " (cutoff:3.500A) Processing helix chain 'L' and resid 32 through 57 removed outlier: 3.591A pdb=" N ILE L 45 " --> pdb=" O SER L 41 " (cutoff:3.500A) Proline residue: L 50 - end of helix Processing helix chain 'L' and resid 84 through 107 Proline residue: L 91 - end of helix removed outlier: 3.623A pdb=" N MET L 105 " --> pdb=" O MET L 101 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N TRP L 106 " --> pdb=" O GLU L 102 " (cutoff:3.500A) Processing helix chain 'L' and resid 114 through 133 removed outlier: 3.546A pdb=" N LEU L 131 " --> pdb=" O THR L 127 " (cutoff:3.500A) Processing helix chain 'L' and resid 137 through 155 removed outlier: 3.586A pdb=" N GLY L 143 " --> pdb=" O GLN L 139 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY L 148 " --> pdb=" O TRP L 144 " (cutoff:3.500A) Processing helix chain 'L' and resid 162 through 192 removed outlier: 4.305A pdb=" N GLY L 181 " --> pdb=" O ILE L 177 " (cutoff:3.500A) removed outlier: 3.577A 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: 4.020A pdb=" N MET L 237 " --> pdb=" O LEU L 233 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N GLU L 238 " --> pdb=" O PRO L 234 " (cutoff:3.500A) Processing helix chain 'L' and resid 241 through 246 Processing helix chain 'L' and resid 252 through 262 removed outlier: 3.653A pdb=" N GLY L 256 " --> pdb=" O VAL L 253 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU L 259 " --> pdb=" O GLY L 256 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE L 261 " --> pdb=" O PHE L 258 " (cutoff:3.500A) Processing helix chain 'L' and resid 264 through 267 No H-bonds generated for 'chain 'L' and resid 264 through 267' Processing helix chain 'L' and resid 271 through 292 removed outlier: 3.661A pdb=" N ILE L 276 " --> pdb=" O TYR L 272 " (cutoff:3.500A) Processing helix chain 'L' and resid 298 through 318 Processing helix chain 'L' and resid 322 through 349 removed outlier: 3.905A pdb=" N PHE L 334 " --> pdb=" O CYS L 330 " (cutoff:3.500A) removed outlier: 3.958A 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 381 Processing helix chain 'L' and resid 387 through 400 removed outlier: 4.169A pdb=" N SER L 391 " --> pdb=" O THR L 387 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N LEU L 394 " --> pdb=" O TYR L 390 " (cutoff:3.500A) Processing helix chain 'L' and resid 406 through 431 removed outlier: 3.613A pdb=" N LEU L 413 " --> pdb=" O LEU L 409 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ILE L 426 " --> pdb=" O TYR L 422 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ILE L 427 " --> pdb=" O SER L 423 " (cutoff:3.500A) Processing helix chain 'L' and resid 448 through 471 removed outlier: 6.053A pdb=" N GLY L 465 " --> pdb=" O SER L 461 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N TYR L 466 " --> pdb=" O LEU L 462 " (cutoff:3.500A) Processing helix chain 'L' and resid 484 through 509 removed outlier: 4.953A pdb=" N ALA L 490 " --> pdb=" O LEU L 486 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N LEU L 491 " --> pdb=" O LYS L 487 " (cutoff:3.500A) removed outlier: 3.532A 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 546 removed outlier: 3.640A pdb=" N PHE L 529 " --> pdb=" O LEU L 526 " (cutoff:3.500A) Proline residue: L 530 - end of helix removed outlier: 3.897A pdb=" N MET L 533 " --> pdb=" O PRO L 530 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N HIS L 534 " --> pdb=" O THR L 531 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU L 536 " --> pdb=" O MET L 533 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N ALA L 537 " --> pdb=" O HIS L 534 " (cutoff:3.500A) Proline residue: L 538 - end of helix removed outlier: 3.737A pdb=" N ASN L 541 " --> pdb=" O PRO L 538 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU L 542 " --> pdb=" O TYR L 539 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N MET L 544 " --> pdb=" O ASN L 541 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLN L 546 " --> pdb=" O SER L 543 " (cutoff:3.500A) Processing helix chain 'M' and resid 5 through 17 removed outlier: 4.340A pdb=" N MET M 12 " --> pdb=" O THR M 8 " (cutoff:3.500A) Proline residue: M 13 - end of helix Processing helix chain 'M' and resid 20 through 42 removed outlier: 4.078A pdb=" N ILE M 23 " --> pdb=" O ASN M 20 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N TRP M 24 " --> pdb=" O ASN M 21 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL M 25 " --> pdb=" O MET M 22 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER M 27 " --> pdb=" O TRP M 24 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N THR M 28 " --> pdb=" O VAL M 25 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N HIS M 30 " --> pdb=" O SER M 27 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER M 31 " --> pdb=" O THR M 28 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU M 32 " --> pdb=" O ALA M 29 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ILE M 34 " --> pdb=" O SER M 31 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N MET M 42 " --> pdb=" O LEU M 39 " (cutoff:3.500A) Processing helix chain 'M' and resid 60 through 80 Proline residue: M 64 - end of helix removed outlier: 3.590A 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 111 removed outlier: 3.591A pdb=" N THR M 111 " --> pdb=" O ILE M 107 " (cutoff:3.500A) Processing helix chain 'M' and resid 115 through 135 removed outlier: 4.700A pdb=" N LEU M 126 " --> pdb=" O PHE M 122 " (cutoff:3.500A) removed outlier: 4.149A 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 145 through 155 removed outlier: 3.738A pdb=" N PHE M 151 " --> pdb=" O TYR M 148 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N THR M 153 " --> pdb=" O LEU M 150 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU M 154 " --> pdb=" O PHE M 151 " (cutoff:3.500A) Processing helix chain 'M' and resid 157 through 171 Processing helix chain 'M' and resid 176 through 182 removed outlier: 3.624A pdb=" N TYR M 181 " --> pdb=" O LEU M 177 " (cutoff:3.500A) Processing helix chain 'M' and resid 190 through 206 removed outlier: 4.570A pdb=" N ALA M 202 " --> pdb=" O ALA M 198 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N PHE M 203 " --> pdb=" O CYS M 199 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LYS M 206 " --> pdb=" O ALA M 202 " (cutoff:3.500A) Processing helix chain 'M' and resid 214 through 222 removed outlier: 3.956A 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: 4.112A pdb=" N GLY M 239 " --> pdb=" O LEU M 235 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLY M 240 " --> pdb=" O LEU M 236 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N LEU M 248 " --> pdb=" O LEU M 244 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N ILE M 249 " --> pdb=" O ARG M 245 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N LEU M 250 " --> pdb=" O ILE M 246 " (cutoff:3.500A) Processing helix chain 'M' and resid 253 through 257 removed outlier: 3.916A pdb=" N MET M 257 " --> pdb=" O THR M 254 " (cutoff:3.500A) Processing helix chain 'M' and resid 259 through 278 removed outlier: 3.950A pdb=" N ILE M 270 " --> pdb=" O LEU M 266 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU M 277 " --> pdb=" O SER M 273 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ARG M 278 " --> pdb=" O SER M 274 " (cutoff:3.500A) Processing helix chain 'M' and resid 282 through 303 removed outlier: 4.042A pdb=" N LEU M 296 " --> pdb=" O SER M 292 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL M 297 " --> pdb=" O HIS M 293 " (cutoff:3.500A) Processing helix chain 'M' and resid 306 through 337 removed outlier: 3.502A pdb=" N MET M 310 " --> pdb=" O PRO M 306 " (cutoff:3.500A) removed outlier: 3.618A 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 367 Processing helix chain 'M' and resid 373 through 388 removed outlier: 3.542A pdb=" N SER M 387 " --> pdb=" O MET M 383 " (cutoff:3.500A) Processing helix chain 'M' and resid 390 through 415 removed outlier: 3.559A pdb=" N MET M 396 " --> pdb=" O ILE M 393 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL M 398 " --> pdb=" O LEU M 395 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASN M 399 " --> pdb=" O MET M 396 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE M 402 " --> pdb=" O ASN M 399 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR M 403 " --> pdb=" O MET M 400 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA M 404 " --> pdb=" O VAL M 401 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N TYR M 406 " --> pdb=" O THR M 403 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N SER M 407 " --> pdb=" O ALA M 404 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TYR M 409 " --> pdb=" O TYR M 406 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N MET M 410 " --> pdb=" O SER M 407 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N MET M 413 " --> pdb=" O MET M 410 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N THR M 414 " --> pdb=" O LEU M 411 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLN M 415 " --> pdb=" O ILE M 412 " (cutoff:3.500A) Processing helix chain 'M' and resid 431 through 448 removed outlier: 3.550A pdb=" N HIS M 440 " --> pdb=" O LEU M 436 " (cutoff:3.500A) Proline residue: M 443 - end of helix removed outlier: 4.216A 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 21 Processing helix chain 'N' and resid 26 through 44 removed outlier: 3.549A pdb=" N ILE N 41 " --> pdb=" O MET N 37 " (cutoff:3.500A) Proline residue: N 42 - end of helix Processing helix chain 'N' and resid 50 through 81 Processing helix chain 'N' and resid 92 through 106 Processing helix chain 'N' and resid 113 through 120 removed outlier: 4.052A pdb=" N GLU N 117 " --> pdb=" O PHE N 113 " (cutoff:3.500A) Processing helix chain 'N' and resid 124 through 148 removed outlier: 4.237A pdb=" N GLN N 134 " --> pdb=" O LEU N 130 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N LYS N 135 " --> pdb=" O LEU N 131 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N LEU N 136 " --> pdb=" O THR N 132 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N ALA N 137 " --> pdb=" O TRP N 133 " (cutoff:3.500A) Proline residue: N 138 - end of helix removed outlier: 3.541A pdb=" N GLN N 144 " --> pdb=" O SER N 140 " (cutoff:3.500A) Proline residue: N 147 - end of helix Processing helix chain 'N' and resid 151 through 167 Processing helix chain 'N' and resid 175 through 192 Processing helix chain 'N' and resid 198 through 222 Processing helix chain 'N' and resid 227 through 236 removed outlier: 3.758A pdb=" N TRP N 234 " --> pdb=" O LEU N 230 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ASN N 235 " --> pdb=" O SER N 231 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LYS N 236 " --> pdb=" O HIS N 232 " (cutoff:3.500A) Processing helix chain 'N' and resid 238 through 252 Processing helix chain 'N' and resid 258 through 272 Proline residue: N 262 - end of helix Processing helix chain 'N' and resid 277 through 302 Processing helix chain 'N' and resid 310 through 316 Processing helix chain 'N' and resid 326 through 334 removed outlier: 3.649A pdb=" N VAL N 331 " --> pdb=" O PRO N 327 " (cutoff:3.500A) Processing helix chain 'N' and resid 337 through 346 Proline residue: N 341 - end of helix removed outlier: 3.590A pdb=" N SER N 344 " --> pdb=" O PRO N 341 " (cutoff:3.500A) 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 58 through 62 Processing helix chain 'O' and resid 71 through 74 No H-bonds generated for '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 128 through 140 removed outlier: 4.355A pdb=" N PHE O 132 " --> pdb=" O ILE O 128 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N VAL O 133 " --> pdb=" O TYR O 129 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N PHE O 134 " --> pdb=" O SER O 130 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LEU O 135 " --> pdb=" O ASP O 131 " (cutoff:3.500A) Processing helix chain 'O' and resid 146 through 162 removed outlier: 3.997A pdb=" N ASP O 150 " --> pdb=" O LYS O 146 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N CYS O 161 " --> pdb=" O LYS O 157 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N GLU O 162 " --> pdb=" O VAL O 158 " (cutoff:3.500A) Processing helix chain 'O' and resid 176 through 186 Processing helix chain 'O' and resid 189 through 193 Processing helix chain 'O' and resid 196 through 208 Processing helix chain 'O' and resid 210 through 217 removed outlier: 3.821A pdb=" N GLU O 216 " --> pdb=" O PRO O 212 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LYS O 217 " --> pdb=" O GLU O 213 " (cutoff:3.500A) Processing helix chain 'O' and resid 225 through 229 removed outlier: 4.308A pdb=" N GLN O 229 " --> pdb=" O ALA O 225 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 225 through 229' Processing helix chain 'O' and resid 231 through 239 Processing helix chain 'O' and resid 247 through 250 Processing helix chain 'O' and resid 253 through 264 Processing helix chain 'O' and resid 266 through 270 Processing helix chain 'O' and resid 286 through 298 removed outlier: 3.830A pdb=" N GLU O 298 " --> pdb=" O GLN O 294 " (cutoff:3.500A) 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: 4.073A pdb=" N TYR P 33 " --> pdb=" O PHE P 29 " (cutoff:3.500A) Processing helix chain 'P' and resid 53 through 62 removed outlier: 4.768A 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: 3.595A pdb=" N ALA P 84 " --> pdb=" O SER P 80 " (cutoff:3.500A) Processing helix chain 'P' and resid 106 through 109 No H-bonds generated for 'chain 'P' and resid 106 through 109' Processing helix chain 'P' and resid 112 through 123 Processing helix chain 'P' and resid 144 through 159 removed outlier: 3.510A pdb=" N ARG P 157 " --> pdb=" O GLU P 153 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU P 158 " --> pdb=" O LYS P 154 " (cutoff:3.500A) Processing helix chain 'P' and resid 179 through 184 Processing helix chain 'P' and resid 197 through 199 No H-bonds generated for 'chain 'P' and resid 197 through 199' Processing helix chain 'P' and resid 207 through 219 Processing helix chain 'P' and resid 238 through 249 Processing helix chain 'P' and resid 281 through 288 removed outlier: 3.641A pdb=" N GLU P 285 " --> pdb=" O ARG P 281 " (cutoff:3.500A) Processing helix chain 'P' and resid 300 through 303 Processing helix chain 'P' and resid 312 through 318 removed outlier: 4.581A pdb=" N GLU P 316 " --> pdb=" O LEU P 312 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N VAL P 317 " --> pdb=" O LYS P 313 " (cutoff:3.500A) Processing helix chain 'Q' and resid 20 through 23 No H-bonds generated for 'chain 'Q' and resid 20 through 23' Processing helix chain 'Q' and resid 27 through 31 removed outlier: 4.202A pdb=" N LYS Q 31 " --> pdb=" O GLU Q 28 " (cutoff:3.500A) Processing helix chain 'Q' and resid 89 through 98 Processing helix chain 'Q' and resid 119 through 121 No H-bonds generated for 'chain 'Q' and resid 119 through 121' Processing helix chain 'R' and resid 23 through 28 Processing helix chain 'R' and resid 40 through 46 removed outlier: 3.577A pdb=" N GLU R 46 " --> pdb=" O ASP R 42 " (cutoff:3.500A) Processing helix chain 'R' and resid 64 through 66 No H-bonds generated for 'chain 'R' and resid 64 through 66' Processing helix chain 'S' and resid 27 through 46 removed outlier: 5.059A pdb=" N GLY S 31 " --> pdb=" O GLY S 28 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ARG S 39 " --> pdb=" O ILE S 36 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N TYR S 40 " --> pdb=" O GLU S 37 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N VAL S 41 " --> pdb=" O LYS S 38 " (cutoff:3.500A) Processing helix chain 'S' and resid 69 through 71 No H-bonds generated for 'chain 'S' and resid 69 through 71' Processing helix chain 'S' and resid 83 through 93 Processing helix chain 'T' and resid 8 through 21 removed outlier: 3.537A pdb=" N LYS T 12 " --> pdb=" O LEU T 8 " (cutoff:3.500A) Processing helix chain 'T' and resid 44 through 58 Processing helix chain 'T' and resid 64 through 69 removed outlier: 4.063A pdb=" N LYS T 69 " --> pdb=" O ILE T 65 " (cutoff:3.500A) Processing helix chain 'T' and resid 73 through 84 Processing helix chain 'U' and resid 8 through 20 Processing helix chain 'U' and resid 44 through 58 removed outlier: 3.554A pdb=" N ASP U 56 " --> pdb=" O MET U 52 " (cutoff:3.500A) Processing helix chain 'U' and resid 64 through 69 removed outlier: 3.895A 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: 4.299A 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: 3.748A 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 removed outlier: 3.679A pdb=" N HIS W 48 " --> pdb=" O PRO W 44 " (cutoff:3.500A) Processing helix chain 'W' and resid 56 through 69 Processing helix chain 'W' and resid 76 through 94 Processing helix chain 'W' and resid 100 through 107 removed outlier: 4.378A pdb=" N PHE W 106 " --> pdb=" O HIS W 102 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N PHE W 107 " --> pdb=" O VAL W 103 " (cutoff:3.500A) Processing helix chain 'W' and resid 118 through 124 removed outlier: 3.532A pdb=" N VAL W 124 " --> pdb=" O SER W 120 " (cutoff:3.500A) Processing helix chain 'X' and resid 9 through 12 Processing helix chain 'X' and resid 21 through 49 removed outlier: 4.852A pdb=" N HIS X 29 " --> pdb=" O LYS X 25 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N HIS X 30 " --> pdb=" O ALA X 26 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ALA X 33 " --> pdb=" O HIS X 29 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASP X 36 " --> pdb=" O GLY X 32 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N LYS X 37 " --> pdb=" O ALA X 33 " (cutoff:3.500A) Proline residue: X 38 - end of helix 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 removed outlier: 3.500A pdb=" N LEU X 61 " --> pdb=" O GLU X 57 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASN X 63 " --> pdb=" O GLY X 59 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ILE X 73 " --> pdb=" O PHE X 69 " (cutoff:3.500A) Processing helix chain 'X' and resid 78 through 90 Processing helix chain 'X' and resid 96 through 98 No H-bonds generated for 'chain 'X' and resid 96 through 98' Processing helix chain 'X' and resid 100 through 113 Processing helix chain 'Y' and resid 86 through 90 Processing helix chain 'Y' and resid 119 through 129 removed outlier: 4.215A pdb=" N LYS Y 125 " --> pdb=" O ALA Y 121 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N MET Y 126 " --> pdb=" O ALA Y 122 " (cutoff:3.500A) Processing helix chain 'Z' and resid 32 through 97 Proline residue: Z 73 - end of helix removed outlier: 4.230A pdb=" N THR Z 96 " --> pdb=" O GLU Z 92 " (cutoff:3.500A) Processing helix chain 'Z' and resid 121 through 124 No H-bonds generated for 'chain 'Z' and resid 121 through 124' Processing helix chain 'Z' and resid 130 through 138 Processing helix chain 'a' and resid 2 through 30 Proline residue: a 7 - end of helix removed outlier: 3.680A pdb=" N ILE a 18 " --> pdb=" O CYS a 15 " (cutoff:3.500A) Proline residue: a 19 - end of helix removed outlier: 3.544A pdb=" N ALA a 22 " --> pdb=" O PRO a 19 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR a 23 " --> pdb=" O GLY a 20 " (cutoff:3.500A) Processing helix chain 'a' and resid 42 through 55 Processing helix chain 'a' and resid 66 through 68 No H-bonds generated for 'chain 'a' and resid 66 through 68' Processing helix chain 'b' and resid 2 through 14 removed outlier: 3.794A pdb=" N PHE b 7 " --> pdb=" O ARG b 3 " (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: 3.718A pdb=" N LEU b 42 " --> pdb=" O THR b 38 " (cutoff:3.500A) Processing helix chain 'b' and resid 78 through 82 removed outlier: 3.540A pdb=" N ARG b 82 " --> pdb=" O GLU b 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 78 through 82' Processing helix chain 'c' and resid 14 through 46 removed outlier: 3.922A pdb=" N VAL c 25 " --> pdb=" O LEU c 21 " (cutoff:3.500A) 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: 3.656A pdb=" N TYR d 74 " --> pdb=" O PHE d 70 " (cutoff:3.500A) Processing helix chain 'd' and resid 98 through 100 No H-bonds generated for 'chain 'd' and resid 98 through 100' Processing helix chain 'e' and resid 5 through 9 Processing helix chain 'e' and resid 15 through 17 No H-bonds generated for 'chain 'e' and resid 15 through 17' Processing helix chain 'e' and resid 25 through 27 No H-bonds generated for 'chain 'e' and resid 25 through 27' Processing helix chain 'e' and resid 33 through 42 Processing helix chain 'e' and resid 47 through 54 removed outlier: 4.216A 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 3 through 37 removed outlier: 5.798A pdb=" N ARG f 8 " --> pdb=" O LEU f 4 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ASP f 9 " --> pdb=" O GLN f 5 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VAL f 12 " --> pdb=" O ARG f 8 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N HIS f 13 " --> pdb=" O ASP f 9 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N VAL f 14 " --> pdb=" O HIS f 10 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N LEU f 15 " --> pdb=" O TRP f 11 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N VAL f 16 " --> pdb=" O VAL f 12 " (cutoff:3.500A) Proline residue: f 17 - end of helix removed outlier: 3.659A pdb=" N ASP f 31 " --> pdb=" O ASP f 27 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLU f 32 " --> pdb=" O ARG f 28 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N LYS f 33 " --> pdb=" O LYS f 29 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LEU f 34 " --> pdb=" O ASN f 30 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N ALA f 36 " --> pdb=" O GLU f 32 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N PHE f 37 " --> pdb=" O LYS f 33 " (cutoff:3.500A) Processing helix chain 'g' and resid 37 through 40 No H-bonds generated for 'chain 'g' and resid 37 through 40' Processing helix chain 'g' and resid 51 through 66 removed outlier: 3.529A pdb=" N TRP g 56 " --> pdb=" O ALA g 52 " (cutoff:3.500A) Processing helix chain 'g' and resid 71 through 78 Processing helix chain 'g' and resid 83 through 103 removed outlier: 5.844A pdb=" N GLU g 87 " --> pdb=" O ARG g 84 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TRP g 88 " --> pdb=" O MET g 85 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LYS g 98 " --> pdb=" O ARG g 95 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ARG g 100 " --> pdb=" O VAL g 97 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N HIS g 103 " --> pdb=" O ARG g 100 " (cutoff:3.500A) Processing helix chain 'h' and resid 16 through 45 removed outlier: 3.919A 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 64 through 66 No H-bonds generated for 'chain 'h' and resid 64 through 66' Processing helix chain 'h' and resid 70 through 78 Processing helix chain 'h' and resid 83 through 117 removed outlier: 3.642A pdb=" N LEU h 108 " --> pdb=" O ARG h 104 " (cutoff:3.500A) Processing helix chain 'i' and resid 5 through 25 Processing helix chain 'i' and resid 41 through 49 removed outlier: 4.115A pdb=" N TRP i 46 " --> pdb=" O VAL i 42 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LYS i 48 " --> pdb=" O ARG i 44 " (cutoff:3.500A) Processing helix chain 'i' and resid 55 through 73 removed outlier: 4.516A pdb=" N ILE i 60 " --> pdb=" O TRP i 56 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N TYR i 61 " --> pdb=" O LYS i 57 " (cutoff:3.500A) Processing helix chain 'i' and resid 75 through 87 Processing helix chain 'j' and resid 19 through 42 removed outlier: 3.576A pdb=" N TRP j 33 " --> pdb=" O SER j 29 " (cutoff:3.500A) Processing helix chain 'j' and resid 45 through 48 No H-bonds generated for 'chain 'j' and resid 45 through 48' Processing helix chain 'j' and resid 56 through 58 No H-bonds generated for 'chain 'j' and resid 56 through 58' Processing helix chain 'j' and resid 61 through 64 No H-bonds generated for 'chain 'j' and resid 61 through 64' Processing helix chain 'k' and resid 27 through 38 removed outlier: 3.639A pdb=" N ARG k 38 " --> pdb=" O LYS k 34 " (cutoff:3.500A) Processing helix chain 'k' and resid 43 through 52 removed outlier: 4.262A pdb=" N ARG k 46 " --> pdb=" O PRO k 43 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N TRP k 50 " --> pdb=" O ASN k 47 " (cutoff:3.500A) Processing helix chain 'k' and resid 62 through 66 Processing helix chain 'k' and resid 70 through 89 Processing helix chain 'l' and resid 17 through 26 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 82 through 84 No H-bonds generated for 'chain 'l' and resid 82 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 20 through 22 No H-bonds generated for 'chain 'm' and resid 20 through 22' Processing helix chain 'm' and resid 26 through 51 removed outlier: 3.657A pdb=" N GLN m 49 " --> pdb=" O GLU m 45 " (cutoff:3.500A) Processing helix chain 'm' and resid 62 through 71 Processing helix chain 'm' and resid 86 through 115 removed outlier: 3.885A pdb=" N GLY m 93 " --> pdb=" O GLY m 89 " (cutoff:3.500A) Proline residue: m 96 - end of helix removed outlier: 3.512A pdb=" N TYR m 102 " --> pdb=" O VAL m 98 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ASP m 107 " --> pdb=" O VAL m 103 " (cutoff:3.500A) Processing helix chain 'n' and resid 10 through 30 Processing helix chain 'n' and resid 33 through 49 Processing helix chain 'n' and resid 56 through 72 removed outlier: 3.619A pdb=" N GLN n 61 " --> pdb=" O VAL n 57 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N HIS n 72 " --> pdb=" O GLU n 68 " (cutoff:3.500A) Processing helix chain 'n' and resid 92 through 95 removed outlier: 4.311A pdb=" N CYS n 95 " --> pdb=" O ARG n 92 " (cutoff:3.500A) No H-bonds generated for 'chain 'n' and resid 92 through 95' Processing helix chain 'n' and resid 100 through 105 Processing helix chain 'n' and resid 108 through 142 removed outlier: 3.844A pdb=" N MET n 113 " --> pdb=" O SER n 109 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N TYR n 114 " --> pdb=" O GLU n 110 " (cutoff:3.500A) Proline residue: n 115 - end of helix removed outlier: 4.298A pdb=" N GLU n 133 " --> pdb=" O ARG n 129 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ARG n 134 " --> pdb=" O GLU n 130 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU n 139 " --> pdb=" O GLU n 135 " (cutoff:3.500A) Processing helix chain 'n' and resid 167 through 171 Processing helix chain 'o' and resid 2 through 8 removed outlier: 3.871A pdb=" N ARG o 6 " --> pdb=" O ALA o 2 " (cutoff:3.500A) 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 57 through 72 removed outlier: 4.411A pdb=" N HIS o 60 " --> pdb=" O TYR o 57 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TYR o 61 " --> pdb=" O CYS o 58 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE o 63 " --> pdb=" O HIS o 60 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG o 70 " --> pdb=" O LYS o 67 " (cutoff:3.500A) Processing helix chain 'o' and resid 78 through 119 removed outlier: 4.591A pdb=" N HIS o 81 " --> pdb=" O ALA o 78 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU o 82 " --> pdb=" O CYS o 79 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG o 103 " --> pdb=" O GLU o 100 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ARG o 106 " --> pdb=" O ARG o 103 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU o 115 " --> pdb=" O LYS o 112 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG o 117 " --> 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 Processing helix chain 'p' and resid 117 through 123 removed outlier: 4.952A 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 172 Processing helix chain 'q' and resid 2 through 16 removed outlier: 3.720A pdb=" N VAL q 14 " --> pdb=" O GLY q 10 " (cutoff:3.500A) Processing helix chain 'q' and resid 20 through 30 removed outlier: 3.531A pdb=" N VAL q 26 " --> pdb=" O GLY q 22 " (cutoff:3.500A) 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: 3.521A pdb=" N ARG q 88 " --> pdb=" O PRO q 84 " (cutoff:3.500A) removed outlier: 4.152A 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: 4.677A 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: 6.034A pdb=" N VAL B 85 " --> pdb=" O MET B 48 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N PHE B 50 " --> pdb=" O VAL B 85 " (cutoff:3.500A) removed outlier: 6.401A 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: 7.704A pdb=" N VAL B 88 " --> pdb=" O TYR B 112 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N VAL B 114 " --> pdb=" O VAL B 88 " (cutoff:3.500A) removed outlier: 6.470A 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: 6.677A pdb=" N ASN C 95 " --> pdb=" O ALA C 76 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N LEU C 78 " --> pdb=" O VAL C 93 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N VAL C 93 " --> pdb=" O LEU C 78 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ALA C 80 " --> pdb=" O GLU C 91 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N GLU C 91 " --> pdb=" O ALA C 80 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N LEU C 48 " --> pdb=" O ARG C 104 " (cutoff:3.500A) removed outlier: 4.981A 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: 3.510A pdb=" N ARG C 182 " --> pdb=" O ASP C 177 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 46 through 50 removed outlier: 3.609A pdb=" N ARG D 63 " --> pdb=" O HIS D 79 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS D 75 " --> pdb=" O GLU D 67 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'D' and resid 361 through 368 Processing sheet with id= F, first strand: chain 'E' and resid 137 through 142 removed outlier: 6.653A pdb=" N TYR E 98 " --> pdb=" O THR E 138 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N ILE E 140 " --> pdb=" O TYR E 98 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ILE E 100 " --> pdb=" O ILE E 140 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N VAL E 142 " --> pdb=" O ILE E 100 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N VAL E 102 " --> pdb=" O VAL E 142 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N CYS E 103 " --> pdb=" O MET E 153 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N MET E 153 " --> pdb=" O CYS E 103 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASN E 159 " --> pdb=" O ILE E 156 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'F' and resid 220 through 224 removed outlier: 7.066A pdb=" N TYR F 92 " --> pdb=" O THR F 221 " (cutoff:3.500A) removed outlier: 8.294A pdb=" N ALA F 223 " --> pdb=" O TYR F 92 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N VAL F 94 " --> pdb=" O ALA F 223 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ALA F 133 " --> pdb=" O LEU F 93 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N VAL F 95 " --> pdb=" O ALA F 133 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N TYR F 135 " --> pdb=" O VAL F 95 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ALA F 97 " --> pdb=" O TYR F 135 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N TYR F 137 " --> pdb=" O ALA F 97 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N ASP F 174 " --> pdb=" O ALA F 134 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N ILE F 136 " --> pdb=" O ASP F 174 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N PHE F 176 " --> pdb=" O ILE F 136 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N ILE F 138 " --> pdb=" O PHE F 176 " (cutoff:3.500A) removed outlier: 6.197A 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 removed outlier: 3.585A pdb=" N ALA F 296 " --> pdb=" O MET F 337 " (cutoff:3.500A) 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 56 through 58 Processing sheet with id= K, first strand: chain 'G' and resid 146 through 148 Processing sheet with id= L, first strand: chain 'G' and resid 173 through 175 Processing sheet with id= M, first strand: chain 'G' and resid 223 through 228 Processing sheet with id= N, first strand: chain 'G' and resid 283 through 285 Processing sheet with id= O, first strand: chain 'G' and resid 343 through 345 removed outlier: 8.410A pdb=" N CYS G 344 " --> pdb=" O VAL G 315 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ALA G 317 " --> pdb=" O CYS G 344 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N MET G 521 " --> pdb=" O ALA G 316 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N ILE G 318 " --> pdb=" O MET G 521 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N PHE G 523 " --> pdb=" O ILE G 318 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N PHE G 542 " --> pdb=" O LEU G 522 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N LEU G 524 " --> pdb=" O PHE G 542 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N VAL G 544 " --> pdb=" O LEU G 524 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N VAL G 559 " --> pdb=" O TYR G 545 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N GLY G 547 " --> pdb=" O VAL G 559 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N LEU G 561 " --> pdb=" O GLY G 547 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'G' and resid 490 through 493 removed outlier: 8.212A pdb=" N ASN G 491 " --> pdb=" O PRO G 449 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N VAL G 451 " --> pdb=" O ASN G 491 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N LEU G 493 " --> pdb=" O VAL G 451 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N LEU G 453 " --> pdb=" O LEU G 493 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N VAL G 376 " --> pdb=" O MET G 450 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N ILE G 452 " --> pdb=" O VAL G 376 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N LEU G 378 " --> pdb=" O ILE G 452 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N GLY G 454 " --> pdb=" O LEU G 378 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N VAL G 380 " --> pdb=" O GLY G 454 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LYS G 405 " --> pdb=" O VAL G 377 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N LEU G 379 " --> pdb=" O LYS G 405 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ALA G 407 " --> pdb=" O LEU G 379 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ASP G 420 " --> pdb=" O LEU G 408 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'G' and resid 572 through 574 Processing sheet with id= R, first strand: chain 'I' and resid 65 through 67 Processing sheet with id= S, first strand: chain 'I' and resid 92 through 98 removed outlier: 5.928A pdb=" N GLU I 97 " --> pdb=" O THR I 106 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N THR I 106 " --> pdb=" O GLU I 97 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'L' and resid 61 through 67 removed outlier: 3.587A pdb=" N ASN L 65 " --> pdb=" O LEU L 78 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N LEU L 78 " --> pdb=" O ASN L 65 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'O' and resid 219 through 223 removed outlier: 6.512A pdb=" N VAL O 122 " --> pdb=" O ILE O 25 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N VAL O 27 " --> pdb=" O VAL O 122 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N LEU O 124 " --> pdb=" O VAL O 27 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N LYS O 49 " --> pdb=" O VAL O 123 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N GLU O 125 " --> pdb=" O LYS O 49 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N PHE O 51 " --> pdb=" O GLU O 125 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'P' and resid 227 through 230 removed outlier: 6.707A pdb=" N ILE P 165 " --> pdb=" O PHE P 228 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N PHE P 230 " --> pdb=" O ILE P 165 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LYS P 167 " --> pdb=" O PHE P 230 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE P 132 " --> pdb=" O ASN P 93 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N GLN P 44 " --> pdb=" O ALA P 21 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N VAL P 23 " --> pdb=" O GLN P 44 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ILE P 46 " --> pdb=" O VAL P 23 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'Q' and resid 102 through 105 Processing sheet with id= X, first strand: chain 'Q' and resid 64 through 66 Processing sheet with id= Y, first strand: chain 'R' and resid 50 through 52 Processing sheet with id= Z, first strand: chain 'R' and resid 56 through 59 Processing sheet with id= AA, first strand: chain 'S' and resid 51 through 56 Processing sheet with id= AB, first strand: chain 'q' and resid 60 through 63 removed outlier: 6.719A pdb=" N GLU q 50 " --> pdb=" O LEU q 38 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N LEU q 38 " --> pdb=" O GLU q 50 " (cutoff:3.500A) 2716 hydrogen bonds defined for protein. 7458 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: 24.50 Time building geometry restraints manager: 27.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.40: 27230 1.40 - 1.62: 39613 1.62 - 1.85: 838 1.85 - 2.08: 0 2.08 - 2.30: 80 Bond restraints: 67761 Sorted by residual: bond pdb=" C15 CHD H 701 " pdb=" C16 CHD H 701 " ideal model delta sigma weight residual 1.541 1.728 -0.187 2.00e-02 2.50e+03 8.74e+01 bond pdb=" C15 CHD L 704 " pdb=" C16 CHD L 704 " ideal model delta sigma weight residual 1.541 1.728 -0.187 2.00e-02 2.50e+03 8.70e+01 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 7.29e+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 6.93e+01 bond pdb=" C11 CHD L 704 " pdb=" C12 CHD L 704 " ideal model delta sigma weight residual 1.533 1.675 -0.142 2.00e-02 2.50e+03 5.01e+01 ... (remaining 67756 not shown) Histogram of bond angle deviations from ideal: 72.50 - 84.81: 76 84.81 - 97.13: 1 97.13 - 109.44: 7052 109.44 - 121.75: 71317 121.75 - 134.07: 13203 Bond angle restraints: 91649 Sorted by residual: angle pdb=" CA 2MR D 85 " pdb=" C 2MR D 85 " pdb=" O 2MR D 85 " ideal model delta sigma weight residual 120.80 107.21 13.59 1.70e+00 3.46e-01 6.39e+01 angle pdb=" C11 CDL L 702 " pdb=" CA5 CDL L 702 " pdb=" OA6 CDL L 702 " ideal model delta sigma weight residual 111.33 120.95 -9.62 1.32e+00 5.72e-01 5.29e+01 angle pdb=" C51 CDL h 201 " pdb=" CB5 CDL h 201 " pdb=" OB6 CDL h 201 " ideal model delta sigma weight residual 111.33 120.71 -9.38 1.32e+00 5.72e-01 5.03e+01 angle pdb=" C11 CDL X 201 " pdb=" CA5 CDL X 201 " pdb=" OA6 CDL X 201 " ideal model delta sigma weight residual 111.33 120.68 -9.35 1.32e+00 5.72e-01 5.00e+01 angle pdb=" C51 CDL X 201 " pdb=" CB5 CDL X 201 " pdb=" OB6 CDL X 201 " ideal model delta sigma weight residual 111.33 120.51 -9.18 1.32e+00 5.72e-01 4.82e+01 ... (remaining 91644 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.75: 40082 34.75 - 69.49: 933 69.49 - 104.24: 151 104.24 - 138.99: 18 138.99 - 173.73: 4 Dihedral angle restraints: 41188 sinusoidal: 17830 harmonic: 23358 Sorted by residual: dihedral pdb=" CB CYS X 77 " pdb=" SG CYS X 77 " pdb=" SG CYS X 109 " pdb=" CB CYS X 109 " ideal model delta sinusoidal sigma weight residual 93.00 161.02 -68.02 1 1.00e+01 1.00e-02 6.01e+01 dihedral pdb=" C51 U10 M 701 " pdb=" C52 U10 M 701 " pdb=" C53 U10 M 701 " pdb=" C54 U10 M 701 " ideal model delta sinusoidal sigma weight residual 282.09 108.35 173.73 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" C10 FMN F 501 " pdb=" C1' FMN F 501 " pdb=" N10 FMN F 501 " pdb=" C2' FMN F 501 " ideal model delta sinusoidal sigma weight residual 257.59 86.31 171.28 1 2.00e+01 2.50e-03 4.77e+01 ... (remaining 41185 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.261: 9892 4.261 - 8.522: 0 8.522 - 12.783: 0 12.783 - 17.044: 0 17.044 - 21.305: 16 Chirality restraints: 9908 Sorted by residual: 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 10.75 -21.31 2.00e-01 2.50e+01 1.13e+04 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 10.75 -21.30 2.00e-01 2.50e+01 1.13e+04 chirality pdb="FE3 SF4 G 802 " pdb=" S1 SF4 G 802 " pdb=" S2 SF4 G 802 " pdb=" S4 SF4 G 802 " both_signs ideal model delta sigma weight residual False -10.55 10.73 -21.29 2.00e-01 2.50e+01 1.13e+04 ... (remaining 9905 not shown) Planarity restraints: 11468 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD 2MR D 85 " 0.212 2.00e-02 2.50e+03 2.35e-01 9.67e+02 pdb=" NE 2MR D 85 " -0.097 2.00e-02 2.50e+03 pdb=" CZ 2MR D 85 " -0.188 2.00e-02 2.50e+03 pdb=" NH1 2MR D 85 " -0.157 2.00e-02 2.50e+03 pdb=" NH2 2MR D 85 " -0.331 2.00e-02 2.50e+03 pdb=" CQ1 2MR D 85 " 0.230 2.00e-02 2.50e+03 pdb=" CQ2 2MR D 85 " 0.332 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SAC i 1 " -0.060 2.00e-02 2.50e+03 1.17e-01 1.37e+02 pdb=" C SAC i 1 " 0.203 2.00e-02 2.50e+03 pdb=" O SAC i 1 " -0.070 2.00e-02 2.50e+03 pdb=" N GLY i 2 " -0.073 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA U 3 " -0.093 5.00e-02 4.00e+02 1.41e-01 3.18e+01 pdb=" N PRO U 4 " 0.244 5.00e-02 4.00e+02 pdb=" CA PRO U 4 " -0.078 5.00e-02 4.00e+02 pdb=" CD PRO U 4 " -0.073 5.00e-02 4.00e+02 ... (remaining 11465 not shown) Histogram of nonbonded interaction distances: 1.46 - 2.19: 21 2.19 - 2.93: 29257 2.93 - 3.67: 114276 3.67 - 4.40: 205279 4.40 - 5.14: 334558 Nonbonded interactions: 683391 Sorted by model distance: nonbonded pdb=" OXT AME d 1 " pdb=" CA MET d 2 " model vdw 1.456 2.776 nonbonded pdb=" O3A GTP O 401 " pdb="MG MG O 402 " model vdw 1.873 2.170 nonbonded pdb=" O ASN m 82 " pdb=" OG SER m 86 " model vdw 1.964 2.440 nonbonded pdb=" O THR G 366 " pdb=" OG1 THR G 367 " model vdw 1.981 2.440 nonbonded pdb=" OG SER N 158 " pdb=" OG1 THR N 191 " model vdw 2.025 2.440 ... (remaining 683386 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 5 through 88 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: 11.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 51.240 Check model and map are aligned: 0.730 Set scattering table: 0.460 Process input model: 164.510 Find NCS groups from input model: 1.990 Set up NCS constraints: 0.290 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 233.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.187 67761 Z= 0.483 Angle : 0.829 15.209 91649 Z= 0.394 Chirality : 0.856 21.305 9908 Planarity : 0.005 0.235 11468 Dihedral : 15.440 173.733 26107 Min Nonbonded Distance : 1.456 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.75 % Favored : 96.22 % Rotamer: Outliers : 0.01 % Allowed : 0.19 % Favored : 99.80 % 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: -0.53 (0.09), residues: 7903 helix: -0.12 (0.08), residues: 4091 sheet: -0.30 (0.25), residues: 404 loop : -0.48 (0.10), residues: 3408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP P 73 HIS 0.024 0.001 HIS e 96 PHE 0.080 0.002 PHE D 171 TYR 0.086 0.002 TYR B 125 ARG 0.007 0.001 ARG P 97 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15806 Ramachandran restraints generated. 7903 Oldfield, 0 Emsley, 7903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15806 Ramachandran restraints generated. 7903 Oldfield, 0 Emsley, 7903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1207 residues out of total 6998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1206 time to evaluate : 5.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 ARG cc_start: 0.6539 (ptt180) cc_final: 0.6197 (ttt90) REVERT: B 102 LYS cc_start: 0.8561 (ttmt) cc_final: 0.8333 (ttpp) REVERT: B 171 LYS cc_start: 0.8245 (mttt) cc_final: 0.8002 (mtmm) REVERT: C 73 LYS cc_start: 0.8830 (mmtt) cc_final: 0.8505 (mttt) REVERT: D 66 MET cc_start: 0.8210 (mtm) cc_final: 0.7988 (mtm) REVERT: D 170 MET cc_start: 0.8407 (mmt) cc_final: 0.7881 (mmt) REVERT: G 642 PHE cc_start: 0.7749 (t80) cc_final: 0.7023 (m-80) REVERT: H 62 ARG cc_start: 0.6310 (mmm160) cc_final: 0.5845 (tpp80) REVERT: H 126 LYS cc_start: 0.7891 (mmtp) cc_final: 0.7659 (mtmm) REVERT: H 268 MET cc_start: 0.7969 (mtm) cc_final: 0.7592 (mtp) REVERT: I 14 MET cc_start: 0.8391 (mmm) cc_final: 0.7974 (tpp) REVERT: L 128 MET cc_start: 0.7963 (tpt) cc_final: 0.7642 (tpt) REVERT: L 366 MET cc_start: 0.7241 (mtp) cc_final: 0.6847 (mmm) REVERT: L 445 GLU cc_start: 0.7193 (pt0) cc_final: 0.6980 (pt0) REVERT: N 14 MET cc_start: 0.7949 (mtp) cc_final: 0.7604 (mtt) REVERT: O 151 HIS cc_start: 0.8263 (t-90) cc_final: 0.8029 (t70) REVERT: O 254 ARG cc_start: 0.7809 (ttp80) cc_final: 0.7380 (tpp-160) REVERT: P 102 GLN cc_start: 0.7826 (mt0) cc_final: 0.7602 (mm-40) REVERT: P 188 PHE cc_start: 0.6809 (p90) cc_final: 0.6415 (t80) REVERT: P 335 GLN cc_start: 0.8082 (tp40) cc_final: 0.7677 (pm20) REVERT: W 25 MET cc_start: 0.8342 (mmm) cc_final: 0.8115 (mmm) REVERT: W 117 ASP cc_start: 0.7962 (p0) cc_final: 0.7722 (p0) REVERT: c 13 ASN cc_start: 0.7932 (t0) cc_final: 0.7713 (t0) REVERT: d 17 GLU cc_start: 0.7643 (pt0) cc_final: 0.7428 (pt0) REVERT: d 20 SER cc_start: 0.8311 (m) cc_final: 0.8095 (p) REVERT: f 39 ASN cc_start: 0.8451 (t0) cc_final: 0.8105 (t0) REVERT: g 55 ILE cc_start: 0.8950 (mt) cc_final: 0.8720 (tt) REVERT: g 107 ILE cc_start: 0.8043 (mm) cc_final: 0.7835 (mt) REVERT: i 100 LYS cc_start: 0.7592 (ptmt) cc_final: 0.7384 (ptpt) REVERT: j 59 TRP cc_start: 0.7838 (m-10) cc_final: 0.7613 (m-10) REVERT: o 43 GLN cc_start: 0.7921 (tp40) cc_final: 0.7462 (tp40) REVERT: r 73 LYS cc_start: 0.8047 (mmtp) cc_final: 0.7776 (mmtm) outliers start: 1 outliers final: 1 residues processed: 1207 average time/residue: 0.7110 time to fit residues: 1434.2058 Evaluate side-chains 865 residues out of total 6998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 864 time to evaluate : 5.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain T residue 44 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 783 random chunks: chunk 661 optimal weight: 10.0000 chunk 593 optimal weight: 10.0000 chunk 329 optimal weight: 0.9990 chunk 202 optimal weight: 6.9990 chunk 400 optimal weight: 1.9990 chunk 317 optimal weight: 2.9990 chunk 613 optimal weight: 0.9980 chunk 237 optimal weight: 1.9990 chunk 373 optimal weight: 0.9990 chunk 456 optimal weight: 0.0040 chunk 711 optimal weight: 0.9990 overall best weight: 0.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 46 ASN D 114 ASN L 328 HIS ** L 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 541 ASN M 144 ASN M 175 ASN M 440 HIS O 92 ASN P 87 HIS Q 44 ASN ** U 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 26 HIS e 76 HIS ** h 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 125 GLN i 127 HIS j 13 GLN k 20 GLN k 90 GLN o 53 GLN r 24 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.279 67761 Z= 0.468 Angle : 1.332 50.786 91649 Z= 0.851 Chirality : 0.258 6.497 9908 Planarity : 0.005 0.093 11468 Dihedral : 13.519 173.649 10235 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.09 % Favored : 97.90 % Rotamer: Outliers : 0.90 % Allowed : 5.79 % Favored : 93.31 % 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: 0.63 (0.09), residues: 7903 helix: 1.03 (0.08), residues: 4156 sheet: -0.16 (0.24), residues: 428 loop : -0.17 (0.11), residues: 3319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP P 278 HIS 0.014 0.001 HIS L 514 PHE 0.036 0.002 PHE D 171 TYR 0.045 0.001 TYR B 125 ARG 0.008 0.000 ARG k 38 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15806 Ramachandran restraints generated. 7903 Oldfield, 0 Emsley, 7903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15806 Ramachandran restraints generated. 7903 Oldfield, 0 Emsley, 7903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1022 residues out of total 6998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 959 time to evaluate : 5.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 ARG cc_start: 0.6545 (ptt180) cc_final: 0.6173 (ttt90) REVERT: B 102 LYS cc_start: 0.8386 (ttmt) cc_final: 0.8144 (ttpp) REVERT: B 171 LYS cc_start: 0.8138 (mttt) cc_final: 0.7938 (mtmm) REVERT: C 73 LYS cc_start: 0.8892 (mmtt) cc_final: 0.8560 (mttt) REVERT: D 170 MET cc_start: 0.8294 (mmt) cc_final: 0.7874 (mmt) REVERT: G 642 PHE cc_start: 0.7612 (t80) cc_final: 0.6905 (m-80) REVERT: H 62 ARG cc_start: 0.6317 (mmm160) cc_final: 0.5806 (tpp80) REVERT: H 268 MET cc_start: 0.7833 (mtm) cc_final: 0.7410 (mtp) REVERT: L 40 ILE cc_start: 0.8609 (OUTLIER) cc_final: 0.8359 (mp) REVERT: L 128 MET cc_start: 0.7859 (tpt) cc_final: 0.7493 (tpt) REVERT: L 411 MET cc_start: 0.8422 (mmp) cc_final: 0.7988 (mmp) REVERT: M 396 MET cc_start: 0.8863 (tpp) cc_final: 0.8540 (mmt) REVERT: N 14 MET cc_start: 0.7671 (mtp) cc_final: 0.7404 (mtt) REVERT: O 151 HIS cc_start: 0.8235 (t-90) cc_final: 0.8028 (t70) REVERT: P 115 GLN cc_start: 0.8270 (tm-30) cc_final: 0.7763 (tm-30) REVERT: P 253 PHE cc_start: 0.6897 (t80) cc_final: 0.6645 (t80) REVERT: P 335 GLN cc_start: 0.8091 (tp40) cc_final: 0.7553 (pp30) REVERT: T 52 MET cc_start: 0.7756 (mtp) cc_final: 0.7398 (mtt) REVERT: d 17 GLU cc_start: 0.7577 (pt0) cc_final: 0.7312 (pt0) REVERT: d 20 SER cc_start: 0.8267 (m) cc_final: 0.7973 (p) REVERT: i 100 LYS cc_start: 0.7699 (ptmt) cc_final: 0.7474 (ptpt) REVERT: n 61 GLN cc_start: 0.7505 (tp40) cc_final: 0.7177 (tp40) REVERT: o 96 LYS cc_start: 0.8754 (mptt) cc_final: 0.8397 (mptt) REVERT: o 98 MET cc_start: 0.7923 (OUTLIER) cc_final: 0.7618 (ttm) REVERT: o 112 LYS cc_start: 0.8420 (ttpp) cc_final: 0.8053 (ttpp) REVERT: r 73 LYS cc_start: 0.7992 (mmtp) cc_final: 0.7769 (mmtm) outliers start: 63 outliers final: 35 residues processed: 985 average time/residue: 0.6465 time to fit residues: 1093.0500 Evaluate side-chains 877 residues out of total 6998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 840 time to evaluate : 5.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 112 GLU Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 59 MET Chi-restraints excluded: chain E residue 26 GLU Chi-restraints excluded: chain E residue 52 ASP Chi-restraints excluded: chain E residue 168 ASP Chi-restraints excluded: chain F residue 77 LEU Chi-restraints excluded: chain F residue 323 ILE Chi-restraints excluded: chain H residue 200 LEU Chi-restraints excluded: chain K residue 10 MET Chi-restraints excluded: chain K residue 24 SER Chi-restraints excluded: chain L residue 40 ILE Chi-restraints excluded: chain M residue 12 MET Chi-restraints excluded: chain N residue 251 MET Chi-restraints excluded: chain R residue 5 SER Chi-restraints excluded: chain T residue 44 SER Chi-restraints excluded: chain U residue 33 ASN Chi-restraints excluded: chain U residue 52 MET Chi-restraints excluded: chain Z residue 51 MET Chi-restraints excluded: chain d residue 10 THR Chi-restraints excluded: chain e residue 86 ILE Chi-restraints excluded: chain i residue 23 LYS Chi-restraints excluded: chain i residue 42 VAL Chi-restraints excluded: chain j residue 40 PHE Chi-restraints excluded: chain j residue 42 HIS Chi-restraints excluded: chain k residue 53 MET Chi-restraints excluded: chain k residue 63 VAL Chi-restraints excluded: chain l residue 102 CYS Chi-restraints excluded: chain l residue 128 VAL Chi-restraints excluded: chain l residue 158 ILE Chi-restraints excluded: chain n residue 57 VAL Chi-restraints excluded: chain o residue 77 LEU Chi-restraints excluded: chain o residue 98 MET Chi-restraints excluded: chain p residue 2 ASP Chi-restraints excluded: chain p residue 7 ASP Chi-restraints excluded: chain q residue 78 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 783 random chunks: chunk 395 optimal weight: 0.7980 chunk 220 optimal weight: 6.9990 chunk 591 optimal weight: 9.9990 chunk 484 optimal weight: 4.9990 chunk 196 optimal weight: 10.0000 chunk 712 optimal weight: 8.9990 chunk 769 optimal weight: 2.9990 chunk 634 optimal weight: 0.9980 chunk 706 optimal weight: 8.9990 chunk 242 optimal weight: 6.9990 chunk 571 optimal weight: 30.0000 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 99 HIS F 416 GLN G 237 ASN G 517 ASN K 52 HIS ** L 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 541 ASN M 51 ASN M 139 GLN O 92 ASN P 243 GLN Q 44 ASN V 75 GLN X 76 HIS ** h 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 127 HIS k 90 GLN m 47 GLN n 13 GLN n 138 GLN o 46 ASN o 60 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.1910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.242 67761 Z= 0.533 Angle : 1.340 50.498 91649 Z= 0.854 Chirality : 0.261 6.531 9908 Planarity : 0.005 0.072 11468 Dihedral : 12.809 172.741 10235 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.71 % Favored : 97.24 % Rotamer: Outliers : 1.69 % Allowed : 7.43 % Favored : 90.88 % 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: 0.56 (0.09), residues: 7903 helix: 1.00 (0.08), residues: 4173 sheet: -0.21 (0.25), residues: 404 loop : -0.24 (0.11), residues: 3326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP G 77 HIS 0.010 0.001 HIS L 514 PHE 0.041 0.002 PHE D 171 TYR 0.046 0.002 TYR B 125 ARG 0.007 0.001 ARG k 51 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15806 Ramachandran restraints generated. 7903 Oldfield, 0 Emsley, 7903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15806 Ramachandran restraints generated. 7903 Oldfield, 0 Emsley, 7903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 979 residues out of total 6998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 861 time to evaluate : 5.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 ARG cc_start: 0.6587 (ptt180) cc_final: 0.6212 (ttt90) REVERT: B 171 LYS cc_start: 0.8203 (mttt) cc_final: 0.7994 (mtmm) REVERT: D 170 MET cc_start: 0.8187 (mmt) cc_final: 0.7860 (mmt) REVERT: G 642 PHE cc_start: 0.7690 (t80) cc_final: 0.6929 (m-80) REVERT: H 62 ARG cc_start: 0.6335 (mmm160) cc_final: 0.5766 (tpp80) REVERT: H 268 MET cc_start: 0.7823 (mtm) cc_final: 0.7386 (mtp) REVERT: L 128 MET cc_start: 0.7912 (tpt) cc_final: 0.7585 (tpt) REVERT: M 42 MET cc_start: 0.8697 (OUTLIER) cc_final: 0.8065 (mtp) REVERT: N 14 MET cc_start: 0.7733 (mtp) cc_final: 0.7426 (mtt) REVERT: N 187 MET cc_start: 0.8309 (mmt) cc_final: 0.7669 (mmt) REVERT: O 151 HIS cc_start: 0.8311 (t-90) cc_final: 0.8061 (t70) REVERT: O 254 ARG cc_start: 0.7584 (ttp80) cc_final: 0.7179 (tpp-160) REVERT: P 115 GLN cc_start: 0.8299 (tm-30) cc_final: 0.7809 (tm-30) REVERT: P 335 GLN cc_start: 0.8083 (tp40) cc_final: 0.7545 (pp30) REVERT: d 17 GLU cc_start: 0.7601 (pt0) cc_final: 0.7324 (pt0) REVERT: d 20 SER cc_start: 0.8324 (m) cc_final: 0.8001 (p) REVERT: e 72 MET cc_start: 0.7430 (mmm) cc_final: 0.7202 (mmm) REVERT: k 12 LYS cc_start: 0.8160 (OUTLIER) cc_final: 0.7888 (pptt) REVERT: n 61 GLN cc_start: 0.7498 (tp40) cc_final: 0.7089 (tp40) REVERT: o 4 LEU cc_start: 0.8242 (tt) cc_final: 0.7971 (tt) REVERT: r 73 LYS cc_start: 0.7971 (mmtp) cc_final: 0.7714 (mmtm) outliers start: 118 outliers final: 80 residues processed: 922 average time/residue: 0.6419 time to fit residues: 1017.6862 Evaluate side-chains 890 residues out of total 6998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 808 time to evaluate : 5.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 112 GLU Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 59 MET Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain E residue 26 GLU Chi-restraints excluded: chain E residue 52 ASP Chi-restraints excluded: chain E residue 113 SER Chi-restraints excluded: chain E residue 168 ASP Chi-restraints excluded: chain F residue 77 LEU Chi-restraints excluded: chain F residue 323 ILE Chi-restraints excluded: chain G residue 424 ASP Chi-restraints excluded: chain H residue 156 MET Chi-restraints excluded: chain H residue 200 LEU Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain I residue 1 THR Chi-restraints excluded: chain J residue 56 VAL Chi-restraints excluded: chain J residue 74 MET Chi-restraints excluded: chain J residue 107 VAL Chi-restraints excluded: chain K residue 24 SER Chi-restraints excluded: chain L residue 254 VAL Chi-restraints excluded: chain L residue 381 THR Chi-restraints excluded: chain L residue 424 THR Chi-restraints excluded: chain M residue 12 MET Chi-restraints excluded: chain M residue 42 MET Chi-restraints excluded: chain M residue 143 LEU Chi-restraints excluded: chain M residue 281 ASP Chi-restraints excluded: chain M residue 384 SER Chi-restraints excluded: chain N residue 173 THR Chi-restraints excluded: chain N residue 251 MET Chi-restraints excluded: chain N residue 270 MET Chi-restraints excluded: chain P residue 196 LEU Chi-restraints excluded: chain P residue 256 TYR Chi-restraints excluded: chain Q residue 11 ILE Chi-restraints excluded: chain Q residue 104 ASP Chi-restraints excluded: chain S residue 17 GLU Chi-restraints excluded: chain S residue 44 LYS Chi-restraints excluded: chain S residue 58 SER Chi-restraints excluded: chain S residue 76 VAL Chi-restraints excluded: chain T residue 21 LEU Chi-restraints excluded: chain T residue 44 SER Chi-restraints excluded: chain U residue 33 ASN Chi-restraints excluded: chain V residue 7 THR Chi-restraints excluded: chain V residue 16 CYS Chi-restraints excluded: chain V residue 103 VAL Chi-restraints excluded: chain W residue 24 ASP Chi-restraints excluded: chain X residue 36 ASP Chi-restraints excluded: chain X residue 120 ASP Chi-restraints excluded: chain X residue 130 VAL Chi-restraints excluded: chain Z residue 51 MET Chi-restraints excluded: chain b residue 33 THR Chi-restraints excluded: chain d residue 10 THR Chi-restraints excluded: chain e residue 86 ILE Chi-restraints excluded: chain e residue 92 THR Chi-restraints excluded: chain e residue 96 HIS Chi-restraints excluded: chain f residue 9 ASP Chi-restraints excluded: chain f residue 31 ASP Chi-restraints excluded: chain g residue 37 LEU Chi-restraints excluded: chain i residue 23 LYS Chi-restraints excluded: chain i residue 33 VAL Chi-restraints excluded: chain i residue 42 VAL Chi-restraints excluded: chain i residue 112 THR Chi-restraints excluded: chain j residue 22 VAL Chi-restraints excluded: chain j residue 42 HIS Chi-restraints excluded: chain k residue 12 LYS Chi-restraints excluded: chain k residue 60 VAL Chi-restraints excluded: chain k residue 63 VAL Chi-restraints excluded: chain l residue 4 ILE Chi-restraints excluded: chain l residue 28 ASN Chi-restraints excluded: chain l residue 81 LEU Chi-restraints excluded: chain l residue 102 CYS Chi-restraints excluded: chain l residue 118 VAL Chi-restraints excluded: chain l residue 128 VAL Chi-restraints excluded: chain m residue 72 SER Chi-restraints excluded: chain n residue 57 VAL Chi-restraints excluded: chain o residue 77 LEU Chi-restraints excluded: chain p residue 2 ASP Chi-restraints excluded: chain q residue 11 LEU Chi-restraints excluded: chain q residue 78 ASP Chi-restraints excluded: chain r residue 15 SER Chi-restraints excluded: chain s residue 47 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 783 random chunks: chunk 703 optimal weight: 10.0000 chunk 535 optimal weight: 1.9990 chunk 369 optimal weight: 3.9990 chunk 78 optimal weight: 20.0000 chunk 339 optimal weight: 4.9990 chunk 478 optimal weight: 7.9990 chunk 714 optimal weight: 6.9990 chunk 756 optimal weight: 1.9990 chunk 373 optimal weight: 0.8980 chunk 677 optimal weight: 0.0370 chunk 203 optimal weight: 5.9990 overall best weight: 1.7864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 237 ASN H 212 ASN L 175 ASN ** L 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 92 ASN Q 44 ASN h 44 ASN ** h 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 127 HIS m 47 GLN n 138 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.245 67761 Z= 0.464 Angle : 1.312 50.571 91649 Z= 0.844 Chirality : 0.258 6.446 9908 Planarity : 0.004 0.066 11468 Dihedral : 12.331 172.803 10235 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.35 % Favored : 97.60 % Rotamer: Outliers : 1.60 % Allowed : 8.77 % Favored : 89.63 % 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: 0.77 (0.09), residues: 7903 helix: 1.21 (0.08), residues: 4153 sheet: -0.15 (0.24), residues: 414 loop : -0.19 (0.11), residues: 3336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP j 59 HIS 0.015 0.001 HIS L 514 PHE 0.024 0.001 PHE U 60 TYR 0.025 0.001 TYR L 422 ARG 0.011 0.000 ARG k 38 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15806 Ramachandran restraints generated. 7903 Oldfield, 0 Emsley, 7903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15806 Ramachandran restraints generated. 7903 Oldfield, 0 Emsley, 7903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 967 residues out of total 6998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 855 time to evaluate : 5.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 ARG cc_start: 0.6542 (ptt180) cc_final: 0.6195 (ttt90) REVERT: A 115 GLU cc_start: 0.6475 (OUTLIER) cc_final: 0.6247 (mt-10) REVERT: B 171 LYS cc_start: 0.8166 (mttt) cc_final: 0.7956 (mtmm) REVERT: D 71 GLU cc_start: 0.7046 (tt0) cc_final: 0.6838 (tt0) REVERT: D 170 MET cc_start: 0.8147 (mmt) cc_final: 0.7861 (mmt) REVERT: H 268 MET cc_start: 0.7771 (mtm) cc_final: 0.7349 (mtp) REVERT: J 99 MET cc_start: 0.6282 (ptt) cc_final: 0.6039 (ptt) REVERT: L 128 MET cc_start: 0.7816 (tpt) cc_final: 0.7477 (tpt) REVERT: M 42 MET cc_start: 0.8690 (OUTLIER) cc_final: 0.8050 (mtp) REVERT: M 140 THR cc_start: 0.5733 (OUTLIER) cc_final: 0.5435 (p) REVERT: N 14 MET cc_start: 0.7679 (mtp) cc_final: 0.7381 (mtt) REVERT: N 187 MET cc_start: 0.8306 (mmt) cc_final: 0.7702 (mmt) REVERT: O 151 HIS cc_start: 0.8298 (t-90) cc_final: 0.8033 (t70) REVERT: P 115 GLN cc_start: 0.8289 (tm-30) cc_final: 0.7789 (tm-30) REVERT: P 335 GLN cc_start: 0.8063 (tp40) cc_final: 0.7537 (pp30) REVERT: R 55 ARG cc_start: 0.8233 (mtp85) cc_final: 0.8016 (mtp-110) REVERT: d 17 GLU cc_start: 0.7551 (pt0) cc_final: 0.7250 (pt0) REVERT: d 20 SER cc_start: 0.8321 (m) cc_final: 0.8004 (p) REVERT: e 87 LYS cc_start: 0.6693 (ptpp) cc_final: 0.6356 (ptpp) REVERT: g 55 ILE cc_start: 0.8804 (mt) cc_final: 0.8582 (tt) REVERT: k 12 LYS cc_start: 0.8011 (OUTLIER) cc_final: 0.7638 (pptt) REVERT: r 73 LYS cc_start: 0.7949 (mmtp) cc_final: 0.7688 (mmtm) outliers start: 112 outliers final: 85 residues processed: 915 average time/residue: 0.6233 time to fit residues: 987.1366 Evaluate side-chains 893 residues out of total 6998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 804 time to evaluate : 5.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 112 GLU Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain B residue 59 MET Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain E residue 26 GLU Chi-restraints excluded: chain E residue 168 ASP Chi-restraints excluded: chain F residue 77 LEU Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 323 ILE Chi-restraints excluded: chain G residue 21 GLU Chi-restraints excluded: chain G residue 295 THR Chi-restraints excluded: chain G residue 424 ASP Chi-restraints excluded: chain G residue 536 ASP Chi-restraints excluded: chain H residue 200 LEU Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain I residue 1 THR Chi-restraints excluded: chain J residue 56 VAL Chi-restraints excluded: chain J residue 74 MET Chi-restraints excluded: chain J residue 107 VAL Chi-restraints excluded: chain K residue 10 MET Chi-restraints excluded: chain K residue 84 THR Chi-restraints excluded: chain L residue 254 VAL Chi-restraints excluded: chain L residue 381 THR Chi-restraints excluded: chain L residue 424 THR Chi-restraints excluded: chain M residue 42 MET Chi-restraints excluded: chain M residue 140 THR Chi-restraints excluded: chain M residue 143 LEU Chi-restraints excluded: chain M residue 281 ASP Chi-restraints excluded: chain M residue 384 SER Chi-restraints excluded: chain N residue 173 THR Chi-restraints excluded: chain N residue 251 MET Chi-restraints excluded: chain N residue 270 MET Chi-restraints excluded: chain O residue 32 CYS Chi-restraints excluded: chain P residue 196 LEU Chi-restraints excluded: chain P residue 256 TYR Chi-restraints excluded: chain Q residue 44 ASN Chi-restraints excluded: chain R residue 7 THR Chi-restraints excluded: chain R residue 81 THR Chi-restraints excluded: chain T residue 21 LEU Chi-restraints excluded: chain T residue 72 CYS Chi-restraints excluded: chain T residue 80 ILE Chi-restraints excluded: chain U residue 30 LEU Chi-restraints excluded: chain U residue 33 ASN Chi-restraints excluded: chain U residue 52 MET Chi-restraints excluded: chain U residue 72 CYS Chi-restraints excluded: chain V residue 7 THR Chi-restraints excluded: chain V residue 16 CYS Chi-restraints excluded: chain V residue 103 VAL Chi-restraints excluded: chain W residue 127 ASP Chi-restraints excluded: chain X residue 36 ASP Chi-restraints excluded: chain X residue 120 ASP Chi-restraints excluded: chain X residue 130 VAL Chi-restraints excluded: chain Z residue 51 MET Chi-restraints excluded: chain Z residue 69 ILE Chi-restraints excluded: chain Z residue 101 VAL Chi-restraints excluded: chain a residue 54 VAL Chi-restraints excluded: chain b residue 33 THR Chi-restraints excluded: chain b residue 81 LYS Chi-restraints excluded: chain d residue 10 THR Chi-restraints excluded: chain e residue 92 THR Chi-restraints excluded: chain e residue 96 HIS Chi-restraints excluded: chain f residue 6 VAL Chi-restraints excluded: chain f residue 9 ASP Chi-restraints excluded: chain f residue 31 ASP Chi-restraints excluded: chain g residue 37 LEU Chi-restraints excluded: chain i residue 33 VAL Chi-restraints excluded: chain i residue 42 VAL Chi-restraints excluded: chain i residue 112 THR Chi-restraints excluded: chain j residue 22 VAL Chi-restraints excluded: chain j residue 29 SER Chi-restraints excluded: chain j residue 42 HIS Chi-restraints excluded: chain j residue 64 LEU Chi-restraints excluded: chain k residue 12 LYS Chi-restraints excluded: chain k residue 63 VAL Chi-restraints excluded: chain l residue 4 ILE Chi-restraints excluded: chain l residue 28 ASN Chi-restraints excluded: chain l residue 59 ASP Chi-restraints excluded: chain l residue 102 CYS Chi-restraints excluded: chain l residue 128 VAL Chi-restraints excluded: chain n residue 57 VAL Chi-restraints excluded: chain n residue 116 ASP Chi-restraints excluded: chain o residue 77 LEU Chi-restraints excluded: chain p residue 2 ASP Chi-restraints excluded: chain q residue 11 LEU Chi-restraints excluded: chain q residue 78 ASP Chi-restraints excluded: chain r residue 15 SER Chi-restraints excluded: chain s residue 47 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 783 random chunks: chunk 630 optimal weight: 1.9990 chunk 429 optimal weight: 10.0000 chunk 10 optimal weight: 8.9990 chunk 563 optimal weight: 8.9990 chunk 312 optimal weight: 0.7980 chunk 645 optimal weight: 0.7980 chunk 523 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 386 optimal weight: 7.9990 chunk 679 optimal weight: 0.9980 chunk 190 optimal weight: 6.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 237 ASN ** L 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 243 GLN Q 44 ASN e 26 HIS h 44 ASN ** h 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 127 HIS m 47 GLN n 138 GLN ** o 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.245 67761 Z= 0.454 Angle : 1.306 50.563 91649 Z= 0.841 Chirality : 0.258 6.421 9908 Planarity : 0.004 0.068 11468 Dihedral : 11.930 172.249 10234 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.42 % Favored : 97.55 % Rotamer: Outliers : 1.59 % Allowed : 9.62 % Favored : 88.80 % 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: 0.93 (0.09), residues: 7903 helix: 1.36 (0.08), residues: 4144 sheet: -0.08 (0.24), residues: 419 loop : -0.14 (0.11), residues: 3340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP j 59 HIS 0.011 0.001 HIS L 514 PHE 0.031 0.001 PHE P 239 TYR 0.025 0.001 TYR L 422 ARG 0.010 0.000 ARG k 38 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15806 Ramachandran restraints generated. 7903 Oldfield, 0 Emsley, 7903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15806 Ramachandran restraints generated. 7903 Oldfield, 0 Emsley, 7903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 946 residues out of total 6998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 835 time to evaluate : 5.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 ARG cc_start: 0.6530 (ptt180) cc_final: 0.6183 (ttt90) REVERT: A 115 GLU cc_start: 0.6403 (OUTLIER) cc_final: 0.6164 (mt-10) REVERT: B 171 LYS cc_start: 0.8162 (mttt) cc_final: 0.7957 (mtmm) REVERT: D 170 MET cc_start: 0.8088 (mmt) cc_final: 0.7817 (mmt) REVERT: H 268 MET cc_start: 0.7692 (mtm) cc_final: 0.7357 (mtp) REVERT: L 40 ILE cc_start: 0.8652 (OUTLIER) cc_final: 0.8259 (mt) REVERT: L 128 MET cc_start: 0.7799 (tpt) cc_final: 0.7456 (tpt) REVERT: M 42 MET cc_start: 0.8698 (OUTLIER) cc_final: 0.8039 (mtp) REVERT: N 14 MET cc_start: 0.7662 (mtp) cc_final: 0.7370 (mtt) REVERT: N 187 MET cc_start: 0.8251 (mmt) cc_final: 0.7703 (mmt) REVERT: O 151 HIS cc_start: 0.8304 (t-90) cc_final: 0.8041 (t70) REVERT: P 335 GLN cc_start: 0.8033 (tp40) cc_final: 0.7530 (pp30) REVERT: e 87 LYS cc_start: 0.6634 (ptpp) cc_final: 0.6364 (ptpp) REVERT: g 55 ILE cc_start: 0.8792 (mt) cc_final: 0.8565 (tt) REVERT: k 12 LYS cc_start: 0.7989 (OUTLIER) cc_final: 0.7535 (pptt) REVERT: l 112 MET cc_start: 0.8705 (mmt) cc_final: 0.7918 (mmt) REVERT: r 73 LYS cc_start: 0.7915 (mmtp) cc_final: 0.7652 (mmtm) outliers start: 111 outliers final: 84 residues processed: 891 average time/residue: 0.7022 time to fit residues: 1090.2950 Evaluate side-chains 889 residues out of total 6998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 801 time to evaluate : 5.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 112 GLU Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 59 MET Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 420 THR Chi-restraints excluded: chain E residue 52 ASP Chi-restraints excluded: chain E residue 168 ASP Chi-restraints excluded: chain F residue 77 LEU Chi-restraints excluded: chain F residue 323 ILE Chi-restraints excluded: chain G residue 21 GLU Chi-restraints excluded: chain G residue 424 ASP Chi-restraints excluded: chain G residue 536 ASP Chi-restraints excluded: chain H residue 156 MET Chi-restraints excluded: chain H residue 200 LEU Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain H residue 236 ILE Chi-restraints excluded: chain I residue 1 THR Chi-restraints excluded: chain J residue 74 MET Chi-restraints excluded: chain J residue 107 VAL Chi-restraints excluded: chain K residue 10 MET Chi-restraints excluded: chain L residue 40 ILE Chi-restraints excluded: chain L residue 254 VAL Chi-restraints excluded: chain M residue 42 MET Chi-restraints excluded: chain M residue 143 LEU Chi-restraints excluded: chain M residue 384 SER Chi-restraints excluded: chain N residue 173 THR Chi-restraints excluded: chain N residue 251 MET Chi-restraints excluded: chain N residue 270 MET Chi-restraints excluded: chain O residue 32 CYS Chi-restraints excluded: chain O residue 250 ASP Chi-restraints excluded: chain P residue 196 LEU Chi-restraints excluded: chain Q residue 28 GLU Chi-restraints excluded: chain Q residue 104 ASP Chi-restraints excluded: chain R residue 7 THR Chi-restraints excluded: chain R residue 81 THR Chi-restraints excluded: chain T residue 21 LEU Chi-restraints excluded: chain T residue 72 CYS Chi-restraints excluded: chain T residue 80 ILE Chi-restraints excluded: chain U residue 30 LEU Chi-restraints excluded: chain U residue 33 ASN Chi-restraints excluded: chain U residue 72 CYS Chi-restraints excluded: chain V residue 7 THR Chi-restraints excluded: chain V residue 16 CYS Chi-restraints excluded: chain W residue 24 ASP Chi-restraints excluded: chain W residue 127 ASP Chi-restraints excluded: chain X residue 36 ASP Chi-restraints excluded: chain X residue 120 ASP Chi-restraints excluded: chain X residue 130 VAL Chi-restraints excluded: chain Z residue 51 MET Chi-restraints excluded: chain Z residue 69 ILE Chi-restraints excluded: chain Z residue 101 VAL Chi-restraints excluded: chain b residue 33 THR Chi-restraints excluded: chain b residue 81 LYS Chi-restraints excluded: chain d residue 10 THR Chi-restraints excluded: chain e residue 92 THR Chi-restraints excluded: chain e residue 96 HIS Chi-restraints excluded: chain f residue 6 VAL Chi-restraints excluded: chain f residue 9 ASP Chi-restraints excluded: chain f residue 31 ASP Chi-restraints excluded: chain g residue 37 LEU Chi-restraints excluded: chain h residue 44 ASN Chi-restraints excluded: chain i residue 33 VAL Chi-restraints excluded: chain i residue 42 VAL Chi-restraints excluded: chain i residue 112 THR Chi-restraints excluded: chain j residue 29 SER Chi-restraints excluded: chain j residue 42 HIS Chi-restraints excluded: chain k residue 12 LYS Chi-restraints excluded: chain k residue 53 MET Chi-restraints excluded: chain k residue 63 VAL Chi-restraints excluded: chain l residue 81 LEU Chi-restraints excluded: chain l residue 101 MET Chi-restraints excluded: chain l residue 102 CYS Chi-restraints excluded: chain l residue 118 VAL Chi-restraints excluded: chain l residue 128 VAL Chi-restraints excluded: chain n residue 57 VAL Chi-restraints excluded: chain n residue 116 ASP Chi-restraints excluded: chain o residue 66 LEU Chi-restraints excluded: chain o residue 77 LEU Chi-restraints excluded: chain p residue 2 ASP Chi-restraints excluded: chain q residue 11 LEU Chi-restraints excluded: chain q residue 78 ASP Chi-restraints excluded: chain r residue 15 SER Chi-restraints excluded: chain s residue 47 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 783 random chunks: chunk 254 optimal weight: 5.9990 chunk 681 optimal weight: 3.9990 chunk 149 optimal weight: 7.9990 chunk 444 optimal weight: 10.0000 chunk 186 optimal weight: 1.9990 chunk 757 optimal weight: 8.9990 chunk 628 optimal weight: 9.9990 chunk 350 optimal weight: 0.6980 chunk 62 optimal weight: 0.5980 chunk 250 optimal weight: 1.9990 chunk 397 optimal weight: 2.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 235 ASN ** L 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 35 HIS f 39 ASN h 143 ASN m 47 GLN n 12 GLN n 138 GLN ** o 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.245 67761 Z= 0.457 Angle : 1.306 50.556 91649 Z= 0.841 Chirality : 0.258 6.424 9908 Planarity : 0.004 0.070 11468 Dihedral : 11.712 172.092 10234 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.42 % Favored : 97.55 % Rotamer: Outliers : 1.80 % Allowed : 10.22 % Favored : 87.98 % 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: 7903 helix: 1.42 (0.08), residues: 4142 sheet: -0.05 (0.25), residues: 420 loop : -0.11 (0.11), residues: 3341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP P 187 HIS 0.014 0.001 HIS R 96 PHE 0.028 0.001 PHE U 60 TYR 0.024 0.001 TYR L 422 ARG 0.010 0.000 ARG k 38 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15806 Ramachandran restraints generated. 7903 Oldfield, 0 Emsley, 7903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15806 Ramachandran restraints generated. 7903 Oldfield, 0 Emsley, 7903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 959 residues out of total 6998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 833 time to evaluate : 7.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 ARG cc_start: 0.6529 (ptt180) cc_final: 0.6168 (ttt90) REVERT: A 115 GLU cc_start: 0.6395 (OUTLIER) cc_final: 0.6122 (mt-10) REVERT: B 171 LYS cc_start: 0.8158 (mttt) cc_final: 0.7952 (mtmm) REVERT: D 170 MET cc_start: 0.8063 (mmt) cc_final: 0.7802 (mmt) REVERT: H 268 MET cc_start: 0.7662 (mtm) cc_final: 0.7344 (mtp) REVERT: L 40 ILE cc_start: 0.8637 (OUTLIER) cc_final: 0.8339 (mt) REVERT: L 128 MET cc_start: 0.7804 (tpt) cc_final: 0.7447 (tpt) REVERT: M 42 MET cc_start: 0.8709 (OUTLIER) cc_final: 0.8063 (mtp) REVERT: N 14 MET cc_start: 0.7667 (mtp) cc_final: 0.7368 (mtt) REVERT: N 187 MET cc_start: 0.8223 (mmt) cc_final: 0.7686 (mmt) REVERT: O 151 HIS cc_start: 0.8321 (t-90) cc_final: 0.8073 (t70) REVERT: T 79 TYR cc_start: 0.7314 (t80) cc_final: 0.6937 (t80) REVERT: U 83 LYS cc_start: 0.8436 (mtpp) cc_final: 0.8002 (ttmm) REVERT: Z 68 ARG cc_start: 0.6851 (mtt180) cc_final: 0.6531 (mtt180) REVERT: e 87 LYS cc_start: 0.6596 (ptpp) cc_final: 0.6334 (ptpp) REVERT: g 55 ILE cc_start: 0.8777 (mt) cc_final: 0.8555 (tt) REVERT: l 112 MET cc_start: 0.8719 (mmt) cc_final: 0.7981 (mmt) outliers start: 126 outliers final: 101 residues processed: 904 average time/residue: 0.6302 time to fit residues: 985.0519 Evaluate side-chains 901 residues out of total 6998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 797 time to evaluate : 5.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 112 GLU Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 59 MET Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 420 THR Chi-restraints excluded: chain E residue 52 ASP Chi-restraints excluded: chain E residue 113 SER Chi-restraints excluded: chain E residue 168 ASP Chi-restraints excluded: chain F residue 77 LEU Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 323 ILE Chi-restraints excluded: chain G residue 21 GLU Chi-restraints excluded: chain G residue 295 THR Chi-restraints excluded: chain G residue 424 ASP Chi-restraints excluded: chain G residue 536 ASP Chi-restraints excluded: chain H residue 5 ASN Chi-restraints excluded: chain H residue 156 MET Chi-restraints excluded: chain H residue 200 LEU Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain I residue 1 THR Chi-restraints excluded: chain J residue 56 VAL Chi-restraints excluded: chain J residue 74 MET Chi-restraints excluded: chain J residue 76 THR Chi-restraints excluded: chain J residue 107 VAL Chi-restraints excluded: chain K residue 10 MET Chi-restraints excluded: chain K residue 84 THR Chi-restraints excluded: chain L residue 40 ILE Chi-restraints excluded: chain L residue 254 VAL Chi-restraints excluded: chain L residue 381 THR Chi-restraints excluded: chain M residue 42 MET Chi-restraints excluded: chain M residue 384 SER Chi-restraints excluded: chain N residue 173 THR Chi-restraints excluded: chain N residue 251 MET Chi-restraints excluded: chain N residue 270 MET Chi-restraints excluded: chain O residue 32 CYS Chi-restraints excluded: chain O residue 250 ASP Chi-restraints excluded: chain P residue 196 LEU Chi-restraints excluded: chain P residue 256 TYR Chi-restraints excluded: chain P residue 315 ILE Chi-restraints excluded: chain Q residue 104 ASP Chi-restraints excluded: chain R residue 7 THR Chi-restraints excluded: chain R residue 81 THR Chi-restraints excluded: chain T residue 21 LEU Chi-restraints excluded: chain T residue 72 CYS Chi-restraints excluded: chain T residue 80 ILE Chi-restraints excluded: chain U residue 30 LEU Chi-restraints excluded: chain U residue 33 ASN Chi-restraints excluded: chain U residue 72 CYS Chi-restraints excluded: chain V residue 7 THR Chi-restraints excluded: chain V residue 16 CYS Chi-restraints excluded: chain V residue 94 ILE Chi-restraints excluded: chain W residue 24 ASP Chi-restraints excluded: chain W residue 96 VAL Chi-restraints excluded: chain W residue 127 ASP Chi-restraints excluded: chain X residue 36 ASP Chi-restraints excluded: chain X residue 120 ASP Chi-restraints excluded: chain X residue 130 VAL Chi-restraints excluded: chain Z residue 51 MET Chi-restraints excluded: chain Z residue 69 ILE Chi-restraints excluded: chain Z residue 101 VAL Chi-restraints excluded: chain a residue 54 VAL Chi-restraints excluded: chain b residue 33 THR Chi-restraints excluded: chain b residue 81 LYS Chi-restraints excluded: chain d residue 10 THR Chi-restraints excluded: chain e residue 92 THR Chi-restraints excluded: chain e residue 96 HIS Chi-restraints excluded: chain f residue 6 VAL Chi-restraints excluded: chain f residue 9 ASP Chi-restraints excluded: chain f residue 31 ASP Chi-restraints excluded: chain g residue 37 LEU Chi-restraints excluded: chain h residue 143 ASN Chi-restraints excluded: chain i residue 33 VAL Chi-restraints excluded: chain i residue 42 VAL Chi-restraints excluded: chain i residue 112 THR Chi-restraints excluded: chain j residue 29 SER Chi-restraints excluded: chain j residue 42 HIS Chi-restraints excluded: chain j residue 64 LEU Chi-restraints excluded: chain k residue 12 LYS Chi-restraints excluded: chain k residue 60 VAL Chi-restraints excluded: chain k residue 63 VAL Chi-restraints excluded: chain k residue 67 LEU Chi-restraints excluded: chain l residue 4 ILE Chi-restraints excluded: chain l residue 59 ASP Chi-restraints excluded: chain l residue 101 MET Chi-restraints excluded: chain l residue 102 CYS Chi-restraints excluded: chain l residue 118 VAL Chi-restraints excluded: chain l residue 128 VAL Chi-restraints excluded: chain m residue 72 SER Chi-restraints excluded: chain n residue 12 GLN Chi-restraints excluded: chain n residue 57 VAL Chi-restraints excluded: chain n residue 116 ASP Chi-restraints excluded: chain o residue 66 LEU Chi-restraints excluded: chain o residue 77 LEU Chi-restraints excluded: chain p residue 2 ASP Chi-restraints excluded: chain q residue 11 LEU Chi-restraints excluded: chain q residue 78 ASP Chi-restraints excluded: chain r residue 15 SER Chi-restraints excluded: chain s residue 47 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 783 random chunks: chunk 730 optimal weight: 0.4980 chunk 85 optimal weight: 0.9990 chunk 431 optimal weight: 0.0010 chunk 553 optimal weight: 0.0570 chunk 428 optimal weight: 9.9990 chunk 637 optimal weight: 1.9990 chunk 423 optimal weight: 0.0970 chunk 754 optimal weight: 6.9990 chunk 472 optimal weight: 8.9990 chunk 460 optimal weight: 3.9990 chunk 348 optimal weight: 3.9990 overall best weight: 0.3304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 243 GLN Q 44 ASN ** S 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 74 GLN f 39 ASN j 50 HIS n 72 HIS n 138 GLN o 46 ASN ** o 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.247 67761 Z= 0.436 Angle : 1.298 50.849 91649 Z= 0.838 Chirality : 0.256 6.462 9908 Planarity : 0.004 0.068 11468 Dihedral : 11.314 171.571 10234 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.19 % Favored : 97.77 % Rotamer: Outliers : 1.23 % Allowed : 11.02 % Favored : 87.75 % 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: 1.22 (0.10), residues: 7903 helix: 1.62 (0.08), residues: 4134 sheet: -0.02 (0.25), residues: 425 loop : -0.02 (0.11), residues: 3344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP P 187 HIS 0.009 0.001 HIS L 514 PHE 0.035 0.001 PHE P 239 TYR 0.028 0.001 TYR T 79 ARG 0.011 0.000 ARG k 38 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15806 Ramachandran restraints generated. 7903 Oldfield, 0 Emsley, 7903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15806 Ramachandran restraints generated. 7903 Oldfield, 0 Emsley, 7903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 959 residues out of total 6998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 873 time to evaluate : 5.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 ARG cc_start: 0.6483 (ptt180) cc_final: 0.6177 (ttt-90) REVERT: A 115 GLU cc_start: 0.6281 (OUTLIER) cc_final: 0.5981 (mt-10) REVERT: B 171 LYS cc_start: 0.8134 (mttt) cc_final: 0.7932 (mtmm) REVERT: H 289 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8820 (tp) REVERT: L 40 ILE cc_start: 0.8579 (OUTLIER) cc_final: 0.8278 (mt) REVERT: L 128 MET cc_start: 0.7791 (tpt) cc_final: 0.7404 (tpt) REVERT: N 14 MET cc_start: 0.7593 (mtp) cc_final: 0.7328 (mtt) REVERT: N 187 MET cc_start: 0.8135 (mmt) cc_final: 0.7661 (mmt) REVERT: O 151 HIS cc_start: 0.8302 (t-90) cc_final: 0.8060 (t70) REVERT: P 57 MET cc_start: 0.8422 (mmm) cc_final: 0.8183 (mmm) REVERT: W 89 GLU cc_start: 0.7471 (tt0) cc_final: 0.7175 (tt0) REVERT: e 87 LYS cc_start: 0.6480 (ptpp) cc_final: 0.6173 (ptpp) REVERT: l 112 MET cc_start: 0.8669 (mmt) cc_final: 0.7870 (mmt) REVERT: o 38 MET cc_start: 0.7141 (tpp) cc_final: 0.6549 (mmp) outliers start: 86 outliers final: 64 residues processed: 922 average time/residue: 0.6327 time to fit residues: 1004.8054 Evaluate side-chains 872 residues out of total 6998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 805 time to evaluate : 5.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 GLU Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 59 MET Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain E residue 52 ASP Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 323 ILE Chi-restraints excluded: chain G residue 21 GLU Chi-restraints excluded: chain G residue 424 ASP Chi-restraints excluded: chain H residue 5 ASN Chi-restraints excluded: chain H residue 156 MET Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain H residue 236 ILE Chi-restraints excluded: chain H residue 289 LEU Chi-restraints excluded: chain I residue 1 THR Chi-restraints excluded: chain J residue 56 VAL Chi-restraints excluded: chain J residue 74 MET Chi-restraints excluded: chain J residue 107 VAL Chi-restraints excluded: chain K residue 6 MET Chi-restraints excluded: chain K residue 10 MET Chi-restraints excluded: chain L residue 40 ILE Chi-restraints excluded: chain L residue 254 VAL Chi-restraints excluded: chain L residue 381 THR Chi-restraints excluded: chain L residue 477 ILE Chi-restraints excluded: chain M residue 143 LEU Chi-restraints excluded: chain N residue 251 MET Chi-restraints excluded: chain N residue 270 MET Chi-restraints excluded: chain O residue 250 ASP Chi-restraints excluded: chain P residue 196 LEU Chi-restraints excluded: chain P residue 256 TYR Chi-restraints excluded: chain Q residue 44 ASN Chi-restraints excluded: chain Q residue 104 ASP Chi-restraints excluded: chain T residue 21 LEU Chi-restraints excluded: chain T residue 65 ILE Chi-restraints excluded: chain T residue 80 ILE Chi-restraints excluded: chain U residue 33 ASN Chi-restraints excluded: chain U residue 72 CYS Chi-restraints excluded: chain V residue 7 THR Chi-restraints excluded: chain V residue 94 ILE Chi-restraints excluded: chain W residue 96 VAL Chi-restraints excluded: chain W residue 127 ASP Chi-restraints excluded: chain X residue 130 VAL Chi-restraints excluded: chain Z residue 51 MET Chi-restraints excluded: chain Z residue 69 ILE Chi-restraints excluded: chain Z residue 101 VAL Chi-restraints excluded: chain a residue 69 ILE Chi-restraints excluded: chain e residue 96 HIS Chi-restraints excluded: chain f residue 6 VAL Chi-restraints excluded: chain f residue 9 ASP Chi-restraints excluded: chain f residue 31 ASP Chi-restraints excluded: chain i residue 33 VAL Chi-restraints excluded: chain i residue 42 VAL Chi-restraints excluded: chain j residue 29 SER Chi-restraints excluded: chain j residue 42 HIS Chi-restraints excluded: chain k residue 12 LYS Chi-restraints excluded: chain k residue 63 VAL Chi-restraints excluded: chain l residue 101 MET Chi-restraints excluded: chain n residue 10 THR Chi-restraints excluded: chain n residue 57 VAL Chi-restraints excluded: chain n residue 116 ASP Chi-restraints excluded: chain o residue 39 VAL Chi-restraints excluded: chain o residue 77 LEU Chi-restraints excluded: chain q residue 11 LEU Chi-restraints excluded: chain q residue 78 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 783 random chunks: chunk 466 optimal weight: 0.8980 chunk 301 optimal weight: 0.7980 chunk 450 optimal weight: 9.9990 chunk 227 optimal weight: 0.0470 chunk 148 optimal weight: 10.0000 chunk 146 optimal weight: 0.1980 chunk 479 optimal weight: 6.9990 chunk 514 optimal weight: 0.3980 chunk 373 optimal weight: 0.9990 chunk 70 optimal weight: 3.9990 chunk 593 optimal weight: 6.9990 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 243 GLN Q 44 ASN ** S 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 39 ASN h 44 ASN ** h 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 50 HIS m 47 GLN n 138 GLN ** o 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.2811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.246 67761 Z= 0.437 Angle : 1.299 50.540 91649 Z= 0.838 Chirality : 0.256 6.379 9908 Planarity : 0.004 0.091 11468 Dihedral : 11.021 171.310 10234 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.13 % Favored : 97.85 % Rotamer: Outliers : 1.19 % Allowed : 11.49 % Favored : 87.32 % 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: 1.34 (0.10), residues: 7903 helix: 1.71 (0.08), residues: 4130 sheet: -0.01 (0.25), residues: 419 loop : 0.06 (0.11), residues: 3354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP j 59 HIS 0.008 0.001 HIS e 97 PHE 0.034 0.001 PHE P 239 TYR 0.025 0.001 TYR L 422 ARG 0.007 0.000 ARG i 65 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15806 Ramachandran restraints generated. 7903 Oldfield, 0 Emsley, 7903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15806 Ramachandran restraints generated. 7903 Oldfield, 0 Emsley, 7903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 926 residues out of total 6998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 843 time to evaluate : 5.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 ARG cc_start: 0.6493 (ptt180) cc_final: 0.6187 (ttt-90) REVERT: A 115 GLU cc_start: 0.6226 (OUTLIER) cc_final: 0.5921 (mt-10) REVERT: B 171 LYS cc_start: 0.8133 (mttt) cc_final: 0.7930 (mtmm) REVERT: H 289 LEU cc_start: 0.9097 (OUTLIER) cc_final: 0.8742 (tp) REVERT: L 40 ILE cc_start: 0.8555 (OUTLIER) cc_final: 0.8277 (mt) REVERT: L 128 MET cc_start: 0.7786 (tpt) cc_final: 0.7396 (tpt) REVERT: M 42 MET cc_start: 0.8677 (OUTLIER) cc_final: 0.8082 (mtp) REVERT: M 87 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.7326 (mt-10) REVERT: N 14 MET cc_start: 0.7569 (mtp) cc_final: 0.7313 (mtt) REVERT: N 187 MET cc_start: 0.8104 (mmt) cc_final: 0.7711 (mmt) REVERT: O 151 HIS cc_start: 0.8268 (t-90) cc_final: 0.8044 (t70) REVERT: P 57 MET cc_start: 0.8420 (mmm) cc_final: 0.8218 (mmm) REVERT: P 335 GLN cc_start: 0.8037 (tp40) cc_final: 0.7680 (pp30) REVERT: U 74 GLN cc_start: 0.8362 (tp40) cc_final: 0.7615 (tp40) REVERT: U 78 ASP cc_start: 0.6853 (m-30) cc_final: 0.6547 (m-30) REVERT: U 83 LYS cc_start: 0.8333 (mtpp) cc_final: 0.7980 (ttmm) REVERT: W 34 GLU cc_start: 0.7479 (mt-10) cc_final: 0.7150 (mt-10) REVERT: W 89 GLU cc_start: 0.7460 (tt0) cc_final: 0.7201 (tt0) REVERT: b 9 LYS cc_start: 0.8313 (ttmt) cc_final: 0.8040 (tttt) REVERT: e 87 LYS cc_start: 0.6417 (ptpp) cc_final: 0.6109 (ptpp) REVERT: l 112 MET cc_start: 0.8686 (mmt) cc_final: 0.7925 (mmt) REVERT: m 94 ILE cc_start: 0.8307 (tt) cc_final: 0.8088 (tp) outliers start: 83 outliers final: 64 residues processed: 890 average time/residue: 0.6437 time to fit residues: 991.4649 Evaluate side-chains 885 residues out of total 6998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 816 time to evaluate : 5.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 112 GLU Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 59 MET Chi-restraints excluded: chain B residue 125 TYR Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain E residue 52 ASP Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain G residue 21 GLU Chi-restraints excluded: chain G residue 424 ASP Chi-restraints excluded: chain H residue 5 ASN Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain H residue 236 ILE Chi-restraints excluded: chain H residue 289 LEU Chi-restraints excluded: chain I residue 1 THR Chi-restraints excluded: chain J residue 56 VAL Chi-restraints excluded: chain J residue 74 MET Chi-restraints excluded: chain J residue 107 VAL Chi-restraints excluded: chain K residue 10 MET Chi-restraints excluded: chain L residue 40 ILE Chi-restraints excluded: chain L residue 129 LEU Chi-restraints excluded: chain L residue 254 VAL Chi-restraints excluded: chain L residue 381 THR Chi-restraints excluded: chain L residue 477 ILE Chi-restraints excluded: chain M residue 42 MET Chi-restraints excluded: chain M residue 87 GLU Chi-restraints excluded: chain M residue 116 ILE Chi-restraints excluded: chain N residue 173 THR Chi-restraints excluded: chain N residue 251 MET Chi-restraints excluded: chain N residue 270 MET Chi-restraints excluded: chain O residue 250 ASP Chi-restraints excluded: chain P residue 196 LEU Chi-restraints excluded: chain Q residue 44 ASN Chi-restraints excluded: chain Q residue 104 ASP Chi-restraints excluded: chain R residue 7 THR Chi-restraints excluded: chain T residue 65 ILE Chi-restraints excluded: chain T residue 71 MET Chi-restraints excluded: chain T residue 80 ILE Chi-restraints excluded: chain U residue 33 ASN Chi-restraints excluded: chain U residue 72 CYS Chi-restraints excluded: chain U residue 82 ASP Chi-restraints excluded: chain V residue 7 THR Chi-restraints excluded: chain V residue 94 ILE Chi-restraints excluded: chain W residue 96 VAL Chi-restraints excluded: chain W residue 127 ASP Chi-restraints excluded: chain X residue 130 VAL Chi-restraints excluded: chain Z residue 51 MET Chi-restraints excluded: chain Z residue 101 VAL Chi-restraints excluded: chain Z residue 120 MET Chi-restraints excluded: chain a residue 54 VAL Chi-restraints excluded: chain a residue 69 ILE Chi-restraints excluded: chain b residue 81 LYS Chi-restraints excluded: chain e residue 96 HIS Chi-restraints excluded: chain f residue 9 ASP Chi-restraints excluded: chain f residue 31 ASP Chi-restraints excluded: chain i residue 37 GLN Chi-restraints excluded: chain j residue 64 LEU Chi-restraints excluded: chain k residue 12 LYS Chi-restraints excluded: chain k residue 63 VAL Chi-restraints excluded: chain l residue 101 MET Chi-restraints excluded: chain n residue 57 VAL Chi-restraints excluded: chain n residue 116 ASP Chi-restraints excluded: chain o residue 77 LEU Chi-restraints excluded: chain p residue 2 ASP Chi-restraints excluded: chain q residue 11 LEU Chi-restraints excluded: chain q residue 78 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 783 random chunks: chunk 686 optimal weight: 9.9990 chunk 723 optimal weight: 0.0770 chunk 659 optimal weight: 6.9990 chunk 703 optimal weight: 2.9990 chunk 722 optimal weight: 0.9980 chunk 423 optimal weight: 0.7980 chunk 306 optimal weight: 9.9990 chunk 552 optimal weight: 0.6980 chunk 215 optimal weight: 10.0000 chunk 635 optimal weight: 1.9990 chunk 665 optimal weight: 0.8980 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 46 ASN C 69 ASN G 437 HIS L 405 ASN ** L 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 180 GLN O 184 GLN Q 44 ASN ** S 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 39 ASN h 44 ASN ** h 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 21 GLN j 42 HIS n 138 GLN ** o 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.2892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.246 67761 Z= 0.438 Angle : 1.300 50.541 91649 Z= 0.838 Chirality : 0.257 6.399 9908 Planarity : 0.004 0.072 11468 Dihedral : 10.816 171.252 10234 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.14 % Favored : 97.84 % Rotamer: Outliers : 1.19 % Allowed : 11.60 % Favored : 87.21 % 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: 1.39 (0.10), residues: 7903 helix: 1.75 (0.08), residues: 4129 sheet: 0.05 (0.25), residues: 419 loop : 0.08 (0.11), residues: 3355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP j 59 HIS 0.010 0.001 HIS e 97 PHE 0.036 0.001 PHE P 239 TYR 0.024 0.001 TYR L 422 ARG 0.014 0.000 ARG k 38 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15806 Ramachandran restraints generated. 7903 Oldfield, 0 Emsley, 7903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15806 Ramachandran restraints generated. 7903 Oldfield, 0 Emsley, 7903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 914 residues out of total 6998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 831 time to evaluate : 5.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 ARG cc_start: 0.6461 (ptt180) cc_final: 0.6163 (ttt-90) REVERT: A 115 GLU cc_start: 0.6191 (OUTLIER) cc_final: 0.5875 (mt-10) REVERT: B 171 LYS cc_start: 0.8139 (mttt) cc_final: 0.7932 (mtmm) REVERT: H 289 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8724 (tp) REVERT: J 103 MET cc_start: 0.5111 (mmm) cc_final: 0.4368 (mmm) REVERT: L 40 ILE cc_start: 0.8573 (OUTLIER) cc_final: 0.8295 (mt) REVERT: L 128 MET cc_start: 0.7796 (tpt) cc_final: 0.7413 (tpt) REVERT: M 42 MET cc_start: 0.8677 (OUTLIER) cc_final: 0.8082 (mtp) REVERT: M 87 GLU cc_start: 0.7617 (OUTLIER) cc_final: 0.7339 (mt-10) REVERT: N 14 MET cc_start: 0.7570 (mtp) cc_final: 0.7319 (mtt) REVERT: N 187 MET cc_start: 0.8082 (mmt) cc_final: 0.7696 (mmt) REVERT: P 335 GLN cc_start: 0.8022 (tp40) cc_final: 0.7669 (pp30) REVERT: T 79 TYR cc_start: 0.7016 (t80) cc_final: 0.6573 (t80) REVERT: U 74 GLN cc_start: 0.8377 (tp40) cc_final: 0.7629 (tp40) REVERT: U 78 ASP cc_start: 0.6832 (m-30) cc_final: 0.6553 (m-30) REVERT: U 83 LYS cc_start: 0.8361 (mtpp) cc_final: 0.8015 (ttmm) REVERT: W 34 GLU cc_start: 0.7472 (mt-10) cc_final: 0.7104 (mt-10) REVERT: W 89 GLU cc_start: 0.7461 (tt0) cc_final: 0.7249 (tt0) REVERT: e 87 LYS cc_start: 0.6436 (ptpp) cc_final: 0.6102 (ptpp) REVERT: g 101 GLU cc_start: 0.6967 (mm-30) cc_final: 0.6750 (mm-30) REVERT: l 112 MET cc_start: 0.8694 (mmt) cc_final: 0.8101 (mmt) REVERT: o 96 LYS cc_start: 0.8438 (mptt) cc_final: 0.7972 (mptt) outliers start: 83 outliers final: 66 residues processed: 877 average time/residue: 0.6259 time to fit residues: 947.8123 Evaluate side-chains 878 residues out of total 6998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 807 time to evaluate : 5.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 GLU Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 59 MET Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 125 TYR Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain E residue 52 ASP Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain G residue 21 GLU Chi-restraints excluded: chain G residue 35 MET Chi-restraints excluded: chain G residue 424 ASP Chi-restraints excluded: chain H residue 5 ASN Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain H residue 236 ILE Chi-restraints excluded: chain H residue 289 LEU Chi-restraints excluded: chain I residue 1 THR Chi-restraints excluded: chain J residue 56 VAL Chi-restraints excluded: chain J residue 107 VAL Chi-restraints excluded: chain K residue 10 MET Chi-restraints excluded: chain L residue 40 ILE Chi-restraints excluded: chain L residue 129 LEU Chi-restraints excluded: chain L residue 254 VAL Chi-restraints excluded: chain L residue 381 THR Chi-restraints excluded: chain L residue 477 ILE Chi-restraints excluded: chain M residue 42 MET Chi-restraints excluded: chain M residue 87 GLU Chi-restraints excluded: chain M residue 116 ILE Chi-restraints excluded: chain M residue 123 GLU Chi-restraints excluded: chain N residue 173 THR Chi-restraints excluded: chain N residue 251 MET Chi-restraints excluded: chain N residue 270 MET Chi-restraints excluded: chain O residue 250 ASP Chi-restraints excluded: chain P residue 196 LEU Chi-restraints excluded: chain P residue 256 TYR Chi-restraints excluded: chain Q residue 44 ASN Chi-restraints excluded: chain Q residue 104 ASP Chi-restraints excluded: chain R residue 7 THR Chi-restraints excluded: chain R residue 19 ASP Chi-restraints excluded: chain T residue 21 LEU Chi-restraints excluded: chain T residue 65 ILE Chi-restraints excluded: chain T residue 80 ILE Chi-restraints excluded: chain U residue 33 ASN Chi-restraints excluded: chain U residue 72 CYS Chi-restraints excluded: chain V residue 7 THR Chi-restraints excluded: chain V residue 94 ILE Chi-restraints excluded: chain W residue 96 VAL Chi-restraints excluded: chain W residue 127 ASP Chi-restraints excluded: chain X residue 120 ASP Chi-restraints excluded: chain X residue 130 VAL Chi-restraints excluded: chain Z residue 51 MET Chi-restraints excluded: chain Z residue 101 VAL Chi-restraints excluded: chain Z residue 120 MET Chi-restraints excluded: chain a residue 54 VAL Chi-restraints excluded: chain a residue 69 ILE Chi-restraints excluded: chain b residue 81 LYS Chi-restraints excluded: chain e residue 96 HIS Chi-restraints excluded: chain f residue 6 VAL Chi-restraints excluded: chain f residue 9 ASP Chi-restraints excluded: chain f residue 31 ASP Chi-restraints excluded: chain i residue 37 GLN Chi-restraints excluded: chain j residue 64 LEU Chi-restraints excluded: chain k residue 12 LYS Chi-restraints excluded: chain k residue 63 VAL Chi-restraints excluded: chain m residue 24 ILE Chi-restraints excluded: chain n residue 57 VAL Chi-restraints excluded: chain o residue 77 LEU Chi-restraints excluded: chain q residue 11 LEU Chi-restraints excluded: chain q residue 78 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 783 random chunks: chunk 700 optimal weight: 8.9990 chunk 461 optimal weight: 1.9990 chunk 743 optimal weight: 4.9990 chunk 453 optimal weight: 10.0000 chunk 352 optimal weight: 7.9990 chunk 516 optimal weight: 3.9990 chunk 780 optimal weight: 0.3980 chunk 717 optimal weight: 0.7980 chunk 621 optimal weight: 0.0070 chunk 64 optimal weight: 9.9990 chunk 479 optimal weight: 6.9990 overall best weight: 1.4402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 46 ASN ** L 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 151 HIS P 243 GLN Q 44 ASN ** S 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 39 ASN h 44 ASN ** h 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 50 HIS n 138 GLN ** o 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.245 67761 Z= 0.452 Angle : 1.308 50.523 91649 Z= 0.841 Chirality : 0.258 6.420 9908 Planarity : 0.004 0.086 11468 Dihedral : 10.765 171.357 10234 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.30 % Favored : 97.67 % Rotamer: Outliers : 1.19 % Allowed : 11.80 % Favored : 87.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.10), residues: 7903 helix: 1.68 (0.08), residues: 4138 sheet: 0.10 (0.25), residues: 426 loop : 0.07 (0.11), residues: 3339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP j 59 HIS 0.010 0.001 HIS e 97 PHE 0.034 0.001 PHE s 33 TYR 0.045 0.001 TYR T 79 ARG 0.011 0.000 ARG R 55 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15806 Ramachandran restraints generated. 7903 Oldfield, 0 Emsley, 7903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15806 Ramachandran restraints generated. 7903 Oldfield, 0 Emsley, 7903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 901 residues out of total 6998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 818 time to evaluate : 5.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 ARG cc_start: 0.6496 (ptt180) cc_final: 0.6173 (ttt-90) REVERT: A 115 GLU cc_start: 0.6269 (OUTLIER) cc_final: 0.5967 (mt-10) REVERT: H 289 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8744 (tp) REVERT: L 40 ILE cc_start: 0.8612 (OUTLIER) cc_final: 0.8312 (mt) REVERT: L 128 MET cc_start: 0.7816 (tpt) cc_final: 0.7416 (tpt) REVERT: M 42 MET cc_start: 0.8693 (OUTLIER) cc_final: 0.8068 (mtp) REVERT: M 87 GLU cc_start: 0.7672 (OUTLIER) cc_final: 0.7388 (mt-10) REVERT: N 14 MET cc_start: 0.7596 (mtp) cc_final: 0.7319 (mtt) REVERT: N 187 MET cc_start: 0.8123 (mmt) cc_final: 0.7737 (mmt) REVERT: P 335 GLN cc_start: 0.8005 (tp40) cc_final: 0.7536 (pp30) REVERT: U 74 GLN cc_start: 0.8437 (tp40) cc_final: 0.7867 (tp40) REVERT: U 83 LYS cc_start: 0.8364 (mtpp) cc_final: 0.8015 (ttmm) REVERT: W 34 GLU cc_start: 0.7482 (mt-10) cc_final: 0.7118 (mt-10) REVERT: e 87 LYS cc_start: 0.6433 (ptpp) cc_final: 0.6093 (ptpp) REVERT: l 112 MET cc_start: 0.8741 (mmt) cc_final: 0.8130 (mmt) REVERT: o 38 MET cc_start: 0.7304 (tpp) cc_final: 0.6954 (mmm) outliers start: 83 outliers final: 74 residues processed: 866 average time/residue: 0.6337 time to fit residues: 952.1783 Evaluate side-chains 877 residues out of total 6998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 798 time to evaluate : 5.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 112 GLU Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 59 MET Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 125 TYR Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 420 THR Chi-restraints excluded: chain E residue 52 ASP Chi-restraints excluded: chain E residue 113 SER Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain G residue 21 GLU Chi-restraints excluded: chain G residue 35 MET Chi-restraints excluded: chain G residue 424 ASP Chi-restraints excluded: chain G residue 536 ASP Chi-restraints excluded: chain H residue 5 ASN Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain H residue 236 ILE Chi-restraints excluded: chain H residue 289 LEU Chi-restraints excluded: chain I residue 1 THR Chi-restraints excluded: chain J residue 56 VAL Chi-restraints excluded: chain J residue 107 VAL Chi-restraints excluded: chain K residue 10 MET Chi-restraints excluded: chain L residue 40 ILE Chi-restraints excluded: chain L residue 129 LEU Chi-restraints excluded: chain L residue 254 VAL Chi-restraints excluded: chain L residue 381 THR Chi-restraints excluded: chain L residue 477 ILE Chi-restraints excluded: chain M residue 42 MET Chi-restraints excluded: chain M residue 87 GLU Chi-restraints excluded: chain M residue 116 ILE Chi-restraints excluded: chain M residue 123 GLU Chi-restraints excluded: chain N residue 173 THR Chi-restraints excluded: chain N residue 251 MET Chi-restraints excluded: chain N residue 270 MET Chi-restraints excluded: chain O residue 250 ASP Chi-restraints excluded: chain P residue 196 LEU Chi-restraints excluded: chain P residue 256 TYR Chi-restraints excluded: chain Q residue 44 ASN Chi-restraints excluded: chain Q residue 104 ASP Chi-restraints excluded: chain R residue 7 THR Chi-restraints excluded: chain R residue 19 ASP Chi-restraints excluded: chain R residue 81 THR Chi-restraints excluded: chain T residue 65 ILE Chi-restraints excluded: chain T residue 76 ILE Chi-restraints excluded: chain T residue 80 ILE Chi-restraints excluded: chain U residue 33 ASN Chi-restraints excluded: chain U residue 72 CYS Chi-restraints excluded: chain U residue 82 ASP Chi-restraints excluded: chain V residue 7 THR Chi-restraints excluded: chain V residue 94 ILE Chi-restraints excluded: chain W residue 24 ASP Chi-restraints excluded: chain W residue 96 VAL Chi-restraints excluded: chain W residue 127 ASP Chi-restraints excluded: chain X residue 120 ASP Chi-restraints excluded: chain X residue 130 VAL Chi-restraints excluded: chain Z residue 51 MET Chi-restraints excluded: chain Z residue 101 VAL Chi-restraints excluded: chain Z residue 120 MET Chi-restraints excluded: chain a residue 54 VAL Chi-restraints excluded: chain a residue 69 ILE Chi-restraints excluded: chain b residue 81 LYS Chi-restraints excluded: chain e residue 96 HIS Chi-restraints excluded: chain f residue 6 VAL Chi-restraints excluded: chain f residue 9 ASP Chi-restraints excluded: chain f residue 31 ASP Chi-restraints excluded: chain i residue 37 GLN Chi-restraints excluded: chain k residue 12 LYS Chi-restraints excluded: chain k residue 63 VAL Chi-restraints excluded: chain l residue 59 ASP Chi-restraints excluded: chain m residue 22 TYR Chi-restraints excluded: chain m residue 23 ASP Chi-restraints excluded: chain n residue 57 VAL Chi-restraints excluded: chain o residue 77 LEU Chi-restraints excluded: chain q residue 11 LEU Chi-restraints excluded: chain q residue 78 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 783 random chunks: chunk 380 optimal weight: 2.9990 chunk 493 optimal weight: 2.9990 chunk 661 optimal weight: 6.9990 chunk 190 optimal weight: 1.9990 chunk 572 optimal weight: 6.9990 chunk 91 optimal weight: 3.9990 chunk 172 optimal weight: 0.6980 chunk 622 optimal weight: 6.9990 chunk 260 optimal weight: 0.9980 chunk 638 optimal weight: 5.9990 chunk 78 optimal weight: 3.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 39 GLN ** L 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 243 GLN Q 44 ASN ** R 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 44 ASN ** h 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 138 GLN ** o 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.084292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.069540 restraints weight = 147931.943| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 1.45 r_work: 0.3043 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.2771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.244 67761 Z= 0.466 Angle : 1.315 50.522 91649 Z= 0.844 Chirality : 0.258 6.434 9908 Planarity : 0.004 0.063 11468 Dihedral : 10.796 171.507 10234 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.44 % Favored : 97.53 % Rotamer: Outliers : 1.21 % Allowed : 11.82 % Favored : 86.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.10), residues: 7903 helix: 1.59 (0.08), residues: 4145 sheet: 0.07 (0.25), residues: 416 loop : 0.05 (0.11), residues: 3342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP X 85 HIS 0.010 0.001 HIS e 97 PHE 0.040 0.001 PHE i 49 TYR 0.030 0.001 TYR o 88 ARG 0.016 0.000 ARG k 38 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18448.93 seconds wall clock time: 323 minutes 41.63 seconds (19421.63 seconds total)