Starting phenix.real_space_refine on Fri Mar 15 07:26:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r43_14261/03_2024/7r43_14261_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r43_14261/03_2024/7r43_14261.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r43_14261/03_2024/7r43_14261_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r43_14261/03_2024/7r43_14261_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r43_14261/03_2024/7r43_14261_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r43_14261/03_2024/7r43_14261.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r43_14261/03_2024/7r43_14261.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r43_14261/03_2024/7r43_14261_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r43_14261/03_2024/7r43_14261_updated.pdb" } resolution = 2.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.007 sd= 1.033 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 34 5.49 5 Mg 1 5.21 5 S 468 5.16 5 C 43631 2.51 5 N 11148 2.21 5 O 13022 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 42": "OD1" <-> "OD2" Residue "A PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 105": "OE1" <-> "OE2" Residue "A GLU 115": "OE1" <-> "OE2" Residue "B ARG 71": "NH1" <-> "NH2" Residue "B GLU 109": "OE1" <-> "OE2" Residue "B ARG 111": "NH1" <-> "NH2" Residue "B GLU 154": "OE1" <-> "OE2" Residue "C ARG 8": "NH1" <-> "NH2" Residue "C ARG 12": "NH1" <-> "NH2" Residue "C ASP 16": "OD1" <-> "OD2" Residue "C GLU 27": "OE1" <-> "OE2" Residue "C PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 77": "OD1" <-> "OD2" Residue "C PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 149": "NH1" <-> "NH2" Residue "C GLU 179": "OE1" <-> "OE2" Residue "C GLU 186": "OE1" <-> "OE2" Residue "C ASP 198": "OD1" <-> "OD2" Residue "D ARG 2": "NH1" <-> "NH2" Residue "D GLU 9": "OE1" <-> "OE2" Residue "D GLU 12": "OE1" <-> "OE2" Residue "D GLU 67": "OE1" <-> "OE2" Residue "D TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 123": "OE1" <-> "OE2" Residue "D PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 179": "OE1" <-> "OE2" Residue "D ARG 221": "NH1" <-> "NH2" Residue "D GLU 226": "OE1" <-> "OE2" Residue "D ARG 233": "NH1" <-> "NH2" Residue "D ASP 279": "OD1" <-> "OD2" Residue "D GLU 343": "OE1" <-> "OE2" Residue "D GLU 427": "OE1" <-> "OE2" Residue "E GLU 26": "OE1" <-> "OE2" Residue "E ASP 52": "OD1" <-> "OD2" Residue "E GLU 71": "OE1" <-> "OE2" Residue "E ARG 190": "NH1" <-> "NH2" Residue "E GLU 204": "OE1" <-> "OE2" Residue "F PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 32": "NH1" <-> "NH2" Residue "F ASP 54": "OD1" <-> "OD2" Residue "F PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 87": "OD1" <-> "OD2" Residue "F GLU 99": "OE1" <-> "OE2" Residue "F ARG 112": "NH1" <-> "NH2" Residue "F ARG 132": "NH1" <-> "NH2" Residue "F ARG 139": "NH1" <-> "NH2" Residue "F GLU 155": "OE1" <-> "OE2" Residue "F PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 249": "NH1" <-> "NH2" Residue "F GLU 278": "OE1" <-> "OE2" Residue "F ASP 338": "OD1" <-> "OD2" Residue "F ARG 349": "NH1" <-> "NH2" Residue "F GLU 352": "OE1" <-> "OE2" Residue "F GLU 357": "OE1" <-> "OE2" Residue "F ASP 370": "OD1" <-> "OD2" Residue "F GLU 428": "OE1" <-> "OE2" Residue "F ARG 429": "NH1" <-> "NH2" Residue "F PHE 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 10": "OE1" <-> "OE2" Residue "G GLU 21": "OE1" <-> "OE2" Residue "G ARG 39": "NH1" <-> "NH2" Residue "G ARG 53": "NH1" <-> "NH2" Residue "G GLU 138": "OE1" <-> "OE2" Residue "G GLU 165": "OE1" <-> "OE2" Residue "G ASP 171": "OD1" <-> "OD2" Residue "G ARG 218": "NH1" <-> "NH2" Residue "G ARG 243": "NH1" <-> "NH2" Residue "G GLU 246": "OE1" <-> "OE2" Residue "G ARG 253": "NH1" <-> "NH2" Residue "G GLU 261": "OE1" <-> "OE2" Residue "G ARG 285": "NH1" <-> "NH2" Residue "G GLU 287": "OE1" <-> "OE2" Residue "G GLU 297": "OE1" <-> "OE2" Residue "G ARG 302": "NH1" <-> "NH2" Residue "G ASP 314": "OD1" <-> "OD2" Residue "G GLU 346": "OE1" <-> "OE2" Residue "G GLU 347": "OE1" <-> "OE2" Residue "G ARG 385": "NH1" <-> "NH2" Residue "G ARG 418": "NH1" <-> "NH2" Residue "G ASP 486": "OD1" <-> "OD2" Residue "G GLU 512": "OE1" <-> "OE2" Residue "G ASP 536": "OD1" <-> "OD2" Residue "G ASP 558": "OD1" <-> "OD2" Residue "G GLU 625": "OE1" <-> "OE2" Residue "G GLU 647": "OE1" <-> "OE2" Residue "G GLU 693": "OE1" <-> "OE2" Residue "H GLU 24": "OE1" <-> "OE2" Residue "H ARG 25": "NH1" <-> "NH2" Residue "H TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 34": "NH1" <-> "NH2" Residue "H PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 62": "NH1" <-> "NH2" Residue "H GLU 143": "OE1" <-> "OE2" Residue "H ASP 199": "OD1" <-> "OD2" Residue "H PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 283": "OD1" <-> "OD2" Residue "I ARG 8": "NH1" <-> "NH2" Residue "I TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 74": "OE1" <-> "OE2" Residue "I GLU 95": "OE1" <-> "OE2" Residue "I ARG 108": "NH1" <-> "NH2" Residue "I GLU 133": "OE1" <-> "OE2" Residue "I PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 118": "OE1" <-> "OE2" Residue "J TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 138": "OE1" <-> "OE2" Residue "J GLU 170": "OE1" <-> "OE2" Residue "J ARG 173": "NH1" <-> "NH2" Residue "L ASP 83": "OD1" <-> "OD2" Residue "L TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 102": "OE1" <-> "OE2" Residue "L PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 161": "NH1" <-> "NH2" Residue "L ASP 163": "OD1" <-> "OD2" Residue "L ASP 179": "OD1" <-> "OD2" Residue "L ASP 208": "OD1" <-> "OD2" Residue "L ARG 262": "NH1" <-> "NH2" Residue "L PHE 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 352": "OD1" <-> "OD2" Residue "L PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 554": "OD1" <-> "OD2" Residue "L GLU 606": "OE1" <-> "OE2" Residue "M ASP 59": "OD1" <-> "OD2" Residue "M GLU 87": "OE1" <-> "OE2" Residue "M PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 142": "NH1" <-> "NH2" Residue "M TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 281": "OD1" <-> "OD2" Residue "M TYR 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 378": "OE1" <-> "OE2" Residue "M TYR 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 432": "NH1" <-> "NH2" Residue "N PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 295": "NH1" <-> "NH2" Residue "N PHE 325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 41": "OE1" <-> "OE2" Residue "O GLU 53": "OE1" <-> "OE2" Residue "O ASP 85": "OD1" <-> "OD2" Residue "O ASP 131": "OD1" <-> "OD2" Residue "O ASP 173": "OD1" <-> "OD2" Residue "O TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 213": "OE1" <-> "OE2" Residue "O TYR 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 253": "OD1" <-> "OD2" Residue "O ARG 302": "NH1" <-> "NH2" Residue "O ARG 305": "NH1" <-> "NH2" Residue "O TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 40": "NH1" <-> "NH2" Residue "P ARG 50": "NH1" <-> "NH2" Residue "P GLU 52": "OE1" <-> "OE2" Residue "P ARG 82": "NH1" <-> "NH2" Residue "P GLU 86": "OE1" <-> "OE2" Residue "P ARG 97": "NH1" <-> "NH2" Residue "P GLU 98": "OE1" <-> "OE2" Residue "P PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 138": "OD1" <-> "OD2" Residue "P TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 147": "NH1" <-> "NH2" Residue "P ARG 157": "NH1" <-> "NH2" Residue "P GLU 162": "OE1" <-> "OE2" Residue "P GLU 175": "OE1" <-> "OE2" Residue "P ARG 235": "NH1" <-> "NH2" Residue "P TYR 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 251": "NH1" <-> "NH2" Residue "P TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 285": "OE1" <-> "OE2" Residue "P ARG 325": "NH1" <-> "NH2" Residue "Q ASP 14": "OD1" <-> "OD2" Residue "Q GLU 15": "OE1" <-> "OE2" Residue "Q GLU 66": "OE1" <-> "OE2" Residue "Q ASP 104": "OD1" <-> "OD2" Residue "R TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 31": "NH1" <-> "NH2" Residue "R ASP 42": "OD1" <-> "OD2" Residue "R GLU 46": "OE1" <-> "OE2" Residue "S GLU 37": "OE1" <-> "OE2" Residue "S GLU 56": "OE1" <-> "OE2" Residue "S GLU 91": "OE1" <-> "OE2" Residue "T TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 28": "OE1" <-> "OE2" Residue "T ASP 43": "OD1" <-> "OD2" Residue "T GLU 68": "OE1" <-> "OE2" Residue "T GLU 75": "OE1" <-> "OE2" Residue "T TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 43": "OD1" <-> "OD2" Residue "U GLU 49": "OE1" <-> "OE2" Residue "U GLU 55": "OE1" <-> "OE2" Residue "U PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 61": "OE1" <-> "OE2" Residue "U TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 17": "OE1" <-> "OE2" Residue "V ARG 22": "NH1" <-> "NH2" Residue "V GLU 48": "OE1" <-> "OE2" Residue "V GLU 78": "OE1" <-> "OE2" Residue "V GLU 84": "OE1" <-> "OE2" Residue "V GLU 86": "OE1" <-> "OE2" Residue "V GLU 104": "OE1" <-> "OE2" Residue "W GLU 27": "OE1" <-> "OE2" Residue "W GLU 34": "OE1" <-> "OE2" Residue "W ASP 53": "OD1" <-> "OD2" Residue "W GLU 109": "OE1" <-> "OE2" Residue "X GLU 10": "OE1" <-> "OE2" Residue "X GLU 16": "OE1" <-> "OE2" Residue "X GLU 41": "OE1" <-> "OE2" Residue "X GLU 48": "OE1" <-> "OE2" Residue "X GLU 49": "OE1" <-> "OE2" Residue "X PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 89": "OD1" <-> "OD2" Residue "X ARG 97": "NH1" <-> "NH2" Residue "X ARG 118": "NH1" <-> "NH2" Residue "X ASP 120": "OD1" <-> "OD2" Residue "X ARG 134": "NH1" <-> "NH2" Residue "X ARG 144": "NH1" <-> "NH2" Residue "X ARG 146": "NH1" <-> "NH2" Residue "X GLU 148": "OE1" <-> "OE2" Residue "X ASP 156": "OD1" <-> "OD2" Residue "Y GLU 13": "OE1" <-> "OE2" Residue "Y TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 50": "OE1" <-> "OE2" Residue "Y ARG 57": "NH1" <-> "NH2" Residue "Y ARG 103": "NH1" <-> "NH2" Residue "Z TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 78": "OE1" <-> "OE2" Residue "Z ARG 82": "NH1" <-> "NH2" Residue "Z GLU 89": "OE1" <-> "OE2" Residue "a GLU 4": "OE1" <-> "OE2" Residue "a TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 49": "OE1" <-> "OE2" Residue "a ARG 59": "NH1" <-> "NH2" Residue "a GLU 67": "OE1" <-> "OE2" Residue "b ARG 3": "NH1" <-> "NH2" Residue "b ARG 57": "NH1" <-> "NH2" Residue "c GLU 6": "OE1" <-> "OE2" Residue "c GLU 41": "OE1" <-> "OE2" Residue "c ARG 44": "NH1" <-> "NH2" Residue "d ASP 45": "OD1" <-> "OD2" Residue "d ARG 51": "NH1" <-> "NH2" Residue "d TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 114": "OE1" <-> "OE2" Residue "e ARG 8": "NH1" <-> "NH2" Residue "e GLU 38": "OE1" <-> "OE2" Residue "e ARG 50": "NH1" <-> "NH2" Residue "e GLU 60": "OE1" <-> "OE2" Residue "e TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ASP 9": "OD1" <-> "OD2" Residue "f ARG 28": "NH1" <-> "NH2" Residue "f ASP 31": "OD1" <-> "OD2" Residue "f ARG 46": "NH1" <-> "NH2" Residue "f GLU 47": "OE1" <-> "OE2" Residue "f GLU 52": "OE1" <-> "OE2" Residue "g ASP 29": "OD1" <-> "OD2" Residue "g GLU 33": "OE1" <-> "OE2" Residue "g GLU 87": "OE1" <-> "OE2" Residue "g GLU 92": "OE1" <-> "OE2" Residue "h PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ARG 20": "NH1" <-> "NH2" Residue "h PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 51": "OE1" <-> "OE2" Residue "h GLU 54": "OE1" <-> "OE2" Residue "h GLU 57": "OE1" <-> "OE2" Residue "h TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 65": "OE1" <-> "OE2" Residue "h ARG 77": "NH1" <-> "NH2" Residue "h TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 88": "OE1" <-> "OE2" Residue "h GLU 102": "OE1" <-> "OE2" Residue "h ARG 112": "NH1" <-> "NH2" Residue "h ASP 129": "OD1" <-> "OD2" Residue "h GLU 131": "OE1" <-> "OE2" Residue "i GLU 7": "OE1" <-> "OE2" Residue "i ARG 18": "NH1" <-> "NH2" Residue "i GLU 26": "OE1" <-> "OE2" Residue "i GLU 31": "OE1" <-> "OE2" Residue "i PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i GLU 98": "OE1" <-> "OE2" Residue "i GLU 111": "OE1" <-> "OE2" Residue "i GLU 114": "OE1" <-> "OE2" Residue "j GLU 8": "OE1" <-> "OE2" Residue "j PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ASP 43": "OD1" <-> "OD2" Residue "k GLU 14": "OE1" <-> "OE2" 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 88": "OE1" <-> "OE2" Residue "l TYR 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l GLU 19": "OE1" <-> "OE2" Residue "l ARG 30": "NH1" <-> "NH2" Residue "l GLU 32": "OE1" <-> "OE2" Residue "l GLU 35": "OE1" <-> "OE2" Residue "l TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ASP 63": "OD1" <-> "OD2" Residue "l GLU 120": "OE1" <-> "OE2" Residue "l TYR 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ARG 142": "NH1" <-> "NH2" Residue "l ASP 145": "OD1" <-> "OD2" Residue "m TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m ASP 18": "OD1" <-> "OD2" Residue "m GLU 27": "OE1" <-> "OE2" Residue "m GLU 34": "OE1" <-> "OE2" Residue "m ARG 39": "NH1" <-> "NH2" Residue "m GLU 60": "OE1" <-> "OE2" Residue "m ARG 71": "NH1" <-> "NH2" Residue "m TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m ASP 107": "OD1" <-> "OD2" Residue "m ASP 109": "OD1" <-> "OD2" Residue "m GLU 112": "OE1" <-> "OE2" Residue "n TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ARG 21": "NH1" <-> "NH2" Residue "n GLU 27": "OE1" <-> "OE2" Residue "n GLU 53": "OE1" <-> "OE2" Residue "n ARG 64": "NH1" <-> "NH2" Residue "n GLU 65": "OE1" <-> "OE2" Residue "n GLU 67": "OE1" <-> "OE2" Residue "n GLU 68": "OE1" <-> "OE2" Residue "n GLU 69": "OE1" <-> "OE2" Residue "n GLU 91": "OE1" <-> "OE2" Residue "n ARG 92": "NH1" <-> "NH2" Residue "n TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n GLU 94": "OE1" <-> "OE2" Residue "n TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n GLU 133": "OE1" <-> "OE2" Residue "n ARG 134": "NH1" <-> "NH2" Residue "n ARG 149": "NH1" <-> "NH2" Residue "n GLU 151": "OE1" <-> "OE2" Residue "o ARG 6": "NH1" <-> "NH2" Residue "o PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o GLU 32": "OE1" <-> "OE2" Residue "o ARG 36": "NH1" <-> "NH2" Residue "o GLU 82": "OE1" <-> "OE2" Residue "o ASP 93": "OD1" <-> "OD2" Residue "o TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ARG 97": "NH1" <-> "NH2" Residue "o ARG 103": "NH1" <-> "NH2" Residue "o ARG 105": "NH1" <-> "NH2" Residue "o ARG 106": "NH1" <-> "NH2" Residue "p ASP 5": "OD1" <-> "OD2" Residue "p PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p GLU 88": "OE1" <-> "OE2" Residue "p ASP 98": "OD1" <-> "OD2" Residue "p GLU 100": "OE1" <-> "OE2" Residue "p GLU 116": "OE1" <-> "OE2" Residue "p TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ARG 21": "NH1" <-> "NH2" Residue "q TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ARG 29": "NH1" <-> "NH2" Residue "q TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q GLU 50": "OE1" <-> "OE2" Residue "q ASP 76": "OD1" <-> "OD2" Residue "q ASP 78": "OD1" <-> "OD2" Residue "q ARG 88": "NH1" <-> "NH2" Residue "q PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r GLU 29": "OE1" <-> "OE2" Residue "r ARG 59": "NH1" <-> "NH2" Residue "r ASP 108": "OD1" <-> "OD2" Residue "r GLU 109": "OE1" <-> "OE2" Residue "s PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s ASP 57": "OD1" <-> "OD2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 68334 Number of models: 1 Model: "" Number of chains: 109 Chain: "A" Number of atoms: 921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 921 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 1230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1230 Classifications: {'peptide': 154} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 143} Chain: "C" Number of atoms: 1721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1721 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 16, 'TRANS': 190} Chain: "D" Number of atoms: 3459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3459 Classifications: {'peptide': 430} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 401} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'2MR:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 1655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1655 Classifications: {'peptide': 213} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 191} Chain: "F" Number of atoms: 3319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3319 Classifications: {'peptide': 431} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 409} Chain: "G" Number of atoms: 5279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 688, 5279 Classifications: {'peptide': 688} Link IDs: {'PTRANS': 32, 'TRANS': 655} Chain: "H" Number of atoms: 2509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2509 Classifications: {'peptide': 318} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 295} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "I" Number of atoms: 1414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1414 Classifications: {'peptide': 176} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 165} Chain: "J" Number of atoms: 1337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1337 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 3, 'TRANS': 170} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "K" Number of atoms: 739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 739 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 1, 'TRANS': 95} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 4756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 601, 4756 Classifications: {'peptide': 601} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 27, 'TRANS': 573} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'FME:plan-2': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "M" Number of atoms: 3654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3654 Classifications: {'peptide': 459} Link IDs: {'PCIS': 3, 'PTRANS': 17, 'TRANS': 438} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "N" Number of atoms: 2733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2733 Classifications: {'peptide': 347} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 325} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "O" Number of atoms: 2589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2589 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 15, 'TRANS': 304} Chain: "P" Number of atoms: 2747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2747 Classifications: {'peptide': 341} Link IDs: {'PTRANS': 22, 'TRANS': 318} Chain: "Q" Number of atoms: 1016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1016 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 6, 'TRANS': 118} Chain: "R" Number of atoms: 730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 730 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "S" Number of atoms: 691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 691 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 4, 'TRANS': 81} Chain: "T" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 612 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "U" Number of atoms: 693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 693 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 5, 'TRANS': 80} Chain: "V" Number of atoms: 923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 923 Classifications: {'peptide': 114} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 105} Chain: "W" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 971 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 6, 'TRANS': 107} Chain: "X" Number of atoms: 1402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1402 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 12, 'TRANS': 158} Chain: "Y" Number of atoms: 1030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1030 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 5, 'TRANS': 134} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'AYA:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "Z" Number of atoms: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1152 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 7, 'TRANS': 133} Chain: "a" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 569 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "b" Number of atoms: 651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 651 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 11, 'TRANS': 71} Chain: "c" Number of atoms: 405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 405 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 3, 'TRANS': 44} Chain: "d" Number of atoms: 934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 934 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 9, 'TRANS': 102} Chain: "e" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 819 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 5, 'TRANS': 91} Chain: "f" Number of atoms: 451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 451 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 2, 'TRANS': 49} Chain: "g" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 824 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 8, 'TRANS': 89} Chain: "h" Number of atoms: 1154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1154 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 10, 'TRANS': 127} Chain: "i" Number of atoms: 912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 912 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 93} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'SAC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "j" Number of atoms: 580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 580 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 7, 'TRANS': 59} Chain: "k" Number of atoms: 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: 1304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1304 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 20, 'TRANS': 134} Chain: "m" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 960 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 6, 'TRANS': 107} Chain breaks: 1 Chain: "n" Number of atoms: 1492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1492 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 15, 'TRANS': 156} Chain: "o" Number of atoms: 1048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1048 Classifications: {'peptide': 122} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 114} Chain: "p" Number of atoms: 1443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1443 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 10, 'TRANS': 160} Chain: "q" Number of atoms: 1209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1209 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 11, 'TRANS': 133} Chain: "r" Number of atoms: 767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 767 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 11, 'TRANS': 82} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'AYA:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "s" Number of atoms: 371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 371 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 3, 'TRANS': 40} Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 56 Unusual residues: {'LMT': 1, 'PC1': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 32 Planarities with less than four sites: {'PC1:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 43 Unusual residues: {'PC1': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 19 Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'FMN': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 21 Unusual residues: {' K': 1, 'FES': 1, 'SF4': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "H" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 78 Unusual residues: {'3PE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'3PE:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "I" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Unusual residues: {'3PE': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "J" Number of atoms: 97 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 97 Unusual residues: {'CDL': 1, 'LMT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 38 Chain: "K" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 71 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 29 Chain: "L" Number of atoms: 198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 198 Unusual residues: {'3PE': 2, 'CDL': 1, 'LMT': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 39 Chain: "M" Number of atoms: 181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 181 Unusual residues: {'3PE': 2, 'LMT': 1, 'PC1': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Chain: "O" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "P" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 102 Unusual residues: {'NDP': 1, 'PC1': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'EHZ': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "U" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'EHZ': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "Y" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 70 Unusual residues: {'3PE': 1, 'LMT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Chain: "b" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'LMT': 1} Classifications: {'undetermined': 1} Chain: "d" Number of atoms: 153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 153 Unusual residues: {'3PE': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "f" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'LMT': 1} Classifications: {'undetermined': 1} Chain: "h" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 102 Unusual residues: {'CDL': 1, 'LMT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 33 Chain: "j" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'LMT': 1} Classifications: {'undetermined': 1} Chain: "l" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'LMT': 1} Classifications: {'undetermined': 1} Chain: "o" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'MYR': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MYR:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "q" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 76 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 24 Chain: "A" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "B" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 48 Classifications: {'water': 48} Link IDs: {None: 47} Chain: "C" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 66 Classifications: {'water': 66} Link IDs: {None: 65} Chain: "D" Number of atoms: 115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 115 Classifications: {'water': 115} Link IDs: {None: 114} Chain: "E" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "F" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 33 Classifications: {'water': 33} Link IDs: {None: 32} Chain: "G" Number of atoms: 135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 135 Classifications: {'water': 135} Link IDs: {None: 134} Chain: "H" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 43 Classifications: {'water': 43} Link IDs: {None: 42} Chain: "I" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 79 Classifications: {'water': 79} Link IDs: {None: 78} Chain: "J" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "K" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "L" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 28 Classifications: {'water': 28} Link IDs: {None: 27} Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 28 Classifications: {'water': 28} Link IDs: {None: 27} Chain: "O" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "P" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 40 Classifications: {'water': 40} Link IDs: {None: 39} Chain: "Q" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 45 Classifications: {'water': 45} Link IDs: {None: 44} Chain: "R" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Chain: "S" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "V" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "W" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "X" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "Y" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "Z" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "a" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "b" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "d" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "e" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "f" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "g" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "h" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "j" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "l" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "m" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "n" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "o" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "p" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "q" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "r" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1657 SG CYS B 119 95.686 93.902 204.909 1.00 28.37 S ATOM 1887 SG CYS B 149 93.481 91.375 209.434 1.00 28.44 S ATOM 1153 SG CYS B 54 90.169 90.210 203.929 1.00 31.97 S ATOM 1159 SG CYS B 55 89.661 95.832 206.929 1.00 30.67 S ATOM 8135 SG CYS E 103 114.445 44.148 258.895 1.00 47.32 S ATOM 8169 SG CYS E 108 112.900 41.395 260.754 1.00 47.32 S ATOM 8449 SG CYS E 144 116.662 40.936 255.435 1.00 45.16 S ATOM 8472 SG CYS E 148 115.417 38.169 256.259 1.00 48.38 S ATOM 11690 SG CYS F 362 119.142 51.502 235.406 1.00 31.54 S ATOM 11710 SG CYS F 365 116.254 50.633 240.284 1.00 32.60 S ATOM 12034 SG CYS F 405 120.851 46.413 239.286 1.00 34.34 S ATOM 11671 SG CYS F 359 122.727 52.238 240.898 1.00 34.33 S ATOM 13131 SG CYS G 114 115.340 70.231 226.739 1.00 29.36 S ATOM 13070 SG CYS G 105 109.448 72.509 228.730 1.00 28.60 S ATOM 13091 SG CYS G 108 114.953 75.025 230.865 1.00 29.03 S ATOM 13463 SG CYS G 156 123.762 64.226 231.303 1.00 30.34 S ATOM 13440 SG CYS G 153 121.010 66.156 237.036 1.00 29.42 S ATOM 13487 SG CYS G 159 127.120 67.301 235.612 1.00 32.81 S ATOM 13817 SG CYS G 203 122.568 70.089 231.866 1.00 31.17 S ATOM 12576 SG CYS G 41 124.294 57.425 228.862 1.00 30.80 S ATOM 12662 SG CYS G 52 120.419 57.883 227.991 1.00 30.77 S ATOM 12687 SG CYS G 55 122.050 53.463 224.487 1.00 32.11 S ATOM 12788 SG CYS G 69 125.170 54.176 225.742 1.00 32.52 S ATOM 21047 SG CYS I 119 96.522 85.384 215.297 1.00 26.67 S ATOM 21021 SG CYS I 116 96.832 91.894 216.330 1.00 27.07 S ATOM 21068 SG CYS I 122 98.087 87.434 220.830 1.00 28.10 S ATOM 20795 SG CYS I 87 102.214 88.350 215.700 1.00 26.81 S ATOM 21097 SG CYS I 126 100.853 84.064 228.233 1.00 28.45 S ATOM 20726 SG CYS I 77 105.687 88.373 229.332 1.00 28.67 S ATOM 20768 SG CYS I 83 104.074 86.744 223.318 1.00 27.76 S ATOM 20745 SG CYS I 80 106.314 82.051 226.741 1.00 28.45 S ATOM 41537 SG CYS R 59 102.734 79.229 243.286 1.00 34.08 S ATOM 41715 SG CYS R 84 105.675 79.941 241.164 1.00 34.99 S ATOM 41737 SG CYS R 87 103.318 82.594 242.032 1.00 33.31 S Time building chain proxies: 27.43, per 1000 atoms: 0.40 Number of scatterers: 68334 At special positions: 0 Unit cell: (186.405, 199.563, 291.669, 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 468 16.00 P 34 15.00 Mg 1 11.99 O 13022 8.00 N 11148 7.00 C 43631 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS Y 17 " - pdb=" SG CYS Y 74 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 94 " - pdb=" SG CYS Y 114 " distance=2.03 Simple disulfide: pdb=" SG CYS e 32 " - pdb=" SG CYS e 65 " distance=2.03 Simple disulfide: pdb=" SG CYS e 42 " - pdb=" SG CYS e 55 " distance=2.04 Simple disulfide: pdb=" SG CYS p 112 " - pdb=" SG CYS p 124 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 21.56 Conformation dependent library (CDL) restraints added in 9.3 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E 301 " pdb="FE1 FES E 301 " - pdb=" SG CYS E 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="FE1 FES G 803 " - pdb=" SG CYS G 52 " 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 41 " pdb=" SF4 B 201 " pdb="FE2 SF4 B 201 " - pdb=" SG CYS B 149 " pdb="FE1 SF4 B 201 " - pdb=" SG CYS B 119 " pdb="FE3 SF4 B 201 " - pdb=" SG CYS B 54 " pdb="FE4 SF4 B 201 " - pdb=" SG CYS B 55 " pdb=" SF4 F 502 " pdb="FE3 SF4 F 502 " - pdb=" SG CYS F 405 " pdb="FE2 SF4 F 502 " - pdb=" SG CYS F 365 " pdb="FE4 SF4 F 502 " - pdb=" SG CYS F 359 " pdb="FE1 SF4 F 502 " - pdb=" SG CYS F 362 " pdb=" SF4 G 801 " pdb="FE3 SF4 G 801 " - pdb=" NE2 HIS G 101 " pdb="FE4 SF4 G 801 " - pdb=" SG CYS G 108 " pdb="FE1 SF4 G 801 " - pdb=" SG CYS G 114 " pdb="FE2 SF4 G 801 " - pdb=" SG CYS G 105 " pdb=" SF4 G 802 " pdb="FE1 SF4 G 802 " - pdb=" SG CYS G 156 " pdb="FE3 SF4 G 802 " - pdb=" SG CYS G 159 " pdb="FE4 SF4 G 802 " - pdb=" SG CYS G 203 " pdb="FE2 SF4 G 802 " - pdb=" SG CYS G 153 " pdb=" SF4 I 202 " pdb="FE3 SF4 I 202 " - pdb=" SG CYS I 122 " pdb="FE2 SF4 I 202 " - pdb=" SG CYS I 116 " pdb="FE4 SF4 I 202 " - pdb=" SG CYS I 87 " pdb="FE1 SF4 I 202 " - pdb=" SG CYS I 119 " pdb=" SF4 I 203 " pdb="FE1 SF4 I 203 " - pdb=" SG CYS I 126 " pdb="FE2 SF4 I 203 " - pdb=" SG CYS I 77 " pdb="FE3 SF4 I 203 " - pdb=" SG CYS I 83 " pdb="FE4 SF4 I 203 " - pdb=" SG CYS I 80 " Number of angles added : 81 Zn2+ tetrahedral coordination pdb=" ZN R 201 " pdb="ZN ZN R 201 " - pdb=" NE2 HIS R 68 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 84 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 87 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 59 " Number of angles added : 3 16154 Ramachandran restraints generated. 8077 Oldfield, 0 Emsley, 8077 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15386 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 359 helices and 30 sheets defined 54.3% alpha, 4.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 11.17 Creating SS restraints... Processing helix chain 'A' and resid 3 through 23 Processing helix chain 'A' and resid 31 through 34 No H-bonds generated for 'chain 'A' and resid 31 through 34' Processing helix chain 'A' and resid 56 through 80 removed outlier: 3.538A pdb=" N LEU A 63 " --> pdb=" O ALA A 59 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU A 67 " --> pdb=" O LEU A 63 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU A 68 " --> pdb=" O LEU A 64 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE A 69 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N ALA A 70 " --> pdb=" O ASP A 66 " (cutoff:3.500A) Proline residue: A 74 - end of helix removed outlier: 5.435A pdb=" N TRP A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N GLN A 80 " --> pdb=" O PRO A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 107 removed outlier: 3.572A pdb=" N THR A 89 " --> pdb=" O ASN A 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 43 Processing helix chain 'B' and resid 54 through 63 Processing helix chain 'B' and resid 69 through 72 Processing helix chain 'B' and resid 80 through 82 No H-bonds generated for 'chain 'B' and resid 80 through 82' Processing helix chain 'B' and resid 94 through 105 Proline residue: B 98 - end of helix Processing helix chain 'B' and resid 117 through 122 Processing helix chain 'B' and resid 124 through 126 No H-bonds generated for 'chain 'B' and resid 124 through 126' Processing helix chain 'B' and resid 136 through 138 No H-bonds generated for 'chain 'B' and resid 136 through 138' Processing helix chain 'B' and resid 153 through 169 removed outlier: 3.525A pdb=" N ARG B 169 " --> pdb=" O LYS B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 178 Processing helix chain 'C' and resid 16 through 32 Processing helix chain 'C' and resid 54 through 66 removed outlier: 4.771A pdb=" N ILE C 58 " --> pdb=" O ASP C 55 " (cutoff:3.500A) Proline residue: C 59 - end of helix removed outlier: 3.656A pdb=" N THR C 62 " --> pdb=" O PRO C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 122 No H-bonds generated for 'chain 'C' and resid 120 through 122' Processing helix chain 'C' and resid 125 through 138 removed outlier: 3.866A pdb=" N TRP C 129 " --> pdb=" O ALA C 126 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU C 131 " --> pdb=" O ASN C 128 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N MET C 137 " --> pdb=" O ILE C 134 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N PHE C 138 " --> pdb=" O TRP C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 209 No H-bonds generated for 'chain 'C' and resid 207 through 209' Processing helix chain 'D' and resid 8 through 14 removed outlier: 3.876A pdb=" N GLN D 13 " --> pdb=" O GLU D 9 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N TYR D 14 " --> pdb=" O TRP D 10 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 25 No H-bonds generated for 'chain 'D' and resid 23 through 25' Processing helix chain 'D' and resid 87 through 93 removed outlier: 3.864A pdb=" N GLU D 92 " --> pdb=" O GLU D 88 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N TYR D 93 " --> pdb=" O LYS D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 104 removed outlier: 3.943A pdb=" N ASP D 104 " --> pdb=" O LEU D 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 100 through 104' Processing helix chain 'D' and resid 111 through 126 Processing helix chain 'D' and resid 132 through 161 Processing helix chain 'D' and resid 165 through 185 removed outlier: 3.910A pdb=" N GLU D 173 " --> pdb=" O TRP D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 229 removed outlier: 3.864A pdb=" N ASN D 217 " --> pdb=" O GLU D 213 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N SER D 219 " --> pdb=" O SER D 215 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N LEU D 220 " --> pdb=" O LYS D 216 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG D 221 " --> pdb=" O ASN D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 239 Processing helix chain 'D' and resid 247 through 252 Processing helix chain 'D' and resid 257 through 263 removed outlier: 3.575A pdb=" N ARG D 261 " --> pdb=" O VAL D 258 " (cutoff:3.500A) removed outlier: 4.848A 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 removed outlier: 3.517A pdb=" N GLN D 313 " --> pdb=" O ARG D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 338 No H-bonds generated for 'chain 'D' and resid 335 through 338' Processing helix chain 'D' and resid 342 through 353 Processing helix chain 'D' and resid 394 through 405 removed outlier: 3.572A pdb=" N LEU D 402 " --> pdb=" O HIS D 398 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N ASP D 403 " --> pdb=" O LEU D 399 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N LYS D 404 " --> pdb=" O ALA D 400 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 421 Processing helix chain 'D' and resid 425 through 429 Processing helix chain 'E' and resid 25 through 37 removed outlier: 3.751A pdb=" N LYS E 29 " --> pdb=" O PRO E 25 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASN E 37 " --> pdb=" O ALA E 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 58 removed outlier: 4.568A pdb=" N LEU E 48 " --> pdb=" O ALA E 45 " (cutoff:3.500A) Proline residue: E 49 - end of helix removed outlier: 3.641A 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: 3.544A pdb=" N VAL E 83 " --> pdb=" O ARG E 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 111 removed outlier: 3.674A pdb=" N ARG E 111 " --> pdb=" O PRO E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 113 through 124 Processing helix chain 'E' and resid 148 through 150 No H-bonds generated for 'chain 'E' and resid 148 through 150' Processing helix chain 'E' and resid 166 through 177 Processing helix chain 'F' and resid 17 through 19 No H-bonds generated for 'chain 'F' and resid 17 through 19' Processing helix chain 'F' and resid 33 through 39 Processing helix chain 'F' and resid 45 through 51 Processing helix chain 'F' and resid 53 through 63 Processing helix chain 'F' and resid 75 through 82 removed outlier: 3.801A pdb=" N PHE F 81 " --> pdb=" O LEU F 77 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N MET F 82 " --> pdb=" O LYS F 78 " (cutoff:3.500A) Processing helix chain 'F' and resid 106 through 113 removed outlier: 3.542A pdb=" N ILE F 110 " --> pdb=" O LYS F 106 " (cutoff:3.500A) Processing helix chain 'F' and resid 115 through 128 Processing helix chain 'F' and resid 143 through 158 Processing helix chain 'F' and resid 166 through 168 No H-bonds generated for 'chain 'F' and resid 166 through 168' Processing helix chain 'F' and resid 184 through 187 Processing helix chain 'F' and resid 189 through 196 Processing helix chain 'F' and resid 215 through 217 No H-bonds generated for 'chain 'F' and resid 215 through 217' Processing helix chain 'F' and resid 225 through 237 removed outlier: 3.862A pdb=" N SER F 231 " --> pdb=" O THR F 227 " (cutoff:3.500A) Proline residue: F 232 - end of helix Processing helix chain 'F' and resid 239 through 244 Processing helix chain 'F' and resid 276 through 284 Processing helix chain 'F' and resid 291 through 293 No H-bonds generated for 'chain 'F' and resid 291 through 293' Processing helix chain 'F' and resid 309 through 312 No H-bonds generated for 'chain 'F' and resid 309 through 312' Processing helix chain 'F' and resid 319 through 324 Processing helix chain 'F' and resid 343 through 357 Processing helix chain 'F' and resid 363 through 381 removed outlier: 4.490A pdb=" N ASP F 370 " --> pdb=" O ARG F 366 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ARG F 381 " --> pdb=" O ALA F 377 " (cutoff:3.500A) Processing helix chain 'F' and resid 386 through 399 removed outlier: 3.579A pdb=" N ASP F 390 " --> pdb=" O ALA F 387 " (cutoff:3.500A) Processing helix chain 'F' and resid 407 through 436 Proline residue: F 414 - end of helix removed outlier: 3.619A pdb=" N ARG F 423 " --> pdb=" O ILE F 419 " (cutoff:3.500A) Proline residue: F 424 - end of helix Processing helix chain 'G' and resid 26 through 33 removed outlier: 3.887A 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 122 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: 3.631A pdb=" N ILE G 202 " --> pdb=" O ILE G 199 " (cutoff:3.500A) Processing helix chain 'G' and resid 219 through 221 No H-bonds generated for 'chain 'G' and resid 219 through 221' Processing helix chain 'G' and resid 265 through 275 removed outlier: 5.419A pdb=" N TYR G 271 " --> pdb=" O THR G 267 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ASP G 272 " --> pdb=" O ARG G 268 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N GLY G 273 " --> pdb=" O PHE G 269 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N LEU G 274 " --> pdb=" O ALA G 270 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N LYS G 275 " --> pdb=" O TYR G 271 " (cutoff:3.500A) Processing helix chain 'G' and resid 296 through 309 removed outlier: 3.539A pdb=" N MET G 306 " --> pdb=" O ARG G 302 " (cutoff:3.500A) Processing helix chain 'G' and resid 312 through 314 No H-bonds generated for 'chain 'G' and resid 312 through 314' Processing helix chain 'G' and resid 325 through 338 removed outlier: 3.696A pdb=" N VAL G 338 " --> pdb=" O LEU G 334 " (cutoff:3.500A) Processing helix chain 'G' and resid 359 through 362 Processing helix chain 'G' and resid 369 through 373 Processing helix chain 'G' and resid 384 through 387 No H-bonds generated for 'chain 'G' and resid 384 through 387' Processing helix chain 'G' and resid 389 through 401 Processing helix chain 'G' and resid 426 through 434 Processing helix chain 'G' and resid 438 through 445 removed outlier: 3.571A pdb=" N VAL G 442 " --> pdb=" O PRO G 438 " (cutoff:3.500A) Processing helix chain 'G' and resid 455 through 459 removed outlier: 3.561A pdb=" N GLN G 459 " --> pdb=" O SER G 456 " (cutoff:3.500A) Processing helix chain 'G' and resid 463 through 479 Processing helix chain 'G' and resid 499 through 504 Processing helix chain 'G' and resid 512 through 516 Processing helix chain 'G' and resid 534 through 536 No H-bonds generated for 'chain 'G' and resid 534 through 536' Processing helix chain 'G' and resid 554 through 556 No H-bonds generated for 'chain 'G' and resid 554 through 556' Processing helix chain 'G' and resid 566 through 568 No H-bonds generated for 'chain 'G' and resid 566 through 568' Processing helix chain 'G' and resid 596 through 607 Processing helix chain 'G' and resid 616 through 626 Processing helix chain 'G' and resid 628 through 631 removed outlier: 3.789A pdb=" N VAL G 631 " --> pdb=" O PRO G 628 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 628 through 631' Processing helix chain 'G' and resid 642 through 650 removed outlier: 3.555A pdb=" N LYS G 650 " --> pdb=" O SER G 646 " (cutoff:3.500A) Processing helix chain 'G' and resid 668 through 670 No H-bonds generated for 'chain 'G' and resid 668 through 670' Processing helix chain 'G' and resid 676 through 679 No H-bonds generated for 'chain 'G' and resid 676 through 679' Processing helix chain 'G' and resid 682 through 692 Processing helix chain 'H' and resid 3 through 31 Proline residue: H 12 - end of helix removed outlier: 3.649A pdb=" N LEU H 22 " --> pdb=" O ALA H 18 " (cutoff:3.500A) Processing helix chain 'H' and resid 42 through 44 No H-bonds generated for 'chain 'H' and resid 42 through 44' Processing helix chain 'H' and resid 47 through 57 Processing helix chain 'H' and resid 68 through 86 Proline residue: H 75 - end of helix removed outlier: 4.266A pdb=" N TRP H 86 " --> pdb=" O ALA H 82 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 123 removed outlier: 3.502A pdb=" N VAL H 113 " --> pdb=" O SER H 109 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N TYR H 114 " --> pdb=" O SER H 110 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N SER H 115 " --> pdb=" O LEU H 111 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ILE H 116 " --> pdb=" O ALA H 112 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER H 119 " --> pdb=" O SER H 115 " (cutoff:3.500A) Processing helix chain 'H' and resid 126 through 157 removed outlier: 4.831A pdb=" N VAL H 144 " --> pdb=" O ILE H 140 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N THR H 145 " --> pdb=" O SER H 141 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N MET H 156 " --> pdb=" O SER H 152 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER H 157 " --> pdb=" O VAL H 153 " (cutoff:3.500A) Processing helix chain 'H' and resid 162 through 168 removed outlier: 3.940A pdb=" N ILE H 166 " --> pdb=" O LEU H 162 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR H 167 " --> pdb=" O SER H 163 " (cutoff:3.500A) Processing helix chain 'H' and resid 174 through 192 Proline residue: H 180 - end of helix Processing helix chain 'H' and resid 204 through 207 No H-bonds generated for 'chain 'H' and resid 204 through 207' Processing helix chain 'H' and resid 210 through 212 No H-bonds generated for 'chain 'H' and resid 210 through 212' Processing helix chain 'H' and resid 217 through 242 removed outlier: 3.666A pdb=" N PHE H 223 " --> pdb=" O PRO H 219 " (cutoff:3.500A) Processing helix chain 'H' and resid 252 through 274 Processing helix chain 'H' and resid 282 through 291 removed outlier: 3.521A pdb=" N MET H 286 " --> pdb=" O TYR H 282 " (cutoff:3.500A) Processing helix chain 'H' and resid 293 through 310 Proline residue: H 308 - end of helix Processing helix chain 'I' and resid 14 through 26 Processing helix chain 'I' and resid 28 through 42 removed outlier: 3.555A pdb=" N MET I 36 " --> pdb=" O ARG I 32 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N THR I 37 " --> pdb=" O GLY I 33 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE I 42 " --> pdb=" O LEU I 38 " (cutoff:3.500A) Processing helix chain 'I' and resid 82 through 86 Processing helix chain 'I' and resid 121 through 125 Processing helix chain 'I' and resid 145 through 147 No H-bonds generated for 'chain 'I' and resid 145 through 147' Processing helix chain 'I' and resid 151 through 175 removed outlier: 5.453A pdb=" N ALA I 163 " --> pdb=" O ASP I 159 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N GLU I 164 " --> pdb=" O LYS I 160 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA I 167 " --> pdb=" O ALA I 163 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N LEU I 174 " --> pdb=" O GLN I 170 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N TYR I 175 " --> pdb=" O ALA I 171 " (cutoff:3.500A) Processing helix chain 'J' and resid 5 through 21 Processing helix chain 'J' and resid 26 through 47 Processing helix chain 'J' and resid 50 through 74 Processing helix chain 'J' and resid 87 through 110 removed outlier: 3.597A pdb=" N MET J 103 " --> pdb=" O MET J 99 " (cutoff:3.500A) Processing helix chain 'J' and resid 124 through 127 removed outlier: 3.577A pdb=" N ILE J 127 " --> pdb=" O ASP J 124 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 124 through 127' Processing helix chain 'J' and resid 138 through 148 removed outlier: 4.122A pdb=" N LEU J 146 " --> pdb=" O GLY J 142 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N TYR J 147 " --> pdb=" O ILE J 143 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N SER J 148 " --> pdb=" O ALA J 144 " (cutoff:3.500A) Processing helix chain 'J' and resid 151 through 172 Processing helix chain 'K' and resid 3 through 20 removed outlier: 3.789A pdb=" N ASN K 7 " --> pdb=" O MET K 3 " (cutoff:3.500A) Processing helix chain 'K' and resid 26 through 51 Processing helix chain 'K' and resid 54 through 85 removed outlier: 3.705A pdb=" N MET K 58 " --> pdb=" O LEU K 55 " (cutoff:3.500A) Proline residue: K 60 - end of helix removed outlier: 3.888A pdb=" N CYS K 69 " --> pdb=" O PHE K 66 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU K 75 " --> pdb=" O ALA K 72 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL K 81 " --> pdb=" O LEU K 78 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASN K 83 " --> pdb=" O MET K 80 " (cutoff:3.500A) Processing helix chain 'K' and resid 90 through 92 No H-bonds generated for 'chain 'K' and resid 90 through 92' Processing helix chain 'L' and resid 3 through 24 removed outlier: 4.116A pdb=" N LEU L 12 " --> pdb=" O SER L 8 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N THR L 16 " --> pdb=" O LEU L 12 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N MET L 17 " --> pdb=" O LEU L 13 " (cutoff:3.500A) Proline residue: L 18 - end of helix Processing helix chain 'L' and resid 29 through 57 removed outlier: 3.916A pdb=" N TYR L 32 " --> pdb=" O PRO L 29 " (cutoff:3.500A) Proline residue: L 33 - end of helix removed outlier: 3.609A pdb=" N PHE L 44 " --> pdb=" O SER L 41 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR L 46 " --> pdb=" O ALA L 43 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE L 49 " --> pdb=" O THR L 46 " (cutoff:3.500A) Proline residue: L 50 - end of helix removed outlier: 3.897A pdb=" N SER L 57 " --> pdb=" O PHE L 54 " (cutoff:3.500A) Processing helix chain 'L' and resid 84 through 107 Proline residue: L 91 - end of helix removed outlier: 3.817A pdb=" N TRP L 106 " --> pdb=" O GLU L 102 " (cutoff:3.500A) Processing helix chain 'L' and resid 114 through 133 Processing helix chain 'L' and resid 137 through 155 removed outlier: 3.578A pdb=" N GLY L 148 " --> pdb=" O TRP L 144 " (cutoff:3.500A) Processing helix chain 'L' and resid 162 through 192 removed outlier: 3.615A pdb=" N ILE L 180 " --> pdb=" O ARG L 176 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N GLY L 181 " --> pdb=" O ILE L 177 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N PHE L 182 " --> pdb=" O GLY L 178 " (cutoff:3.500A) Processing helix chain 'L' and resid 198 through 204 Processing helix chain 'L' and resid 210 through 224 removed outlier: 3.552A pdb=" N GLY L 222 " --> pdb=" O LEU L 218 " (cutoff:3.500A) Processing helix chain 'L' and resid 231 through 238 removed outlier: 3.985A pdb=" N MET L 237 " --> pdb=" O LEU L 233 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N GLU L 238 " --> pdb=" O PRO L 234 " (cutoff:3.500A) Processing helix chain 'L' and resid 241 through 247 Processing helix chain 'L' and resid 252 through 262 removed outlier: 4.270A pdb=" N GLY L 256 " --> pdb=" O MET L 252 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N ILE L 257 " --> pdb=" O VAL L 253 " (cutoff:3.500A) Processing helix chain 'L' and resid 264 through 269 removed outlier: 4.434A pdb=" N ASN L 269 " --> pdb=" O PRO L 265 " (cutoff:3.500A) Processing helix chain 'L' and resid 271 through 294 removed outlier: 4.485A pdb=" N THR L 294 " --> pdb=" O MET L 290 " (cutoff:3.500A) Processing helix chain 'L' and resid 298 through 318 Processing helix chain 'L' and resid 322 through 349 removed outlier: 3.862A pdb=" N PHE L 334 " --> pdb=" O CYS L 330 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N PHE L 335 " --> pdb=" O THR L 331 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA L 337 " --> pdb=" O ALA L 333 " (cutoff:3.500A) Processing helix chain 'L' and resid 356 through 358 No H-bonds generated for 'chain 'L' and resid 356 through 358' Processing helix chain 'L' and resid 362 through 365 No H-bonds generated for 'chain 'L' and resid 362 through 365' Processing helix chain 'L' and resid 367 through 381 Processing helix chain 'L' and resid 389 through 400 removed outlier: 4.985A pdb=" N LEU L 394 " --> pdb=" O TYR L 390 " (cutoff:3.500A) Processing helix chain 'L' and resid 406 through 430 removed outlier: 3.681A pdb=" N ALA L 420 " --> pdb=" O THR L 416 " (cutoff:3.500A) Processing helix chain 'L' and resid 448 through 471 removed outlier: 5.810A pdb=" N GLY L 465 " --> pdb=" O SER L 461 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N TYR L 466 " --> pdb=" O LEU L 462 " (cutoff:3.500A) Processing helix chain 'L' and resid 484 through 487 No H-bonds generated for 'chain 'L' and resid 484 through 487' Processing helix chain 'L' and resid 489 through 509 removed outlier: 4.288A 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 542 Proline residue: L 530 - end of helix removed outlier: 3.839A pdb=" N MET L 533 " --> pdb=" O PRO L 530 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N HIS L 534 " --> pdb=" O THR L 531 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N ALA L 537 " --> pdb=" O HIS L 534 " (cutoff:3.500A) Proline residue: L 538 - end of helix removed outlier: 3.621A pdb=" N LEU L 542 " --> pdb=" O TYR L 539 " (cutoff:3.500A) Processing helix chain 'L' and resid 552 through 559 Processing helix chain 'L' and resid 563 through 578 Processing helix chain 'L' and resid 584 through 600 Processing helix chain 'M' and resid 5 through 17 removed outlier: 4.184A pdb=" N MET M 12 " --> pdb=" O THR M 8 " (cutoff:3.500A) Proline residue: M 13 - end of helix Processing helix chain 'M' and resid 20 through 42 removed outlier: 3.895A pdb=" N ILE M 23 " --> pdb=" O ASN M 20 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N TRP M 24 " --> pdb=" O ASN M 21 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ASN M 26 " --> pdb=" O ILE M 23 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N SER M 27 " --> pdb=" O TRP M 24 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N THR M 28 " --> pdb=" O VAL M 25 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N HIS M 30 " --> pdb=" O SER M 27 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER M 31 " --> pdb=" O THR M 28 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE M 34 " --> pdb=" O SER M 31 " (cutoff:3.500A) Processing helix chain 'M' and resid 60 through 80 Proline residue: M 64 - end of helix removed outlier: 3.576A 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 Processing helix chain 'M' and resid 115 through 136 removed outlier: 4.785A pdb=" N LEU M 126 " --> pdb=" O PHE M 122 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N VAL M 127 " --> pdb=" O GLU M 123 " (cutoff:3.500A) Proline residue: M 128 - end of helix Processing helix chain 'M' and resid 140 through 171 removed outlier: 3.589A pdb=" N ALA M 145 " --> pdb=" O ARG M 142 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N TYR M 148 " --> pdb=" O ALA M 145 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N TYR M 152 " --> pdb=" O PHE M 149 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU M 154 " --> pdb=" O PHE M 151 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA M 155 " --> pdb=" O TYR M 152 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N LEU M 158 " --> pdb=" O ALA M 155 " (cutoff:3.500A) Proline residue: M 159 - end of helix removed outlier: 3.526A pdb=" N GLN M 168 " --> pdb=" O ILE M 165 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL M 171 " --> pdb=" O GLN M 168 " (cutoff:3.500A) Processing helix chain 'M' and resid 176 through 182 removed outlier: 3.858A pdb=" N TYR M 181 " --> pdb=" O LEU M 177 " (cutoff:3.500A) Processing helix chain 'M' and resid 190 through 206 removed outlier: 4.454A pdb=" N ALA M 202 " --> pdb=" O ALA M 198 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N PHE M 203 " --> pdb=" O CYS M 199 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LYS M 206 " --> pdb=" O ALA M 202 " (cutoff:3.500A) Processing helix chain 'M' and resid 214 through 222 removed outlier: 3.927A pdb=" N LYS M 218 " --> pdb=" O LEU M 214 " (cutoff:3.500A) Processing helix chain 'M' and resid 225 through 233 Processing helix chain 'M' and resid 235 through 249 removed outlier: 4.255A pdb=" N GLY M 239 " --> pdb=" O LEU M 235 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLY M 240 " --> pdb=" O LEU M 236 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N LEU M 248 " --> pdb=" O LEU M 244 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N ILE M 249 " --> pdb=" O ARG M 245 " (cutoff:3.500A) Processing helix chain 'M' and resid 253 through 278 removed outlier: 3.878A pdb=" N MET M 257 " --> pdb=" O THR M 254 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ALA M 258 " --> pdb=" O ASP M 255 " (cutoff:3.500A) Proline residue: M 260 - end of helix removed outlier: 3.658A pdb=" N LEU M 264 " --> pdb=" O PHE M 261 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N TRP M 267 " --> pdb=" O LEU M 264 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLY M 268 " --> pdb=" O SER M 265 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N MET M 269 " --> pdb=" O LEU M 266 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N THR M 272 " --> pdb=" O MET M 269 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER M 273 " --> pdb=" O ILE M 270 " (cutoff:3.500A) Processing helix chain 'M' and resid 282 through 303 removed outlier: 3.883A pdb=" N LEU M 296 " --> pdb=" O SER M 292 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL M 297 " --> pdb=" O HIS M 293 " (cutoff:3.500A) Processing helix chain 'M' and resid 306 through 337 removed outlier: 3.697A pdb=" N ARG M 336 " --> pdb=" O SER M 332 " (cutoff:3.500A) Processing helix chain 'M' and resid 348 through 351 No H-bonds generated for 'chain 'M' and resid 348 through 351' Processing helix chain 'M' and resid 353 through 366 Processing helix chain 'M' and resid 373 through 388 Processing helix chain 'M' and resid 390 through 415 removed outlier: 3.547A pdb=" N MET M 396 " --> pdb=" O ILE M 393 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR M 403 " --> pdb=" O MET M 400 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N TYR M 406 " --> pdb=" O THR M 403 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER M 407 " --> pdb=" O ALA M 404 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU M 408 " --> pdb=" O LEU M 405 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TYR M 409 " --> pdb=" O TYR M 406 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N MET M 410 " --> pdb=" O SER M 407 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N MET M 413 " --> pdb=" O MET M 410 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N THR M 414 " --> pdb=" O LEU M 411 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLN M 415 " --> pdb=" O ILE M 412 " (cutoff:3.500A) Processing helix chain 'M' and resid 431 through 454 removed outlier: 3.506A pdb=" N HIS M 440 " --> pdb=" O LEU M 436 " (cutoff:3.500A) Proline residue: M 443 - end of helix removed outlier: 4.193A pdb=" N THR M 448 " --> pdb=" O LEU M 444 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N LEU M 449 " --> pdb=" O LEU M 445 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ASN M 450 " --> pdb=" O LEU M 446 " (cutoff:3.500A) Proline residue: M 451 - end of helix removed outlier: 5.180A pdb=" N ILE M 454 " --> pdb=" O ASN M 450 " (cutoff:3.500A) Processing helix chain 'N' and resid 3 through 22 Processing helix chain 'N' and resid 26 through 44 removed outlier: 3.533A 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 79 Processing helix chain 'N' and resid 92 through 106 Processing helix chain 'N' and resid 113 through 121 removed outlier: 4.127A pdb=" N GLU N 117 " --> pdb=" O PHE N 113 " (cutoff:3.500A) Processing helix chain 'N' and resid 124 through 131 Processing helix chain 'N' and resid 133 through 148 removed outlier: 4.332A pdb=" N ALA N 137 " --> pdb=" O GLN N 134 " (cutoff:3.500A) Proline residue: N 138 - end of helix removed outlier: 3.540A pdb=" N ILE N 145 " --> pdb=" O LEU N 142 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N PHE N 146 " --> pdb=" O TYR N 143 " (cutoff:3.500A) Proline residue: N 147 - end of helix Processing helix chain 'N' and resid 151 through 171 removed outlier: 3.885A pdb=" N LEU N 170 " --> pdb=" O GLY N 166 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ASN N 171 " --> pdb=" O TRP N 167 " (cutoff:3.500A) Processing helix chain 'N' and resid 175 through 194 removed outlier: 3.744A pdb=" N TRP N 189 " --> pdb=" O ALA N 185 " (cutoff:3.500A) Processing helix chain 'N' and resid 198 through 222 removed outlier: 3.625A pdb=" N ASN N 222 " --> pdb=" O MET N 218 " (cutoff:3.500A) Processing helix chain 'N' and resid 227 through 235 removed outlier: 3.709A pdb=" N HIS N 232 " --> pdb=" O LEU N 228 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N THR N 233 " --> pdb=" O SER N 229 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N TRP N 234 " --> pdb=" O LEU N 230 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N ASN N 235 " --> pdb=" O SER N 231 " (cutoff:3.500A) Processing helix chain 'N' and resid 238 through 251 Processing helix chain 'N' and resid 258 through 273 Proline residue: N 262 - end of helix removed outlier: 3.521A pdb=" N ILE N 266 " --> pdb=" O LYS N 263 " (cutoff:3.500A) Processing helix chain 'N' and resid 277 through 300 removed outlier: 3.669A pdb=" N LEU N 287 " --> pdb=" O ALA N 283 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N LEU N 288 " --> pdb=" O ILE N 284 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ASN N 289 " --> pdb=" O THR N 285 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LEU N 296 " --> pdb=" O PHE N 292 " (cutoff:3.500A) Processing helix chain 'N' and resid 309 through 316 Processing helix chain 'N' and resid 326 through 332 Processing helix chain 'N' and resid 337 through 346 Proline residue: N 341 - end of helix Processing helix chain 'O' and resid 5 through 9 Processing helix chain 'O' and resid 14 through 16 No H-bonds generated for 'chain 'O' and resid 14 through 16' Processing helix chain 'O' and resid 35 through 46 Processing helix chain 'O' and resid 58 through 62 removed outlier: 3.549A pdb=" N THR O 62 " --> pdb=" O TYR O 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 58 through 62' Processing helix chain 'O' and resid 71 through 74 Processing helix chain 'O' and resid 79 through 84 Processing helix chain 'O' and resid 92 through 118 Processing helix chain 'O' and resid 131 through 140 Processing helix chain 'O' and resid 146 through 157 Processing helix chain 'O' and resid 160 through 162 No H-bonds generated for 'chain 'O' and resid 160 through 162' Processing helix chain 'O' and resid 176 through 186 Processing helix chain 'O' and resid 190 through 193 Processing helix chain 'O' and resid 196 through 216 removed outlier: 5.215A pdb=" N LEU O 211 " --> pdb=" O LYS O 207 " (cutoff:3.500A) Proline residue: O 212 - end of helix removed outlier: 3.580A pdb=" N GLU O 216 " --> pdb=" O PRO O 212 " (cutoff:3.500A) Processing helix chain 'O' and resid 225 through 229 Processing helix chain 'O' and resid 231 through 240 removed outlier: 3.518A pdb=" N TYR O 240 " --> pdb=" O GLU O 236 " (cutoff:3.500A) Processing helix chain 'O' and resid 247 through 250 Processing helix chain 'O' and resid 253 through 263 Processing helix chain 'O' and resid 266 through 269 No H-bonds generated for 'chain 'O' and resid 266 through 269' Processing helix chain 'O' and resid 271 through 274 removed outlier: 3.777A pdb=" N SER O 274 " --> pdb=" O ASN O 271 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 271 through 274' Processing helix chain 'O' and resid 286 through 298 Processing helix chain 'O' and resid 310 through 312 No H-bonds generated for 'chain 'O' and resid 310 through 312' Processing helix chain 'O' and resid 317 through 319 No H-bonds generated for 'chain 'O' and resid 317 through 319' Processing helix chain 'P' and resid 3 through 5 No H-bonds generated for 'chain 'P' and resid 3 through 5' Processing helix chain 'P' and resid 29 through 40 removed outlier: 4.096A pdb=" N TYR P 33 " --> pdb=" O PHE P 29 " (cutoff:3.500A) Processing helix chain 'P' and resid 53 through 62 removed outlier: 5.226A 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 79 through 85 removed outlier: 3.804A pdb=" N ALA P 84 " --> pdb=" O SER P 80 " (cutoff:3.500A) Processing helix chain 'P' and resid 106 through 110 Processing helix chain 'P' and resid 112 through 124 Processing helix chain 'P' and resid 144 through 159 Processing helix chain 'P' and resid 179 through 188 removed outlier: 3.514A pdb=" N ILE P 185 " --> pdb=" O TYR P 181 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ARG P 186 " --> pdb=" O PHE P 182 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N TRP P 187 " --> pdb=" O ALA P 183 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N PHE P 188 " --> pdb=" O ASN P 184 " (cutoff:3.500A) Processing helix chain 'P' and resid 194 through 197 Processing helix chain 'P' and resid 207 through 219 removed outlier: 3.505A pdb=" N LYS P 219 " --> pdb=" O ILE P 215 " (cutoff:3.500A) Processing helix chain 'P' and resid 221 through 223 No H-bonds generated for 'chain 'P' and resid 221 through 223' Processing helix chain 'P' and resid 238 through 249 Processing helix chain 'P' and resid 260 through 272 removed outlier: 3.600A pdb=" N GLY P 267 " --> pdb=" O TYR P 263 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ILE P 272 " --> pdb=" O ARG P 268 " (cutoff:3.500A) Processing helix chain 'P' and resid 281 through 287 Processing helix chain 'P' and resid 300 through 303 Processing helix chain 'P' and resid 310 through 321 removed outlier: 5.034A pdb=" N ILE P 315 " --> pdb=" O GLU P 311 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N GLU P 316 " --> pdb=" O LEU P 312 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL P 317 " --> pdb=" O LYS P 313 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N ARG P 320 " --> pdb=" O GLU P 316 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N HIS P 321 " --> pdb=" O VAL P 317 " (cutoff:3.500A) Processing helix chain 'P' and resid 324 through 326 No H-bonds generated for 'chain 'P' and resid 324 through 326' Processing helix chain 'P' and resid 331 through 333 No H-bonds generated for 'chain 'P' and resid 331 through 333' Processing helix chain 'Q' and resid 20 through 22 No H-bonds generated for 'chain 'Q' and resid 20 through 22' Processing helix chain 'Q' and resid 27 through 31 removed outlier: 3.911A pdb=" N LYS Q 31 " --> pdb=" O GLU Q 28 " (cutoff:3.500A) Processing helix chain 'Q' and resid 89 through 99 Processing helix chain 'Q' and resid 118 through 122 Processing helix chain 'R' and resid 23 through 28 Processing helix chain 'R' and resid 40 through 46 removed outlier: 3.663A pdb=" N ALA R 45 " --> pdb=" O ILE R 41 " (cutoff:3.500A) removed outlier: 3.517A 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: 5.172A pdb=" N GLY S 31 " --> pdb=" O GLY S 28 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ARG S 39 " --> pdb=" O ILE S 36 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N TYR S 40 " --> pdb=" O GLU S 37 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N VAL S 41 " --> pdb=" O LYS S 38 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLU S 42 " --> pdb=" O ARG S 39 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LYS S 44 " --> pdb=" O VAL S 41 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS S 45 " --> pdb=" O GLU S 42 " (cutoff:3.500A) Processing helix chain 'S' and resid 69 through 71 No H-bonds generated for 'chain 'S' and resid 69 through 71' Processing helix chain 'S' and resid 83 through 94 Processing helix chain 'T' and resid 8 through 21 removed outlier: 3.592A pdb=" N LYS T 12 " --> pdb=" O LEU T 8 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASP T 13 " --> pdb=" O GLU T 9 " (cutoff:3.500A) Processing helix chain 'T' and resid 44A through 58 Processing helix chain 'T' and resid 64 through 67 No H-bonds generated for 'chain 'T' and resid 64 through 67' Processing helix chain 'T' and resid 73 through 81 Processing helix chain 'U' and resid 8 through 21 Processing helix chain 'U' and resid 44A through 58 Processing helix chain 'U' and resid 64 through 69 removed outlier: 4.882A pdb=" N LYS U 69 " --> pdb=" O ILE U 65 " (cutoff:3.500A) Processing helix chain 'U' and resid 73 through 83 Processing helix chain 'V' and resid 19 through 36 removed outlier: 4.276A 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: 3.741A pdb=" N GLN V 95 " --> pdb=" O ARG V 91 " (cutoff:3.500A) Processing helix chain 'W' and resid 25 through 49 Proline residue: W 44 - end of helix Processing helix chain 'W' and resid 56 through 70 removed outlier: 4.289A pdb=" N ASN W 70 " --> pdb=" O MET W 66 " (cutoff:3.500A) Processing helix chain 'W' and resid 76 through 94 removed outlier: 3.500A pdb=" N THR W 93 " --> pdb=" O GLU W 89 " (cutoff:3.500A) Processing helix chain 'W' and resid 100 through 106 removed outlier: 4.590A pdb=" N PHE W 106 " --> pdb=" O HIS W 102 " (cutoff:3.500A) Processing helix chain 'W' and resid 118 through 124 Processing helix chain 'X' and resid 9 through 12 No H-bonds generated for 'chain 'X' and resid 9 through 12' Processing helix chain 'X' and resid 21 through 26 Processing helix chain 'X' and resid 28 through 34 Processing helix chain 'X' and resid 36 through 49 Processing helix chain 'X' and resid 52 through 76 removed outlier: 3.929A pdb=" N LEU X 56 " --> pdb=" O ARG X 53 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N GLU X 57 " --> pdb=" O ARG X 54 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL X 62 " --> pdb=" O GLY X 59 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLN X 64 " --> pdb=" O LEU X 61 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N CYS X 65 " --> pdb=" O VAL X 62 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU X 67 " --> pdb=" O GLN X 64 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLU X 68 " --> pdb=" O CYS X 65 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE X 73 " --> pdb=" O PHE X 70 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LYS X 74 " --> pdb=" O ARG X 71 " (cutoff:3.500A) Processing helix chain 'X' and resid 78 through 90 Processing helix chain 'X' and resid 100 through 113 Processing helix chain 'Y' and resid 3 through 10 Processing helix chain 'Y' and resid 17 through 42 Processing helix chain 'Y' and resid 48 through 80 Processing helix chain 'Y' and resid 86 through 104 Processing helix chain 'Y' and resid 107 through 130 Processing helix chain 'Z' and resid 32 through 97 Proline residue: Z 73 - end of helix Processing helix chain 'Z' and resid 121 through 124 No H-bonds generated for 'chain 'Z' and resid 121 through 124' Processing helix chain 'Z' and resid 130 through 142 removed outlier: 5.893A pdb=" N PHE Z 140 " --> pdb=" O ALA Z 136 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N ILE Z 141 " --> pdb=" O THR Z 137 " (cutoff:3.500A) Processing helix chain 'a' and resid 2 through 31 Proline residue: a 7 - end of helix removed outlier: 3.739A pdb=" N VAL a 11 " --> pdb=" O GLY a 8 " (cutoff:3.500A) Proline residue: a 19 - end of helix removed outlier: 3.588A pdb=" N ALA a 22 " --> pdb=" O PRO a 19 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N THR a 23 " --> pdb=" O GLY a 20 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE a 26 " --> pdb=" O THR a 23 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N HIS a 27 " --> pdb=" O ALA a 24 " (cutoff:3.500A) Processing helix chain 'a' and resid 42 through 55 Processing helix chain 'a' and resid 66 through 68 No H-bonds generated for 'chain 'a' and resid 66 through 68' Processing helix chain 'b' and resid 2 through 14 Processing helix chain 'b' and resid 16 through 34 Proline residue: b 32 - end of helix Processing helix chain 'b' and resid 38 through 47 removed outlier: 4.044A pdb=" N LEU b 42 " --> pdb=" O THR b 38 " (cutoff:3.500A) Processing helix chain 'b' and resid 78 through 81 No H-bonds generated for 'chain 'b' and resid 78 through 81' Processing helix chain 'c' and resid 14 through 45 removed outlier: 3.567A pdb=" N LEU c 40 " --> pdb=" O ASN c 36 " (cutoff:3.500A) Processing helix chain 'd' and resid 16 through 20 Processing helix chain 'd' and resid 29 through 49 Processing helix chain 'd' and resid 58 through 96 removed outlier: 3.660A pdb=" N TYR d 74 " --> pdb=" O PHE d 70 " (cutoff:3.500A) Processing helix chain 'd' and resid 98 through 100 No H-bonds generated for 'chain 'd' and resid 98 through 100' Processing helix chain 'e' and resid 5 through 9 Processing helix chain 'e' and resid 15 through 17 No H-bonds generated for 'chain 'e' and resid 15 through 17' Processing helix chain 'e' and resid 25 through 27 No H-bonds generated for 'chain 'e' and resid 25 through 27' Processing helix chain 'e' and resid 33 through 43 Processing helix chain 'e' and resid 48 through 54 removed outlier: 4.149A pdb=" N LYS e 53 " --> pdb=" O ILE e 49 " (cutoff:3.500A) Processing helix chain 'e' and resid 56 through 67 Processing helix chain 'e' and resid 69 through 87 Processing helix chain 'f' and resid 12 through 34 removed outlier: 4.897A pdb=" N VAL f 16 " --> pdb=" O HIS f 13 " (cutoff:3.500A) Proline residue: f 17 - end of helix Processing helix chain 'g' and resid 37 through 40 No H-bonds generated for 'chain 'g' and resid 37 through 40' Processing helix chain 'g' and resid 51 through 66 Processing helix chain 'g' and resid 69 through 78 Processing helix chain 'g' and resid 83 through 102 removed outlier: 3.727A pdb=" N GLN g 86 " --> pdb=" O TYR g 83 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N GLU g 87 " --> pdb=" O ARG g 84 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N TRP g 88 " --> pdb=" O MET g 85 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA g 89 " --> pdb=" O GLN g 86 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ARG g 100 " --> pdb=" O VAL g 97 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLU g 101 " --> pdb=" O LYS g 98 " (cutoff:3.500A) Processing helix chain 'g' and resid 115 through 117 No H-bonds generated for 'chain 'g' and resid 115 through 117' Processing helix chain 'h' and resid 16 through 46 removed outlier: 3.997A pdb=" N THR h 32 " --> pdb=" O TYR h 28 " (cutoff:3.500A) Proline residue: h 35 - end of helix Processing helix chain 'h' and resid 63 through 66 removed outlier: 3.646A pdb=" N TYR h 66 " --> pdb=" O HIS h 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 63 through 66' Processing helix chain 'h' and resid 70 through 79 Processing helix chain 'h' and resid 83 through 117 Processing helix chain 'h' and resid 130 through 132 No H-bonds generated for 'chain 'h' and resid 130 through 132' Processing helix chain 'i' and resid 5 through 25 Processing helix chain 'i' and resid 59 through 73 Processing helix chain 'i' and resid 75 through 87 Processing helix chain 'j' and resid 19 through 48 removed outlier: 7.529A pdb=" N ASP j 45 " --> pdb=" O TRP j 41 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ALA j 46 " --> pdb=" O HIS j 42 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N VAL j 47 " --> pdb=" O ASP j 43 " (cutoff:3.500A) Processing helix chain 'j' and resid 56 through 58 No H-bonds generated for 'chain 'j' and resid 56 through 58' Processing helix chain 'j' and resid 61 through 64 No H-bonds generated for 'chain 'j' and resid 61 through 64' Processing helix chain 'k' and resid 18 through 20 No H-bonds generated for 'chain 'k' and resid 18 through 20' Processing helix chain 'k' and resid 27 through 38 removed outlier: 3.606A pdb=" N ARG k 38 " --> pdb=" O LYS k 34 " (cutoff:3.500A) Processing helix chain 'k' and resid 45 through 52 removed outlier: 4.937A pdb=" N TRP k 50 " --> pdb=" O ASN k 47 " (cutoff:3.500A) Processing helix chain 'k' and resid 54 through 56 No H-bonds generated for 'chain 'k' and resid 54 through 56' Processing helix chain 'k' and resid 62 through 66 Processing helix chain 'k' and resid 70 through 90 Processing helix chain 'l' and resid 6 through 8 No H-bonds generated for 'chain 'l' and resid 6 through 8' Processing helix chain 'l' and resid 17 through 26 Processing helix chain 'l' and resid 55 through 57 No H-bonds generated for 'chain 'l' and resid 55 through 57' Processing helix chain 'l' and resid 81 through 84 No H-bonds generated for 'chain 'l' and resid 81 through 84' Processing helix chain 'l' and resid 98 through 121 Processing helix chain 'l' and resid 134 through 138 Processing helix chain 'm' and resid 15 through 17 No H-bonds generated for 'chain 'm' and resid 15 through 17' Processing helix chain 'm' and resid 19 through 21 No H-bonds generated for 'chain 'm' and resid 19 through 21' Processing helix chain 'm' and resid 26 through 50 removed outlier: 3.837A 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 94 through 116 Processing helix chain 'n' and resid 11 through 30 Processing helix chain 'n' and resid 33 through 49 Processing helix chain 'n' and resid 56 through 73 Processing helix chain 'n' and resid 94 through 96 No H-bonds generated for 'chain 'n' and resid 94 through 96' Processing helix chain 'n' and resid 100 through 105 Processing helix chain 'n' and resid 108 through 140 removed outlier: 3.892A pdb=" N MET n 113 " --> pdb=" O SER n 109 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N TYR n 114 " --> pdb=" O GLU n 110 " (cutoff:3.500A) Proline residue: n 115 - end of helix removed outlier: 4.760A pdb=" N GLU n 133 " --> pdb=" O ARG n 129 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N ARG n 134 " --> pdb=" O GLU n 130 " (cutoff:3.500A) Processing helix chain 'n' and resid 167 through 170 No H-bonds generated for 'chain 'n' and resid 167 through 170' Processing helix chain 'o' and resid 2 through 9 Processing helix chain 'o' and resid 42 through 47 Processing helix chain 'o' and resid 52 through 54 No H-bonds generated for 'chain 'o' and resid 52 through 54' Processing helix chain 'o' and resid 59 through 71 Processing helix chain 'o' and resid 80 through 120 Processing helix chain 'p' and resid 28 through 39 Processing helix chain 'p' and resid 41 through 56 Processing helix chain 'p' and resid 73 through 75 No H-bonds generated for 'chain 'p' and resid 73 through 75' Processing helix chain 'p' and resid 81 through 123 removed outlier: 3.757A pdb=" N GLU p 86 " --> pdb=" O LEU p 82 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLY p 117 " --> pdb=" O GLN p 113 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N GLU p 118 " --> pdb=" O GLN p 114 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N SER p 119 " --> pdb=" O ARG p 115 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N HIS p 120 " --> pdb=" O GLU p 116 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N ARG p 121 " --> pdb=" O GLY p 117 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N GLN p 122 " --> pdb=" O GLU p 118 " (cutoff:3.500A) Processing helix chain 'p' and resid 125 through 142 Processing helix chain 'p' and resid 151 through 171 Processing helix chain 'q' and resid 2 through 16 removed outlier: 3.604A pdb=" N LEU q 11 " --> pdb=" O LEU q 7 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL q 14 " --> pdb=" O GLY q 10 " (cutoff:3.500A) Processing helix chain 'q' and resid 20 through 30 Processing helix chain 'q' and resid 79 through 81 No H-bonds generated for 'chain 'q' and resid 79 through 81' Processing helix chain 'q' and resid 84 through 90 removed outlier: 4.050A 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 58 through 61 No H-bonds generated for 'chain 'r' and resid 58 through 61' Processing helix chain 's' and resid 42 through 45 Processing helix chain 's' and resid 50 through 60 removed outlier: 4.612A pdb=" N LYS s 60 " --> pdb=" O LEU s 56 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 85 through 89 removed outlier: 6.535A pdb=" N TYR B 112 " --> pdb=" O MET B 86 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N VAL B 88 " --> pdb=" O TYR B 112 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL B 114 " --> pdb=" O VAL B 88 " (cutoff:3.500A) removed outlier: 6.388A 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: 6.706A pdb=" N ASN C 95 " --> pdb=" O ALA C 76 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N LEU C 78 " --> pdb=" O VAL C 93 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N VAL C 93 " --> pdb=" O LEU C 78 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ALA C 80 " --> pdb=" O GLU C 91 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N GLU C 91 " --> pdb=" O ALA C 80 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N LEU C 48 " --> pdb=" O ARG C 104 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N TYR C 110 " --> pdb=" O ILE C 52 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 172 through 177 Processing sheet with id= D, first strand: chain 'D' and resid 47 through 51 removed outlier: 6.244A pdb=" N SER D 69 " --> pdb=" O VAL D 73 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N VAL D 73 " --> pdb=" O SER D 69 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'D' and resid 361 through 369 Processing sheet with id= F, first strand: chain 'E' and resid 137 through 142 removed outlier: 6.598A pdb=" N TYR E 98 " --> pdb=" O THR E 138 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N ILE E 140 " --> pdb=" O TYR E 98 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ILE E 100 " --> pdb=" O ILE E 140 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N VAL E 142 " --> pdb=" O ILE E 100 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N VAL E 102 " --> pdb=" O VAL E 142 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'F' and resid 220 through 224 removed outlier: 7.073A pdb=" N TYR F 92 " --> pdb=" O THR F 221 " (cutoff:3.500A) removed outlier: 8.243A pdb=" N ALA F 223 " --> pdb=" O TYR F 92 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N VAL F 94 " --> pdb=" O ALA F 223 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ALA F 133 " --> pdb=" O LEU F 93 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N VAL F 95 " --> pdb=" O ALA F 133 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N TYR F 135 " --> pdb=" O VAL F 95 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N ALA F 97 " --> pdb=" O TYR F 135 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N TYR F 137 " --> pdb=" O ALA F 97 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ASP F 174 " --> pdb=" O ALA F 134 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N ILE F 136 " --> pdb=" O ASP F 174 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N PHE F 176 " --> pdb=" O ILE F 136 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N ILE F 138 " --> pdb=" O PHE F 176 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N VAL F 178 " --> pdb=" O ILE F 138 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'F' and resid 266 through 271 Processing sheet with id= I, first strand: chain 'G' and resid 9 through 13 Processing sheet with id= J, first strand: chain 'G' and resid 146 through 148 Processing sheet with id= K, first strand: chain 'G' and resid 173 through 175 Processing sheet with id= L, first strand: chain 'G' and resid 223 through 228 removed outlier: 6.333A pdb=" N ARG G 243 " --> pdb=" O VAL G 247 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N VAL G 247 " --> pdb=" O ARG G 243 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'G' and resid 283 through 285 Processing sheet with id= N, first strand: chain 'G' and resid 343 through 345 removed outlier: 8.367A pdb=" N CYS G 344 " --> pdb=" O VAL G 315 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N ALA G 317 " --> pdb=" O CYS G 344 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N MET G 521 " --> pdb=" O ALA G 316 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N ILE G 318 " --> pdb=" O MET G 521 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N PHE G 523 " --> pdb=" O ILE G 318 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N PHE G 542 " --> pdb=" O LEU G 522 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N LEU G 524 " --> pdb=" O PHE G 542 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N VAL G 544 " --> pdb=" O LEU G 524 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N VAL G 559 " --> pdb=" O TYR G 545 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N GLY G 547 " --> pdb=" O VAL G 559 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N LEU G 561 " --> pdb=" O GLY G 547 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'G' and resid 490 through 493 removed outlier: 8.174A pdb=" N ASN G 491 " --> pdb=" O PRO G 449 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N VAL G 451 " --> pdb=" O ASN G 491 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N LEU G 493 " --> pdb=" O VAL G 451 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N LEU G 453 " --> pdb=" O LEU G 493 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N VAL G 376 " --> pdb=" O MET G 450 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N ILE G 452 " --> pdb=" O VAL G 376 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N LEU G 378 " --> pdb=" O ILE G 452 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N GLY G 454 " --> pdb=" O LEU G 378 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N VAL G 380 " --> pdb=" O GLY G 454 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N LYS G 405 " --> pdb=" O VAL G 377 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N LEU G 379 " --> pdb=" O LYS G 405 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ALA G 407 " --> pdb=" O LEU G 379 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ASP G 420 " --> pdb=" O LEU G 408 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'G' and resid 572 through 574 Processing sheet with id= Q, first strand: chain 'I' and resid 65 through 67 Processing sheet with id= R, first strand: chain 'I' and resid 92 through 98 removed outlier: 6.085A pdb=" N GLU I 97 " --> pdb=" O THR I 106 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N THR I 106 " --> pdb=" O GLU I 97 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'J' and resid 112 through 115 Processing sheet with id= T, first strand: chain 'L' and resid 69 through 71 Processing sheet with id= U, first strand: chain 'L' and resid 61 through 67 removed outlier: 6.756A pdb=" N LEU L 78 " --> pdb=" O ASN L 65 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'O' and resid 219 through 223 removed outlier: 6.256A pdb=" N VAL O 122 " --> pdb=" O ILE O 25 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N VAL O 27 " --> pdb=" O VAL O 122 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N LEU O 124 " --> pdb=" O VAL O 27 " (cutoff:3.500A) removed outlier: 8.605A pdb=" N GLY O 29 " --> pdb=" O LEU O 124 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N LYS O 49 " --> pdb=" O VAL O 123 " (cutoff:3.500A) removed outlier: 8.309A pdb=" N GLU O 125 " --> pdb=" O LYS O 49 " (cutoff:3.500A) removed outlier: 8.427A pdb=" N PHE O 51 " --> pdb=" O GLU O 125 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'P' and resid 227 through 230 removed outlier: 6.514A pdb=" N ILE P 165 " --> pdb=" O PHE P 228 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N PHE P 230 " --> pdb=" O ILE P 165 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N LYS P 167 " --> pdb=" O PHE P 230 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N GLN P 44 " --> pdb=" O ALA P 21 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N VAL P 23 " --> pdb=" O GLN P 44 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ILE P 46 " --> pdb=" O VAL P 23 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'P' and resid 191 through 193 Processing sheet with id= Y, first strand: chain 'Q' and resid 102 through 105 Processing sheet with id= Z, first strand: chain 'Q' and resid 64 through 66 Processing sheet with id= AA, first strand: chain 'R' and resid 50 through 52 Processing sheet with id= AB, first strand: chain 'R' and resid 56 through 59 Processing sheet with id= AC, first strand: chain 'S' and resid 51 through 56 removed outlier: 3.561A pdb=" N LEU S 22 " --> pdb=" O ARG S 55 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ARG S 67 " --> pdb=" O ARG S 16 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ILE S 18 " --> pdb=" O TRP S 65 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N TRP S 65 " --> pdb=" O ILE S 18 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ILE S 20 " --> pdb=" O LYS S 63 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N LYS S 63 " --> pdb=" O ILE S 20 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'q' and resid 60 through 63 removed outlier: 6.515A pdb=" N GLU q 50 " --> pdb=" O LEU q 38 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N LEU q 38 " --> pdb=" O GLU q 50 " (cutoff:3.500A) 2886 hydrogen bonds defined for protein. 7764 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: 27.44 Time building geometry restraints manager: 23.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.40: 27834 1.40 - 1.63: 40411 1.63 - 1.85: 826 1.85 - 2.08: 0 2.08 - 2.30: 80 Bond restraints: 69151 Sorted by residual: bond pdb=" C5 GTP O 401 " pdb=" N7 GTP O 401 " ideal model delta sigma weight residual 1.350 1.523 -0.173 2.00e-02 2.50e+03 7.45e+01 bond pdb=" C6 GTP O 401 " pdb=" O6 GTP O 401 " ideal model delta sigma weight residual 1.230 1.396 -0.166 2.00e-02 2.50e+03 6.86e+01 bond pdb=" CB7 CDL q 201 " pdb=" OB8 CDL q 201 " ideal model delta sigma weight residual 1.334 1.403 -0.069 1.10e-02 8.26e+03 3.91e+01 bond pdb=" C 2MR D 85 " pdb=" O 2MR D 85 " ideal model delta sigma weight residual 1.231 1.352 -0.121 2.00e-02 2.50e+03 3.66e+01 bond pdb=" CA7 CDL J 701 " pdb=" OA8 CDL J 701 " ideal model delta sigma weight residual 1.334 1.399 -0.065 1.10e-02 8.26e+03 3.54e+01 ... (remaining 69146 not shown) Histogram of bond angle deviations from ideal: 72.56 - 84.87: 76 84.87 - 97.18: 2 97.18 - 109.49: 7530 109.49 - 121.80: 72703 121.80 - 134.11: 13267 Bond angle restraints: 93578 Sorted by residual: angle pdb=" O 2MR D 85 " pdb=" C 2MR D 85 " pdb=" N GLY D 86 " ideal model delta sigma weight residual 123.00 97.15 25.85 1.60e+00 3.91e-01 2.61e+02 angle pdb=" C51 CDL J 701 " pdb=" CB5 CDL J 701 " pdb=" OB6 CDL J 701 " ideal model delta sigma weight residual 111.33 121.58 -10.25 1.32e+00 5.72e-01 6.01e+01 angle pdb=" C51 CDL h1001 " pdb=" CB5 CDL h1001 " pdb=" OB6 CDL h1001 " ideal model delta sigma weight residual 111.33 120.91 -9.58 1.32e+00 5.72e-01 5.26e+01 angle pdb=" C11 CDL h1001 " pdb=" CA5 CDL h1001 " pdb=" OA6 CDL h1001 " ideal model delta sigma weight residual 111.33 120.37 -9.04 1.32e+00 5.72e-01 4.68e+01 angle pdb=" C11 CDL J 701 " pdb=" CA5 CDL J 701 " pdb=" OA6 CDL J 701 " ideal model delta sigma weight residual 111.33 120.15 -8.82 1.32e+00 5.72e-01 4.45e+01 ... (remaining 93573 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.56: 40900 34.56 - 69.12: 1082 69.12 - 103.68: 139 103.68 - 138.24: 24 138.24 - 172.79: 6 Dihedral angle restraints: 42151 sinusoidal: 18285 harmonic: 23866 Sorted by residual: dihedral pdb=" C10 FMN F 501 " pdb=" C1' FMN F 501 " pdb=" N10 FMN F 501 " pdb=" C2' FMN F 501 " ideal model delta sinusoidal sigma weight residual 257.59 84.80 172.79 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" O3B GTP O 401 " pdb=" O3A GTP O 401 " pdb=" PB GTP O 401 " pdb=" PA GTP O 401 " ideal model delta sinusoidal sigma weight residual -68.92 84.02 -152.94 1 2.00e+01 2.50e-03 4.54e+01 dihedral pdb=" O5' GTP O 401 " pdb=" O3A GTP O 401 " pdb=" PA GTP O 401 " pdb=" PB GTP O 401 " ideal model delta sinusoidal sigma weight residual 274.12 124.58 149.55 1 2.00e+01 2.50e-03 4.47e+01 ... (remaining 42148 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.264: 10194 4.264 - 8.528: 0 8.528 - 12.792: 0 12.792 - 17.057: 0 17.057 - 21.321: 16 Chirality restraints: 10210 Sorted by residual: chirality pdb="FE1 SF4 I 202 " pdb=" S2 SF4 I 202 " pdb=" S3 SF4 I 202 " pdb=" S4 SF4 I 202 " both_signs ideal model delta sigma weight residual False -10.55 10.77 -21.32 2.00e-01 2.50e+01 1.14e+04 chirality pdb="FE4 SF4 I 202 " pdb=" S1 SF4 I 202 " pdb=" S2 SF4 I 202 " pdb=" S3 SF4 I 202 " both_signs ideal model delta sigma weight residual False 10.55 -10.75 21.30 2.00e-01 2.50e+01 1.13e+04 chirality pdb="FE2 SF4 G 802 " pdb=" S1 SF4 G 802 " pdb=" S3 SF4 G 802 " pdb=" S4 SF4 G 802 " both_signs ideal model delta sigma weight residual False 10.55 -10.73 21.28 2.00e-01 2.50e+01 1.13e+04 ... (remaining 10207 not shown) Planarity restraints: 11671 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA 2MR D 85 " 0.123 2.00e-02 2.50e+03 2.07e-01 4.27e+02 pdb=" C 2MR D 85 " -0.358 2.00e-02 2.50e+03 pdb=" O 2MR D 85 " 0.111 2.00e-02 2.50e+03 pdb=" N GLY D 86 " 0.124 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 125 " 0.049 2.00e-02 2.50e+03 3.71e-02 2.75e+01 pdb=" CG TYR B 125 " -0.089 2.00e-02 2.50e+03 pdb=" CD1 TYR B 125 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TYR B 125 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR B 125 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR B 125 " 0.012 2.00e-02 2.50e+03 pdb=" CZ TYR B 125 " 0.007 2.00e-02 2.50e+03 pdb=" OH TYR B 125 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE K 53 " -0.021 2.00e-02 2.50e+03 2.68e-02 1.26e+01 pdb=" CG PHE K 53 " 0.060 2.00e-02 2.50e+03 pdb=" CD1 PHE K 53 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 PHE K 53 " -0.012 2.00e-02 2.50e+03 pdb=" CE1 PHE K 53 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 PHE K 53 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE K 53 " -0.006 2.00e-02 2.50e+03 ... (remaining 11668 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.55: 607 2.55 - 3.20: 64366 3.20 - 3.84: 142801 3.84 - 4.49: 208675 4.49 - 5.14: 317844 Nonbonded interactions: 734293 Sorted by model distance: nonbonded pdb=" OD1 ASN p 58 " pdb=" O6B LMT h1002 " model vdw 1.899 2.440 nonbonded pdb=" OE1 GLU H 24 " pdb=" OH TYR H 228 " model vdw 1.927 2.440 nonbonded pdb=" O HOH B 348 " pdb=" O HOH I 373 " model vdw 1.940 2.440 nonbonded pdb=" OD1 ASN X 139 " pdb=" O HOH X 201 " model vdw 1.940 2.440 nonbonded pdb=" O HOH D 573 " pdb=" O HOH D 611 " model vdw 1.964 2.440 ... (remaining 734288 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'T' selection = (chain 'U' and (resid 7 through 82 or resid 101)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 14.990 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: 0.070 Extract box with map and model: 57.990 Check model and map are aligned: 0.770 Set scattering table: 0.460 Process input model: 168.040 Find NCS groups from input model: 2.530 Set up NCS constraints: 0.310 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:12.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 257.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 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 0.173 69151 Z= 0.471 Angle : 0.795 25.851 93578 Z= 0.370 Chirality : 0.842 21.321 10210 Planarity : 0.004 0.207 11671 Dihedral : 16.086 172.794 26750 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.54 % Favored : 97.44 % Rotamer: Outliers : 0.01 % Allowed : 0.20 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.09), residues: 8077 helix: 0.54 (0.08), residues: 4274 sheet: -0.20 (0.24), residues: 423 loop : 0.15 (0.11), residues: 3380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP P 73 HIS 0.008 0.001 HIS C 160 PHE 0.060 0.002 PHE K 53 TYR 0.089 0.002 TYR B 125 ARG 0.016 0.001 ARG p 14 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16154 Ramachandran restraints generated. 8077 Oldfield, 0 Emsley, 8077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16154 Ramachandran restraints generated. 8077 Oldfield, 0 Emsley, 8077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1063 residues out of total 7140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1062 time to evaluate : 6.170 Fit side-chains revert: symmetry clash REVERT: D 429 ASP cc_start: 0.8238 (m-30) cc_final: 0.7847 (m-30) REVERT: E 52 ASP cc_start: 0.8692 (t70) cc_final: 0.8453 (t70) REVERT: G 311 GLN cc_start: 0.7909 (mt0) cc_final: 0.7627 (mt0) REVERT: G 475 GLN cc_start: 0.7924 (tm-30) cc_final: 0.7696 (tp40) REVERT: L 572 LYS cc_start: 0.7894 (mttp) cc_final: 0.7662 (mptt) REVERT: P 119 GLN cc_start: 0.8277 (tm-30) cc_final: 0.8059 (tp40) REVERT: P 188 PHE cc_start: 0.8218 (m-80) cc_final: 0.7854 (m-80) REVERT: P 268 ARG cc_start: 0.6886 (tpt170) cc_final: 0.6681 (ttt90) REVERT: T 19 LEU cc_start: 0.8457 (mm) cc_final: 0.8238 (mm) REVERT: Y 84 ASP cc_start: 0.6817 (p0) cc_final: 0.6431 (p0) REVERT: Y 128 GLN cc_start: 0.8085 (pp30) cc_final: 0.7876 (pp30) REVERT: f 18 MET cc_start: 0.7230 (ttp) cc_final: 0.6962 (ttp) REVERT: i 124 ASP cc_start: 0.6166 (m-30) cc_final: 0.5665 (t70) REVERT: r 17 ARG cc_start: 0.7889 (mmt-90) cc_final: 0.7524 (mmm160) REVERT: s 34 ASP cc_start: 0.7720 (t0) cc_final: 0.7293 (t0) outliers start: 1 outliers final: 1 residues processed: 1063 average time/residue: 1.7671 time to fit residues: 2366.1069 Evaluate side-chains 912 residues out of total 7140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 911 time to evaluate : 6.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 44 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 800 random chunks: chunk 675 optimal weight: 6.9990 chunk 606 optimal weight: 10.0000 chunk 336 optimal weight: 3.9990 chunk 207 optimal weight: 9.9990 chunk 409 optimal weight: 0.9980 chunk 323 optimal weight: 0.8980 chunk 627 optimal weight: 0.0570 chunk 242 optimal weight: 5.9990 chunk 381 optimal weight: 0.9980 chunk 466 optimal weight: 0.0370 chunk 726 optimal weight: 9.9990 overall best weight: 0.5976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN D 114 ASN E 121 GLN F 257 ASN G 237 ASN G 402 ASN G 472 ASN M 82 HIS M 175 ASN N 316 GLN S 30 GLN S 92 ASN Y 128 GLN Z 85 GLN c 34 GLN c 46 ASN d 61 GLN e 69 GLN f 10 HIS l 136 ASN l 147 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.1205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.314 69151 Z= 0.423 Angle : 1.306 51.044 93578 Z= 0.838 Chirality : 0.251 6.512 10210 Planarity : 0.004 0.055 11671 Dihedral : 12.633 171.645 10586 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.46 % Favored : 98.53 % Rotamer: Outliers : 0.78 % Allowed : 5.79 % Favored : 93.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.09), residues: 8077 helix: 1.40 (0.08), residues: 4275 sheet: -0.08 (0.26), residues: 364 loop : 0.34 (0.11), residues: 3438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP j 38 HIS 0.006 0.001 HIS G 101 PHE 0.028 0.001 PHE N 292 TYR 0.038 0.001 TYR B 125 ARG 0.005 0.000 ARG R 92 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16154 Ramachandran restraints generated. 8077 Oldfield, 0 Emsley, 8077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16154 Ramachandran restraints generated. 8077 Oldfield, 0 Emsley, 8077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1057 residues out of total 7140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 1001 time to evaluate : 6.395 Fit side-chains revert: symmetry clash REVERT: G 311 GLN cc_start: 0.7802 (mt0) cc_final: 0.7524 (mt0) REVERT: H 8 MET cc_start: 0.8309 (OUTLIER) cc_final: 0.7993 (mmt) REVERT: L 411 MET cc_start: 0.7740 (mmp) cc_final: 0.7356 (mmp) REVERT: L 572 LYS cc_start: 0.7656 (mttp) cc_final: 0.7375 (mptt) REVERT: N 104 MET cc_start: 0.8681 (mtt) cc_final: 0.8467 (mtt) REVERT: P 170 GLU cc_start: 0.7476 (OUTLIER) cc_final: 0.7156 (mp0) REVERT: P 188 PHE cc_start: 0.8191 (m-80) cc_final: 0.7856 (m-80) REVERT: P 264 ARG cc_start: 0.7738 (mtp85) cc_final: 0.7490 (mtp85) REVERT: Y 43 LYS cc_start: 0.8122 (mtpp) cc_final: 0.7878 (mtmt) REVERT: Y 75 ILE cc_start: 0.7785 (mp) cc_final: 0.7578 (mp) REVERT: Y 84 ASP cc_start: 0.6626 (p0) cc_final: 0.6177 (p0) REVERT: e 90 LYS cc_start: 0.6668 (mmpt) cc_final: 0.6270 (mmtt) REVERT: f 47 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7087 (mp0) REVERT: i 124 ASP cc_start: 0.6030 (m-30) cc_final: 0.5628 (t70) REVERT: j 70 ASP cc_start: 0.7710 (OUTLIER) cc_final: 0.7481 (p0) REVERT: k 33 GLU cc_start: 0.7930 (OUTLIER) cc_final: 0.7591 (mm-30) REVERT: m 21 GLU cc_start: 0.6539 (mm-30) cc_final: 0.6334 (mm-30) REVERT: q 21 ARG cc_start: 0.6794 (ttt90) cc_final: 0.6543 (ttt180) REVERT: q 101 LYS cc_start: 0.8091 (OUTLIER) cc_final: 0.7817 (mmtt) REVERT: r 5 ARG cc_start: 0.7522 (mtm-85) cc_final: 0.7211 (mtm-85) REVERT: r 17 ARG cc_start: 0.7816 (mmt-90) cc_final: 0.7492 (mmm-85) outliers start: 56 outliers final: 8 residues processed: 1022 average time/residue: 1.7527 time to fit residues: 2265.8207 Evaluate side-chains 935 residues out of total 7140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 921 time to evaluate : 6.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 237 ASN Chi-restraints excluded: chain H residue 8 MET Chi-restraints excluded: chain L residue 500 LEU Chi-restraints excluded: chain M residue 126 LEU Chi-restraints excluded: chain P residue 170 GLU Chi-restraints excluded: chain P residue 195 SER Chi-restraints excluded: chain R residue 37 GLU Chi-restraints excluded: chain U residue 44 SER Chi-restraints excluded: chain X residue 13 LYS Chi-restraints excluded: chain f residue 47 GLU Chi-restraints excluded: chain j residue 70 ASP Chi-restraints excluded: chain k residue 33 GLU Chi-restraints excluded: chain q residue 53 LYS Chi-restraints excluded: chain q residue 101 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 800 random chunks: chunk 403 optimal weight: 2.9990 chunk 225 optimal weight: 3.9990 chunk 604 optimal weight: 8.9990 chunk 494 optimal weight: 2.9990 chunk 200 optimal weight: 0.6980 chunk 727 optimal weight: 10.0000 chunk 786 optimal weight: 4.9990 chunk 648 optimal weight: 10.0000 chunk 721 optimal weight: 10.0000 chunk 248 optimal weight: 6.9990 chunk 583 optimal weight: 2.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN ** D 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 257 ASN G 16 GLN ** G 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 441 GLN G 472 ASN G 475 GLN H 292 ASN M 304 GLN N 316 GLN S 75 ASN S 92 ASN T 74 GLN Y 7 GLN Y 128 GLN Z 85 GLN c 46 ASN f 10 HIS j 24 GLN k 32 GLN l 136 ASN l 147 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.1207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.252 69151 Z= 0.457 Angle : 1.307 50.510 93578 Z= 0.838 Chirality : 0.257 6.538 10210 Planarity : 0.004 0.056 11671 Dihedral : 11.821 171.108 10586 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.22 % Allowed : 7.45 % Favored : 91.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.09), residues: 8077 helix: 1.43 (0.08), residues: 4296 sheet: 0.00 (0.25), residues: 373 loop : 0.33 (0.11), residues: 3408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP n 71 HIS 0.007 0.001 HIS C 160 PHE 0.028 0.002 PHE M 122 TYR 0.040 0.002 TYR B 125 ARG 0.008 0.000 ARG k 41 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16154 Ramachandran restraints generated. 8077 Oldfield, 0 Emsley, 8077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16154 Ramachandran restraints generated. 8077 Oldfield, 0 Emsley, 8077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1016 residues out of total 7140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 929 time to evaluate : 6.117 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 425 GLU cc_start: 0.7204 (OUTLIER) cc_final: 0.6899 (mm-30) REVERT: F 427 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.8148 (mt-10) REVERT: G 311 GLN cc_start: 0.7796 (mt0) cc_final: 0.7511 (mt0) REVERT: G 490 MET cc_start: 0.8604 (tpt) cc_final: 0.8246 (tpt) REVERT: H 8 MET cc_start: 0.8346 (OUTLIER) cc_final: 0.8055 (mmt) REVERT: L 314 MET cc_start: 0.8678 (tpp) cc_final: 0.8448 (tpp) REVERT: L 411 MET cc_start: 0.7804 (mmp) cc_final: 0.7511 (mmp) REVERT: P 170 GLU cc_start: 0.7500 (OUTLIER) cc_final: 0.7207 (mp0) REVERT: Q 106 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7911 (mt-10) REVERT: X 108 GLU cc_start: 0.7489 (OUTLIER) cc_final: 0.6510 (mp0) REVERT: Y 2 LYS cc_start: 0.5982 (OUTLIER) cc_final: 0.4172 (tptp) REVERT: Y 43 LYS cc_start: 0.8200 (mtpp) cc_final: 0.7978 (mtmt) REVERT: Y 84 ASP cc_start: 0.6736 (p0) cc_final: 0.6215 (p0) REVERT: b 30 ILE cc_start: 0.9200 (OUTLIER) cc_final: 0.8945 (mp) REVERT: e 17 MET cc_start: 0.8851 (OUTLIER) cc_final: 0.8582 (ttm) REVERT: e 90 LYS cc_start: 0.6676 (mmpt) cc_final: 0.6346 (mmtt) REVERT: f 24 TYR cc_start: 0.8234 (t80) cc_final: 0.7888 (t80) REVERT: f 47 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7041 (mp0) REVERT: i 124 ASP cc_start: 0.6117 (m-30) cc_final: 0.5627 (t70) REVERT: j 70 ASP cc_start: 0.7784 (OUTLIER) cc_final: 0.7574 (p0) REVERT: k 33 GLU cc_start: 0.7938 (OUTLIER) cc_final: 0.7021 (mp0) REVERT: k 66 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8648 (mp) REVERT: p 37 ASP cc_start: 0.7658 (OUTLIER) cc_final: 0.7341 (t0) REVERT: q 21 ARG cc_start: 0.6909 (ttt90) cc_final: 0.6563 (ttt-90) REVERT: r 17 ARG cc_start: 0.7888 (mmt-90) cc_final: 0.7508 (mmm-85) outliers start: 87 outliers final: 29 residues processed: 967 average time/residue: 1.7655 time to fit residues: 2152.6205 Evaluate side-chains 945 residues out of total 7140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 902 time to evaluate : 6.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 425 GLU Chi-restraints excluded: chain F residue 427 GLU Chi-restraints excluded: chain G residue 403 ASP Chi-restraints excluded: chain G residue 420 ASP Chi-restraints excluded: chain H residue 8 MET Chi-restraints excluded: chain L residue 52 MET Chi-restraints excluded: chain L residue 500 LEU Chi-restraints excluded: chain M residue 86 LYS Chi-restraints excluded: chain M residue 126 LEU Chi-restraints excluded: chain N residue 320 MET Chi-restraints excluded: chain P residue 170 GLU Chi-restraints excluded: chain P residue 195 SER Chi-restraints excluded: chain Q residue 106 GLU Chi-restraints excluded: chain R residue 37 GLU Chi-restraints excluded: chain R residue 80 LYS Chi-restraints excluded: chain S residue 26 SER Chi-restraints excluded: chain S residue 90 LEU Chi-restraints excluded: chain T residue 44 SER Chi-restraints excluded: chain U residue 44 SER Chi-restraints excluded: chain X residue 108 GLU Chi-restraints excluded: chain Y residue 2 LYS Chi-restraints excluded: chain Y residue 49 LEU Chi-restraints excluded: chain Y residue 52 VAL Chi-restraints excluded: chain Y residue 124 VAL Chi-restraints excluded: chain Z residue 120 MET Chi-restraints excluded: chain b residue 30 ILE Chi-restraints excluded: chain d residue 20 SER Chi-restraints excluded: chain d residue 92 SER Chi-restraints excluded: chain d residue 96 SER Chi-restraints excluded: chain e residue 17 MET Chi-restraints excluded: chain e residue 75 LEU Chi-restraints excluded: chain f residue 29 LYS Chi-restraints excluded: chain f residue 47 GLU Chi-restraints excluded: chain i residue 67 SER Chi-restraints excluded: chain j residue 20 SER Chi-restraints excluded: chain j residue 70 ASP Chi-restraints excluded: chain k residue 33 GLU Chi-restraints excluded: chain k residue 66 LEU Chi-restraints excluded: chain l residue 42 THR Chi-restraints excluded: chain p residue 37 ASP Chi-restraints excluded: chain q residue 53 LYS Chi-restraints excluded: chain q residue 101 LYS Chi-restraints excluded: chain q residue 144 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 800 random chunks: chunk 719 optimal weight: 0.9990 chunk 547 optimal weight: 7.9990 chunk 377 optimal weight: 10.0000 chunk 80 optimal weight: 1.9990 chunk 347 optimal weight: 6.9990 chunk 488 optimal weight: 10.0000 chunk 730 optimal weight: 6.9990 chunk 773 optimal weight: 2.9990 chunk 381 optimal weight: 4.9990 chunk 692 optimal weight: 0.0570 chunk 208 optimal weight: 5.9990 overall best weight: 2.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN ** D 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 121 GLN G 237 ASN G 441 GLN G 472 ASN G 475 GLN M 304 GLN N 316 GLN P 87 HIS S 92 ASN T 74 GLN Y 7 GLN Y 128 GLN j 24 GLN l 136 ASN l 147 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.1336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.249 69151 Z= 0.435 Angle : 1.294 50.531 93578 Z= 0.834 Chirality : 0.255 6.491 10210 Planarity : 0.004 0.057 11671 Dihedral : 11.436 171.329 10586 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.72 % Favored : 98.27 % Rotamer: Outliers : 1.34 % Allowed : 8.14 % Favored : 90.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.09), residues: 8077 helix: 1.51 (0.08), residues: 4293 sheet: -0.02 (0.25), residues: 374 loop : 0.36 (0.11), residues: 3410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP X 85 HIS 0.006 0.001 HIS C 160 PHE 0.029 0.001 PHE N 292 TYR 0.022 0.001 TYR C 28 ARG 0.007 0.000 ARG k 41 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16154 Ramachandran restraints generated. 8077 Oldfield, 0 Emsley, 8077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16154 Ramachandran restraints generated. 8077 Oldfield, 0 Emsley, 8077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1025 residues out of total 7140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 929 time to evaluate : 6.351 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 29 LYS cc_start: 0.8386 (OUTLIER) cc_final: 0.7833 (mppt) REVERT: G 311 GLN cc_start: 0.7774 (mt0) cc_final: 0.7487 (mt0) REVERT: G 490 MET cc_start: 0.8699 (tpt) cc_final: 0.8363 (tpt) REVERT: H 8 MET cc_start: 0.8308 (OUTLIER) cc_final: 0.8009 (mmt) REVERT: I 29 GLU cc_start: 0.8629 (OUTLIER) cc_final: 0.7549 (pm20) REVERT: J 98 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8255 (mm) REVERT: L 314 MET cc_start: 0.8673 (tpp) cc_final: 0.8375 (tpp) REVERT: L 411 MET cc_start: 0.7834 (mmp) cc_final: 0.7594 (mmp) REVERT: M 114 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.7633 (tm-30) REVERT: P 170 GLU cc_start: 0.7481 (OUTLIER) cc_final: 0.7188 (mp0) REVERT: Q 106 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7930 (mt-10) REVERT: T 71 MET cc_start: 0.7532 (mmm) cc_final: 0.7246 (mmm) REVERT: U 12 LYS cc_start: 0.8788 (ttpp) cc_final: 0.8561 (tttt) REVERT: X 108 GLU cc_start: 0.7504 (OUTLIER) cc_final: 0.6466 (mp0) REVERT: X 138 GLU cc_start: 0.6935 (mp0) cc_final: 0.6725 (mp0) REVERT: Y 2 LYS cc_start: 0.5959 (OUTLIER) cc_final: 0.4197 (tptp) REVERT: Y 84 ASP cc_start: 0.6642 (p0) cc_final: 0.6123 (p0) REVERT: c 48 LEU cc_start: 0.6875 (OUTLIER) cc_final: 0.6493 (mp) REVERT: e 17 MET cc_start: 0.8859 (OUTLIER) cc_final: 0.8584 (ttm) REVERT: e 90 LYS cc_start: 0.6665 (mmpt) cc_final: 0.6324 (mmtt) REVERT: f 24 TYR cc_start: 0.8219 (t80) cc_final: 0.7913 (t80) REVERT: f 29 LYS cc_start: 0.8350 (OUTLIER) cc_final: 0.8150 (mmpt) REVERT: f 47 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7030 (mp0) REVERT: i 124 ASP cc_start: 0.6063 (m-30) cc_final: 0.5620 (t70) REVERT: k 33 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.7039 (mp0) REVERT: k 66 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8642 (mp) REVERT: p 37 ASP cc_start: 0.7663 (OUTLIER) cc_final: 0.7354 (t0) REVERT: q 21 ARG cc_start: 0.6876 (ttt90) cc_final: 0.6543 (ttt-90) REVERT: r 17 ARG cc_start: 0.7873 (mmt-90) cc_final: 0.7497 (mmm-85) outliers start: 96 outliers final: 40 residues processed: 974 average time/residue: 1.7196 time to fit residues: 2125.3817 Evaluate side-chains 952 residues out of total 7140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 896 time to evaluate : 6.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain D residue 29 LYS Chi-restraints excluded: chain G residue 403 ASP Chi-restraints excluded: chain G residue 420 ASP Chi-restraints excluded: chain H residue 8 MET Chi-restraints excluded: chain I residue 29 GLU Chi-restraints excluded: chain J residue 98 LEU Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain L residue 393 ASP Chi-restraints excluded: chain L residue 440 LEU Chi-restraints excluded: chain L residue 500 LEU Chi-restraints excluded: chain M residue 86 LYS Chi-restraints excluded: chain M residue 114 GLU Chi-restraints excluded: chain M residue 126 LEU Chi-restraints excluded: chain N residue 320 MET Chi-restraints excluded: chain O residue 224 SER Chi-restraints excluded: chain P residue 170 GLU Chi-restraints excluded: chain P residue 195 SER Chi-restraints excluded: chain Q residue 106 GLU Chi-restraints excluded: chain R residue 37 GLU Chi-restraints excluded: chain R residue 80 LYS Chi-restraints excluded: chain S residue 26 SER Chi-restraints excluded: chain S residue 84 ASP Chi-restraints excluded: chain S residue 90 LEU Chi-restraints excluded: chain T residue 44 SER Chi-restraints excluded: chain U residue 44 SER Chi-restraints excluded: chain X residue 108 GLU Chi-restraints excluded: chain Y residue 2 LYS Chi-restraints excluded: chain Y residue 49 LEU Chi-restraints excluded: chain Y residue 52 VAL Chi-restraints excluded: chain Y residue 124 VAL Chi-restraints excluded: chain Z residue 120 MET Chi-restraints excluded: chain c residue 48 LEU Chi-restraints excluded: chain d residue 20 SER Chi-restraints excluded: chain d residue 92 SER Chi-restraints excluded: chain d residue 96 SER Chi-restraints excluded: chain d residue 107 LYS Chi-restraints excluded: chain d residue 111 GLU Chi-restraints excluded: chain e residue 7 LYS Chi-restraints excluded: chain e residue 17 MET Chi-restraints excluded: chain e residue 75 LEU Chi-restraints excluded: chain f residue 29 LYS Chi-restraints excluded: chain f residue 47 GLU Chi-restraints excluded: chain g residue 26 TRP Chi-restraints excluded: chain h residue 143 ASN Chi-restraints excluded: chain j residue 20 SER Chi-restraints excluded: chain k residue 33 GLU Chi-restraints excluded: chain k residue 66 LEU Chi-restraints excluded: chain l residue 42 THR Chi-restraints excluded: chain l residue 128 VAL Chi-restraints excluded: chain p residue 37 ASP Chi-restraints excluded: chain q residue 53 LYS Chi-restraints excluded: chain q residue 101 LYS Chi-restraints excluded: chain q residue 135 GLN Chi-restraints excluded: chain q residue 144 TYR Chi-restraints excluded: chain s residue 71 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 800 random chunks: chunk 644 optimal weight: 6.9990 chunk 438 optimal weight: 1.9990 chunk 11 optimal weight: 9.9990 chunk 575 optimal weight: 9.9990 chunk 319 optimal weight: 9.9990 chunk 659 optimal weight: 3.9990 chunk 534 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 394 optimal weight: 4.9990 chunk 694 optimal weight: 1.9990 chunk 195 optimal weight: 0.2980 overall best weight: 2.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN ** D 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 402 ASN G 441 GLN G 472 ASN M 304 GLN N 316 GLN S 92 ASN Y 7 GLN Y 128 GLN j 24 GLN k 32 GLN l 147 ASN n 140 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.1334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.248 69151 Z= 0.451 Angle : 1.300 50.536 93578 Z= 0.836 Chirality : 0.256 6.516 10210 Planarity : 0.004 0.057 11671 Dihedral : 11.330 171.350 10586 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.88 % Favored : 98.11 % Rotamer: Outliers : 1.53 % Allowed : 8.70 % Favored : 89.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.09), residues: 8077 helix: 1.50 (0.08), residues: 4291 sheet: -0.01 (0.25), residues: 376 loop : 0.34 (0.11), residues: 3410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP X 85 HIS 0.007 0.001 HIS C 160 PHE 0.029 0.002 PHE N 292 TYR 0.023 0.002 TYR P 263 ARG 0.009 0.000 ARG k 41 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16154 Ramachandran restraints generated. 8077 Oldfield, 0 Emsley, 8077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16154 Ramachandran restraints generated. 8077 Oldfield, 0 Emsley, 8077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1016 residues out of total 7140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 907 time to evaluate : 6.194 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 29 LYS cc_start: 0.8405 (OUTLIER) cc_final: 0.7803 (mppt) REVERT: F 427 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.8148 (mt-10) REVERT: G 311 GLN cc_start: 0.7743 (mt0) cc_final: 0.7502 (mt0) REVERT: G 490 MET cc_start: 0.8790 (tpt) cc_final: 0.8469 (tpt) REVERT: H 8 MET cc_start: 0.8320 (OUTLIER) cc_final: 0.8033 (mmt) REVERT: I 29 GLU cc_start: 0.8618 (OUTLIER) cc_final: 0.7597 (pm20) REVERT: J 98 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8295 (mm) REVERT: L 314 MET cc_start: 0.8670 (tpp) cc_final: 0.8367 (tpp) REVERT: L 568 LEU cc_start: 0.8003 (tp) cc_final: 0.7784 (mt) REVERT: M 114 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.7598 (tm-30) REVERT: P 170 GLU cc_start: 0.7486 (OUTLIER) cc_final: 0.7193 (mp0) REVERT: Q 106 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7942 (mt-10) REVERT: T 71 MET cc_start: 0.7376 (mmm) cc_final: 0.7071 (mmm) REVERT: U 12 LYS cc_start: 0.8796 (ttpp) cc_final: 0.8573 (tttt) REVERT: X 108 GLU cc_start: 0.7513 (OUTLIER) cc_final: 0.6473 (mp0) REVERT: Y 2 LYS cc_start: 0.5935 (OUTLIER) cc_final: 0.4214 (tptp) REVERT: Y 84 ASP cc_start: 0.6589 (p0) cc_final: 0.6072 (p0) REVERT: c 34 GLN cc_start: 0.8372 (tm-30) cc_final: 0.7971 (tp-100) REVERT: e 17 MET cc_start: 0.8864 (OUTLIER) cc_final: 0.8589 (ttm) REVERT: e 90 LYS cc_start: 0.6658 (mmpt) cc_final: 0.6307 (mmtt) REVERT: f 24 TYR cc_start: 0.8227 (t80) cc_final: 0.7932 (t80) REVERT: f 47 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7032 (mp0) REVERT: g 50 ASP cc_start: 0.8144 (t0) cc_final: 0.7927 (t0) REVERT: i 8 LYS cc_start: 0.8404 (OUTLIER) cc_final: 0.8054 (ttpt) REVERT: i 124 ASP cc_start: 0.6128 (m-30) cc_final: 0.5622 (t70) REVERT: k 33 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.6930 (mp0) REVERT: k 66 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8647 (mp) REVERT: p 37 ASP cc_start: 0.7697 (OUTLIER) cc_final: 0.7394 (t0) REVERT: q 21 ARG cc_start: 0.6886 (ttt180) cc_final: 0.6557 (ttt-90) REVERT: r 17 ARG cc_start: 0.7885 (mmt-90) cc_final: 0.7500 (mmm-85) REVERT: r 39 LYS cc_start: 0.8786 (tttp) cc_final: 0.8542 (tmtm) outliers start: 109 outliers final: 54 residues processed: 967 average time/residue: 1.7655 time to fit residues: 2160.2629 Evaluate side-chains 973 residues out of total 7140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 903 time to evaluate : 6.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 125 TYR Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain D residue 29 LYS Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain F residue 427 GLU Chi-restraints excluded: chain F residue 428 GLU Chi-restraints excluded: chain G residue 403 ASP Chi-restraints excluded: chain G residue 456 SER Chi-restraints excluded: chain H residue 8 MET Chi-restraints excluded: chain I residue 29 GLU Chi-restraints excluded: chain J residue 98 LEU Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain L residue 393 ASP Chi-restraints excluded: chain L residue 440 LEU Chi-restraints excluded: chain L residue 500 LEU Chi-restraints excluded: chain L residue 508 THR Chi-restraints excluded: chain M residue 86 LYS Chi-restraints excluded: chain M residue 111 THR Chi-restraints excluded: chain M residue 114 GLU Chi-restraints excluded: chain M residue 126 LEU Chi-restraints excluded: chain N residue 320 MET Chi-restraints excluded: chain O residue 224 SER Chi-restraints excluded: chain P residue 139 ILE Chi-restraints excluded: chain P residue 170 GLU Chi-restraints excluded: chain P residue 195 SER Chi-restraints excluded: chain Q residue 106 GLU Chi-restraints excluded: chain R residue 37 GLU Chi-restraints excluded: chain R residue 80 LYS Chi-restraints excluded: chain S residue 26 SER Chi-restraints excluded: chain S residue 84 ASP Chi-restraints excluded: chain S residue 90 LEU Chi-restraints excluded: chain T residue 44 SER Chi-restraints excluded: chain U residue 9 GLU Chi-restraints excluded: chain U residue 44 SER Chi-restraints excluded: chain V residue 94 ILE Chi-restraints excluded: chain X residue 3 ILE Chi-restraints excluded: chain X residue 108 GLU Chi-restraints excluded: chain Y residue 2 LYS Chi-restraints excluded: chain Y residue 43 LYS Chi-restraints excluded: chain Y residue 49 LEU Chi-restraints excluded: chain Y residue 52 VAL Chi-restraints excluded: chain Y residue 124 VAL Chi-restraints excluded: chain Z residue 120 MET Chi-restraints excluded: chain d residue 20 SER Chi-restraints excluded: chain d residue 92 SER Chi-restraints excluded: chain d residue 96 SER Chi-restraints excluded: chain d residue 107 LYS Chi-restraints excluded: chain d residue 111 GLU Chi-restraints excluded: chain e residue 7 LYS Chi-restraints excluded: chain e residue 17 MET Chi-restraints excluded: chain e residue 53 LYS Chi-restraints excluded: chain e residue 75 LEU Chi-restraints excluded: chain f residue 47 GLU Chi-restraints excluded: chain g residue 26 TRP Chi-restraints excluded: chain g residue 55 ILE Chi-restraints excluded: chain h residue 143 ASN Chi-restraints excluded: chain i residue 8 LYS Chi-restraints excluded: chain j residue 20 SER Chi-restraints excluded: chain k residue 33 GLU Chi-restraints excluded: chain k residue 66 LEU Chi-restraints excluded: chain l residue 42 THR Chi-restraints excluded: chain l residue 128 VAL Chi-restraints excluded: chain l residue 154 VAL Chi-restraints excluded: chain p residue 37 ASP Chi-restraints excluded: chain q residue 53 LYS Chi-restraints excluded: chain q residue 101 LYS Chi-restraints excluded: chain q residue 135 GLN Chi-restraints excluded: chain q residue 144 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 800 random chunks: chunk 260 optimal weight: 1.9990 chunk 696 optimal weight: 4.9990 chunk 152 optimal weight: 0.4980 chunk 454 optimal weight: 3.9990 chunk 190 optimal weight: 3.9990 chunk 774 optimal weight: 9.9990 chunk 642 optimal weight: 5.9990 chunk 358 optimal weight: 3.9990 chunk 64 optimal weight: 5.9990 chunk 256 optimal weight: 5.9990 chunk 406 optimal weight: 1.9990 overall best weight: 2.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN ** D 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 402 ASN G 441 GLN G 472 ASN M 304 GLN N 316 GLN S 92 ASN Y 7 GLN Y 128 GLN c 46 ASN j 24 GLN k 32 GLN l 147 ASN n 140 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.1382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.248 69151 Z= 0.444 Angle : 1.297 50.529 93578 Z= 0.835 Chirality : 0.256 6.513 10210 Planarity : 0.004 0.056 11671 Dihedral : 11.169 171.418 10586 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.78 % Favored : 98.20 % Rotamer: Outliers : 1.58 % Allowed : 9.04 % Favored : 89.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.09), residues: 8077 helix: 1.52 (0.08), residues: 4294 sheet: -0.01 (0.25), residues: 376 loop : 0.35 (0.11), residues: 3407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP X 85 HIS 0.006 0.001 HIS C 160 PHE 0.029 0.002 PHE N 292 TYR 0.023 0.001 TYR C 28 ARG 0.010 0.000 ARG k 41 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16154 Ramachandran restraints generated. 8077 Oldfield, 0 Emsley, 8077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16154 Ramachandran restraints generated. 8077 Oldfield, 0 Emsley, 8077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1033 residues out of total 7140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 920 time to evaluate : 6.289 Fit side-chains revert: symmetry clash REVERT: D 29 LYS cc_start: 0.8372 (OUTLIER) cc_final: 0.7793 (mppt) REVERT: D 72 MET cc_start: 0.8333 (mmm) cc_final: 0.7732 (mmm) REVERT: F 427 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.8145 (mt-10) REVERT: G 311 GLN cc_start: 0.7740 (mt0) cc_final: 0.7503 (mt0) REVERT: G 490 MET cc_start: 0.8783 (tpt) cc_final: 0.8482 (tpt) REVERT: H 8 MET cc_start: 0.8307 (OUTLIER) cc_final: 0.8034 (mmt) REVERT: I 29 GLU cc_start: 0.8597 (OUTLIER) cc_final: 0.7615 (pm20) REVERT: J 98 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8310 (mm) REVERT: L 314 MET cc_start: 0.8670 (tpp) cc_final: 0.8370 (tpp) REVERT: L 572 LYS cc_start: 0.7893 (mtpt) cc_final: 0.7611 (mtmt) REVERT: M 114 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.7603 (tm-30) REVERT: P 170 GLU cc_start: 0.7495 (OUTLIER) cc_final: 0.7208 (mp0) REVERT: Q 106 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7951 (mt-10) REVERT: U 12 LYS cc_start: 0.8791 (ttpp) cc_final: 0.8565 (tttt) REVERT: X 108 GLU cc_start: 0.7534 (OUTLIER) cc_final: 0.6496 (mp0) REVERT: Y 2 LYS cc_start: 0.5956 (OUTLIER) cc_final: 0.4252 (tptp) REVERT: Y 84 ASP cc_start: 0.6572 (p0) cc_final: 0.6053 (p0) REVERT: e 17 MET cc_start: 0.8858 (OUTLIER) cc_final: 0.8578 (ttm) REVERT: e 90 LYS cc_start: 0.6640 (mmpt) cc_final: 0.6283 (mmtt) REVERT: f 24 TYR cc_start: 0.8239 (t80) cc_final: 0.7938 (t80) REVERT: f 47 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7029 (mp0) REVERT: g 50 ASP cc_start: 0.8150 (t0) cc_final: 0.7918 (t0) REVERT: i 8 LYS cc_start: 0.8391 (OUTLIER) cc_final: 0.8041 (ttpt) REVERT: i 124 ASP cc_start: 0.6109 (m-30) cc_final: 0.5601 (t70) REVERT: k 33 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.6921 (mp0) REVERT: k 66 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8624 (mp) REVERT: q 21 ARG cc_start: 0.6860 (ttt180) cc_final: 0.6535 (ttt-90) REVERT: r 17 ARG cc_start: 0.7888 (mmt-90) cc_final: 0.7502 (mmm-85) REVERT: r 39 LYS cc_start: 0.8788 (OUTLIER) cc_final: 0.8496 (tmtm) outliers start: 113 outliers final: 55 residues processed: 981 average time/residue: 1.7586 time to fit residues: 2183.4663 Evaluate side-chains 967 residues out of total 7140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 896 time to evaluate : 8.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 125 TYR Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain D residue 29 LYS Chi-restraints excluded: chain D residue 420 THR Chi-restraints excluded: chain F residue 427 GLU Chi-restraints excluded: chain F residue 428 GLU Chi-restraints excluded: chain G residue 403 ASP Chi-restraints excluded: chain G residue 456 SER Chi-restraints excluded: chain H residue 8 MET Chi-restraints excluded: chain I residue 29 GLU Chi-restraints excluded: chain J residue 98 LEU Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain L residue 393 ASP Chi-restraints excluded: chain L residue 500 LEU Chi-restraints excluded: chain L residue 508 THR Chi-restraints excluded: chain M residue 86 LYS Chi-restraints excluded: chain M residue 111 THR Chi-restraints excluded: chain M residue 114 GLU Chi-restraints excluded: chain M residue 126 LEU Chi-restraints excluded: chain N residue 320 MET Chi-restraints excluded: chain O residue 24 LEU Chi-restraints excluded: chain O residue 224 SER Chi-restraints excluded: chain P residue 139 ILE Chi-restraints excluded: chain P residue 170 GLU Chi-restraints excluded: chain P residue 195 SER Chi-restraints excluded: chain Q residue 106 GLU Chi-restraints excluded: chain R residue 37 GLU Chi-restraints excluded: chain R residue 80 LYS Chi-restraints excluded: chain S residue 26 SER Chi-restraints excluded: chain S residue 84 ASP Chi-restraints excluded: chain S residue 90 LEU Chi-restraints excluded: chain U residue 9 GLU Chi-restraints excluded: chain U residue 44 SER Chi-restraints excluded: chain V residue 94 ILE Chi-restraints excluded: chain X residue 108 GLU Chi-restraints excluded: chain Y residue 2 LYS Chi-restraints excluded: chain Y residue 43 LYS Chi-restraints excluded: chain Y residue 49 LEU Chi-restraints excluded: chain Y residue 52 VAL Chi-restraints excluded: chain Y residue 124 VAL Chi-restraints excluded: chain Z residue 120 MET Chi-restraints excluded: chain d residue 20 SER Chi-restraints excluded: chain d residue 92 SER Chi-restraints excluded: chain d residue 96 SER Chi-restraints excluded: chain d residue 107 LYS Chi-restraints excluded: chain d residue 111 GLU Chi-restraints excluded: chain e residue 7 LYS Chi-restraints excluded: chain e residue 17 MET Chi-restraints excluded: chain e residue 53 LYS Chi-restraints excluded: chain e residue 75 LEU Chi-restraints excluded: chain f residue 47 GLU Chi-restraints excluded: chain g residue 26 TRP Chi-restraints excluded: chain h residue 143 ASN Chi-restraints excluded: chain i residue 8 LYS Chi-restraints excluded: chain j residue 20 SER Chi-restraints excluded: chain k residue 33 GLU Chi-restraints excluded: chain k residue 66 LEU Chi-restraints excluded: chain l residue 42 THR Chi-restraints excluded: chain l residue 128 VAL Chi-restraints excluded: chain l residue 154 VAL Chi-restraints excluded: chain p residue 37 ASP Chi-restraints excluded: chain q residue 53 LYS Chi-restraints excluded: chain q residue 101 LYS Chi-restraints excluded: chain q residue 135 GLN Chi-restraints excluded: chain q residue 144 TYR Chi-restraints excluded: chain r residue 39 LYS Chi-restraints excluded: chain s residue 71 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 800 random chunks: chunk 746 optimal weight: 0.3980 chunk 87 optimal weight: 6.9990 chunk 441 optimal weight: 7.9990 chunk 565 optimal weight: 0.6980 chunk 437 optimal weight: 2.9990 chunk 651 optimal weight: 0.0970 chunk 432 optimal weight: 1.9990 chunk 771 optimal weight: 7.9990 chunk 482 optimal weight: 2.9990 chunk 470 optimal weight: 9.9990 chunk 355 optimal weight: 2.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN ** D 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 441 GLN G 472 ASN M 304 GLN N 316 GLN O 200 GLN S 92 ASN Y 7 GLN Y 128 GLN ** e 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 147 ASN n 140 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.247 69151 Z= 0.412 Angle : 1.282 50.564 93578 Z= 0.829 Chirality : 0.254 6.430 10210 Planarity : 0.004 0.057 11671 Dihedral : 10.758 170.984 10586 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.76 % Favored : 98.23 % Rotamer: Outliers : 1.34 % Allowed : 9.68 % Favored : 88.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.09), residues: 8077 helix: 1.67 (0.08), residues: 4296 sheet: -0.03 (0.25), residues: 384 loop : 0.44 (0.11), residues: 3397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP X 85 HIS 0.005 0.001 HIS L 332 PHE 0.030 0.001 PHE N 292 TYR 0.022 0.001 TYR C 28 ARG 0.011 0.000 ARG k 41 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16154 Ramachandran restraints generated. 8077 Oldfield, 0 Emsley, 8077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16154 Ramachandran restraints generated. 8077 Oldfield, 0 Emsley, 8077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1036 residues out of total 7140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 940 time to evaluate : 6.310 Fit side-chains revert: symmetry clash REVERT: D 23 LYS cc_start: 0.7992 (ttpp) cc_final: 0.7787 (tppp) REVERT: D 29 LYS cc_start: 0.8332 (OUTLIER) cc_final: 0.7782 (mppt) REVERT: D 72 MET cc_start: 0.8330 (mmm) cc_final: 0.7744 (mmm) REVERT: H 8 MET cc_start: 0.8222 (OUTLIER) cc_final: 0.7940 (mmt) REVERT: J 98 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8238 (mm) REVERT: L 101 MET cc_start: 0.8474 (OUTLIER) cc_final: 0.8222 (mtt) REVERT: L 314 MET cc_start: 0.8673 (tpp) cc_final: 0.8370 (tpp) REVERT: L 572 LYS cc_start: 0.7840 (mtpt) cc_final: 0.7572 (mtmt) REVERT: M 114 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.7677 (tm-30) REVERT: P 170 GLU cc_start: 0.7484 (OUTLIER) cc_final: 0.7207 (mp0) REVERT: U 9 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7682 (tp30) REVERT: X 108 GLU cc_start: 0.7523 (OUTLIER) cc_final: 0.6487 (mp0) REVERT: Y 2 LYS cc_start: 0.5922 (OUTLIER) cc_final: 0.4239 (tptp) REVERT: Y 84 ASP cc_start: 0.6523 (p0) cc_final: 0.6040 (p0) REVERT: c 34 GLN cc_start: 0.8349 (tm-30) cc_final: 0.7988 (tp-100) REVERT: e 17 MET cc_start: 0.8835 (OUTLIER) cc_final: 0.8562 (ttm) REVERT: e 90 LYS cc_start: 0.6640 (OUTLIER) cc_final: 0.6262 (mmtt) REVERT: f 24 TYR cc_start: 0.8219 (t80) cc_final: 0.7949 (t80) REVERT: f 47 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7044 (mp0) REVERT: g 50 ASP cc_start: 0.8134 (t0) cc_final: 0.7866 (t0) REVERT: i 124 ASP cc_start: 0.6066 (m-30) cc_final: 0.5587 (t70) REVERT: k 33 GLU cc_start: 0.7773 (OUTLIER) cc_final: 0.6932 (mp0) REVERT: p 37 ASP cc_start: 0.7673 (OUTLIER) cc_final: 0.7365 (t0) REVERT: q 21 ARG cc_start: 0.6850 (ttt180) cc_final: 0.6510 (ttt180) REVERT: r 39 LYS cc_start: 0.8765 (OUTLIER) cc_final: 0.8503 (tmtm) outliers start: 96 outliers final: 43 residues processed: 990 average time/residue: 1.7231 time to fit residues: 2167.1173 Evaluate side-chains 972 residues out of total 7140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 914 time to evaluate : 6.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 125 TYR Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain D residue 29 LYS Chi-restraints excluded: chain D residue 420 THR Chi-restraints excluded: chain G residue 403 ASP Chi-restraints excluded: chain G residue 456 SER Chi-restraints excluded: chain H residue 8 MET Chi-restraints excluded: chain J residue 98 LEU Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain L residue 101 MET Chi-restraints excluded: chain L residue 393 ASP Chi-restraints excluded: chain L residue 440 LEU Chi-restraints excluded: chain L residue 500 LEU Chi-restraints excluded: chain L residue 508 THR Chi-restraints excluded: chain M residue 111 THR Chi-restraints excluded: chain M residue 114 GLU Chi-restraints excluded: chain M residue 126 LEU Chi-restraints excluded: chain N residue 263 LYS Chi-restraints excluded: chain N residue 322 LYS Chi-restraints excluded: chain O residue 24 LEU Chi-restraints excluded: chain P residue 170 GLU Chi-restraints excluded: chain P residue 195 SER Chi-restraints excluded: chain R residue 37 GLU Chi-restraints excluded: chain R residue 80 LYS Chi-restraints excluded: chain S residue 84 ASP Chi-restraints excluded: chain S residue 90 LEU Chi-restraints excluded: chain T residue 44 SER Chi-restraints excluded: chain U residue 9 GLU Chi-restraints excluded: chain U residue 44 SER Chi-restraints excluded: chain V residue 94 ILE Chi-restraints excluded: chain X residue 108 GLU Chi-restraints excluded: chain Y residue 2 LYS Chi-restraints excluded: chain Y residue 49 LEU Chi-restraints excluded: chain d residue 20 SER Chi-restraints excluded: chain d residue 92 SER Chi-restraints excluded: chain d residue 107 LYS Chi-restraints excluded: chain d residue 111 GLU Chi-restraints excluded: chain e residue 17 MET Chi-restraints excluded: chain e residue 73 LYS Chi-restraints excluded: chain e residue 75 LEU Chi-restraints excluded: chain e residue 90 LYS Chi-restraints excluded: chain f residue 47 GLU Chi-restraints excluded: chain g residue 26 TRP Chi-restraints excluded: chain h residue 143 ASN Chi-restraints excluded: chain j residue 20 SER Chi-restraints excluded: chain k residue 33 GLU Chi-restraints excluded: chain l residue 42 THR Chi-restraints excluded: chain l residue 128 VAL Chi-restraints excluded: chain l residue 154 VAL Chi-restraints excluded: chain p residue 37 ASP Chi-restraints excluded: chain q residue 53 LYS Chi-restraints excluded: chain q residue 101 LYS Chi-restraints excluded: chain q residue 135 GLN Chi-restraints excluded: chain q residue 144 TYR Chi-restraints excluded: chain r residue 39 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 800 random chunks: chunk 477 optimal weight: 0.9990 chunk 307 optimal weight: 7.9990 chunk 460 optimal weight: 7.9990 chunk 232 optimal weight: 0.8980 chunk 151 optimal weight: 10.0000 chunk 149 optimal weight: 5.9990 chunk 490 optimal weight: 5.9990 chunk 525 optimal weight: 5.9990 chunk 381 optimal weight: 0.6980 chunk 71 optimal weight: 9.9990 chunk 606 optimal weight: 2.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN ** D 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 121 GLN G 441 GLN G 472 ASN M 188 ASN M 304 GLN N 316 GLN O 252 ASN S 92 ASN Y 7 GLN Y 128 GLN j 24 GLN k 58 ASN l 147 ASN m 116 GLN n 140 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.1501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.247 69151 Z= 0.440 Angle : 1.295 50.547 93578 Z= 0.833 Chirality : 0.255 6.489 10210 Planarity : 0.004 0.056 11671 Dihedral : 10.755 170.892 10586 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.84 % Favored : 98.14 % Rotamer: Outliers : 1.43 % Allowed : 10.02 % Favored : 88.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.09), residues: 8077 helix: 1.61 (0.08), residues: 4291 sheet: 0.04 (0.25), residues: 376 loop : 0.43 (0.11), residues: 3410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP r 9 HIS 0.007 0.001 HIS C 160 PHE 0.028 0.002 PHE M 122 TYR 0.022 0.001 TYR C 28 ARG 0.012 0.000 ARG k 41 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16154 Ramachandran restraints generated. 8077 Oldfield, 0 Emsley, 8077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16154 Ramachandran restraints generated. 8077 Oldfield, 0 Emsley, 8077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1014 residues out of total 7140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 912 time to evaluate : 6.431 Fit side-chains revert: symmetry clash REVERT: D 29 LYS cc_start: 0.8317 (OUTLIER) cc_final: 0.7754 (mppt) REVERT: G 490 MET cc_start: 0.8613 (tpt) cc_final: 0.8281 (tpt) REVERT: H 8 MET cc_start: 0.8264 (OUTLIER) cc_final: 0.7973 (mmt) REVERT: I 29 GLU cc_start: 0.8591 (OUTLIER) cc_final: 0.7469 (pm20) REVERT: J 98 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8315 (mm) REVERT: L 101 MET cc_start: 0.8489 (OUTLIER) cc_final: 0.8229 (mtt) REVERT: L 314 MET cc_start: 0.8676 (tpp) cc_final: 0.8403 (tpp) REVERT: L 572 LYS cc_start: 0.7864 (mtpt) cc_final: 0.7599 (mtmt) REVERT: M 114 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.7676 (tm-30) REVERT: P 170 GLU cc_start: 0.7492 (OUTLIER) cc_final: 0.7222 (mp0) REVERT: X 108 GLU cc_start: 0.7511 (OUTLIER) cc_final: 0.6493 (mp0) REVERT: Y 2 LYS cc_start: 0.5949 (OUTLIER) cc_final: 0.4254 (tptp) REVERT: Y 84 ASP cc_start: 0.6569 (p0) cc_final: 0.6085 (p0) REVERT: c 34 GLN cc_start: 0.8376 (tm-30) cc_final: 0.8004 (tp-100) REVERT: e 17 MET cc_start: 0.8858 (OUTLIER) cc_final: 0.8585 (ttm) REVERT: e 90 LYS cc_start: 0.6663 (OUTLIER) cc_final: 0.6288 (mmtt) REVERT: f 24 TYR cc_start: 0.8240 (t80) cc_final: 0.7929 (t80) REVERT: f 47 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7070 (mp0) REVERT: i 124 ASP cc_start: 0.6110 (m-30) cc_final: 0.5600 (t70) REVERT: k 33 GLU cc_start: 0.7754 (OUTLIER) cc_final: 0.6871 (mp0) REVERT: k 66 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8606 (mp) REVERT: p 37 ASP cc_start: 0.7670 (OUTLIER) cc_final: 0.7354 (t0) REVERT: p 66 GLU cc_start: 0.7028 (OUTLIER) cc_final: 0.6402 (mp0) REVERT: q 21 ARG cc_start: 0.6876 (ttt180) cc_final: 0.6528 (ttt180) REVERT: r 39 LYS cc_start: 0.8784 (OUTLIER) cc_final: 0.8493 (tmtm) REVERT: r 101 LYS cc_start: 0.8013 (mmmm) cc_final: 0.7524 (mtpm) outliers start: 102 outliers final: 53 residues processed: 967 average time/residue: 1.7751 time to fit residues: 2166.3161 Evaluate side-chains 965 residues out of total 7140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 895 time to evaluate : 6.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 125 TYR Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain D residue 29 LYS Chi-restraints excluded: chain D residue 420 THR Chi-restraints excluded: chain F residue 428 GLU Chi-restraints excluded: chain G residue 403 ASP Chi-restraints excluded: chain G residue 420 ASP Chi-restraints excluded: chain G residue 456 SER Chi-restraints excluded: chain H residue 8 MET Chi-restraints excluded: chain I residue 29 GLU Chi-restraints excluded: chain J residue 98 LEU Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain L residue 17 MET Chi-restraints excluded: chain L residue 101 MET Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain L residue 149 ILE Chi-restraints excluded: chain L residue 393 ASP Chi-restraints excluded: chain L residue 440 LEU Chi-restraints excluded: chain L residue 500 LEU Chi-restraints excluded: chain L residue 508 THR Chi-restraints excluded: chain M residue 111 THR Chi-restraints excluded: chain M residue 114 GLU Chi-restraints excluded: chain M residue 126 LEU Chi-restraints excluded: chain N residue 263 LYS Chi-restraints excluded: chain N residue 322 LYS Chi-restraints excluded: chain O residue 24 LEU Chi-restraints excluded: chain P residue 170 GLU Chi-restraints excluded: chain P residue 195 SER Chi-restraints excluded: chain R residue 37 GLU Chi-restraints excluded: chain R residue 80 LYS Chi-restraints excluded: chain S residue 84 ASP Chi-restraints excluded: chain S residue 90 LEU Chi-restraints excluded: chain T residue 44 SER Chi-restraints excluded: chain U residue 9 GLU Chi-restraints excluded: chain U residue 44 SER Chi-restraints excluded: chain W residue 101 THR Chi-restraints excluded: chain X residue 108 GLU Chi-restraints excluded: chain Y residue 2 LYS Chi-restraints excluded: chain Y residue 49 LEU Chi-restraints excluded: chain d residue 20 SER Chi-restraints excluded: chain d residue 92 SER Chi-restraints excluded: chain d residue 96 SER Chi-restraints excluded: chain d residue 107 LYS Chi-restraints excluded: chain d residue 111 GLU Chi-restraints excluded: chain e residue 7 LYS Chi-restraints excluded: chain e residue 17 MET Chi-restraints excluded: chain e residue 73 LYS Chi-restraints excluded: chain e residue 75 LEU Chi-restraints excluded: chain e residue 90 LYS Chi-restraints excluded: chain f residue 47 GLU Chi-restraints excluded: chain g residue 26 TRP Chi-restraints excluded: chain h residue 143 ASN Chi-restraints excluded: chain j residue 20 SER Chi-restraints excluded: chain k residue 33 GLU Chi-restraints excluded: chain k residue 66 LEU Chi-restraints excluded: chain l residue 42 THR Chi-restraints excluded: chain l residue 128 VAL Chi-restraints excluded: chain l residue 154 VAL Chi-restraints excluded: chain p residue 37 ASP Chi-restraints excluded: chain p residue 66 GLU Chi-restraints excluded: chain q residue 53 LYS Chi-restraints excluded: chain q residue 101 LYS Chi-restraints excluded: chain q residue 135 GLN Chi-restraints excluded: chain q residue 144 TYR Chi-restraints excluded: chain r residue 39 LYS Chi-restraints excluded: chain s residue 41 LEU Chi-restraints excluded: chain s residue 71 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 800 random chunks: chunk 701 optimal weight: 1.9990 chunk 738 optimal weight: 6.9990 chunk 673 optimal weight: 1.9990 chunk 718 optimal weight: 0.9980 chunk 432 optimal weight: 5.9990 chunk 313 optimal weight: 0.9990 chunk 564 optimal weight: 4.9990 chunk 220 optimal weight: 9.9990 chunk 649 optimal weight: 0.6980 chunk 679 optimal weight: 0.8980 chunk 716 optimal weight: 3.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 441 GLN G 472 ASN L 579 ASN M 304 GLN N 316 GLN S 92 ASN Y 7 GLN j 24 GLN k 58 ASN l 147 ASN m 116 GLN n 140 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.247 69151 Z= 0.410 Angle : 1.282 50.552 93578 Z= 0.828 Chirality : 0.254 6.416 10210 Planarity : 0.004 0.057 11671 Dihedral : 10.454 170.801 10586 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.71 % Favored : 98.28 % Rotamer: Outliers : 1.09 % Allowed : 10.52 % Favored : 88.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.09), residues: 8077 helix: 1.72 (0.08), residues: 4307 sheet: 0.01 (0.25), residues: 382 loop : 0.48 (0.11), residues: 3388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP r 9 HIS 0.005 0.001 HIS L 332 PHE 0.030 0.001 PHE N 292 TYR 0.022 0.001 TYR L 422 ARG 0.012 0.000 ARG k 41 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16154 Ramachandran restraints generated. 8077 Oldfield, 0 Emsley, 8077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16154 Ramachandran restraints generated. 8077 Oldfield, 0 Emsley, 8077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 997 residues out of total 7140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 919 time to evaluate : 6.264 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.8038 (mtm) cc_final: 0.7819 (mpp) REVERT: D 29 LYS cc_start: 0.8320 (OUTLIER) cc_final: 0.7802 (mppt) REVERT: D 72 MET cc_start: 0.8336 (mmm) cc_final: 0.7773 (mmm) REVERT: I 29 GLU cc_start: 0.8526 (OUTLIER) cc_final: 0.7411 (pm20) REVERT: J 139 GLU cc_start: 0.7883 (tt0) cc_final: 0.7653 (tt0) REVERT: L 101 MET cc_start: 0.8466 (OUTLIER) cc_final: 0.8214 (mtt) REVERT: M 114 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.7731 (tm-30) REVERT: N 37 MET cc_start: 0.8562 (ttp) cc_final: 0.8354 (ttm) REVERT: P 170 GLU cc_start: 0.7463 (OUTLIER) cc_final: 0.7084 (mp0) REVERT: P 188 PHE cc_start: 0.8341 (m-80) cc_final: 0.7927 (m-80) REVERT: X 108 GLU cc_start: 0.7497 (OUTLIER) cc_final: 0.6470 (mp0) REVERT: Y 2 LYS cc_start: 0.5921 (OUTLIER) cc_final: 0.4246 (tptp) REVERT: Y 84 ASP cc_start: 0.6533 (p0) cc_final: 0.6049 (p0) REVERT: c 34 GLN cc_start: 0.8365 (tm-30) cc_final: 0.7993 (tp-100) REVERT: e 90 LYS cc_start: 0.6623 (OUTLIER) cc_final: 0.6236 (mmtt) REVERT: f 24 TYR cc_start: 0.8213 (t80) cc_final: 0.7911 (t80) REVERT: i 124 ASP cc_start: 0.6069 (m-30) cc_final: 0.5611 (t70) REVERT: k 66 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8572 (mp) REVERT: p 37 ASP cc_start: 0.7667 (OUTLIER) cc_final: 0.7362 (t0) REVERT: q 21 ARG cc_start: 0.6858 (ttt180) cc_final: 0.6521 (ttt180) REVERT: r 39 LYS cc_start: 0.8750 (OUTLIER) cc_final: 0.8489 (tmtm) REVERT: r 101 LYS cc_start: 0.8020 (mmmm) cc_final: 0.7538 (mtpm) outliers start: 78 outliers final: 42 residues processed: 949 average time/residue: 1.7323 time to fit residues: 2085.1426 Evaluate side-chains 958 residues out of total 7140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 905 time to evaluate : 6.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 125 TYR Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain D residue 29 LYS Chi-restraints excluded: chain D residue 420 THR Chi-restraints excluded: chain G residue 403 ASP Chi-restraints excluded: chain G residue 456 SER Chi-restraints excluded: chain I residue 29 GLU Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain L residue 101 MET Chi-restraints excluded: chain L residue 149 ILE Chi-restraints excluded: chain L residue 440 LEU Chi-restraints excluded: chain L residue 500 LEU Chi-restraints excluded: chain L residue 508 THR Chi-restraints excluded: chain M residue 111 THR Chi-restraints excluded: chain M residue 114 GLU Chi-restraints excluded: chain M residue 126 LEU Chi-restraints excluded: chain N residue 263 LYS Chi-restraints excluded: chain O residue 24 LEU Chi-restraints excluded: chain P residue 170 GLU Chi-restraints excluded: chain P residue 195 SER Chi-restraints excluded: chain R residue 37 GLU Chi-restraints excluded: chain R residue 80 LYS Chi-restraints excluded: chain S residue 26 SER Chi-restraints excluded: chain S residue 84 ASP Chi-restraints excluded: chain S residue 90 LEU Chi-restraints excluded: chain T residue 44 SER Chi-restraints excluded: chain W residue 101 THR Chi-restraints excluded: chain X residue 13 LYS Chi-restraints excluded: chain X residue 108 GLU Chi-restraints excluded: chain Y residue 2 LYS Chi-restraints excluded: chain Y residue 124 VAL Chi-restraints excluded: chain d residue 20 SER Chi-restraints excluded: chain d residue 92 SER Chi-restraints excluded: chain d residue 107 LYS Chi-restraints excluded: chain d residue 111 GLU Chi-restraints excluded: chain e residue 53 LYS Chi-restraints excluded: chain e residue 73 LYS Chi-restraints excluded: chain e residue 75 LEU Chi-restraints excluded: chain e residue 90 LYS Chi-restraints excluded: chain g residue 26 TRP Chi-restraints excluded: chain h residue 143 ASN Chi-restraints excluded: chain k residue 33 GLU Chi-restraints excluded: chain k residue 66 LEU Chi-restraints excluded: chain l residue 42 THR Chi-restraints excluded: chain l residue 128 VAL Chi-restraints excluded: chain l residue 154 VAL Chi-restraints excluded: chain p residue 37 ASP Chi-restraints excluded: chain q residue 53 LYS Chi-restraints excluded: chain q residue 101 LYS Chi-restraints excluded: chain q residue 135 GLN Chi-restraints excluded: chain q residue 144 TYR Chi-restraints excluded: chain r residue 39 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 800 random chunks: chunk 471 optimal weight: 9.9990 chunk 759 optimal weight: 0.6980 chunk 463 optimal weight: 0.9990 chunk 360 optimal weight: 2.9990 chunk 528 optimal weight: 10.0000 chunk 797 optimal weight: 4.9990 chunk 733 optimal weight: 10.0000 chunk 634 optimal weight: 4.9990 chunk 65 optimal weight: 8.9990 chunk 490 optimal weight: 4.9990 chunk 389 optimal weight: 2.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 GLN ** D 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 398 GLN G 441 GLN ** L 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 316 GLN S 92 ASN Y 7 GLN j 13 GLN k 58 ASN l 137 ASN l 147 ASN n 61 GLN n 140 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.1529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.247 69151 Z= 0.447 Angle : 1.298 50.535 93578 Z= 0.835 Chirality : 0.256 6.535 10210 Planarity : 0.004 0.057 11671 Dihedral : 10.576 170.811 10585 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.80 % Favored : 98.19 % Rotamer: Outliers : 0.99 % Allowed : 10.84 % Favored : 88.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.09), residues: 8077 helix: 1.62 (0.08), residues: 4292 sheet: 0.05 (0.25), residues: 376 loop : 0.45 (0.11), residues: 3409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP r 9 HIS 0.007 0.001 HIS C 160 PHE 0.029 0.002 PHE M 122 TYR 0.022 0.002 TYR C 28 ARG 0.013 0.000 ARG k 41 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16154 Ramachandran restraints generated. 8077 Oldfield, 0 Emsley, 8077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16154 Ramachandran restraints generated. 8077 Oldfield, 0 Emsley, 8077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 982 residues out of total 7140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 911 time to evaluate : 6.870 Fit side-chains revert: symmetry clash REVERT: D 29 LYS cc_start: 0.8332 (OUTLIER) cc_final: 0.7802 (mppt) REVERT: G 260 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7989 (mt-10) REVERT: I 29 GLU cc_start: 0.8583 (OUTLIER) cc_final: 0.7478 (pm20) REVERT: L 101 MET cc_start: 0.8496 (OUTLIER) cc_final: 0.8232 (mtt) REVERT: M 114 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.7691 (tm-30) REVERT: P 170 GLU cc_start: 0.7495 (OUTLIER) cc_final: 0.7222 (mp0) REVERT: P 188 PHE cc_start: 0.8346 (m-80) cc_final: 0.7875 (m-80) REVERT: P 260 HIS cc_start: 0.6953 (t-90) cc_final: 0.6405 (t-90) REVERT: T 71 MET cc_start: 0.7513 (mmm) cc_final: 0.6974 (mmm) REVERT: U 9 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.7693 (tp30) REVERT: X 108 GLU cc_start: 0.7516 (OUTLIER) cc_final: 0.6499 (mp0) REVERT: Y 2 LYS cc_start: 0.5965 (OUTLIER) cc_final: 0.4285 (tptp) REVERT: Y 84 ASP cc_start: 0.6564 (p0) cc_final: 0.6090 (p0) REVERT: e 90 LYS cc_start: 0.6625 (OUTLIER) cc_final: 0.6248 (mmtt) REVERT: f 24 TYR cc_start: 0.8240 (t80) cc_final: 0.7972 (t80) REVERT: g 50 ASP cc_start: 0.8134 (t0) cc_final: 0.7888 (t0) REVERT: i 124 ASP cc_start: 0.6124 (m-30) cc_final: 0.5620 (t70) REVERT: j 70 ASP cc_start: 0.7742 (p0) cc_final: 0.7464 (p0) REVERT: k 33 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.6877 (mp0) REVERT: k 66 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8590 (mp) REVERT: p 37 ASP cc_start: 0.7674 (OUTLIER) cc_final: 0.7365 (t0) REVERT: q 21 ARG cc_start: 0.6890 (ttt180) cc_final: 0.6538 (ttt180) REVERT: r 101 LYS cc_start: 0.8012 (mmmm) cc_final: 0.7531 (mtpm) outliers start: 71 outliers final: 48 residues processed: 946 average time/residue: 1.7970 time to fit residues: 2150.6920 Evaluate side-chains 963 residues out of total 7140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 902 time to evaluate : 6.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 125 TYR Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain D residue 29 LYS Chi-restraints excluded: chain D residue 420 THR Chi-restraints excluded: chain F residue 428 GLU Chi-restraints excluded: chain G residue 260 GLU Chi-restraints excluded: chain G residue 403 ASP Chi-restraints excluded: chain G residue 456 SER Chi-restraints excluded: chain I residue 29 GLU Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain L residue 52 MET Chi-restraints excluded: chain L residue 101 MET Chi-restraints excluded: chain L residue 149 ILE Chi-restraints excluded: chain L residue 440 LEU Chi-restraints excluded: chain L residue 500 LEU Chi-restraints excluded: chain L residue 508 THR Chi-restraints excluded: chain M residue 111 THR Chi-restraints excluded: chain M residue 114 GLU Chi-restraints excluded: chain M residue 126 LEU Chi-restraints excluded: chain N residue 263 LYS Chi-restraints excluded: chain N residue 322 LYS Chi-restraints excluded: chain O residue 24 LEU Chi-restraints excluded: chain P residue 170 GLU Chi-restraints excluded: chain P residue 195 SER Chi-restraints excluded: chain R residue 37 GLU Chi-restraints excluded: chain R residue 80 LYS Chi-restraints excluded: chain S residue 26 SER Chi-restraints excluded: chain S residue 84 ASP Chi-restraints excluded: chain S residue 90 LEU Chi-restraints excluded: chain T residue 44 SER Chi-restraints excluded: chain U residue 9 GLU Chi-restraints excluded: chain W residue 101 THR Chi-restraints excluded: chain X residue 3 ILE Chi-restraints excluded: chain X residue 108 GLU Chi-restraints excluded: chain Y residue 2 LYS Chi-restraints excluded: chain Y residue 43 LYS Chi-restraints excluded: chain Y residue 124 VAL Chi-restraints excluded: chain d residue 20 SER Chi-restraints excluded: chain d residue 92 SER Chi-restraints excluded: chain d residue 107 LYS Chi-restraints excluded: chain d residue 111 GLU Chi-restraints excluded: chain e residue 7 LYS Chi-restraints excluded: chain e residue 73 LYS Chi-restraints excluded: chain e residue 75 LEU Chi-restraints excluded: chain e residue 90 LYS Chi-restraints excluded: chain g residue 26 TRP Chi-restraints excluded: chain h residue 143 ASN Chi-restraints excluded: chain k residue 33 GLU Chi-restraints excluded: chain k residue 66 LEU Chi-restraints excluded: chain l residue 42 THR Chi-restraints excluded: chain l residue 128 VAL Chi-restraints excluded: chain l residue 154 VAL Chi-restraints excluded: chain p residue 37 ASP Chi-restraints excluded: chain q residue 53 LYS Chi-restraints excluded: chain q residue 101 LYS Chi-restraints excluded: chain q residue 144 TYR Chi-restraints excluded: chain s residue 41 LEU Chi-restraints excluded: chain s residue 71 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 800 random chunks: chunk 504 optimal weight: 9.9990 chunk 676 optimal weight: 5.9990 chunk 194 optimal weight: 2.9990 chunk 585 optimal weight: 10.0000 chunk 93 optimal weight: 0.6980 chunk 176 optimal weight: 8.9990 chunk 635 optimal weight: 4.9990 chunk 266 optimal weight: 0.9980 chunk 652 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 117 optimal weight: 0.7980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 441 GLN G 472 ASN S 92 ASN Y 7 GLN c 34 GLN k 58 ASN l 147 ASN n 61 GLN n 140 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.096149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.081656 restraints weight = 87596.814| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 1.22 r_work: 0.2990 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 2.81 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8804 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.247 69151 Z= 0.410 Angle : 1.283 50.562 93578 Z= 0.829 Chirality : 0.254 6.434 10210 Planarity : 0.004 0.058 11671 Dihedral : 10.333 170.870 10585 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.73 % Favored : 98.25 % Rotamer: Outliers : 0.95 % Allowed : 10.94 % Favored : 88.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.09), residues: 8077 helix: 1.72 (0.08), residues: 4308 sheet: 0.01 (0.25), residues: 384 loop : 0.48 (0.11), residues: 3385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP r 9 HIS 0.007 0.001 HIS D 27 PHE 0.030 0.001 PHE N 292 TYR 0.022 0.001 TYR C 28 ARG 0.014 0.000 ARG k 41 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 29920.22 seconds wall clock time: 518 minutes 58.85 seconds (31138.85 seconds total)