Starting phenix.real_space_refine on Fri Mar 15 15:19:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r42_14256/03_2024/7r42_14256_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r42_14256/03_2024/7r42_14256.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r42_14256/03_2024/7r42_14256_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r42_14256/03_2024/7r42_14256_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r42_14256/03_2024/7r42_14256_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r42_14256/03_2024/7r42_14256.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r42_14256/03_2024/7r42_14256.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r42_14256/03_2024/7r42_14256_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r42_14256/03_2024/7r42_14256_updated.pdb" } resolution = 2.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.007 sd= 1.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 11 Type Number sf(0) Gaussians I 1 10.91 5 K 1 8.98 5 Fe 28 7.16 5 Zn 1 6.06 5 P 37 5.49 5 Mg 1 5.21 5 S 468 5.16 5 Cl 1 4.86 5 C 43953 2.51 5 N 11184 2.21 5 O 13805 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 32": "OE1" <-> "OE2" Residue "A PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 42": "OD1" <-> "OD2" Residue "A PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 115": "OE1" <-> "OE2" Residue "B ASP 35": "OD1" <-> "OD2" Residue "B ARG 71": "NH1" <-> "NH2" Residue "B PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 109": "OE1" <-> "OE2" Residue "B ARG 111": "NH1" <-> "NH2" Residue "B ASP 143": "OD1" <-> "OD2" 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 ASP 77": "OD1" <-> "OD2" Residue "C TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 149": "NH1" <-> "NH2" Residue "C PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 158": "OE1" <-> "OE2" Residue "C ASP 177": "OD1" <-> "OD2" 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 24": "OE1" <-> "OE2" Residue "D ASP 37": "OD1" <-> "OD2" Residue "D PHE 51": "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 ASP 210": "OD1" <-> "OD2" 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 282": "OE1" <-> "OE2" Residue "D GLU 343": "OE1" <-> "OE2" Residue "D GLU 427": "OE1" <-> "OE2" Residue "D ASP 429": "OD1" <-> "OD2" Residue "E GLU 26": "OE1" <-> "OE2" Residue "E GLU 40": "OE1" <-> "OE2" Residue "E ASP 52": "OD1" <-> "OD2" Residue "E GLU 71": "OE1" <-> "OE2" Residue "E GLU 82": "OE1" <-> "OE2" Residue "E ASP 114": "OD1" <-> "OD2" Residue "E TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 162": "OE1" <-> "OE2" Residue "E ASP 168": "OD1" <-> "OD2" Residue "E GLU 170": "OE1" <-> "OE2" Residue "E ARG 190": "NH1" <-> "NH2" Residue "F ARG 32": "NH1" <-> "NH2" Residue "F TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 54": "OD1" <-> "OD2" Residue "F PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 87": "OD1" <-> "OD2" Residue "F GLU 101": "OE1" <-> "OE2" Residue "F ARG 112": "NH1" <-> "NH2" Residue "F ARG 132": "NH1" <-> "NH2" Residue "F ARG 139": "NH1" <-> "NH2" Residue "F GLU 189": "OE1" <-> "OE2" Residue "F GLU 194": "OE1" <-> "OE2" Residue "F GLU 248": "OE1" <-> "OE2" Residue "F ARG 249": "NH1" <-> "NH2" Residue "F PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 278": "OE1" <-> "OE2" Residue "F GLU 281": "OE1" <-> "OE2" Residue "F ARG 349": "NH1" <-> "NH2" Residue "F GLU 357": "OE1" <-> "OE2" Residue "F ASP 370": "OD1" <-> "OD2" Residue "F ARG 429": "NH1" <-> "NH2" Residue "G GLU 10": "OE1" <-> "OE2" Residue "G GLU 21": "OE1" <-> "OE2" Residue "G GLU 31": "OE1" <-> "OE2" Residue "G ARG 39": "NH1" <-> "NH2" Residue "G ARG 53": "NH1" <-> "NH2" Residue "G GLU 60": "OE1" <-> "OE2" Residue "G GLU 84": "OE1" <-> "OE2" Residue "G GLU 138": "OE1" <-> "OE2" Residue "G GLU 165": "OE1" <-> "OE2" Residue "G ARG 218": "NH1" <-> "NH2" Residue "G ARG 243": "NH1" <-> "NH2" Residue "G GLU 246": "OE1" <-> "OE2" Residue "G ARG 253": "NH1" <-> "NH2" Residue "G GLU 260": "OE1" <-> "OE2" Residue "G GLU 261": "OE1" <-> "OE2" Residue "G ARG 285": "NH1" <-> "NH2" Residue "G GLU 287": "OE1" <-> "OE2" Residue "G GLU 297": "OE1" <-> "OE2" Residue "G ARG 302": "NH1" <-> "NH2" Residue "G ASP 314": "OD1" <-> "OD2" Residue "G ASP 339": "OD1" <-> "OD2" Residue "G GLU 347": "OE1" <-> "OE2" Residue "G GLU 373": "OE1" <-> "OE2" Residue "G ASP 375": "OD1" <-> "OD2" Residue "G ARG 385": "NH1" <-> "NH2" Residue "G ARG 418": "NH1" <-> "NH2" Residue "G ASP 486": "OD1" <-> "OD2" Residue "G ASP 614": "OD1" <-> "OD2" Residue "G ASP 617": "OD1" <-> "OD2" Residue "G GLU 624": "OE1" <-> "OE2" Residue "G GLU 625": "OE1" <-> "OE2" Residue "G ASP 634": "OD1" <-> "OD2" Residue "G GLU 637": "OE1" <-> "OE2" Residue "H GLU 24": "OE1" <-> "OE2" Residue "H ARG 25": "NH1" <-> "NH2" Residue "H ARG 34": "NH1" <-> "NH2" Residue "H ARG 62": "NH1" <-> "NH2" Residue "H TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 192": "OE1" <-> "OE2" Residue "H GLU 202": "OE1" <-> "OE2" Residue "H GLU 204": "OE1" <-> "OE2" Residue "H PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 214": "OE1" <-> "OE2" Residue "I ARG 8": "NH1" <-> "NH2" Residue "I TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 74": "OE1" <-> "OE2" Residue "I GLU 95": "OE1" <-> "OE2" Residue "I ARG 108": "NH1" <-> "NH2" Residue "I PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 77": "OE1" <-> "OE2" Residue "J GLU 81": "OE1" <-> "OE2" Residue "J GLU 100": "OE1" <-> "OE2" Residue "J GLU 112": "OE1" <-> "OE2" Residue "J TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 139": "OE1" <-> "OE2" Residue "J GLU 170": "OE1" <-> "OE2" Residue "J ARG 173": "NH1" <-> "NH2" Residue "K GLU 34": "OE1" <-> "OE2" Residue "K GLU 70": "OE1" <-> "OE2" Residue "L GLU 102": "OE1" <-> "OE2" Residue "L ARG 161": "NH1" <-> "NH2" Residue "L ASP 163": "OD1" <-> "OD2" Residue "L ASP 179": "OD1" <-> "OD2" Residue "L PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 262": "NH1" <-> "NH2" Residue "L GLU 268": "OE1" <-> "OE2" Residue "L GLU 353": "OE1" <-> "OE2" Residue "L PHE 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 393": "OD1" <-> "OD2" Residue "L GLU 397": "OE1" <-> "OE2" Residue "L PHE 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 503": "OE1" <-> "OE2" Residue "L GLU 559": "OE1" <-> "OE2" Residue "L PHE 588": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 606": "OE1" <-> "OE2" Residue "M ASP 59": "OD1" <-> "OD2" Residue "M GLU 87": "OE1" <-> "OE2" Residue "M PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 114": "OE1" <-> "OE2" Residue "M PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 141": "OE1" <-> "OE2" Residue "M ARG 142": "NH1" <-> "NH2" Residue "M TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 222": "OE1" <-> "OE2" Residue "M GLU 378": "OE1" <-> "OE2" Residue "M TYR 419": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 432": "NH1" <-> "NH2" Residue "N GLU 34": "OE1" <-> "OE2" Residue "N GLU 54": "OE1" <-> "OE2" Residue "N GLU 117": "OE1" <-> "OE2" Residue "N PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 295": "NH1" <-> "NH2" Residue "N PHE 325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 347": "OE1" <-> "OE2" Residue "O GLU 12": "OE1" <-> "OE2" Residue "O GLU 41": "OE1" <-> "OE2" Residue "O GLU 53": "OE1" <-> "OE2" Residue "O ASP 85": "OD1" <-> "OD2" Residue "O TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 131": "OD1" <-> "OD2" Residue "O GLU 203": "OE1" <-> "OE2" Residue "O GLU 216": "OE1" <-> "OE2" Residue "O GLU 227": "OE1" <-> "OE2" Residue "O GLU 232": "OE1" <-> "OE2" Residue "O GLU 239": "OE1" <-> "OE2" Residue "O ASP 244": "OD1" <-> "OD2" Residue "O ARG 302": "NH1" <-> "NH2" Residue "O ARG 305": "NH1" <-> "NH2" Residue "O GLU 310": "OE1" <-> "OE2" Residue "P ARG 40": "NH1" <-> "NH2" Residue "P ARG 50": "NH1" <-> "NH2" Residue "P GLU 52": "OE1" <-> "OE2" Residue "P ASP 79": "OD1" <-> "OD2" Residue "P ARG 82": "NH1" <-> "NH2" Residue "P ARG 97": "NH1" <-> "NH2" Residue "P GLU 98": "OE1" <-> "OE2" Residue "P GLU 127": "OE1" <-> "OE2" Residue "P ARG 147": "NH1" <-> "NH2" Residue "P ARG 157": "NH1" <-> "NH2" Residue "P GLU 158": "OE1" <-> "OE2" Residue "P GLU 162": "OE1" <-> "OE2" Residue "P GLU 170": "OE1" <-> "OE2" Residue "P PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 175": "OE1" <-> "OE2" Residue "P PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 235": "NH1" <-> "NH2" Residue "P PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 251": "NH1" <-> "NH2" Residue "P TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 285": "OE1" <-> "OE2" Residue "P GLU 316": "OE1" <-> "OE2" Residue "P ARG 325": "NH1" <-> "NH2" Residue "P ASP 333": "OD1" <-> "OD2" Residue "Q GLU 27": "OE1" <-> "OE2" Residue "Q GLU 28": "OE1" <-> "OE2" Residue "Q GLU 58": "OE1" <-> "OE2" Residue "Q GLU 66": "OE1" <-> "OE2" Residue "Q GLU 97": "OE1" <-> "OE2" Residue "Q GLU 106": "OE1" <-> "OE2" Residue "R ARG 31": "NH1" <-> "NH2" Residue "R GLU 34": "OE1" <-> "OE2" Residue "R GLU 78": "OE1" <-> "OE2" Residue "S GLU 17": "OE1" <-> "OE2" Residue "S GLU 37": "OE1" <-> "OE2" Residue "S ASP 49": "OD1" <-> "OD2" Residue "S GLU 56": "OE1" <-> "OE2" Residue "S ASP 84": "OD1" <-> "OD2" Residue "T GLU 9": "OE1" <-> "OE2" Residue "T ASP 13": "OD1" <-> "OD2" Residue "T ASP 23": "OD1" <-> "OD2" Residue "T ASP 26": "OD1" <-> "OD2" Residue "T GLU 28": "OE1" <-> "OE2" Residue "T ASP 43": "OD1" <-> "OD2" Residue "T GLU 55": "OE1" <-> "OE2" Residue "T GLU 57": "OE1" <-> "OE2" Residue "T GLU 68": "OE1" <-> "OE2" Residue "T GLU 75": "OE1" <-> "OE2" Residue "T ASP 78": "OD1" <-> "OD2" Residue "T TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 82": "OD1" <-> "OD2" Residue "U TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 39": "OD1" <-> "OD2" Residue "U ASP 43": "OD1" <-> "OD2" Residue "U GLU 49": "OE1" <-> "OE2" Residue "U GLU 55": "OE1" <-> "OE2" Residue "U GLU 61": "OE1" <-> "OE2" Residue "U GLU 68": "OE1" <-> "OE2" Residue "U TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 88": "OE1" <-> "OE2" Residue "V GLU 21": "OE1" <-> "OE2" Residue "V ARG 22": "NH1" <-> "NH2" Residue "V ASP 32": "OD1" <-> "OD2" Residue "V GLU 78": "OE1" <-> "OE2" Residue "V GLU 84": "OE1" <-> "OE2" Residue "V GLU 104": "OE1" <-> "OE2" Residue "W GLU 27": "OE1" <-> "OE2" Residue "W PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 61": "OD1" <-> "OD2" Residue "W GLU 89": "OE1" <-> "OE2" Residue "W GLU 91": "OE1" <-> "OE2" Residue "W GLU 111": "OE1" <-> "OE2" Residue "W PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 GLU 79": "OE1" <-> "OE2" Residue "X ARG 97": "NH1" <-> "NH2" Residue "X GLU 108": "OE1" <-> "OE2" Residue "X ASP 112": "OD1" <-> "OD2" Residue "X ARG 118": "NH1" <-> "NH2" Residue "X ASP 120": "OD1" <-> "OD2" Residue "X ASP 133": "OD1" <-> "OD2" Residue "X ARG 134": "NH1" <-> "NH2" Residue "X GLU 138": "OE1" <-> "OE2" Residue "X ARG 144": "NH1" <-> "NH2" Residue "X ARG 146": "NH1" <-> "NH2" Residue "X GLU 148": "OE1" <-> "OE2" Residue "X GLU 152": "OE1" <-> "OE2" Residue "X GLU 154": "OE1" <-> "OE2" Residue "Y GLU 13": "OE1" <-> "OE2" Residue "Y GLU 16": "OE1" <-> "OE2" Residue "Y TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 57": "NH1" <-> "NH2" Residue "Y GLU 81": "OE1" <-> "OE2" Residue "Y ARG 103": "NH1" <-> "NH2" Residue "Y TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 130": "OE1" <-> "OE2" 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 "Z GLU 92": "OE1" <-> "OE2" Residue "Z GLU 93": "OE1" <-> "OE2" Residue "Z GLU 108": "OE1" <-> "OE2" Residue "Z GLU 131": "OE1" <-> "OE2" Residue "Z GLU 132": "OE1" <-> "OE2" Residue "a GLU 4": "OE1" <-> "OE2" Residue "a ARG 59": "NH1" <-> "NH2" Residue "a ASP 70": "OD1" <-> "OD2" Residue "b ARG 3": "NH1" <-> "NH2" Residue "b ARG 57": "NH1" <-> "NH2" Residue "b ASP 64": "OD1" <-> "OD2" Residue "c GLU 6": "OE1" <-> "OE2" Residue "c GLU 37": "OE1" <-> "OE2" Residue "c GLU 41": "OE1" <-> "OE2" Residue "c ARG 44": "NH1" <-> "NH2" Residue "d ARG 51": "NH1" <-> "NH2" Residue "d TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 111": "OE1" <-> "OE2" Residue "d GLU 114": "OE1" <-> "OE2" Residue "d GLU 115": "OE1" <-> "OE2" Residue "e ARG 8": "NH1" <-> "NH2" Residue "e GLU 23": "OE1" <-> "OE2" Residue "e GLU 38": "OE1" <-> "OE2" Residue "e ARG 50": "NH1" <-> "NH2" Residue "e GLU 60": "OE1" <-> "OE2" Residue "e GLU 83": "OE1" <-> "OE2" Residue "f ASP 9": "OD1" <-> "OD2" Residue "f ARG 28": "NH1" <-> "NH2" Residue "f ASP 31": "OD1" <-> "OD2" Residue "f GLU 32": "OE1" <-> "OE2" Residue "f ARG 46": "NH1" <-> "NH2" Residue "f GLU 47": "OE1" <-> "OE2" Residue "f GLU 52": "OE1" <-> "OE2" Residue "g GLU 28": "OE1" <-> "OE2" Residue "g ASP 29": "OD1" <-> "OD2" Residue "g GLU 31": "OE1" <-> "OE2" Residue "g GLU 33": "OE1" <-> "OE2" Residue "g ASP 34": "OD1" <-> "OD2" Residue "g GLU 39": "OE1" <-> "OE2" Residue "g GLU 87": "OE1" <-> "OE2" Residue "g GLU 92": "OE1" <-> "OE2" Residue "g GLU 122": "OE1" <-> "OE2" Residue "h PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ARG 20": "NH1" <-> "NH2" Residue "h GLU 51": "OE1" <-> "OE2" Residue "h GLU 57": "OE1" <-> "OE2" Residue "h TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 62": "OE1" <-> "OE2" Residue "h 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 GLU 131": "OE1" <-> "OE2" Residue "i GLU 16": "OE1" <-> "OE2" Residue "i ARG 18": "NH1" <-> "NH2" Residue "i GLU 26": "OE1" <-> "OE2" Residue "i PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i GLU 114": "OE1" <-> "OE2" Residue "i GLU 121": "OE1" <-> "OE2" Residue "i ASP 124": "OD1" <-> "OD2" Residue "j PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j GLU 26": "OE1" <-> "OE2" Residue "j PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j GLU 62": "OE1" <-> "OE2" Residue "j ASP 70": "OD1" <-> "OD2" Residue "j GLU 71": "OE1" <-> "OE2" Residue "k GLU 14": "OE1" <-> "OE2" Residue "k ASP 17": "OD1" <-> "OD2" Residue "k GLU 24": "OE1" <-> "OE2" Residue "k GLU 29": "OE1" <-> "OE2" Residue "k GLU 33": "OE1" <-> "OE2" Residue "k ARG 38": "NH1" <-> "NH2" Residue "k ARG 41": "NH1" <-> "NH2" Residue "k TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ASP 7": "OD1" <-> "OD2" 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 ASP 63": "OD1" <-> "OD2" Residue "l GLU 75": "OE1" <-> "OE2" Residue "l TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ARG 142": "NH1" <-> "NH2" Residue "l GLU 151": "OE1" <-> "OE2" Residue "l GLU 157": "OE1" <-> "OE2" Residue "m ARG 39": "NH1" <-> "NH2" Residue "m GLU 45": "OE1" <-> "OE2" Residue "m ARG 71": "NH1" <-> "NH2" Residue "m PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m ASP 109": "OD1" <-> "OD2" Residue "m GLU 112": "OE1" <-> "OE2" Residue "m GLU 117": "OE1" <-> "OE2" Residue "n ARG 21": "NH1" <-> "NH2" Residue "n GLU 27": "OE1" <-> "OE2" Residue "n ARG 64": "NH1" <-> "NH2" 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 ARG 134": "NH1" <-> "NH2" Residue "n ARG 149": "NH1" <-> "NH2" Residue "n GLU 151": "OE1" <-> "OE2" Residue "n ASP 161": "OD1" <-> "OD2" Residue "n GLU 175": "OE1" <-> "OE2" Residue "o ARG 6": "NH1" <-> "NH2" Residue "o TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o GLU 32": "OE1" <-> "OE2" Residue "o ARG 36": "NH1" <-> "NH2" Residue "o ASP 56": "OD1" <-> "OD2" Residue "o ARG 97": "NH1" <-> "NH2" Residue "o ARG 103": "NH1" <-> "NH2" Residue "o ARG 105": "NH1" <-> "NH2" Residue "o ARG 106": "NH1" <-> "NH2" Residue "p ASP 5": "OD1" <-> "OD2" Residue "p TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p GLU 75": "OE1" <-> "OE2" Residue "p GLU 86": "OE1" <-> "OE2" Residue "p GLU 100": "OE1" <-> "OE2" Residue "p GLU 116": "OE1" <-> "OE2" Residue "p GLU 171": "OE1" <-> "OE2" Residue "q GLU 2": "OE1" <-> "OE2" Residue "q ARG 21": "NH1" <-> "NH2" Residue "q ARG 29": "NH1" <-> "NH2" Residue "q ASP 32": "OD1" <-> "OD2" Residue "q TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ASP 76": "OD1" <-> "OD2" Residue "q ASP 78": "OD1" <-> "OD2" Residue "q ARG 88": "NH1" <-> "NH2" Residue "q ASP 96": "OD1" <-> "OD2" Residue "q GLU 136": "OE1" <-> "OE2" Residue "r TYR 27": "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 "r TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s ASP 57": "OD1" <-> "OD2" Residue "s GLU 71": "OE1" <-> "OE2" Time to flip residues: 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 69480 Number of models: 1 Model: "" Number of chains: 114 Chain: "A" Number of atoms: 921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 921 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 1241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1241 Classifications: {'peptide': 155} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 144} Chain: "C" Number of atoms: 1721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1721 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 16, 'TRANS': 190} Chain: "D" Number of atoms: 3459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3459 Classifications: {'peptide': 430} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 401} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'2MR:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 1655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1655 Classifications: {'peptide': 213} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 191} Chain: "F" Number of atoms: 3319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3319 Classifications: {'peptide': 431} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 409} Chain: "G" Number of atoms: 5279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 688, 5279 Classifications: {'peptide': 688} Link IDs: {'PTRANS': 32, 'TRANS': 655} Chain: "H" Number of atoms: 2509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2509 Classifications: {'peptide': 318} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 295} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "I" Number of atoms: 1414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1414 Classifications: {'peptide': 176} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 165} Chain: "J" Number of atoms: 1337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1337 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 3, 'TRANS': 170} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "K" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 745 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 1, 'TRANS': 96} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 4780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4780 Classifications: {'peptide': 606} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 27, 'TRANS': 578} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'FME:plan-2': 1, 'PHE:plan': 1, 'ASN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "M" Number of atoms: 3654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3654 Classifications: {'peptide': 459} Link IDs: {'PCIS': 3, 'PTRANS': 17, 'TRANS': 438} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "N" Number of atoms: 2733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2733 Classifications: {'peptide': 347} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 325} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "O" Number of atoms: 2589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2589 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 15, 'TRANS': 304} Chain: "P" Number of atoms: 2747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2747 Classifications: {'peptide': 341} Link IDs: {'PTRANS': 22, 'TRANS': 318} Chain: "Q" Number of atoms: 1016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1016 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 6, 'TRANS': 118} Chain: "R" Number of atoms: 730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 730 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "S" Number of atoms: 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: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 945 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 9, 'TRANS': 103} 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: 898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 898 Classifications: {'peptide': 104} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 91} 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: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 644 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 3, 'TRANS': 76} Chain: "l" Number of atoms: 1304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1304 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 20, 'TRANS': 134} Chain: "m" Number of atoms: 1061 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1061 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 8, 'TRANS': 118} Chain: "n" Number of atoms: 1492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1492 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 15, 'TRANS': 156} Chain: "o" Number of atoms: 1035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 1035 Classifications: {'peptide': 120} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 112} Chain: "p" Number of atoms: 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: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 91 Unusual residues: {'LMT': 2, 'PC1': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: 97 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 97 Unusual residues: {'PC1': 2, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 129 Unusual residues: {'3PE': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'SF4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 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: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 106 Unusual residues: {'CDL': 1, 'LMT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 29 Chain: "L" Number of atoms: 317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 317 Unusual residues: {'3PE': 2, 'CDL': 1, 'LMT': 3, 'PC1': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 44 Chain: "M" Number of atoms: 202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 202 Unusual residues: {'3PE': 2, 'LMT': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "N" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 87 Unusual residues: {'3PE': 2, 'I49': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 32 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: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 85 Unusual residues: {'3PE': 1, 'NDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 14 Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'EHZ': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "U" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'EHZ': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "X" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Chain: "Y" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 140 Unusual residues: {'3PE': 1, 'LMT': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} 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: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 102 Unusual residues: {'3PE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 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: "r" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 76 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 24 Chain: "A" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 30 Classifications: {'water': 30} Link IDs: {None: 29} Chain: "B" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 65 Classifications: {'water': 65} Link IDs: {None: 64} Chain: "C" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 92 Classifications: {'water': 92} Link IDs: {None: 91} Chain: "D" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 168 Classifications: {'water': 168} Link IDs: {None: 167} Chain: "E" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "F" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 63 Classifications: {'water': 63} Link IDs: {None: 62} Chain: "G" Number of atoms: 203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 203 Classifications: {'water': 203} Link IDs: {None: 202} Chain: "H" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 70 Classifications: {'water': 70} Link IDs: {None: 69} Chain: "I" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 92 Classifications: {'water': 92} Link IDs: {None: 91} Chain: "J" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "K" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "L" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 52 Classifications: {'water': 52} Link IDs: {None: 51} Chain: "M" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 65 Classifications: {'water': 65} Link IDs: {None: 64} Chain: "N" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 52 Classifications: {'water': 52} Link IDs: {None: 51} Chain: "O" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "P" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 80 Classifications: {'water': 80} Link IDs: {None: 79} Chain: "Q" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 64 Classifications: {'water': 64} Link IDs: {None: 63} Chain: "R" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 44 Classifications: {'water': 44} Link IDs: {None: 43} Chain: "S" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "U" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "V" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "W" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 28 Classifications: {'water': 28} Link IDs: {None: 27} Chain: "Y" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "Z" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "a" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "b" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "d" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "e" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "f" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "g" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "h" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 23 Classifications: {'water': 23} Link IDs: {None: 22} Chain: "i" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "j" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "k" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "l" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "m" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "n" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} 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: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "q" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 47 Classifications: {'water': 47} Link IDs: {None: 46} Chain: "r" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 33 Classifications: {'water': 33} Link IDs: {None: 32} Chain: "s" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1668 SG CYS B 119 95.742 93.983 203.258 1.00 24.56 S ATOM 1898 SG CYS B 149 93.548 91.403 207.817 1.00 23.56 S ATOM 1164 SG CYS B 54 90.286 90.570 202.062 1.00 27.18 S ATOM 1170 SG CYS B 55 89.860 96.036 205.322 1.00 26.53 S ATOM 8146 SG CYS E 103 114.214 43.768 256.918 1.00 46.82 S ATOM 8180 SG CYS E 108 112.661 41.069 258.805 1.00 46.94 S ATOM 8460 SG CYS E 144 116.503 40.623 253.436 1.00 44.30 S ATOM 8483 SG CYS E 148 115.234 37.848 254.418 1.00 47.29 S ATOM 11701 SG CYS F 362 119.071 51.301 233.646 1.00 30.12 S ATOM 11721 SG CYS F 365 116.221 50.570 238.453 1.00 31.49 S ATOM 12045 SG CYS F 405 120.791 46.104 237.439 1.00 33.15 S ATOM 11682 SG CYS F 359 122.707 52.000 239.104 1.00 33.18 S ATOM 13142 SG CYS G 114 115.288 70.110 225.038 1.00 26.88 S ATOM 13081 SG CYS G 105 109.317 72.417 226.889 1.00 25.96 S ATOM 13102 SG CYS G 108 114.896 74.908 229.104 1.00 26.68 S ATOM 13474 SG CYS G 156 123.660 63.958 229.641 1.00 28.82 S ATOM 13451 SG CYS G 153 120.848 66.036 235.376 1.00 28.35 S ATOM 13498 SG CYS G 159 127.027 67.065 233.920 1.00 31.20 S ATOM 13828 SG CYS G 203 122.470 69.930 230.242 1.00 28.86 S ATOM 12587 SG CYS G 41 124.145 57.248 227.189 1.00 28.43 S ATOM 12673 SG CYS G 52 120.349 57.735 226.200 1.00 28.28 S ATOM 12698 SG CYS G 55 121.888 53.338 222.802 1.00 30.30 S ATOM 12799 SG CYS G 69 125.166 54.038 223.901 1.00 31.01 S ATOM 21058 SG CYS I 119 96.658 85.364 213.636 1.00 22.82 S ATOM 21032 SG CYS I 116 96.969 91.908 214.673 1.00 22.91 S ATOM 21079 SG CYS I 122 98.223 87.357 219.174 1.00 24.15 S ATOM 20806 SG CYS I 87 102.308 88.306 214.045 1.00 23.51 S ATOM 21108 SG CYS I 126 100.878 83.927 226.584 1.00 25.28 S ATOM 20737 SG CYS I 77 105.714 88.229 227.713 1.00 26.00 S ATOM 20779 SG CYS I 83 104.155 86.677 221.651 1.00 24.80 S ATOM 20756 SG CYS I 80 106.319 81.908 225.076 1.00 25.59 S ATOM 41578 SG CYS R 59 102.506 78.928 241.595 1.00 32.61 S ATOM 41756 SG CYS R 84 105.554 79.697 239.561 1.00 32.74 S ATOM 41778 SG CYS R 87 103.269 82.305 240.393 1.00 30.94 S Time building chain proxies: 27.36, per 1000 atoms: 0.39 Number of scatterers: 69480 At special positions: 0 Unit cell: (184.943, 197.37, 290.207, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 11 Type Number sf(0) I 1 52.95 Zn 1 29.99 Fe 28 26.01 K 1 19.00 Cl 1 17.00 S 468 16.00 P 37 15.00 Mg 1 11.99 O 13805 8.00 N 11184 7.00 C 43953 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=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 23.94 Conformation dependent library (CDL) restraints added in 8.9 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E 301 " pdb="FE1 FES E 301 " - pdb=" SG CYS E 103 " pdb="FE1 FES E 301 " - pdb=" SG CYS E 108 " pdb="FE2 FES E 301 " - pdb=" SG CYS E 144 " pdb="FE2 FES E 301 " - pdb=" SG CYS E 148 " pdb=" FES G 803 " pdb="FE1 FES G 803 " - pdb=" SG CYS G 52 " pdb="FE2 FES G 803 " - pdb=" SG CYS G 55 " pdb="FE2 FES G 803 " - pdb=" SG CYS G 69 " pdb="FE1 FES G 803 " - pdb=" SG CYS G 41 " pdb=" SF4 B 201 " pdb="FE1 SF4 B 201 " - pdb=" SG CYS B 119 " pdb="FE2 SF4 B 201 " - pdb=" SG CYS B 149 " 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="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="FE3 SF4 F 502 " - pdb=" SG CYS F 405 " pdb=" SF4 G 801 " pdb="FE3 SF4 G 801 " - pdb=" NE2 HIS G 101 " pdb="FE1 SF4 G 801 " - pdb=" SG CYS G 114 " pdb="FE4 SF4 G 801 " - pdb=" SG CYS G 108 " pdb="FE2 SF4 G 801 " - pdb=" SG CYS G 105 " pdb=" SF4 G 802 " pdb="FE4 SF4 G 802 " - pdb=" SG CYS G 203 " pdb="FE3 SF4 G 802 " - pdb=" SG CYS G 159 " pdb="FE2 SF4 G 802 " - pdb=" SG CYS G 153 " pdb="FE1 SF4 G 802 " - pdb=" SG CYS G 156 " pdb=" SF4 I 201 " pdb="FE3 SF4 I 201 " - pdb=" SG CYS I 122 " pdb="FE2 SF4 I 201 " - pdb=" SG CYS I 116 " pdb="FE4 SF4 I 201 " - pdb=" SG CYS I 87 " pdb="FE1 SF4 I 201 " - pdb=" SG CYS I 119 " pdb=" SF4 I 202 " pdb="FE1 SF4 I 202 " - pdb=" SG CYS I 126 " pdb="FE3 SF4 I 202 " - pdb=" SG CYS I 83 " pdb="FE2 SF4 I 202 " - pdb=" SG CYS I 77 " pdb="FE4 SF4 I 202 " - 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 16194 Ramachandran restraints generated. 8097 Oldfield, 0 Emsley, 8097 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15416 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 367 helices and 30 sheets defined 54.2% alpha, 4.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.33 Creating SS restraints... Processing helix chain 'A' and resid 3 through 24 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: 3.563A pdb=" N LEU A 64 " --> pdb=" O ILE A 60 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA A 70 " --> pdb=" O ASP A 66 " (cutoff:3.500A) Proline residue: A 74 - end of helix removed outlier: 5.423A pdb=" N TRP A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLN A 80 " --> pdb=" O PRO A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 107 Processing helix chain 'B' and resid 26 through 44 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 168 Processing helix chain 'B' and resid 172 through 177 Processing helix chain 'C' and resid 16 through 32 Processing helix chain 'C' and resid 54 through 66 removed outlier: 4.648A pdb=" N ILE C 58 " --> pdb=" O ASP C 55 " (cutoff:3.500A) Proline residue: C 59 - end of helix removed outlier: 3.645A pdb=" N THR C 62 " --> pdb=" O PRO C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 138 removed outlier: 3.935A pdb=" N TRP C 129 " --> pdb=" O ALA C 126 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N MET C 137 " --> pdb=" O ILE C 134 " (cutoff:3.500A) removed outlier: 3.821A 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: 3.785A pdb=" N GLN D 13 " --> pdb=" O GLU D 9 " (cutoff:3.500A) removed outlier: 4.451A 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: 3.932A pdb=" N GLU D 92 " --> pdb=" O GLU D 88 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N TYR D 93 " --> pdb=" O LYS D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 104 Proline residue: D 101 - end of helix removed outlier: 3.940A pdb=" N ASP D 104 " --> pdb=" O LEU D 100 " (cutoff:3.500A) 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: 3.801A pdb=" N GLU D 173 " --> pdb=" O TRP D 169 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N PHE D 180 " --> pdb=" O LYS D 176 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 229 removed outlier: 3.857A pdb=" N ASN D 217 " --> pdb=" O GLU D 213 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N SER D 219 " --> pdb=" O SER D 215 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N LEU D 220 " --> pdb=" O LYS D 216 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ARG D 221 " --> pdb=" O ASN D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 239 Processing helix chain 'D' and resid 247 through 252 Processing helix chain 'D' and resid 257 through 263 removed outlier: 4.742A pdb=" N GLY D 262 " --> pdb=" O MET D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 272 No H-bonds generated for 'chain 'D' and resid 269 through 272' Processing helix chain 'D' and resid 278 through 280 No H-bonds generated for 'chain 'D' and resid 278 through 280' Processing helix chain 'D' and resid 293 through 317 Processing helix chain 'D' and resid 335 through 338 No H-bonds generated for 'chain 'D' and resid 335 through 338' Processing helix chain 'D' and resid 342 through 351 Processing helix chain 'D' and resid 394 through 405 removed outlier: 4.717A pdb=" N ASP D 403 " --> pdb=" O LEU D 399 " (cutoff:3.500A) removed outlier: 5.086A 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: 3.608A pdb=" N ASN E 37 " --> pdb=" O ALA E 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 58 removed outlier: 4.394A pdb=" N LEU E 48 " --> pdb=" O ALA E 45 " (cutoff:3.500A) Proline residue: E 49 - end of helix Processing helix chain 'E' and resid 63 through 73 Processing helix chain 'E' and resid 77 through 86 Processing helix chain 'E' and resid 106 through 111 removed outlier: 3.693A 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 38 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: 3.713A pdb=" N PHE F 81 " --> pdb=" O LEU F 77 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N MET F 82 " --> pdb=" O LYS F 78 " (cutoff:3.500A) Processing helix chain 'F' and resid 106 through 113 Processing helix chain 'F' and resid 115 through 129 Processing helix chain 'F' and resid 143 through 158 Processing helix chain 'F' and resid 166 through 168 No H-bonds generated for 'chain 'F' and resid 166 through 168' Processing helix chain 'F' and resid 184 through 187 Processing helix chain 'F' and resid 189 through 196 Processing helix chain 'F' and resid 215 through 217 No H-bonds generated for 'chain 'F' and resid 215 through 217' Processing helix chain 'F' and resid 225 through 229 Processing helix chain 'F' and resid 231 through 237 Processing helix chain 'F' and resid 239 through 244 Processing helix chain 'F' and resid 276 through 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: 4.363A pdb=" N ASP F 370 " --> pdb=" O ARG F 366 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG F 381 " --> pdb=" O ALA F 377 " (cutoff:3.500A) Processing helix chain 'F' and resid 386 through 399 Processing helix chain 'F' and resid 407 through 437 Proline residue: F 414 - end of helix removed outlier: 3.557A 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: 3.879A pdb=" N VAL G 33 " --> pdb=" O ALA G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 84 through 99 Processing helix chain 'G' and resid 105 through 107 No H-bonds generated for 'chain 'G' and resid 105 through 107' Processing helix chain 'G' and resid 115 through 123 Processing helix chain 'G' and resid 150 through 152 No H-bonds generated for 'chain 'G' and resid 150 through 152' Processing helix chain 'G' and resid 158 through 165 Processing helix chain 'G' and resid 178 through 180 No H-bonds generated for 'chain 'G' and resid 178 through 180' Processing helix chain 'G' and resid 196 through 202 removed outlier: 3.614A 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: 5.236A pdb=" N TYR G 271 " --> pdb=" O THR G 267 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ASP G 272 " --> pdb=" O ARG G 268 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N GLY G 273 " --> pdb=" O PHE G 269 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N LEU G 274 " --> pdb=" O ALA G 270 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N LYS G 275 " --> pdb=" O TYR G 271 " (cutoff:3.500A) Processing helix chain 'G' and resid 296 through 309 removed outlier: 3.527A 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: 3.676A 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 372 Processing helix chain 'G' and resid 384 through 387 No H-bonds generated for 'chain 'G' and resid 384 through 387' Processing helix chain 'G' and resid 389 through 401 Processing helix chain 'G' and resid 426 through 434 removed outlier: 3.517A pdb=" N ILE G 432 " --> pdb=" O LEU G 429 " (cutoff:3.500A) Processing helix chain 'G' and resid 438 through 444 removed outlier: 3.689A pdb=" N VAL G 442 " --> pdb=" O PRO G 438 " (cutoff:3.500A) Processing helix chain 'G' and resid 457 through 459 No H-bonds generated for 'chain 'G' and resid 457 through 459' Processing helix chain 'G' and resid 463 through 479 Processing helix chain 'G' and resid 499 through 504 Processing helix chain 'G' and resid 512 through 516 Processing helix chain 'G' and resid 554 through 556 No H-bonds generated for 'chain 'G' and resid 554 through 556' Processing helix chain 'G' and resid 566 through 568 No H-bonds generated for 'chain 'G' and resid 566 through 568' Processing helix chain 'G' and resid 596 through 606 Processing helix chain 'G' and resid 616 through 626 Processing helix chain 'G' and resid 628 through 631 removed outlier: 3.777A pdb=" N VAL G 631 " --> pdb=" O PRO G 628 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 628 through 631' Processing helix chain 'G' and resid 642 through 650 Processing helix chain 'G' and resid 668 through 670 No H-bonds generated for 'chain 'G' and resid 668 through 670' Processing helix chain 'G' and resid 676 through 680 Processing helix chain 'G' and resid 682 through 690 Processing helix chain 'H' and resid 3 through 32 Proline residue: H 12 - end of helix removed outlier: 3.657A 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: 4.212A pdb=" N TRP H 86 " --> pdb=" O ALA H 82 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 123 removed outlier: 3.576A pdb=" N VAL H 113 " --> pdb=" O SER H 109 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N TYR H 114 " --> pdb=" O SER H 110 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N SER H 115 " --> pdb=" O LEU H 111 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ILE H 116 " --> pdb=" O ALA H 112 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER H 119 " --> pdb=" O SER H 115 " (cutoff:3.500A) Processing helix chain 'H' and resid 126 through 157 removed outlier: 4.933A pdb=" N VAL H 144 " --> pdb=" O ILE H 140 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N THR H 145 " --> pdb=" O SER H 141 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N MET H 156 " --> pdb=" O SER H 152 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER H 157 " --> pdb=" O VAL H 153 " (cutoff:3.500A) Processing helix chain 'H' and resid 162 through 168 removed outlier: 4.005A pdb=" N ILE H 166 " --> pdb=" O LEU H 162 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR H 167 " --> pdb=" O SER H 163 " (cutoff:3.500A) Processing helix chain 'H' and resid 174 through 177 No H-bonds generated for 'chain 'H' and resid 174 through 177' Processing helix chain 'H' and resid 179 through 192 Processing helix chain 'H' and resid 204 through 207 No H-bonds generated for 'chain 'H' and resid 204 through 207' Processing helix chain 'H' and resid 210 through 212 No H-bonds generated for 'chain 'H' and resid 210 through 212' Processing helix chain 'H' and resid 217 through 242 removed outlier: 3.613A 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: 3.563A pdb=" N MET H 286 " --> pdb=" O TYR H 282 " (cutoff:3.500A) Processing helix chain 'H' and resid 293 through 310 Proline residue: H 308 - end of helix Processing helix chain 'I' and resid 14 through 26 Processing helix chain 'I' and resid 28 through 41 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: 5.540A pdb=" N ALA I 163 " --> pdb=" O ASP I 159 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N GLU I 164 " --> pdb=" O LYS I 160 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA I 167 " --> pdb=" O ALA I 163 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N LEU I 174 " --> pdb=" O GLN I 170 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N TYR I 175 " --> pdb=" O ALA I 171 " (cutoff:3.500A) Processing helix chain 'J' and resid 5 through 21 Processing helix chain 'J' and resid 26 through 47 removed outlier: 3.510A pdb=" N PHE J 47 " --> pdb=" O ILE J 43 " (cutoff:3.500A) Processing helix chain 'J' and resid 50 through 74 Processing helix chain 'J' and resid 87 through 107 Processing helix chain 'J' and resid 124 through 127 removed outlier: 3.627A pdb=" N ILE J 127 " --> pdb=" O ASP J 124 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 124 through 127' Processing helix chain 'J' and resid 138 through 147 removed outlier: 3.954A pdb=" N LEU J 146 " --> pdb=" O GLY J 142 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N TYR J 147 " --> pdb=" O ILE J 143 " (cutoff:3.500A) Processing helix chain 'J' and resid 151 through 171 Processing helix chain 'K' and resid 3 through 20 removed outlier: 3.654A 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: 3.536A pdb=" N MET K 58 " --> pdb=" O LEU K 55 " (cutoff:3.500A) Proline residue: K 60 - end of helix removed outlier: 3.609A pdb=" N CYS K 69 " --> pdb=" O PHE K 66 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA K 72 " --> pdb=" O CYS K 69 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU K 77 " --> pdb=" O GLY K 74 " (cutoff:3.500A) Processing helix chain 'K' and resid 90 through 92 No H-bonds generated for 'chain 'K' and resid 90 through 92' Processing helix chain 'K' and resid 95 through 97 No H-bonds generated for 'chain 'K' and resid 95 through 97' Processing helix chain 'L' and resid 3 through 24 removed outlier: 4.304A pdb=" N LEU L 12 " --> pdb=" O SER L 8 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR L 16 " --> pdb=" O LEU L 12 " (cutoff:3.500A) Proline residue: L 18 - end of helix Processing helix chain 'L' and resid 29 through 57 removed outlier: 3.931A pdb=" N TYR L 32 " --> pdb=" O PRO L 29 " (cutoff:3.500A) Proline residue: L 33 - end of helix removed outlier: 3.569A pdb=" N ILE L 49 " --> pdb=" O THR L 46 " (cutoff:3.500A) Proline residue: L 50 - end of helix removed outlier: 3.531A 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: 3.727A 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 193 removed outlier: 4.271A pdb=" N GLY L 181 " --> pdb=" O ILE L 177 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N PHE L 182 " --> pdb=" O GLY L 178 " (cutoff:3.500A) Processing helix chain 'L' and resid 198 through 204 Processing helix chain 'L' and resid 210 through 223 Processing helix chain 'L' and resid 231 through 238 removed outlier: 3.501A pdb=" N SER L 235 " --> pdb=" O PRO L 231 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N MET L 237 " --> pdb=" O LEU L 233 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N GLU L 238 " --> pdb=" O PRO L 234 " (cutoff:3.500A) Processing helix chain 'L' and resid 241 through 249 Processing helix chain 'L' and resid 251 through 262 removed outlier: 3.634A pdb=" N ALA L 255 " --> pdb=" O THR L 251 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N GLY L 256 " --> pdb=" O MET L 252 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N ILE L 257 " --> pdb=" O VAL L 253 " (cutoff:3.500A) Processing helix chain 'L' and resid 264 through 269 removed outlier: 4.517A pdb=" N ASN L 269 " --> pdb=" O PRO L 265 " (cutoff:3.500A) Processing helix chain 'L' and resid 271 through 294 removed outlier: 4.592A 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: 3.984A pdb=" N PHE L 334 " --> pdb=" O CYS L 330 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N PHE L 335 " --> pdb=" O THR L 331 " (cutoff:3.500A) Processing helix chain 'L' and resid 356 through 358 No H-bonds generated for 'chain 'L' and resid 356 through 358' Processing helix chain 'L' and resid 367 through 380 Processing helix chain 'L' and resid 387 through 399 removed outlier: 3.977A pdb=" N LYS L 392 " --> pdb=" O PHE L 389 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N ASP L 393 " --> pdb=" O TYR L 390 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLU L 397 " --> pdb=" O LEU L 394 " (cutoff:3.500A) Processing helix chain 'L' and resid 406 through 430 removed outlier: 3.551A pdb=" N ALA L 420 " --> pdb=" O THR L 416 " (cutoff:3.500A) Processing helix chain 'L' and resid 448 through 471 removed outlier: 3.520A pdb=" N LEU L 457 " --> pdb=" O SER L 453 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N GLY L 465 " --> pdb=" O SER L 461 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N TYR L 466 " --> pdb=" O LEU L 462 " (cutoff:3.500A) Processing helix chain 'L' and resid 484 through 487 No H-bonds generated for 'chain 'L' and resid 484 through 487' Processing helix chain 'L' and resid 489 through 509 removed outlier: 3.732A pdb=" N THR L 508 " --> pdb=" O ILE L 504 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N LYS L 509 " --> pdb=" O SER L 505 " (cutoff:3.500A) Processing helix chain 'L' and resid 518 through 524 Processing helix chain 'L' and resid 526 through 547 Proline residue: L 530 - end of helix removed outlier: 3.898A pdb=" N MET L 533 " --> pdb=" O PRO L 530 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N HIS L 534 " --> pdb=" O THR L 531 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU L 536 " --> pdb=" O MET L 533 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N ALA L 537 " --> pdb=" O HIS L 534 " (cutoff:3.500A) Proline residue: L 538 - end of helix removed outlier: 3.618A pdb=" N ASN L 541 " --> pdb=" O PRO L 538 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER L 543 " --> pdb=" O MET L 540 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS L 547 " --> pdb=" O MET L 544 " (cutoff:3.500A) Processing helix chain 'L' and resid 557 through 560 No H-bonds generated for 'chain 'L' and resid 557 through 560' Processing helix chain 'L' and resid 563 through 578 Processing helix chain 'L' and resid 584 through 600 Processing helix chain 'M' and resid 5 through 16 removed outlier: 4.255A pdb=" N MET M 12 " --> pdb=" O THR M 8 " (cutoff:3.500A) Proline residue: M 13 - end of helix Processing helix chain 'M' and resid 23 through 42 removed outlier: 4.195A pdb=" N LEU M 39 " --> pdb=" O SER M 35 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N LEU M 40 " --> pdb=" O PHE M 36 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N LEU M 41 " --> pdb=" O THR M 37 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N MET M 42 " --> pdb=" O SER M 38 " (cutoff:3.500A) Processing helix chain 'M' and resid 60 through 80 Proline residue: M 64 - end of helix removed outlier: 3.515A pdb=" N LEU M 73 " --> pdb=" O THR M 69 " (cutoff:3.500A) Proline residue: M 74 - end of helix Processing helix chain 'M' and resid 89 through 109 Processing helix chain 'M' and resid 115 through 136 removed outlier: 4.697A pdb=" N LEU M 126 " --> pdb=" O PHE M 122 " (cutoff:3.500A) removed outlier: 4.427A 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: 3.519A pdb=" N PHE M 151 " --> pdb=" O TYR M 148 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N TYR M 152 " --> pdb=" O PHE M 149 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR M 153 " --> pdb=" O LEU M 150 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU M 154 " --> pdb=" O PHE M 151 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA M 155 " --> pdb=" O TYR M 152 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N LEU M 158 " --> pdb=" O ALA M 155 " (cutoff:3.500A) Proline residue: M 159 - end of helix removed outlier: 3.758A pdb=" N VAL M 171 " --> pdb=" O GLN M 168 " (cutoff:3.500A) Processing helix chain 'M' and resid 176 through 182 removed outlier: 3.751A pdb=" N TYR M 181 " --> pdb=" O LEU M 177 " (cutoff:3.500A) Processing helix chain 'M' and resid 190 through 206 removed outlier: 4.739A pdb=" N ALA M 202 " --> pdb=" O ALA M 198 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N PHE M 203 " --> pdb=" O CYS M 199 " (cutoff:3.500A) Processing helix chain 'M' and resid 214 through 222 removed outlier: 3.885A pdb=" N LYS M 218 " --> pdb=" O LEU M 214 " (cutoff:3.500A) Processing helix chain 'M' and resid 225 through 233 Processing helix chain 'M' and resid 235 through 250 removed outlier: 4.071A pdb=" N GLY M 239 " --> pdb=" O LEU M 235 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLY M 240 " --> pdb=" O LEU M 236 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N LEU M 248 " --> pdb=" O LEU M 244 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N ILE M 249 " --> pdb=" O ARG M 245 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU M 250 " --> pdb=" O ILE M 246 " (cutoff:3.500A) Processing helix chain 'M' and resid 253 through 257 removed outlier: 3.646A pdb=" N MET M 257 " --> pdb=" O THR M 254 " (cutoff:3.500A) Processing helix chain 'M' and resid 259 through 278 removed outlier: 3.851A pdb=" N ILE M 270 " --> pdb=" O LEU M 266 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N CYS M 276 " --> pdb=" O THR M 272 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU M 277 " --> pdb=" O SER M 273 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ARG M 278 " --> pdb=" O SER M 274 " (cutoff:3.500A) Processing helix chain 'M' and resid 282 through 303 removed outlier: 3.902A pdb=" N LEU M 296 " --> pdb=" O SER M 292 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL M 297 " --> pdb=" O HIS M 293 " (cutoff:3.500A) Processing helix chain 'M' and resid 306 through 337 removed outlier: 3.528A 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: 3.633A pdb=" N MET M 396 " --> pdb=" O ILE M 393 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY M 397 " --> pdb=" O ILE M 394 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N THR M 403 " --> pdb=" O MET M 400 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TYR M 406 " --> pdb=" O THR M 403 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU M 408 " --> pdb=" O LEU M 405 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N MET M 410 " --> pdb=" O SER M 407 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N MET M 413 " --> pdb=" O MET M 410 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N THR M 414 " --> pdb=" O LEU M 411 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLN M 415 " --> pdb=" O ILE M 412 " (cutoff:3.500A) Processing helix chain 'M' and resid 431 through 454 removed outlier: 3.648A pdb=" N HIS M 440 " --> pdb=" O LEU M 436 " (cutoff:3.500A) Proline residue: M 443 - end of helix removed outlier: 4.069A pdb=" N THR M 448 " --> pdb=" O LEU M 444 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N LEU M 449 " --> pdb=" O LEU M 445 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ASN M 450 " --> pdb=" O LEU M 446 " (cutoff:3.500A) Proline residue: M 451 - end of helix removed outlier: 5.173A 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: 3.594A 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: 4.071A 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: 4.307A pdb=" N ALA N 137 " --> pdb=" O GLN N 134 " (cutoff:3.500A) Proline residue: N 138 - end of helix removed outlier: 3.515A pdb=" N TYR N 143 " --> pdb=" O SER N 140 " (cutoff:3.500A) removed outlier: 4.608A 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: 3.688A pdb=" N LEU N 170 " --> pdb=" O GLY N 166 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ASN N 171 " --> pdb=" O TRP N 167 " (cutoff:3.500A) Processing helix chain 'N' and resid 175 through 192 removed outlier: 3.581A pdb=" N TRP N 189 " --> pdb=" O ALA N 185 " (cutoff:3.500A) Processing helix chain 'N' and resid 198 through 222 removed outlier: 3.550A pdb=" N ASN N 222 " --> pdb=" O MET N 218 " (cutoff:3.500A) Processing helix chain 'N' and resid 227 through 235 removed outlier: 3.659A pdb=" N HIS N 232 " --> pdb=" O LEU N 228 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N THR N 233 " --> pdb=" O SER N 229 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N TRP N 234 " --> pdb=" O LEU N 230 " (cutoff:3.500A) removed outlier: 5.508A 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: 3.571A pdb=" N LYS N 272 " --> pdb=" O GLU N 269 " (cutoff:3.500A) Processing helix chain 'N' and resid 277 through 300 removed outlier: 3.594A pdb=" N LEU N 287 " --> pdb=" O ALA N 283 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N LEU N 288 " --> pdb=" O ILE N 284 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ASN N 289 " --> pdb=" O THR N 285 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU N 296 " --> pdb=" O PHE N 292 " (cutoff:3.500A) Processing helix chain 'N' and resid 309 through 316 removed outlier: 3.621A pdb=" N GLN N 316 " --> pdb=" O MET N 313 " (cutoff:3.500A) Processing helix chain 'N' and resid 326 through 334 Processing helix chain 'N' and resid 337 through 346 Proline residue: N 341 - end of helix Processing helix chain 'O' and resid 5 through 10 Processing helix chain 'O' and resid 14 through 17 No H-bonds generated for 'chain 'O' and resid 14 through 17' Processing helix chain 'O' and resid 35 through 46 Processing helix chain 'O' and resid 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 162 removed outlier: 3.526A pdb=" N VAL O 158 " --> pdb=" O GLN O 154 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N CYS O 161 " --> pdb=" O LYS O 157 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N GLU O 162 " --> pdb=" O VAL O 158 " (cutoff:3.500A) Processing helix chain 'O' and resid 176 through 186 Processing helix chain 'O' and resid 191 through 193 No H-bonds generated for 'chain 'O' and resid 191 through 193' Processing helix chain 'O' and resid 196 through 208 Processing helix chain 'O' and resid 210 through 216 removed outlier: 3.864A pdb=" N GLU O 216 " --> pdb=" O PRO O 212 " (cutoff:3.500A) Processing helix chain 'O' and resid 225 through 229 removed outlier: 3.566A pdb=" N GLN O 229 " --> pdb=" O ALA O 225 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 225 through 229' Processing helix chain 'O' and resid 231 through 240 removed outlier: 3.679A 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: 3.882A 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 297 Processing helix chain 'O' and resid 310 through 312 No H-bonds generated for 'chain 'O' and resid 310 through 312' Processing helix chain 'O' and resid 317 through 319 No H-bonds generated for 'chain 'O' and resid 317 through 319' Processing helix chain 'P' and resid 3 through 5 No H-bonds generated for 'chain 'P' and resid 3 through 5' Processing helix chain 'P' and resid 29 through 41 removed outlier: 4.042A pdb=" N TYR P 33 " --> pdb=" O PHE P 29 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N MET P 41 " --> pdb=" O HIS P 37 " (cutoff:3.500A) Processing helix chain 'P' and resid 53 through 62 removed outlier: 5.089A pdb=" N HIS P 58 " --> pdb=" O ASP P 55 " (cutoff:3.500A) Proline residue: P 61 - end of helix Processing helix chain 'P' and resid 78 through 85 Processing helix chain 'P' and resid 106 through 110 Processing helix chain 'P' and resid 112 through 123 Processing helix chain 'P' and resid 144 through 159 Processing helix chain 'P' and resid 179 through 188 removed outlier: 4.257A pdb=" N ARG P 186 " --> pdb=" O PHE P 182 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N TRP P 187 " --> pdb=" O ALA P 183 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N PHE P 188 " --> pdb=" O ASN P 184 " (cutoff:3.500A) Processing helix chain 'P' and resid 194 through 197 Processing helix chain 'P' and resid 207 through 219 Processing helix chain 'P' and resid 221 through 223 No H-bonds generated for 'chain 'P' and resid 221 through 223' Processing helix chain 'P' and resid 238 through 248 Processing helix chain 'P' and resid 260 through 272 removed outlier: 3.552A 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 301 through 303 No H-bonds generated for 'chain 'P' and resid 301 through 303' Processing helix chain 'P' and resid 310 through 321 removed outlier: 5.435A pdb=" N ILE P 315 " --> pdb=" O GLU P 311 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N GLU P 316 " --> pdb=" O LEU P 312 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N ARG P 320 " --> pdb=" O GLU P 316 " (cutoff:3.500A) removed outlier: 5.263A 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 27 through 31 removed outlier: 3.916A pdb=" N LYS Q 31 " --> pdb=" O GLU Q 28 " (cutoff:3.500A) Processing helix chain 'Q' and resid 50 through 52 No H-bonds generated for 'chain 'Q' and resid 50 through 52' Processing helix chain 'Q' and resid 89 through 99 Processing helix chain 'Q' and resid 118 through 122 Processing helix chain 'R' and resid 23 through 28 Processing helix chain 'R' and resid 40 through 46 removed outlier: 3.562A pdb=" N ALA R 45 " --> pdb=" O ILE R 41 " (cutoff:3.500A) Processing helix chain 'R' and resid 64 through 66 No H-bonds generated for 'chain 'R' and resid 64 through 66' Processing helix chain 'S' and resid 27 through 46 removed outlier: 4.921A pdb=" N GLY S 31 " --> pdb=" O GLY S 28 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE S 36 " --> pdb=" O ARG S 33 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ARG S 39 " --> pdb=" O ILE S 36 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N TYR S 40 " --> pdb=" O GLU S 37 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N VAL S 41 " --> pdb=" O LYS S 38 " (cutoff:3.500A) Processing helix chain 'S' and resid 69 through 71 No H-bonds generated for 'chain 'S' and resid 69 through 71' Processing helix chain 'S' and resid 83 through 95 Processing helix chain 'T' and resid 8 through 21 removed outlier: 3.944A pdb=" N ASP T 13 " --> pdb=" O GLU T 9 " (cutoff:3.500A) Processing helix chain 'T' and resid 27 through 29 No H-bonds generated for 'chain 'T' and resid 27 through 29' Processing helix chain 'T' and resid 44A through 58 Processing helix chain 'T' and resid 64 through 69 removed outlier: 4.617A pdb=" N LYS T 69 " --> pdb=" O ILE T 65 " (cutoff:3.500A) Processing helix chain 'T' and resid 73 through 81 Processing helix chain 'U' and resid 8 through 21 Processing helix chain 'U' and resid 44A through 58 Processing helix chain 'U' and resid 64 through 69 removed outlier: 4.464A 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: 4.196A pdb=" N HIS V 36 " --> pdb=" O ASP V 32 " (cutoff:3.500A) Processing helix chain 'V' and resid 42 through 59 Processing helix chain 'V' and resid 64 through 71 Processing helix chain 'V' and resid 76 through 96 removed outlier: 3.797A pdb=" N GLN V 95 " --> pdb=" O ARG V 91 " (cutoff:3.500A) Processing helix chain 'W' and resid 25 through 50 removed outlier: 3.513A pdb=" N ARG W 30 " --> pdb=" O ASN W 26 " (cutoff:3.500A) Proline residue: W 44 - end of helix Processing helix chain 'W' and resid 56 through 70 removed outlier: 4.204A pdb=" N ASN W 70 " --> pdb=" O MET W 66 " (cutoff:3.500A) Processing helix chain 'W' and resid 76 through 94 Processing helix chain 'W' and resid 100 through 106 removed outlier: 4.337A pdb=" N PHE W 106 " --> pdb=" O HIS W 102 " (cutoff:3.500A) Processing helix chain 'W' and resid 118 through 124 Processing helix chain 'X' and resid 21 through 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 54 No H-bonds generated for 'chain 'X' and resid 52 through 54' Processing helix chain 'X' and resid 56 through 76 Processing helix chain 'X' and resid 78 through 90 Processing helix chain 'X' and resid 96 through 98 No H-bonds generated for 'chain 'X' and resid 96 through 98' Processing helix chain 'X' and resid 100 through 113 Processing helix chain 'X' and resid 123 through 125 No H-bonds generated for 'chain 'X' and resid 123 through 125' Processing helix chain 'Y' and resid 3 through 10 removed outlier: 3.566A pdb=" N TYR Y 8 " --> pdb=" O VAL Y 4 " (cutoff:3.500A) Processing helix chain 'Y' and resid 17 through 42 Processing helix chain 'Y' and resid 48 through 80 Processing helix chain 'Y' and resid 86 through 104 Processing helix chain 'Y' and resid 107 through 130 Processing helix chain 'Z' and resid 32 through 97 Proline residue: Z 73 - end of helix removed outlier: 3.604A pdb=" N THR Z 96 " --> pdb=" O GLU Z 92 " (cutoff:3.500A) Processing helix chain 'Z' and resid 121 through 124 No H-bonds generated for 'chain 'Z' and resid 121 through 124' Processing helix chain 'Z' and resid 130 through 138 Processing helix chain 'a' and resid 2 through 31 Proline residue: a 7 - end of helix Proline residue: a 19 - end of helix removed outlier: 3.539A pdb=" N ALA a 22 " --> pdb=" O PRO a 19 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR a 23 " --> pdb=" O GLY a 20 " (cutoff:3.500A) Processing helix chain 'a' and resid 42 through 55 Processing helix chain 'a' and resid 66 through 68 No H-bonds generated for 'chain 'a' and resid 66 through 68' Processing helix chain 'b' and resid 2 through 14 Processing helix chain 'b' and resid 16 through 34 Proline residue: b 32 - end of helix Processing helix chain 'b' and resid 38 through 47 removed outlier: 3.947A 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 Processing helix chain 'd' and resid 16 through 20 Processing helix chain 'd' and resid 29 through 48 Processing helix chain 'd' and resid 58 through 96 removed outlier: 3.721A 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: 4.263A pdb=" N LYS e 53 " --> pdb=" O ILE e 49 " (cutoff:3.500A) Processing helix chain 'e' and resid 56 through 67 Processing helix chain 'e' and resid 69 through 88 removed outlier: 3.514A pdb=" N LYS e 87 " --> pdb=" O GLU e 83 " (cutoff:3.500A) Processing helix chain 'f' and resid 11 through 33 removed outlier: 3.512A pdb=" N LEU f 15 " --> pdb=" O VAL f 12 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N VAL f 16 " --> pdb=" O HIS f 13 " (cutoff:3.500A) Proline residue: f 17 - end of helix removed outlier: 3.512A pdb=" N PHE f 22 " --> pdb=" O GLY f 19 " (cutoff:3.500A) Processing helix chain 'g' and resid 37 through 40 No H-bonds generated for 'chain 'g' and resid 37 through 40' Processing helix chain 'g' and resid 51 through 65 Processing helix chain 'g' and resid 69 through 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: 5.740A pdb=" N GLU g 87 " --> pdb=" O ARG g 84 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N TRP g 88 " --> pdb=" O MET g 85 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA g 89 " --> pdb=" O GLN g 86 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LYS g 98 " --> pdb=" O ARG g 95 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU g 101 " --> pdb=" O LYS g 98 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA g 102 " --> pdb=" O TYR g 99 " (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: 3.980A 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: 3.839A 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 62 through 73 removed outlier: 3.508A pdb=" N PHE i 69 " --> pdb=" O ARG i 65 " (cutoff:3.500A) Processing helix chain 'i' and resid 75 through 87 Processing helix chain 'j' and resid 19 through 42 Processing helix chain 'j' and resid 44 through 48 Processing helix chain 'j' and resid 56 through 58 No H-bonds generated for 'chain 'j' and resid 56 through 58' Processing helix chain 'j' and resid 61 through 64 No H-bonds generated for 'chain 'j' and resid 61 through 64' Processing helix chain 'k' and resid 18 through 20 No H-bonds generated for 'chain 'k' and resid 18 through 20' Processing helix chain 'k' and resid 27 through 38 removed outlier: 4.088A pdb=" N ARG k 38 " --> pdb=" O LYS k 34 " (cutoff:3.500A) Processing helix chain 'k' and resid 45 through 47 No H-bonds generated for 'chain 'k' and resid 45 through 47' Processing helix chain 'k' and resid 49 through 52 Processing helix chain 'k' and resid 54 through 56 No H-bonds generated for 'chain 'k' and resid 54 through 56' Processing helix chain 'k' and resid 62 through 66 Processing helix chain 'k' and resid 70 through 89 Processing helix chain 'l' and resid 6 through 8 No H-bonds generated for 'chain 'l' and resid 6 through 8' Processing helix chain 'l' and resid 17 through 26 Processing helix chain 'l' and resid 55 through 57 No H-bonds generated for 'chain 'l' and resid 55 through 57' Processing helix chain 'l' and resid 81 through 83 No H-bonds generated for 'chain 'l' and resid 81 through 83' 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: 3.690A pdb=" N GLN m 49 " --> pdb=" O GLU m 45 " (cutoff:3.500A) Processing helix chain 'm' and resid 62 through 70 Processing helix chain 'm' and resid 73 through 78 Proline residue: m 77 - end of helix No H-bonds generated for 'chain 'm' and resid 73 through 78' Processing helix chain 'm' and resid 83 through 93 Processing helix chain 'm' and resid 95 through 117 Processing helix chain 'n' and resid 11 through 30 Processing helix chain 'n' and resid 33 through 50 removed outlier: 3.962A pdb=" N HIS n 50 " --> pdb=" O ARG n 46 " (cutoff:3.500A) Processing helix chain 'n' and resid 56 through 73 Processing helix chain 'n' and resid 94 through 96 No H-bonds generated for 'chain 'n' and resid 94 through 96' Processing helix chain 'n' and resid 100 through 105 Processing helix chain 'n' and resid 108 through 142 removed outlier: 3.948A pdb=" N MET n 113 " --> pdb=" O SER n 109 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N TYR n 114 " --> pdb=" O GLU n 110 " (cutoff:3.500A) Proline residue: n 115 - end of helix removed outlier: 4.490A pdb=" N GLU n 133 " --> pdb=" O ARG n 129 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N ARG n 134 " --> pdb=" O GLU n 130 " (cutoff:3.500A) Processing helix chain 'n' and resid 167 through 170 No H-bonds generated for 'chain 'n' and resid 167 through 170' Processing helix chain 'o' and resid 2 through 8 Processing helix chain 'o' and resid 12 through 14 No H-bonds generated for 'chain 'o' and resid 12 through 14' Processing helix chain 'o' and resid 42 through 48 Processing helix chain 'o' and resid 52 through 54 No H-bonds generated for 'chain 'o' and resid 52 through 54' Processing helix chain 'o' and resid 59 through 72 Processing helix chain 'o' and resid 80 through 119 removed outlier: 3.821A pdb=" N GLU o 118 " --> pdb=" O ARG o 114 " (cutoff:3.500A) Processing helix chain 'p' and resid 28 through 39 Processing helix chain 'p' and resid 41 through 57 removed outlier: 3.703A pdb=" N LYS p 57 " --> pdb=" O ARG p 53 " (cutoff:3.500A) Processing helix chain 'p' and resid 73 through 75 No H-bonds generated for 'chain 'p' and resid 73 through 75' Processing helix chain 'p' and resid 81 through 123 removed outlier: 3.722A pdb=" N GLU p 86 " --> pdb=" O LEU p 82 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLY p 117 " --> pdb=" O GLN p 113 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N GLU p 118 " --> pdb=" O GLN p 114 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N SER p 119 " --> pdb=" O ARG p 115 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N HIS p 120 " --> pdb=" O GLU p 116 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N ARG p 121 " --> pdb=" O GLY p 117 " (cutoff:3.500A) removed outlier: 6.376A 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: 3.525A pdb=" N LEU q 7 " --> pdb=" O LEU q 3 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N VAL q 14 " --> pdb=" O GLY q 10 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N SER q 15 " --> pdb=" O LEU q 11 " (cutoff:3.500A) Processing helix chain 'q' and resid 19 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: 4.309A 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 56 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 61 removed outlier: 4.801A pdb=" N LYS s 60 " --> pdb=" O LEU s 56 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N PHE s 61 " --> pdb=" O ASP s 57 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 85 through 89 removed outlier: 6.530A pdb=" N TYR B 112 " --> pdb=" O MET B 86 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N VAL B 88 " --> pdb=" O TYR B 112 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N VAL B 114 " --> pdb=" O VAL B 88 " (cutoff:3.500A) removed outlier: 6.346A 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: 6.698A pdb=" N ASN C 95 " --> pdb=" O ALA C 76 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N LEU C 78 " --> pdb=" O VAL C 93 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL C 93 " --> pdb=" O LEU C 78 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ALA C 80 " --> pdb=" O GLU C 91 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N GLU C 91 " --> pdb=" O ALA C 80 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N LEU C 48 " --> pdb=" O ARG C 104 " (cutoff:3.500A) removed outlier: 4.835A 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: 6.461A pdb=" N SER D 69 " --> pdb=" O VAL D 73 " (cutoff:3.500A) removed outlier: 5.354A 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: 6.363A pdb=" N TYR E 98 " --> pdb=" O THR E 138 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N ILE E 140 " --> pdb=" O TYR E 98 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ILE E 100 " --> pdb=" O ILE E 140 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N VAL E 142 " --> pdb=" O ILE E 100 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N VAL E 102 " --> pdb=" O VAL E 142 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'F' and resid 220 through 224 removed outlier: 6.962A pdb=" N TYR F 92 " --> pdb=" O THR F 221 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N ALA F 223 " --> pdb=" O TYR F 92 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N VAL F 94 " --> pdb=" O ALA F 223 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ALA F 133 " --> pdb=" O LEU F 93 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N VAL F 95 " --> pdb=" O ALA F 133 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N TYR F 135 " --> pdb=" O VAL F 95 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ALA F 97 " --> pdb=" O TYR F 135 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N TYR F 137 " --> pdb=" O ALA F 97 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ASP F 174 " --> pdb=" O ALA F 134 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N ILE F 136 " --> pdb=" O ASP F 174 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N PHE F 176 " --> pdb=" O ILE F 136 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N ILE F 138 " --> pdb=" O PHE F 176 " (cutoff:3.500A) removed outlier: 6.290A 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: 6.322A pdb=" N ARG G 243 " --> pdb=" O VAL G 247 " (cutoff:3.500A) removed outlier: 5.354A 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 342 through 345 removed outlier: 4.701A pdb=" N THR G 342 " --> pdb=" O VAL G 315 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N MET G 521 " --> pdb=" O ALA G 316 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N ILE G 318 " --> pdb=" O MET G 521 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N PHE G 523 " --> pdb=" O ILE G 318 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N PHE G 542 " --> pdb=" O LEU G 522 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N LEU G 524 " --> pdb=" O PHE G 542 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N VAL G 544 " --> pdb=" O LEU G 524 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N VAL G 559 " --> pdb=" O TYR G 545 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N GLY G 547 " --> pdb=" O VAL G 559 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N LEU G 561 " --> pdb=" O GLY G 547 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'G' and resid 490 through 493 removed outlier: 7.964A pdb=" N ASN G 491 " --> pdb=" O PRO G 449 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N VAL G 451 " --> pdb=" O ASN G 491 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N LEU G 493 " --> pdb=" O VAL G 451 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LEU G 453 " --> pdb=" O LEU G 493 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N VAL G 376 " --> pdb=" O MET G 450 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N ILE G 452 " --> pdb=" O VAL G 376 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N LEU G 378 " --> pdb=" O ILE G 452 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N GLY G 454 " --> pdb=" O LEU G 378 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N VAL G 380 " --> pdb=" O GLY G 454 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N LYS G 405 " --> pdb=" O VAL G 377 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N LEU G 379 " --> pdb=" O LYS G 405 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ALA G 407 " --> pdb=" O LEU G 379 " (cutoff:3.500A) removed outlier: 6.648A 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: 6.044A pdb=" N GLU I 97 " --> pdb=" O THR I 106 " (cutoff:3.500A) removed outlier: 5.355A 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 removed outlier: 3.514A pdb=" N VAL J 115 " --> pdb=" O PHE J 117 " (cutoff:3.500A) 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: 6.699A pdb=" N LEU L 78 " --> pdb=" O ASN L 65 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'O' and resid 122 through 125 removed outlier: 6.585A pdb=" N VAL O 168 " --> pdb=" O THR O 26 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N ASP O 28 " --> pdb=" O VAL O 168 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N VAL O 170 " --> pdb=" O ASP O 28 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N GLU O 219 " --> pdb=" O VAL O 169 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N TYR O 171 " --> pdb=" O GLU O 219 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N LEU O 221 " --> pdb=" O TYR O 171 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N ASP O 173 " --> pdb=" O LEU O 221 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N TYR O 223 " --> pdb=" O ASP O 173 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'P' and resid 227 through 230 removed outlier: 6.508A pdb=" N ILE P 165 " --> pdb=" O PHE P 228 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N PHE P 230 " --> pdb=" O ILE P 165 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N LYS P 167 " --> pdb=" O PHE P 230 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N GLN P 44 " --> pdb=" O ALA P 21 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N VAL P 23 " --> pdb=" O GLN P 44 " (cutoff:3.500A) removed outlier: 6.658A 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 194 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: 3.518A pdb=" N LEU S 22 " --> pdb=" O ARG S 55 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ARG S 67 " --> pdb=" O ARG S 16 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ILE S 18 " --> pdb=" O TRP S 65 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N TRP S 65 " --> pdb=" O ILE S 18 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ILE S 20 " --> pdb=" O LYS S 63 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N LYS S 63 " --> pdb=" O ILE S 20 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLN S 72 " --> pdb=" O TYR S 68 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'q' and resid 60 through 63 removed outlier: 6.567A pdb=" N GLU q 50 " --> pdb=" O LEU q 38 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N LEU q 38 " --> pdb=" O GLU q 50 " (cutoff:3.500A) 2900 hydrogen bonds defined for protein. 7872 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 24.22 Time building geometry restraints manager: 26.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.40: 27876 1.40 - 1.63: 40856 1.63 - 1.85: 832 1.85 - 2.08: 0 2.08 - 2.30: 81 Bond restraints: 69645 Sorted by residual: bond pdb=" C5 GTP O 401 " pdb=" N7 GTP O 401 " ideal model delta sigma weight residual 1.350 1.521 -0.171 2.00e-02 2.50e+03 7.29e+01 bond pdb=" C6 GTP O 401 " pdb=" O6 GTP O 401 " ideal model delta sigma weight residual 1.230 1.395 -0.165 2.00e-02 2.50e+03 6.83e+01 bond pdb=" CB7 CDL K 502 " pdb=" OB8 CDL K 502 " ideal model delta sigma weight residual 1.334 1.402 -0.068 1.10e-02 8.26e+03 3.87e+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 3.65e+01 bond pdb=" CB7 CDL r 201 " pdb=" OB8 CDL r 201 " ideal model delta sigma weight residual 1.334 1.399 -0.065 1.10e-02 8.26e+03 3.47e+01 ... (remaining 69640 not shown) Histogram of bond angle deviations from ideal: 72.65 - 84.94: 76 84.94 - 97.24: 2 97.24 - 109.54: 8031 109.54 - 121.84: 72939 121.84 - 134.14: 13166 Bond angle restraints: 94214 Sorted by residual: angle pdb=" C51 CDL h1001 " pdb=" CB5 CDL h1001 " pdb=" OB6 CDL h1001 " ideal model delta sigma weight residual 111.33 121.82 -10.49 1.32e+00 5.72e-01 6.30e+01 angle pdb=" C51 CDL J 701 " pdb=" CB5 CDL J 701 " pdb=" OB6 CDL J 701 " ideal model delta sigma weight residual 111.33 120.74 -9.41 1.32e+00 5.72e-01 5.07e+01 angle pdb=" C11 CDL h1001 " pdb=" CA5 CDL h1001 " pdb=" OA6 CDL h1001 " ideal model delta sigma weight residual 111.33 120.22 -8.89 1.32e+00 5.72e-01 4.52e+01 angle pdb=" C11 CDL r 201 " pdb=" CA5 CDL r 201 " pdb=" OA6 CDL r 201 " ideal model delta sigma weight residual 111.33 119.67 -8.34 1.32e+00 5.72e-01 3.98e+01 angle pdb=" C51 CDL r 201 " pdb=" CB5 CDL r 201 " pdb=" OB6 CDL r 201 " ideal model delta sigma weight residual 111.33 119.61 -8.28 1.32e+00 5.72e-01 3.93e+01 ... (remaining 94209 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.28: 40818 34.28 - 68.55: 1690 68.55 - 102.83: 210 102.83 - 137.11: 41 137.11 - 171.38: 6 Dihedral angle restraints: 42765 sinusoidal: 18851 harmonic: 23914 Sorted by residual: dihedral pdb=" CA TYR D 275 " pdb=" C TYR D 275 " pdb=" N ASP D 276 " pdb=" CA ASP D 276 " ideal model delta harmonic sigma weight residual -180.00 -131.76 -48.24 0 5.00e+00 4.00e-02 9.31e+01 dihedral pdb=" C10 FMN F 501 " pdb=" C1' FMN F 501 " pdb=" N10 FMN F 501 " pdb=" C2' FMN F 501 " ideal model delta sinusoidal sigma weight residual 257.59 86.21 171.38 1 2.00e+01 2.50e-03 4.77e+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 85.06 -153.98 1 2.00e+01 2.50e-03 4.56e+01 ... (remaining 42762 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.267: 10283 4.267 - 8.534: 0 8.534 - 12.800: 0 12.800 - 17.067: 0 17.067 - 21.334: 16 Chirality restraints: 10299 Sorted by residual: chirality pdb="FE1 SF4 I 201 " pdb=" S2 SF4 I 201 " pdb=" S3 SF4 I 201 " pdb=" S4 SF4 I 201 " both_signs ideal model delta sigma weight residual False -10.55 10.78 -21.33 2.00e-01 2.50e+01 1.14e+04 chirality pdb="FE2 SF4 G 801 " pdb=" S1 SF4 G 801 " pdb=" S3 SF4 G 801 " pdb=" S4 SF4 G 801 " both_signs ideal model delta sigma weight residual False 10.55 -10.77 21.32 2.00e-01 2.50e+01 1.14e+04 chirality pdb="FE1 SF4 G 802 " pdb=" S2 SF4 G 802 " pdb=" S3 SF4 G 802 " pdb=" S4 SF4 G 802 " both_signs ideal model delta sigma weight residual False -10.55 10.76 -21.31 2.00e-01 2.50e+01 1.14e+04 ... (remaining 10296 not shown) Planarity restraints: 11704 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C08 I49 N 703 " 0.037 2.00e-02 2.50e+03 4.86e-01 4.72e+03 pdb=" C14 I49 N 703 " -0.129 2.00e-02 2.50e+03 pdb=" C15 I49 N 703 " -0.066 2.00e-02 2.50e+03 pdb=" N01 I49 N 703 " -0.504 2.00e-02 2.50e+03 pdb=" N02 I49 N 703 " -0.684 2.00e-02 2.50e+03 pdb=" N03 I49 N 703 " 0.727 2.00e-02 2.50e+03 pdb=" N04 I49 N 703 " 0.769 2.00e-02 2.50e+03 pdb=" N05 I49 N 703 " -0.151 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA 2MR D 85 " 0.052 2.00e-02 2.50e+03 1.04e-01 1.07e+02 pdb=" C 2MR D 85 " -0.179 2.00e-02 2.50e+03 pdb=" O 2MR D 85 " 0.062 2.00e-02 2.50e+03 pdb=" N GLY D 86 " 0.065 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN N 2 " 0.033 5.00e-02 4.00e+02 4.93e-02 3.88e+00 pdb=" N PRO N 3 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO N 3 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO N 3 " 0.028 5.00e-02 4.00e+02 ... (remaining 11701 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.56: 894 2.56 - 3.21: 67338 3.21 - 3.85: 150448 3.85 - 4.50: 215521 4.50 - 5.14: 324746 Nonbonded interactions: 758947 Sorted by model distance: nonbonded pdb=" O1G GTP O 401 " pdb="MG MG O 402 " model vdw 1.921 2.170 nonbonded pdb=" O CYS P 51 " pdb=" O HOH P 601 " model vdw 1.929 2.440 nonbonded pdb=" OH TYR O 83 " pdb=" O3' GTP O 401 " model vdw 1.953 2.440 nonbonded pdb=" OB4 CDL J 701 " pdb=" O HOH J 801 " model vdw 1.967 2.440 nonbonded pdb=" OE2 GLU P 98 " pdb=" O HOH P 602 " model vdw 1.968 2.440 ... (remaining 758942 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'T' selection = (chain 'U' and (resid 7 through 82 or resid 101)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 11.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.090 Extract box with map and model: 57.900 Check model and map are aligned: 0.750 Set scattering table: 0.510 Process input model: 168.780 Find NCS groups from input model: 2.150 Set up NCS constraints: 0.280 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:10.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 252.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.171 69645 Z= 0.501 Angle : 0.852 15.533 94214 Z= 0.383 Chirality : 0.840 21.334 10299 Planarity : 0.006 0.486 11704 Dihedral : 18.391 171.382 27334 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.57 % Favored : 97.42 % Rotamer: Outliers : 1.23 % Allowed : 11.99 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.09), residues: 8097 helix: 0.63 (0.08), residues: 4307 sheet: -0.00 (0.24), residues: 405 loop : 0.27 (0.11), residues: 3385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP O 226 HIS 0.007 0.001 HIS C 160 PHE 0.023 0.002 PHE D 425 TYR 0.020 0.002 TYR H 282 ARG 0.019 0.001 ARG e 80 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16194 Ramachandran restraints generated. 8097 Oldfield, 0 Emsley, 8097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16194 Ramachandran restraints generated. 8097 Oldfield, 0 Emsley, 8097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1022 residues out of total 7155 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 934 time to evaluate : 6.240 Fit side-chains REVERT: G 16 GLN cc_start: 0.8131 (tm-30) cc_final: 0.7829 (tp40) REVERT: G 535 GLN cc_start: 0.7819 (mp10) cc_final: 0.7608 (mp10) REVERT: K 82 SER cc_start: 0.8867 (t) cc_final: 0.8648 (t) REVERT: L 237 MET cc_start: 0.8031 (mmp) cc_final: 0.7810 (mmp) REVERT: Z 85 GLN cc_start: 0.8418 (tt0) cc_final: 0.8196 (tt0) REVERT: a 61 TYR cc_start: 0.8834 (p90) cc_final: 0.8614 (p90) REVERT: b 46 ARG cc_start: 0.7924 (mtm110) cc_final: 0.7656 (mtm-85) REVERT: b 71 ASP cc_start: 0.8263 (m-30) cc_final: 0.8054 (m-30) REVERT: s 45 ASP cc_start: 0.8392 (m-30) cc_final: 0.8188 (m-30) outliers start: 88 outliers final: 74 residues processed: 1009 average time/residue: 1.7686 time to fit residues: 2253.4391 Evaluate side-chains 970 residues out of total 7155 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 896 time to evaluate : 6.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 GLU Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain E residue 26 GLU Chi-restraints excluded: chain F residue 18 GLU Chi-restraints excluded: chain F residue 62 THR Chi-restraints excluded: chain F residue 231 SER Chi-restraints excluded: chain F residue 415 VAL Chi-restraints excluded: chain F residue 435 GLN Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain G residue 292 THR Chi-restraints excluded: chain G residue 484 THR Chi-restraints excluded: chain H residue 176 LEU Chi-restraints excluded: chain I residue 9 GLU Chi-restraints excluded: chain I residue 11 SER Chi-restraints excluded: chain I residue 103 SER Chi-restraints excluded: chain K residue 46 LEU Chi-restraints excluded: chain L residue 235 SER Chi-restraints excluded: chain L residue 254 VAL Chi-restraints excluded: chain L residue 505 SER Chi-restraints excluded: chain L residue 554 ASP Chi-restraints excluded: chain L residue 565 THR Chi-restraints excluded: chain M residue 31 SER Chi-restraints excluded: chain M residue 72 LEU Chi-restraints excluded: chain M residue 116 ILE Chi-restraints excluded: chain M residue 144 ASN Chi-restraints excluded: chain M residue 427 SER Chi-restraints excluded: chain N residue 125 SER Chi-restraints excluded: chain O residue 1 LEU Chi-restraints excluded: chain O residue 17 LYS Chi-restraints excluded: chain O residue 60 ASP Chi-restraints excluded: chain O residue 203 GLU Chi-restraints excluded: chain O residue 206 TYR Chi-restraints excluded: chain O residue 232 GLU Chi-restraints excluded: chain O residue 250 ASP Chi-restraints excluded: chain O residue 289 SER Chi-restraints excluded: chain O residue 317 ILE Chi-restraints excluded: chain P residue 142 SER Chi-restraints excluded: chain P residue 170 GLU Chi-restraints excluded: chain R residue 2 VAL Chi-restraints excluded: chain S residue 13 LEU Chi-restraints excluded: chain S residue 91 GLU Chi-restraints excluded: chain S residue 95 SER Chi-restraints excluded: chain T residue 43 ASP Chi-restraints excluded: chain T residue 82 ASP Chi-restraints excluded: chain W residue 68 LYS Chi-restraints excluded: chain X residue 154 GLU Chi-restraints excluded: chain Z residue 109 SER Chi-restraints excluded: chain b residue 4 VAL Chi-restraints excluded: chain b residue 33 THR Chi-restraints excluded: chain e residue 5 VAL Chi-restraints excluded: chain e residue 15 ARG Chi-restraints excluded: chain g residue 112 CYS Chi-restraints excluded: chain h residue 32 THR Chi-restraints excluded: chain i residue 67 SER Chi-restraints excluded: chain i residue 120 LYS Chi-restraints excluded: chain j residue 7 ILE Chi-restraints excluded: chain j residue 40 PHE Chi-restraints excluded: chain k residue 11 SER Chi-restraints excluded: chain k residue 41 ARG Chi-restraints excluded: chain k residue 87 LEU Chi-restraints excluded: chain n residue 150 THR Chi-restraints excluded: chain o residue 58 CYS Chi-restraints excluded: chain o residue 115 GLU Chi-restraints excluded: chain p residue 30 THR Chi-restraints excluded: chain p residue 74 THR Chi-restraints excluded: chain q residue 11 LEU Chi-restraints excluded: chain q residue 26 VAL Chi-restraints excluded: chain q residue 107 LYS Chi-restraints excluded: chain q residue 141 SER Chi-restraints excluded: chain s residue 37 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 801 random chunks: chunk 676 optimal weight: 6.9990 chunk 607 optimal weight: 8.9990 chunk 336 optimal weight: 2.9990 chunk 207 optimal weight: 9.9990 chunk 409 optimal weight: 4.9990 chunk 324 optimal weight: 0.9980 chunk 627 optimal weight: 5.9990 chunk 242 optimal weight: 7.9990 chunk 381 optimal weight: 0.8980 chunk 467 optimal weight: 0.4980 chunk 727 optimal weight: 4.9990 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 214 GLN F 431 GLN G 475 GLN H 317 GLN I 23 GLN L 442 ASN N 204 ASN O 89 ASN R 51 GLN R 95 HIS S 30 GLN ** S 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 58 GLN W 126 HIS X 15 GLN X 64 GLN b 61 ASN ** m 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 61 GLN q 52 ASN s 35 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.0841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.247 69645 Z= 0.481 Angle : 1.318 50.785 94214 Z= 0.840 Chirality : 0.258 6.610 10299 Planarity : 0.004 0.054 11704 Dihedral : 14.448 171.157 11271 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.67 % Favored : 98.31 % Rotamer: Outliers : 2.10 % Allowed : 11.59 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.09), residues: 8097 helix: 1.39 (0.08), residues: 4304 sheet: 0.14 (0.26), residues: 374 loop : 0.35 (0.11), residues: 3419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP L 144 HIS 0.006 0.001 HIS G 101 PHE 0.024 0.002 PHE M 122 TYR 0.021 0.001 TYR I 118 ARG 0.008 0.000 ARG M 340 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16194 Ramachandran restraints generated. 8097 Oldfield, 0 Emsley, 8097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16194 Ramachandran restraints generated. 8097 Oldfield, 0 Emsley, 8097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1078 residues out of total 7155 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 928 time to evaluate : 6.282 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 14 GLU cc_start: 0.7495 (OUTLIER) cc_final: 0.6547 (pp20) REVERT: E 181 ILE cc_start: 0.8111 (OUTLIER) cc_final: 0.7869 (tp) REVERT: G 16 GLN cc_start: 0.8127 (tm-30) cc_final: 0.7848 (tp40) REVERT: G 430 GLN cc_start: 0.8122 (mt0) cc_final: 0.7895 (mt0) REVERT: H 24 GLU cc_start: 0.8555 (OUTLIER) cc_final: 0.7805 (tt0) REVERT: H 227 GLU cc_start: 0.7889 (OUTLIER) cc_final: 0.7378 (tp30) REVERT: J 87 LYS cc_start: 0.7470 (OUTLIER) cc_final: 0.6639 (tttt) REVERT: L 52 MET cc_start: 0.8084 (OUTLIER) cc_final: 0.7800 (mtp) REVERT: T 69 LYS cc_start: 0.7694 (mtmt) cc_final: 0.7237 (mttt) REVERT: V 56 SER cc_start: 0.8783 (m) cc_final: 0.8426 (p) REVERT: Y 103 ARG cc_start: 0.7941 (mmm160) cc_final: 0.7616 (mmm160) REVERT: Z 64 ASP cc_start: 0.7759 (OUTLIER) cc_final: 0.7504 (t70) REVERT: a 61 TYR cc_start: 0.8816 (p90) cc_final: 0.8573 (p90) REVERT: b 8 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8387 (mp) REVERT: b 46 ARG cc_start: 0.7882 (mtm110) cc_final: 0.7593 (mtm-85) REVERT: b 71 ASP cc_start: 0.8237 (m-30) cc_final: 0.8008 (m-30) REVERT: i 12 GLN cc_start: 0.7973 (tm-30) cc_final: 0.7745 (tp40) REVERT: o 109 GLN cc_start: 0.8172 (OUTLIER) cc_final: 0.7966 (tp40) REVERT: q 8 LYS cc_start: 0.8286 (mttt) cc_final: 0.8011 (ttpt) REVERT: r 29 GLU cc_start: 0.8899 (pm20) cc_final: 0.8693 (pm20) outliers start: 150 outliers final: 65 residues processed: 1017 average time/residue: 1.8089 time to fit residues: 2322.0711 Evaluate side-chains 979 residues out of total 7155 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 905 time to evaluate : 6.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 LEU Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 125 TYR Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain D residue 420 THR Chi-restraints excluded: chain E residue 14 GLU Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain F residue 62 THR Chi-restraints excluded: chain F residue 105 CYS Chi-restraints excluded: chain F residue 272 MET Chi-restraints excluded: chain G residue 174 THR Chi-restraints excluded: chain G residue 484 THR Chi-restraints excluded: chain G residue 640 ASN Chi-restraints excluded: chain G residue 653 ASN Chi-restraints excluded: chain G residue 692 THR Chi-restraints excluded: chain H residue 24 GLU Chi-restraints excluded: chain H residue 176 LEU Chi-restraints excluded: chain H residue 202 GLU Chi-restraints excluded: chain H residue 227 GLU Chi-restraints excluded: chain I residue 1 THR Chi-restraints excluded: chain I residue 9 GLU Chi-restraints excluded: chain I residue 11 SER Chi-restraints excluded: chain J residue 87 LYS Chi-restraints excluded: chain K residue 46 LEU Chi-restraints excluded: chain L residue 52 MET Chi-restraints excluded: chain L residue 252 MET Chi-restraints excluded: chain L residue 254 VAL Chi-restraints excluded: chain L residue 554 ASP Chi-restraints excluded: chain M residue 144 ASN Chi-restraints excluded: chain M residue 427 SER Chi-restraints excluded: chain M residue 437 MET Chi-restraints excluded: chain O residue 1 LEU Chi-restraints excluded: chain O residue 19 THR Chi-restraints excluded: chain O residue 203 GLU Chi-restraints excluded: chain O residue 206 TYR Chi-restraints excluded: chain O residue 232 GLU Chi-restraints excluded: chain O residue 289 SER Chi-restraints excluded: chain P residue 170 GLU Chi-restraints excluded: chain P residue 263 TYR Chi-restraints excluded: chain R residue 19 ASP Chi-restraints excluded: chain S residue 13 LEU Chi-restraints excluded: chain T residue 16 LEU Chi-restraints excluded: chain T residue 19 LEU Chi-restraints excluded: chain T residue 43 ASP Chi-restraints excluded: chain T residue 82 ASP Chi-restraints excluded: chain X residue 11 ASP Chi-restraints excluded: chain X residue 63 ASN Chi-restraints excluded: chain X residue 154 GLU Chi-restraints excluded: chain Y residue 114 CYS Chi-restraints excluded: chain Z residue 52 LYS Chi-restraints excluded: chain Z residue 64 ASP Chi-restraints excluded: chain b residue 4 VAL Chi-restraints excluded: chain b residue 8 LEU Chi-restraints excluded: chain b residue 33 THR Chi-restraints excluded: chain e residue 75 LEU Chi-restraints excluded: chain f residue 18 MET Chi-restraints excluded: chain i residue 28 SER Chi-restraints excluded: chain i residue 34 LEU Chi-restraints excluded: chain i residue 67 SER Chi-restraints excluded: chain j residue 40 PHE Chi-restraints excluded: chain k residue 11 SER Chi-restraints excluded: chain k residue 84 GLU Chi-restraints excluded: chain m residue 25 SER Chi-restraints excluded: chain o residue 13 SER Chi-restraints excluded: chain o residue 30 PHE Chi-restraints excluded: chain o residue 109 GLN Chi-restraints excluded: chain p residue 16 THR Chi-restraints excluded: chain p residue 20 SER Chi-restraints excluded: chain s residue 37 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 801 random chunks: chunk 404 optimal weight: 4.9990 chunk 225 optimal weight: 0.7980 chunk 605 optimal weight: 6.9990 chunk 495 optimal weight: 10.0000 chunk 200 optimal weight: 0.1980 chunk 728 optimal weight: 9.9990 chunk 787 optimal weight: 7.9990 chunk 648 optimal weight: 8.9990 chunk 722 optimal weight: 1.9990 chunk 248 optimal weight: 9.9990 chunk 584 optimal weight: 6.9990 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 214 GLN F 431 GLN F 435 GLN L 442 ASN M 304 GLN P 74 ASN R 95 HIS S 72 GLN ** S 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 15 GLN X 64 GLN Z 85 GLN c 46 ASN k 58 ASN l 126 GLN ** m 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 61 GLN n 140 GLN p 58 ASN q 52 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.0904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.245 69645 Z= 0.523 Angle : 1.319 50.597 94214 Z= 0.841 Chirality : 0.257 6.607 10299 Planarity : 0.004 0.052 11704 Dihedral : 13.157 171.085 11187 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.07 % Favored : 97.91 % Rotamer: Outliers : 1.97 % Allowed : 12.08 % Favored : 85.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.09), residues: 8097 helix: 1.48 (0.08), residues: 4311 sheet: 0.12 (0.25), residues: 375 loop : 0.34 (0.11), residues: 3411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP X 85 HIS 0.006 0.001 HIS G 101 PHE 0.025 0.002 PHE M 122 TYR 0.022 0.002 TYR O 94 ARG 0.008 0.000 ARG M 340 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16194 Ramachandran restraints generated. 8097 Oldfield, 0 Emsley, 8097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16194 Ramachandran restraints generated. 8097 Oldfield, 0 Emsley, 8097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1064 residues out of total 7155 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 923 time to evaluate : 6.209 Fit side-chains revert: symmetry clash REVERT: D 43 LEU cc_start: 0.4627 (OUTLIER) cc_final: 0.4248 (mm) REVERT: E 181 ILE cc_start: 0.8110 (OUTLIER) cc_final: 0.7867 (tp) REVERT: G 16 GLN cc_start: 0.8154 (tm-30) cc_final: 0.7857 (tp40) REVERT: G 188 GLU cc_start: 0.7755 (OUTLIER) cc_final: 0.7342 (mm-30) REVERT: H 8 MET cc_start: 0.8034 (mmm) cc_final: 0.7823 (mmp) REVERT: H 24 GLU cc_start: 0.8598 (OUTLIER) cc_final: 0.7878 (tt0) REVERT: H 227 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7397 (tp30) REVERT: J 87 LYS cc_start: 0.7490 (OUTLIER) cc_final: 0.6715 (tttm) REVERT: J 135 PHE cc_start: 0.8989 (OUTLIER) cc_final: 0.8256 (t80) REVERT: O 89 ASN cc_start: 0.7915 (OUTLIER) cc_final: 0.7613 (t0) REVERT: S 88 ARG cc_start: 0.7557 (mpp-170) cc_final: 0.7254 (mtm-85) REVERT: T 69 LYS cc_start: 0.7683 (mtmt) cc_final: 0.7275 (mttt) REVERT: U 84 LYS cc_start: 0.8882 (OUTLIER) cc_final: 0.8670 (mmtt) REVERT: Y 57 ARG cc_start: 0.8229 (ttp80) cc_final: 0.7962 (ttp80) REVERT: Y 74 CYS cc_start: 0.6555 (t) cc_final: 0.6048 (t) REVERT: Z 64 ASP cc_start: 0.7825 (t70) cc_final: 0.7585 (t70) REVERT: a 61 TYR cc_start: 0.8833 (p90) cc_final: 0.8532 (p90) REVERT: b 8 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8330 (mp) REVERT: b 46 ARG cc_start: 0.7937 (mtm110) cc_final: 0.7661 (mtm-85) REVERT: b 78 GLU cc_start: 0.7262 (OUTLIER) cc_final: 0.6344 (pp20) REVERT: e 52 GLU cc_start: 0.7764 (OUTLIER) cc_final: 0.7545 (mt-10) REVERT: j 63 GLU cc_start: 0.8028 (mt-10) cc_final: 0.7814 (tt0) REVERT: m 24 ILE cc_start: 0.7156 (OUTLIER) cc_final: 0.6772 (pp) REVERT: m 34 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7592 (pt0) REVERT: o 109 GLN cc_start: 0.8185 (OUTLIER) cc_final: 0.7983 (tp40) REVERT: p 75 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7621 (mm-30) REVERT: q 8 LYS cc_start: 0.8311 (mttt) cc_final: 0.8022 (ttpt) REVERT: q 11 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8347 (mp) REVERT: r 29 GLU cc_start: 0.8881 (pm20) cc_final: 0.8677 (pm20) REVERT: r 61 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7472 (mt-10) outliers start: 141 outliers final: 70 residues processed: 1004 average time/residue: 1.8067 time to fit residues: 2289.2669 Evaluate side-chains 988 residues out of total 7155 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 900 time to evaluate : 7.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 LEU Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 125 TYR Chi-restraints excluded: chain D residue 43 LEU Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain D residue 420 THR Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain F residue 105 CYS Chi-restraints excluded: chain F residue 435 GLN Chi-restraints excluded: chain G residue 188 GLU Chi-restraints excluded: chain G residue 351 THR Chi-restraints excluded: chain G residue 484 THR Chi-restraints excluded: chain G residue 640 ASN Chi-restraints excluded: chain G residue 653 ASN Chi-restraints excluded: chain G residue 692 THR Chi-restraints excluded: chain H residue 24 GLU Chi-restraints excluded: chain H residue 176 LEU Chi-restraints excluded: chain H residue 227 GLU Chi-restraints excluded: chain I residue 9 GLU Chi-restraints excluded: chain I residue 37 THR Chi-restraints excluded: chain J residue 87 LYS Chi-restraints excluded: chain J residue 110 ASP Chi-restraints excluded: chain J residue 118 GLU Chi-restraints excluded: chain J residue 135 PHE Chi-restraints excluded: chain K residue 46 LEU Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 252 MET Chi-restraints excluded: chain L residue 254 VAL Chi-restraints excluded: chain L residue 371 THR Chi-restraints excluded: chain L residue 554 ASP Chi-restraints excluded: chain M residue 31 SER Chi-restraints excluded: chain M residue 144 ASN Chi-restraints excluded: chain M residue 437 MET Chi-restraints excluded: chain O residue 1 LEU Chi-restraints excluded: chain O residue 19 THR Chi-restraints excluded: chain O residue 89 ASN Chi-restraints excluded: chain O residue 203 GLU Chi-restraints excluded: chain O residue 206 TYR Chi-restraints excluded: chain O residue 232 GLU Chi-restraints excluded: chain O residue 250 ASP Chi-restraints excluded: chain O residue 289 SER Chi-restraints excluded: chain P residue 140 LYS Chi-restraints excluded: chain P residue 170 GLU Chi-restraints excluded: chain P residue 263 TYR Chi-restraints excluded: chain R residue 19 ASP Chi-restraints excluded: chain S residue 13 LEU Chi-restraints excluded: chain S residue 91 GLU Chi-restraints excluded: chain T residue 16 LEU Chi-restraints excluded: chain T residue 19 LEU Chi-restraints excluded: chain T residue 43 ASP Chi-restraints excluded: chain T residue 82 ASP Chi-restraints excluded: chain U residue 84 LYS Chi-restraints excluded: chain X residue 11 ASP Chi-restraints excluded: chain X residue 154 GLU Chi-restraints excluded: chain Y residue 109 ILE Chi-restraints excluded: chain Y residue 114 CYS Chi-restraints excluded: chain Z residue 52 LYS Chi-restraints excluded: chain Z residue 144 THR Chi-restraints excluded: chain b residue 4 VAL Chi-restraints excluded: chain b residue 8 LEU Chi-restraints excluded: chain b residue 33 THR Chi-restraints excluded: chain b residue 78 GLU Chi-restraints excluded: chain e residue 52 GLU Chi-restraints excluded: chain e residue 75 LEU Chi-restraints excluded: chain f residue 18 MET Chi-restraints excluded: chain i residue 28 SER Chi-restraints excluded: chain i residue 34 LEU Chi-restraints excluded: chain i residue 67 SER Chi-restraints excluded: chain j residue 40 PHE Chi-restraints excluded: chain k residue 11 SER Chi-restraints excluded: chain k residue 87 LEU Chi-restraints excluded: chain m residue 24 ILE Chi-restraints excluded: chain m residue 25 SER Chi-restraints excluded: chain m residue 34 GLU Chi-restraints excluded: chain m residue 85 THR Chi-restraints excluded: chain o residue 13 SER Chi-restraints excluded: chain o residue 30 PHE Chi-restraints excluded: chain o residue 109 GLN Chi-restraints excluded: chain p residue 16 THR Chi-restraints excluded: chain p residue 20 SER Chi-restraints excluded: chain p residue 75 GLU Chi-restraints excluded: chain q residue 11 LEU Chi-restraints excluded: chain q residue 26 VAL Chi-restraints excluded: chain r residue 61 GLU Chi-restraints excluded: chain s residue 37 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.2248 > 50: distance: 61 - 62: 55.294 distance: 62 - 63: 39.928 distance: 62 - 65: 23.650 distance: 63 - 64: 57.365 distance: 63 - 67: 39.554 distance: 65 - 66: 32.729 distance: 67 - 68: 40.055 distance: 68 - 69: 40.394 distance: 68 - 71: 39.675 distance: 69 - 70: 39.750 distance: 69 - 76: 47.957 distance: 71 - 72: 29.135 distance: 72 - 73: 7.543 distance: 73 - 74: 29.109 distance: 74 - 75: 12.486 distance: 76 - 77: 38.384 distance: 77 - 78: 48.308 distance: 77 - 80: 24.338 distance: 78 - 84: 40.493 distance: 80 - 81: 29.553 distance: 81 - 82: 42.116 distance: 82 - 83: 40.455 distance: 84 - 85: 15.734 distance: 85 - 86: 44.525 distance: 85 - 88: 45.246 distance: 86 - 87: 42.361 distance: 86 - 93: 57.745 distance: 88 - 89: 7.769 distance: 89 - 90: 19.384 distance: 90 - 91: 21.352 distance: 90 - 92: 38.468 distance: 93 - 94: 3.973 distance: 94 - 95: 43.435 distance: 94 - 97: 37.188 distance: 95 - 96: 40.856 distance: 95 - 101: 18.943 distance: 97 - 98: 34.994 distance: 98 - 99: 39.811 distance: 98 - 100: 43.997 distance: 101 - 102: 11.086 distance: 101 - 107: 12.600 distance: 102 - 103: 26.462 distance: 102 - 105: 46.130 distance: 103 - 104: 57.848 distance: 103 - 108: 57.536 distance: 105 - 106: 6.636 distance: 106 - 107: 31.080 distance: 108 - 109: 49.639 distance: 109 - 110: 42.497 distance: 109 - 112: 40.263 distance: 110 - 111: 35.193 distance: 110 - 116: 9.491 distance: 112 - 113: 40.365 distance: 113 - 114: 12.837 distance: 113 - 115: 28.651 distance: 116 - 117: 29.726 distance: 117 - 118: 19.067 distance: 117 - 120: 33.142 distance: 118 - 119: 20.778 distance: 118 - 128: 23.997 distance: 120 - 121: 26.985 distance: 121 - 122: 31.583 distance: 122 - 124: 21.407 distance: 123 - 125: 22.751 distance: 124 - 126: 13.119 distance: 125 - 126: 11.860 distance: 126 - 127: 5.555 distance: 128 - 129: 28.626 distance: 129 - 130: 29.828 distance: 129 - 132: 17.290 distance: 130 - 131: 49.075 distance: 130 - 137: 16.534 distance: 132 - 133: 24.762 distance: 133 - 134: 23.092 distance: 134 - 135: 14.354 distance: 135 - 136: 38.737