Starting phenix.real_space_refine on Wed Mar 13 01:09:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r4f_14302/03_2024/7r4f_14302_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r4f_14302/03_2024/7r4f_14302.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r4f_14302/03_2024/7r4f_14302_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r4f_14302/03_2024/7r4f_14302_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r4f_14302/03_2024/7r4f_14302_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r4f_14302/03_2024/7r4f_14302.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r4f_14302/03_2024/7r4f_14302.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r4f_14302/03_2024/7r4f_14302_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r4f_14302/03_2024/7r4f_14302_updated.pdb" } resolution = 2.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.011 sd= 1.086 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 34 5.49 5 Mg 1 5.21 5 S 454 5.16 5 Cl 1 4.86 5 C 41399 2.51 5 N 10637 2.21 5 O 12937 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 27": "OE1" <-> "OE2" Residue "B ARG 71": "NH1" <-> "NH2" Residue "B ARG 77": "NH1" <-> "NH2" Residue "B ARG 111": "NH1" <-> "NH2" Residue "B ASP 143": "OD1" <-> "OD2" Residue "B GLU 154": "OE1" <-> "OE2" Residue "B GLU 170": "OE1" <-> "OE2" Residue "C ARG 8": "NH1" <-> "NH2" Residue "C ARG 12": "NH1" <-> "NH2" Residue "C ASP 16": "OD1" <-> "OD2" Residue "C GLU 27": "OE1" <-> "OE2" Residue "C GLU 31": "OE1" <-> "OE2" Residue "C PHE 45": "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 PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 173": "OE1" <-> "OE2" Residue "C GLU 179": "OE1" <-> "OE2" Residue "C GLU 186": "OE1" <-> "OE2" Residue "C GLU 193": "OE1" <-> "OE2" Residue "C GLU 204": "OE1" <-> "OE2" Residue "D GLU 67": "OE1" <-> "OE2" Residue "D TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 123": "OE1" <-> "OE2" Residue "D PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 179": "OE1" <-> "OE2" Residue "D ARG 221": "NH1" <-> "NH2" Residue "D ARG 233": "NH1" <-> "NH2" Residue "D GLU 248": "OE1" <-> "OE2" Residue "D ASP 249": "OD1" <-> "OD2" Residue "D GLU 282": "OE1" <-> "OE2" Residue "D GLU 337": "OE1" <-> "OE2" Residue "D GLU 343": "OE1" <-> "OE2" Residue "D GLU 427": "OE1" <-> "OE2" Residue "E GLU 14": "OE1" <-> "OE2" Residue "E GLU 26": "OE1" <-> "OE2" Residue "E GLU 82": "OE1" <-> "OE2" Residue "E ASP 114": "OD1" <-> "OD2" Residue "E GLU 118": "OE1" <-> "OE2" Residue "E ASP 134": "OD1" <-> "OD2" Residue "E ASP 163": "OD1" <-> "OD2" Residue "E GLU 171": "OE1" <-> "OE2" Residue "E ASP 174": "OD1" <-> "OD2" Residue "E ARG 190": "NH1" <-> "NH2" Residue "F ARG 32": "NH1" <-> "NH2" Residue "F ASP 54": "OD1" <-> "OD2" Residue "F PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 109": "OE1" <-> "OE2" Residue "F ARG 112": "NH1" <-> "NH2" Residue "F ASP 114": "OD1" <-> "OD2" Residue "F ARG 132": "NH1" <-> "NH2" Residue "F TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 139": "NH1" <-> "NH2" Residue "F GLU 158": "OE1" <-> "OE2" Residue "F GLU 226": "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 269": "OE1" <-> "OE2" Residue "F GLU 270": "OE1" <-> "OE2" Residue "F GLU 278": "OE1" <-> "OE2" Residue "F ASP 292": "OD1" <-> "OD2" Residue "F GLU 313": "OE1" <-> "OE2" Residue "F ASP 318": "OD1" <-> "OD2" Residue "F ARG 349": "NH1" <-> "NH2" Residue "F GLU 352": "OE1" <-> "OE2" Residue "F GLU 367": "OE1" <-> "OE2" Residue "F GLU 394": "OE1" <-> "OE2" Residue "F ARG 429": "NH1" <-> "NH2" Residue "F PHE 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 21": "OE1" <-> "OE2" Residue "G GLU 31": "OE1" <-> "OE2" Residue "G ARG 39": "NH1" <-> "NH2" Residue "G GLU 44": "OE1" <-> "OE2" Residue "G ARG 53": "NH1" <-> "NH2" Residue "G GLU 60": "OE1" <-> "OE2" Residue "G GLU 95": "OE1" <-> "OE2" Residue "G PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 165": "OE1" <-> "OE2" Residue "G ASP 170": "OD1" <-> "OD2" Residue "G ASP 180": "OD1" <-> "OD2" Residue "G GLU 188": "OE1" <-> "OE2" Residue "G ARG 218": "NH1" <-> "NH2" Residue "G GLU 226": "OE1" <-> "OE2" Residue "G ASP 232": "OD1" <-> "OD2" 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 297": "OE1" <-> "OE2" Residue "G ASP 298": "OD1" <-> "OD2" Residue "G ARG 302": "NH1" <-> "NH2" Residue "G GLU 347": "OE1" <-> "OE2" Residue "G ARG 385": "NH1" <-> "NH2" Residue "G ASP 403": "OD1" <-> "OD2" Residue "G ARG 418": "NH1" <-> "NH2" Residue "G TYR 419": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 420": "OD1" <-> "OD2" Residue "G ASP 431": "OD1" <-> "OD2" Residue "G PHE 523": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 536": "OD1" <-> "OD2" Residue "G ASP 558": "OD1" <-> "OD2" Residue "G GLU 577": "OE1" <-> "OE2" Residue "G ASP 596": "OD1" <-> "OD2" Residue "G GLU 605": "OE1" <-> "OE2" Residue "G GLU 624": "OE1" <-> "OE2" Residue "G GLU 637": "OE1" <-> "OE2" Residue "G ASP 659": "OD1" <-> "OD2" Residue "G ASP 675": "OD1" <-> "OD2" Residue "G GLU 693": "OE1" <-> "OE2" Residue "H GLU 24": "OE1" <-> "OE2" Residue "H ARG 25": "NH1" <-> "NH2" Residue "H TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 34": "NH1" <-> "NH2" Residue "H TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 59": "OE1" <-> "OE2" Residue "H ARG 62": "NH1" <-> "NH2" Residue "H TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 206": "OE1" <-> "OE2" Residue "H TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 227": "OE1" <-> "OE2" Residue "H PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 8": "NH1" <-> "NH2" Residue "I GLU 9": "OE1" <-> "OE2" Residue "I ASP 13": "OD1" <-> "OD2" Residue "I ASP 19": "OD1" <-> "OD2" Residue "I GLU 74": "OE1" <-> "OE2" Residue "I GLU 95": "OE1" <-> "OE2" Residue "I ARG 108": "NH1" <-> "NH2" Residue "I GLU 146": "OE1" <-> "OE2" Residue "I GLU 152": "OE1" <-> "OE2" Residue "J ASP 132": "OD1" <-> "OD2" Residue "J GLU 138": "OE1" <-> "OE2" Residue "J GLU 170": "OE1" <-> "OE2" Residue "J ARG 173": "NH1" <-> "NH2" Residue "K PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 88": "OD1" <-> "OD2" Residue "L GLU 60": "OE1" <-> "OE2" Residue "L GLU 102": "OE1" <-> "OE2" Residue "L TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 161": "NH1" <-> "NH2" Residue "L ASP 179": "OD1" <-> "OD2" Residue "L ASP 208": "OD1" <-> "OD2" Residue "L GLU 238": "OE1" <-> "OE2" Residue "L PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 262": "NH1" <-> "NH2" Residue "L PHE 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 268": "OE1" <-> "OE2" Residue "L ASP 297": "OD1" <-> "OD2" Residue "L TYR 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 352": "OD1" <-> "OD2" Residue "L PHE 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 393": "OD1" <-> "OD2" Residue "L PHE 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 456": "NH1" <-> "NH2" Residue "L TYR 466": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 503": "OE1" <-> "OE2" Residue "L PHE 520": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 222": "OE1" <-> "OE2" Residue "M PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 346": "NH1" <-> "NH2" Residue "M ARG 432": "NH1" <-> "NH2" Residue "M TYR 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 34": "OE1" <-> "OE2" Residue "N PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 295": "NH1" <-> "NH2" Residue "O GLU 12": "OE1" <-> "OE2" Residue "O GLU 20": "OE1" <-> "OE2" Residue "O GLU 44": "OE1" <-> "OE2" Residue "O PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 53": "OE1" <-> "OE2" Residue "O GLU 80": "OE1" <-> "OE2" Residue "O ASP 85": "OD1" <-> "OD2" Residue "O ARG 104": "NH1" <-> "NH2" Residue "O GLU 113": "OE1" <-> "OE2" Residue "O ARG 126": "NH1" <-> "NH2" Residue "O ASP 131": "OD1" <-> "OD2" Residue "O PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 178": "OE1" <-> "OE2" Residue "O GLU 213": "OE1" <-> "OE2" Residue "O GLU 219": "OE1" <-> "OE2" Residue "O ASP 230": "OD1" <-> "OD2" Residue "O GLU 232": "OE1" <-> "OE2" Residue "O GLU 236": "OE1" <-> "OE2" Residue "O ASP 244": "OD1" <-> "OD2" Residue "O GLU 281": "OE1" <-> "OE2" Residue "O PHE 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 295": "OE1" <-> "OE2" Residue "O ARG 302": "NH1" <-> "NH2" Residue "O ARG 305": "NH1" <-> "NH2" Residue "O TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 40": "NH1" <-> "NH2" Residue "P ARG 50": "NH1" <-> "NH2" Residue "P TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 82": "NH1" <-> "NH2" Residue "P GLU 86": "OE1" <-> "OE2" Residue "P ARG 97": "NH1" <-> "NH2" Residue "P PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 105": "OD1" <-> "OD2" Residue "P GLU 107": "OE1" <-> "OE2" Residue "P GLU 127": "OE1" <-> "OE2" Residue "P PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 138": "OD1" <-> "OD2" Residue "P ARG 147": "NH1" <-> "NH2" Residue "P ARG 157": "NH1" <-> "NH2" Residue "P GLU 162": "OE1" <-> "OE2" Residue "P GLU 175": "OE1" <-> "OE2" Residue "P TYR 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 235": "NH1" <-> "NH2" Residue "P PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 240": "OD1" <-> "OD2" Residue "P PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 251": "NH1" <-> "NH2" Residue "Q GLU 27": "OE1" <-> "OE2" Residue "Q GLU 28": "OE1" <-> "OE2" Residue "Q GLU 58": "OE1" <-> "OE2" Residue "Q GLU 90": "OE1" <-> "OE2" Residue "Q TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 104": "OD1" <-> "OD2" Residue "R ASP 19": "OD1" <-> "OD2" Residue "R TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 31": "NH1" <-> "NH2" Residue "R GLU 46": "OE1" <-> "OE2" Residue "R GLU 78": "OE1" <-> "OE2" Residue "S GLU 17": "OE1" <-> "OE2" Residue "S GLU 42": "OE1" <-> "OE2" Residue "S ASP 49": "OD1" <-> "OD2" Residue "S GLU 91": "OE1" <-> "OE2" Residue "T ASP 13": "OD1" <-> "OD2" Residue "T ASP 26": "OD1" <-> "OD2" Residue "T GLU 28": "OE1" <-> "OE2" Residue "T ASP 39": "OD1" <-> "OD2" Residue "T GLU 55": "OE1" <-> "OE2" Residue "T GLU 57": "OE1" <-> "OE2" Residue "T ASP 66": "OD1" <-> "OD2" Residue "T GLU 75": "OE1" <-> "OE2" Residue "U GLU 9": "OE1" <-> "OE2" Residue "U ASP 13": "OD1" <-> "OD2" Residue "U TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 23": "OD1" <-> "OD2" Residue "U GLU 28": "OE1" <-> "OE2" Residue "U ASP 43": "OD1" <-> "OD2" Residue "U ASP 46": "OD1" <-> "OD2" Residue "U ASP 56": "OD1" <-> "OD2" Residue "U GLU 57": "OE1" <-> "OE2" Residue "U ASP 64": "OD1" <-> "OD2" Residue "U ASP 66": "OD1" <-> "OD2" Residue "U GLU 75": "OE1" <-> "OE2" Residue "V GLU 17": "OE1" <-> "OE2" Residue "V GLU 21": "OE1" <-> "OE2" Residue "V ARG 22": "NH1" <-> "NH2" Residue "V ASP 32": "OD1" <-> "OD2" Residue "V GLU 53": "OE1" <-> "OE2" Residue "V GLU 61": "OE1" <-> "OE2" Residue "V GLU 68": "OE1" <-> "OE2" Residue "V GLU 69": "OE1" <-> "OE2" Residue "V GLU 77": "OE1" <-> "OE2" Residue "V GLU 78": "OE1" <-> "OE2" Residue "V GLU 84": "OE1" <-> "OE2" Residue "V GLU 86": "OE1" <-> "OE2" Residue "V GLU 100": "OE1" <-> "OE2" Residue "W ARG 30": "NH1" <-> "NH2" Residue "W GLU 34": "OE1" <-> "OE2" Residue "W GLU 42": "OE1" <-> "OE2" Residue "W PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 61": "OD1" <-> "OD2" Residue "W GLU 65": "OE1" <-> "OE2" Residue "W GLU 89": "OE1" <-> "OE2" Residue "W GLU 91": "OE1" <-> "OE2" Residue "W PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 109": "OE1" <-> "OE2" Residue "W GLU 111": "OE1" <-> "OE2" Residue "W ASP 117": "OD1" <-> "OD2" Residue "W ASP 127": "OD1" <-> "OD2" Residue "X ASP 11": "OD1" <-> "OD2" Residue "X ASP 36": "OD1" <-> "OD2" Residue "X GLU 41": "OE1" <-> "OE2" Residue "X GLU 49": "OE1" <-> "OE2" Residue "X GLU 57": "OE1" <-> "OE2" Residue "X TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 97": "NH1" <-> "NH2" Residue "X GLU 108": "OE1" <-> "OE2" Residue "X ARG 118": "NH1" <-> "NH2" Residue "X ASP 120": "OD1" <-> "OD2" Residue "X ARG 134": "NH1" <-> "NH2" Residue "X GLU 138": "OE1" <-> "OE2" Residue "X TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 144": "NH1" <-> "NH2" Residue "X ARG 146": "NH1" <-> "NH2" Residue "Z TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 56": "OE1" <-> "OE2" Residue "Z ARG 82": "NH1" <-> "NH2" Residue "Z GLU 93": "OE1" <-> "OE2" Residue "Z GLU 108": "OE1" <-> "OE2" Residue "Z TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 131": "OE1" <-> "OE2" Residue "Z GLU 132": "OE1" <-> "OE2" Residue "Z TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 4": "OE1" <-> "OE2" Residue "a GLU 49": "OE1" <-> "OE2" Residue "a ASP 51": "OD1" <-> "OD2" Residue "a ARG 59": "NH1" <-> "NH2" Residue "b GLU 2": "OE1" <-> "OE2" Residue "b GLU 15": "OE1" <-> "OE2" Residue "b ARG 57": "NH1" <-> "NH2" Residue "b ASP 58": "OD1" <-> "OD2" Residue "b ASP 71": "OD1" <-> "OD2" Residue "c PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 41": "OE1" <-> "OE2" Residue "c ARG 44": "NH1" <-> "NH2" Residue "d ASP 16": "OD1" <-> "OD2" Residue "d ARG 51": "NH1" <-> "NH2" Residue "d PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 86": "NH1" <-> "NH2" Residue "d GLU 99": "OE1" <-> "OE2" Residue "d ASP 100": "OD1" <-> "OD2" Residue "d PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 103": "OE1" <-> "OE2" Residue "d ASP 105": "OD1" <-> "OD2" 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 ASP 12": "OD1" <-> "OD2" Residue "e GLU 36": "OE1" <-> "OE2" Residue "e GLU 38": "OE1" <-> "OE2" Residue "e GLU 41": "OE1" <-> "OE2" Residue "e ARG 50": "NH1" <-> "NH2" Residue "e GLU 58": "OE1" <-> "OE2" Residue "e GLU 60": "OE1" <-> "OE2" Residue "e TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 "g GLU 35": "OE1" <-> "OE2" Residue "g GLU 39": "OE1" <-> "OE2" Residue "g ASP 43": "OD1" <-> "OD2" Residue "g ASP 50": "OD1" <-> "OD2" Residue "g PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 87": "OE1" <-> "OE2" Residue "g GLU 94": "OE1" <-> "OE2" Residue "g TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 122": "OE1" <-> "OE2" Residue "h ARG 20": "NH1" <-> "NH2" Residue "h GLU 49": "OE1" <-> "OE2" Residue "h GLU 62": "OE1" <-> "OE2" Residue "h GLU 65": "OE1" <-> "OE2" Residue "h ARG 77": "NH1" <-> "NH2" Residue "h GLU 84": "OE1" <-> "OE2" Residue "h TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 88": "OE1" <-> "OE2" Residue "h ARG 112": "NH1" <-> "NH2" Residue "h GLU 131": "OE1" <-> "OE2" Residue "h ASP 142": "OD1" <-> "OD2" Residue "i GLU 6": "OE1" <-> "OE2" Residue "i GLU 16": "OE1" <-> "OE2" Residue "i ARG 18": "NH1" <-> "NH2" Residue "i GLU 26": "OE1" <-> "OE2" Residue "i GLU 98": "OE1" <-> "OE2" Residue "i GLU 111": "OE1" <-> "OE2" Residue "i ASP 124": "OD1" <-> "OD2" Residue "j PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ASP 43": "OD1" <-> "OD2" Residue "j ASP 45": "OD1" <-> "OD2" Residue "j ASP 55": "OD1" <-> "OD2" Residue "j GLU 62": "OE1" <-> "OE2" Residue "j GLU 63": "OE1" <-> "OE2" Residue "j ASP 70": "OD1" <-> "OD2" Residue "k GLU 14": "OE1" <-> "OE2" Residue "k ASP 17": "OD1" <-> "OD2" Residue "k GLU 29": "OE1" <-> "OE2" Residue "k ARG 38": "NH1" <-> "NH2" Residue "k ARG 41": "NH1" <-> "NH2" Residue "k ASP 42": "OD1" <-> "OD2" Residue "k TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k GLU 88": "OE1" <-> "OE2" Residue "l TYR 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l GLU 18": "OE1" <-> "OE2" Residue "l ARG 30": "NH1" <-> "NH2" Residue "l GLU 32": "OE1" <-> "OE2" Residue "l GLU 35": "OE1" <-> "OE2" Residue "l ASP 40": "OD1" <-> "OD2" Residue "l GLU 57": "OE1" <-> "OE2" Residue "l ASP 59": "OD1" <-> "OD2" Residue "l ASP 63": "OD1" <-> "OD2" Residue "l PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ARG 142": "NH1" <-> "NH2" Residue "l GLU 149": "OE1" <-> "OE2" Residue "l GLU 151": "OE1" <-> "OE2" Residue "l TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l GLU 157": "OE1" <-> "OE2" Residue "m TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m ASP 23": "OD1" <-> "OD2" Residue "m GLU 27": "OE1" <-> "OE2" Residue "m ARG 39": "NH1" <-> "NH2" Residue "m TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m ASP 52": "OD1" <-> "OD2" Residue "m ARG 55": "NH1" <-> "NH2" Residue "m TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m ARG 71": "NH1" <-> "NH2" Residue "m PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m ASP 107": "OD1" <-> "OD2" Residue "m ASP 109": "OD1" <-> "OD2" Residue "m GLU 112": "OE1" <-> "OE2" Residue "m GLU 117": "OE1" <-> "OE2" Residue "m ASP 121": "OD1" <-> "OD2" Residue "n ARG 21": "NH1" <-> "NH2" Residue "n ARG 24": "NH1" <-> "NH2" Residue "n GLU 27": "OE1" <-> "OE2" Residue "n ARG 33": "NH1" <-> "NH2" Residue "n ASP 34": "OD1" <-> "OD2" Residue "n ASP 48": "OD1" <-> "OD2" Residue "n ASP 55": "OD1" <-> "OD2" Residue "n ARG 64": "NH1" <-> "NH2" Residue "n TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n GLU 83": "OE1" <-> "OE2" Residue "n ARG 92": "NH1" <-> "NH2" Residue "n GLU 122": "OE1" <-> "OE2" Residue "n GLU 130": "OE1" <-> "OE2" Residue "n GLU 133": "OE1" <-> "OE2" Residue "n ARG 149": "NH1" <-> "NH2" Residue "n GLU 175": "OE1" <-> "OE2" Residue "o ARG 6": "NH1" <-> "NH2" Residue "o ASP 27": "OD1" <-> "OD2" Residue "o TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o GLU 32": "OE1" <-> "OE2" Residue "o GLU 35": "OE1" <-> "OE2" Residue "o ARG 36": "NH1" <-> "NH2" Residue "o GLU 44": "OE1" <-> "OE2" Residue "o PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o GLU 90": "OE1" <-> "OE2" Residue "o ASP 93": "OD1" <-> "OD2" Residue "o ARG 97": "NH1" <-> "NH2" Residue "o GLU 100": "OE1" <-> "OE2" Residue "o GLU 102": "OE1" <-> "OE2" Residue "o ARG 103": "NH1" <-> "NH2" Residue "o GLU 104": "OE1" <-> "OE2" Residue "o ARG 105": "NH1" <-> "NH2" Residue "o ARG 106": "NH1" <-> "NH2" Residue "o GLU 115": "OE1" <-> "OE2" Residue "p ASP 5": "OD1" <-> "OD2" Residue "p TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p ARG 15": "NH1" <-> "NH2" Residue "p TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p ASP 37": "OD1" <-> "OD2" Residue "p GLU 52": "OE1" <-> "OE2" Residue "p TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p GLU 66": "OE1" <-> "OE2" Residue "p PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p ASP 72": "OD1" <-> "OD2" Residue "p GLU 88": "OE1" <-> "OE2" Residue "p GLU 100": "OE1" <-> "OE2" Residue "p GLU 107": "OE1" <-> "OE2" Residue "p GLU 116": "OE1" <-> "OE2" Residue "p GLU 118": "OE1" <-> "OE2" Residue "p GLU 127": "OE1" <-> "OE2" Residue "p GLU 129": "OE1" <-> "OE2" Residue "p GLU 171": "OE1" <-> "OE2" Residue "q ARG 21": "NH1" <-> "NH2" Residue "q PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ARG 29": "NH1" <-> "NH2" Residue "q ASP 32": "OD1" <-> "OD2" Residue "q TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q GLU 50": "OE1" <-> "OE2" Residue "q GLU 67": "OE1" <-> "OE2" Residue "q GLU 85": "OE1" <-> "OE2" Residue "q ARG 88": "NH1" <-> "NH2" Residue "q GLU 136": "OE1" <-> "OE2" Residue "q TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r ARG 59": "NH1" <-> "NH2" Residue "r GLU 61": "OE1" <-> "OE2" Residue "r GLU 104": "OE1" <-> "OE2" Residue "s PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s ASP 34": "OD1" <-> "OD2" Residue "s ASP 57": "OD1" <-> "OD2" Residue "s GLU 71": "OE1" <-> "OE2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 65494 Number of models: 1 Model: "" Number of chains: 114 Chain: "A" Number of atoms: 769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 769 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 4, 'TRANS': 90} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 1230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1230 Classifications: {'peptide': 154} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 143} Chain: "C" Number of atoms: 1714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1714 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 16, 'TRANS': 189} Chain: "D" Number of atoms: 3095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3095 Classifications: {'peptide': 386} Link IDs: {'PTRANS': 21, 'TRANS': 364} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'2MR:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 1655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1655 Classifications: {'peptide': 213} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 191} Chain: "F" Number of atoms: 3301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3301 Classifications: {'peptide': 429} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 407} Chain: "G" Number of atoms: 5279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 688, 5279 Classifications: {'peptide': 688} Link IDs: {'PTRANS': 32, 'TRANS': 655} Chain: "H" Number of atoms: 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: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 877 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 2, 'TRANS': 116} Chain breaks: 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: 4312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 547, 4312 Classifications: {'peptide': 547} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 26, 'TRANS': 520} 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: 3606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3606 Classifications: {'peptide': 453} Link IDs: {'PCIS': 3, 'PTRANS': 17, 'TRANS': 432} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "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: 2289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2289 Classifications: {'peptide': 288} Link IDs: {'PTRANS': 15, 'TRANS': 272} Chain breaks: 3 Chain: "Q" Number of atoms: 1016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1016 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 6, 'TRANS': 118} Chain: "R" Number of atoms: 720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 720 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 3, 'TRANS': 90} Chain: "S" Number of atoms: 663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 663 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 4, 'TRANS': 77} Chain: "T" Number of atoms: 584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 584 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 3, 'TRANS': 68} Chain: "U" Number of atoms: 681 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 681 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 3, 'TRANS': 80} Chain: "V" Number of atoms: 903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 903 Classifications: {'peptide': 111} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 102} 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: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 154 Classifications: {'peptide': 20} Link IDs: {'PTRANS': 1, 'TRANS': 18} Chain: "Z" Number of atoms: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1152 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 7, 'TRANS': 133} Chain: "a" Number of atoms: 561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 561 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 3, 'TRANS': 65} Chain: "b" Number of atoms: 651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 651 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 11, 'TRANS': 71} Chain: "c" Number of atoms: 405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 405 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 3, 'TRANS': 44} Chain: "d" Number of atoms: 934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 934 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 9, 'TRANS': 102} Chain: "e" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 799 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 5, 'TRANS': 89} Chain: "f" Number of atoms: 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: 733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 733 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 6, 'TRANS': 81} Chain: "h" Number of atoms: 1154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1154 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 10, 'TRANS': 127} Chain: "i" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 884 Classifications: {'peptide': 103} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 90} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'SAC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "j" Number of atoms: 580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 580 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 7, 'TRANS': 59} Chain: "k" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 638 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "l" Number of atoms: 1304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1304 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 20, 'TRANS': 134} Chain: "m" Number of atoms: 908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 908 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain breaks: 1 Chain: "n" Number of atoms: 1487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1487 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 15, 'TRANS': 155} Chain: "o" Number of atoms: 1027 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 1027 Classifications: {'peptide': 119} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 111} Chain: "p" Number of atoms: 1435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1435 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 10, 'TRANS': 159} Chain: "q" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1192 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 11, 'TRANS': 131} Chain: "r" Number of atoms: 767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 767 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 11, 'TRANS': 82} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'AYA:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "s" Number of atoms: 364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 364 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 3, 'TRANS': 39} Chain: "A" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 87 Unusual residues: {'LMT': 1, 'PC1': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 43 Unusual residues: {'PC1': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 19 Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'FMN': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 21 Unusual residues: {' K': 1, 'FES': 1, 'SF4': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "H" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 107 Unusual residues: {'3PE': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 45 Planarities with less than four sites: {'3PE:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "I" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Unusual residues: {'3PE': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "J" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'LMT': 1} Classifications: {'undetermined': 1} Chain: "K" 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: 163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 163 Unusual residues: {'3PE': 2, 'CDL': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 39 Chain: "M" Number of atoms: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 73 Unusual residues: {'3PE': 1, 'PC1': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 32 Chain: "N" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 78 Unusual residues: {'CDL': 1, 'I49': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 39 Chain: "O" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "P" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NDP': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'EHZ': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "U" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'EHZ': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "X" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 48 Chain: "Y" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Chain: "Z" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 33 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 18 Chain: "d" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 116 Unusual residues: {'3PE': 1, 'CDL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 35 Chain: "f" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'LMT': 1} Classifications: {'undetermined': 1} Chain: "h" Number of atoms: 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: "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: "p" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'LMT': 1} Classifications: {'undetermined': 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: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "B" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 60 Classifications: {'water': 60} Link IDs: {None: 59} Chain: "C" Number of atoms: 99 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 99 Classifications: {'water': 99} Link IDs: {None: 98} Chain: "D" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 160 Classifications: {'water': 160} Link IDs: {None: 159} Chain: "E" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Chain: "F" Number of atoms: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 73 Classifications: {'water': 73} Link IDs: {None: 72} Chain: "G" Number of atoms: 221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 221 Classifications: {'water': 221} Link IDs: {None: 220} Chain: "H" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 54 Classifications: {'water': 54} Link IDs: {None: 53} Chain: "I" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 104 Classifications: {'water': 104} Link IDs: {None: 103} Chain: "J" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "M" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 53 Classifications: {'water': 53} Link IDs: {None: 52} Chain: "N" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "P" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 42 Classifications: {'water': 42} Link IDs: {None: 41} Chain: "Q" Number of atoms: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 73 Classifications: {'water': 73} Link IDs: {None: 72} Chain: "R" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 40 Classifications: {'water': 40} Link IDs: {None: 39} Chain: "S" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "U" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "V" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "W" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "X" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 24 Classifications: {'water': 24} Link IDs: {None: 23} 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: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "a" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "b" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "d" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "e" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "f" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "g" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "h" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 21 Classifications: {'water': 21} Link IDs: {None: 20} Chain: "i" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "j" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "k" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "l" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "m" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "n" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 26 Classifications: {'water': 26} Link IDs: {None: 25} Chain: "o" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "p" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 26 Classifications: {'water': 26} Link IDs: {None: 25} Chain: "q" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 42 Classifications: {'water': 42} Link IDs: {None: 41} Chain: "r" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 30 Classifications: {'water': 30} Link IDs: {None: 29} Chain: "s" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1505 SG CYS B 119 96.326 94.877 209.066 1.00 26.69 S ATOM 1735 SG CYS B 149 93.843 92.536 213.609 1.00 26.61 S ATOM 1001 SG CYS B 54 90.709 91.637 207.890 1.00 30.47 S ATOM 1007 SG CYS B 55 90.441 97.307 210.856 1.00 30.45 S ATOM 7612 SG CYS E 103 111.533 46.176 265.238 1.00 49.96 S ATOM 7646 SG CYS E 108 109.712 43.570 267.124 1.00 50.77 S ATOM 7926 SG CYS E 144 113.599 42.717 261.872 1.00 47.36 S ATOM 7949 SG CYS E 148 112.153 40.065 262.870 1.00 51.51 S ATOM 11158 SG CYS F 362 117.045 52.517 241.565 1.00 31.31 S ATOM 11178 SG CYS F 365 114.081 52.034 246.389 1.00 33.08 S ATOM 11502 SG CYS F 405 118.422 47.394 245.616 1.00 34.76 S ATOM 11139 SG CYS F 359 120.612 53.295 247.091 1.00 35.48 S ATOM 12590 SG CYS G 114 114.300 71.030 232.005 1.00 29.03 S ATOM 12529 SG CYS G 105 108.498 73.625 233.802 1.00 28.30 S ATOM 12550 SG CYS G 108 114.172 76.008 235.976 1.00 28.99 S ATOM 12922 SG CYS G 156 122.414 64.705 237.152 1.00 30.56 S ATOM 12899 SG CYS G 153 119.602 67.116 242.692 1.00 30.60 S ATOM 12946 SG CYS G 159 125.870 67.897 241.337 1.00 33.75 S ATOM 13276 SG CYS G 203 121.416 70.743 237.483 1.00 31.69 S ATOM 12035 SG CYS G 41 122.619 57.869 234.916 1.00 30.12 S ATOM 12121 SG CYS G 52 118.820 58.483 233.912 1.00 30.23 S ATOM 12146 SG CYS G 55 120.220 53.971 230.579 1.00 31.93 S ATOM 12247 SG CYS G 69 123.462 54.462 231.786 1.00 33.02 S ATOM 20506 SG CYS I 119 96.579 86.622 219.774 1.00 27.10 S ATOM 20480 SG CYS I 116 97.222 93.207 220.571 1.00 27.02 S ATOM 20527 SG CYS I 122 98.155 88.755 225.242 1.00 27.00 S ATOM 20254 SG CYS I 87 102.348 89.240 220.113 1.00 26.87 S ATOM 20556 SG CYS I 126 100.528 85.514 232.783 1.00 27.41 S ATOM 20185 SG CYS I 77 105.595 89.565 233.910 1.00 29.15 S ATOM 20227 SG CYS I 83 104.045 87.877 227.916 1.00 26.97 S ATOM 20204 SG CYS I 80 105.995 83.183 231.549 1.00 28.00 S ATOM 39592 SG CYS R 59 101.781 81.107 248.052 1.00 36.23 S ATOM 39770 SG CYS R 84 104.970 81.776 245.969 1.00 36.74 S ATOM 39792 SG CYS R 87 102.683 84.403 246.741 1.00 35.23 S Time building chain proxies: 26.11, per 1000 atoms: 0.40 Number of scatterers: 65494 At special positions: 0 Unit cell: (184.943, 198.832, 298.979, 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 454 16.00 P 34 15.00 Mg 1 11.99 O 12937 8.00 N 10637 7.00 C 41399 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS X 45 " - pdb=" SG CYS X 55 " distance=2.04 Simple disulfide: pdb=" SG CYS e 32 " - pdb=" SG CYS e 65 " distance=2.03 Simple disulfide: pdb=" SG CYS e 42 " - pdb=" SG CYS e 55 " distance=2.04 Simple disulfide: pdb=" SG CYS p 112 " - pdb=" SG CYS p 124 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 22.93 Conformation dependent library (CDL) restraints added in 8.7 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="FE2 FES G 803 " - pdb=" SG CYS G 55 " pdb="FE1 FES G 803 " - pdb=" SG CYS G 52 " pdb="FE1 FES G 803 " - pdb=" SG CYS G 41 " pdb="FE2 FES G 803 " - pdb=" SG CYS G 69 " pdb=" SF4 B 201 " pdb="FE2 SF4 B 201 " - pdb=" SG CYS B 149 " pdb="FE1 SF4 B 201 " - pdb=" SG CYS B 119 " pdb="FE3 SF4 B 201 " - pdb=" SG CYS B 54 " pdb="FE4 SF4 B 201 " - pdb=" SG CYS B 55 " pdb=" SF4 F 502 " pdb="FE2 SF4 F 502 " - pdb=" SG CYS F 365 " pdb="FE3 SF4 F 502 " - pdb=" SG CYS F 405 " pdb="FE4 SF4 F 502 " - pdb=" SG CYS F 359 " pdb="FE1 SF4 F 502 " - pdb=" SG CYS F 362 " pdb=" SF4 G 801 " pdb="FE3 SF4 G 801 " - pdb=" NE2 HIS G 101 " pdb="FE1 SF4 G 801 " - pdb=" SG CYS G 114 " pdb="FE2 SF4 G 801 " - pdb=" SG CYS G 105 " pdb="FE4 SF4 G 801 " - pdb=" SG CYS G 108 " pdb=" SF4 G 802 " pdb="FE2 SF4 G 802 " - pdb=" SG CYS G 153 " pdb="FE3 SF4 G 802 " - pdb=" SG CYS G 159 " pdb="FE4 SF4 G 802 " - pdb=" SG CYS G 203 " pdb="FE1 SF4 G 802 " - pdb=" SG CYS G 156 " pdb=" SF4 I 202 " pdb="FE3 SF4 I 202 " - pdb=" SG CYS I 122 " pdb="FE2 SF4 I 202 " - pdb=" SG CYS I 116 " pdb="FE4 SF4 I 202 " - pdb=" SG CYS I 87 " pdb="FE1 SF4 I 202 " - pdb=" SG CYS I 119 " pdb=" SF4 I 203 " pdb="FE3 SF4 I 203 " - pdb=" SG CYS I 83 " pdb="FE1 SF4 I 203 " - pdb=" SG CYS I 126 " pdb="FE2 SF4 I 203 " - pdb=" SG CYS I 77 " pdb="FE4 SF4 I 203 " - pdb=" SG CYS I 80 " Number of angles added : 81 Zn2+ tetrahedral coordination pdb=" ZN R 201 " pdb="ZN ZN R 201 " - pdb=" NE2 HIS R 68 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 84 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 87 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 59 " Number of angles added : 3 15338 Ramachandran restraints generated. 7669 Oldfield, 0 Emsley, 7669 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14648 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 346 helices and 28 sheets defined 54.2% alpha, 4.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.76 Creating SS restraints... Processing helix chain 'A' and resid 3 through 26 Proline residue: A 25 - end of helix Processing helix chain 'A' and resid 53 through 80 removed outlier: 3.570A pdb=" N GLU A 68 " --> pdb=" O LEU A 64 " (cutoff:3.500A) Proline residue: A 74 - end of helix removed outlier: 5.431A pdb=" N TRP A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 4.816A 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 27 through 43 Processing helix chain 'B' and resid 54 through 63 Processing helix chain 'B' and resid 69 through 72 Processing helix chain 'B' and resid 80 through 82 No H-bonds generated for 'chain 'B' and resid 80 through 82' Processing helix chain 'B' and resid 94 through 106 Proline residue: B 98 - end of helix Processing helix chain 'B' and resid 117 through 122 Processing helix chain 'B' and resid 124 through 126 No H-bonds generated for 'chain 'B' and resid 124 through 126' Processing helix chain 'B' and resid 136 through 138 No H-bonds generated for 'chain 'B' and resid 136 through 138' Processing helix chain 'B' and resid 153 through 168 Processing helix chain 'B' and resid 172 through 177 Processing helix chain 'C' and resid 16 through 32 Processing helix chain 'C' and resid 54 through 66 removed outlier: 4.603A pdb=" N ILE C 58 " --> pdb=" O ASP C 55 " (cutoff:3.500A) Proline residue: C 59 - end of helix Processing helix chain 'C' and resid 125 through 138 removed outlier: 3.942A pdb=" N TRP C 129 " --> pdb=" O ALA C 126 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU C 131 " --> pdb=" O ASN C 128 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N MET C 137 " --> pdb=" O ILE C 134 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N PHE C 138 " --> pdb=" O TRP C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 209 No H-bonds generated for 'chain 'C' and resid 207 through 209' Processing helix chain 'D' and resid 87 through 93 removed outlier: 3.909A pdb=" N GLU D 92 " --> pdb=" O GLU D 88 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N TYR D 93 " --> pdb=" O LYS D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 105 removed outlier: 3.545A pdb=" N LEU D 100 " --> pdb=" O TYR D 96 " (cutoff:3.500A) Proline residue: D 101 - end of helix removed outlier: 3.954A pdb=" N ASP D 104 " --> pdb=" O LEU D 100 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ARG D 105 " --> pdb=" O PRO D 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 96 through 105' 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: 3.788A pdb=" N GLU D 173 " --> pdb=" O TRP D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 229 removed outlier: 3.840A pdb=" N ASN D 217 " --> pdb=" O GLU D 213 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N SER D 219 " --> pdb=" O SER D 215 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N LEU D 220 " --> pdb=" O LYS D 216 " (cutoff:3.500A) removed outlier: 3.567A 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: 4.722A 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 353 Processing helix chain 'D' and resid 394 through 406 removed outlier: 3.601A pdb=" N LEU D 402 " --> pdb=" O HIS D 398 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N ASP D 403 " --> pdb=" O LEU D 399 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N LYS D 404 " --> pdb=" O ALA D 400 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 421 removed outlier: 3.901A pdb=" N VAL D 415 " --> pdb=" O LEU D 411 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA D 416 " --> pdb=" O ALA D 412 " (cutoff:3.500A) Processing helix chain 'D' and resid 425 through 429 Processing helix chain 'E' and resid 25 through 37 removed outlier: 3.673A pdb=" N ASN E 37 " --> pdb=" O ALA E 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 58 removed outlier: 4.441A pdb=" N LEU E 48 " --> pdb=" O ALA E 45 " (cutoff:3.500A) Proline residue: E 49 - end of helix removed outlier: 3.580A pdb=" N GLN E 57 " --> pdb=" O ALA E 54 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASN E 58 " --> pdb=" O GLN E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 73 Processing helix chain 'E' and resid 77 through 86 removed outlier: 3.565A pdb=" N VAL E 83 " --> pdb=" O ARG E 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 110 Processing helix chain 'E' and resid 113 through 124 Processing helix chain 'E' and resid 148 through 150 No H-bonds generated for 'chain 'E' and resid 148 through 150' Processing helix chain 'E' and resid 166 through 177 Processing helix chain 'F' and resid 17 through 19 No H-bonds generated for 'chain 'F' and resid 17 through 19' Processing helix chain 'F' and resid 33 through 39 Processing helix chain 'F' and resid 45 through 51 Processing helix chain 'F' and resid 53 through 62 Processing helix chain 'F' and resid 75 through 82 removed outlier: 3.659A pdb=" N PHE F 81 " --> pdb=" O LEU F 77 " (cutoff:3.500A) removed outlier: 4.654A 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 282 Processing helix chain 'F' and resid 291 through 293 No H-bonds generated for 'chain 'F' and resid 291 through 293' Processing helix chain 'F' and resid 309 through 313 Processing helix chain 'F' and resid 319 through 324 Processing helix chain 'F' and resid 343 through 357 Processing helix chain 'F' and resid 363 through 381 removed outlier: 4.311A pdb=" N ASP F 370 " --> pdb=" O ARG F 366 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ARG F 381 " --> pdb=" O ALA F 377 " (cutoff:3.500A) Processing helix chain 'F' and resid 386 through 399 removed outlier: 3.529A pdb=" N ASP F 390 " --> pdb=" O ALA F 387 " (cutoff:3.500A) Processing helix chain 'F' and resid 407 through 435 Proline residue: F 414 - end of helix removed outlier: 3.578A 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: 3.780A 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: 3.617A 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: 5.216A pdb=" N TYR G 271 " --> pdb=" O THR G 267 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ASP G 272 " --> pdb=" O ARG G 268 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N GLY G 273 " --> pdb=" O PHE G 269 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N LEU G 274 " --> pdb=" O ALA G 270 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LYS G 275 " --> pdb=" O TYR G 271 " (cutoff:3.500A) Processing helix chain 'G' and resid 296 through 307 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: 3.734A pdb=" N VAL G 338 " --> pdb=" O LEU G 334 " (cutoff:3.500A) Processing helix chain 'G' and resid 359 through 361 No H-bonds generated for 'chain 'G' and resid 359 through 361' Processing helix chain 'G' and resid 369 through 373 Processing helix chain 'G' and resid 384 through 387 No H-bonds generated for 'chain 'G' and resid 384 through 387' Processing helix chain 'G' and resid 389 through 401 Processing helix chain 'G' and resid 426 through 434 Processing helix chain 'G' and resid 438 through 445 removed outlier: 3.803A 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 505 Processing helix chain 'G' and resid 512 through 516 Processing helix chain 'G' and resid 534 through 536 No H-bonds generated for 'chain 'G' and resid 534 through 536' Processing helix chain 'G' and resid 554 through 556 No H-bonds generated for 'chain 'G' and resid 554 through 556' Processing helix chain 'G' and resid 566 through 568 No H-bonds generated for 'chain 'G' and resid 566 through 568' Processing helix chain 'G' and resid 596 through 606 Processing helix chain 'G' and resid 616 through 626 Processing helix chain 'G' and resid 628 through 631 Processing helix chain 'G' and resid 642 through 649 Processing helix chain 'G' and resid 668 through 670 No H-bonds generated for 'chain 'G' and resid 668 through 670' Processing helix chain 'G' and resid 676 through 679 No H-bonds generated for 'chain 'G' and resid 676 through 679' Processing helix chain 'G' and resid 682 through 692 Processing helix chain 'H' and resid 3 through 32 Proline residue: H 12 - end of helix removed outlier: 3.930A 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: 4.201A pdb=" N TRP H 86 " --> pdb=" O ALA H 82 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 122 removed outlier: 3.693A pdb=" N LEU H 111 " --> pdb=" O ALA H 107 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA H 112 " --> pdb=" O MET H 108 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N VAL H 113 " --> pdb=" O SER H 109 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N TYR H 114 " --> pdb=" O SER H 110 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N SER H 115 " --> pdb=" O LEU H 111 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ILE H 116 " --> pdb=" O ALA H 112 " (cutoff:3.500A) Processing helix chain 'H' and resid 126 through 157 removed outlier: 4.082A pdb=" N THR H 145 " --> pdb=" O SER H 141 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N MET H 156 " --> pdb=" O SER H 152 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER H 157 " --> pdb=" O VAL H 153 " (cutoff:3.500A) Processing helix chain 'H' and resid 162 through 168 removed outlier: 3.992A pdb=" N ILE H 166 " --> pdb=" O LEU H 162 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR H 167 " --> pdb=" O SER H 163 " (cutoff:3.500A) Processing helix chain 'H' and resid 174 through 177 No H-bonds generated for 'chain 'H' and resid 174 through 177' Processing helix chain 'H' and resid 179 through 192 Processing helix chain 'H' and resid 200 through 207 removed outlier: 3.751A pdb=" N LEU H 207 " --> pdb=" O GLY H 203 " (cutoff:3.500A) Processing helix chain 'H' and resid 217 through 242 Processing helix chain 'H' and resid 252 through 274 removed outlier: 3.504A pdb=" N LEU H 271 " --> pdb=" O THR H 267 " (cutoff:3.500A) Processing helix chain 'H' and resid 282 through 290 Processing helix chain 'H' and resid 293 through 311 Proline residue: H 308 - end of helix Processing helix chain 'I' and resid 14 through 26 Processing helix chain 'I' and resid 28 through 42 removed outlier: 3.518A pdb=" N PHE I 42 " --> pdb=" O LEU I 38 " (cutoff:3.500A) Processing helix chain 'I' and resid 82 through 86 Processing helix chain 'I' and resid 121 through 125 Processing helix chain 'I' and resid 145 through 147 No H-bonds generated for 'chain 'I' and resid 145 through 147' Processing helix chain 'I' and resid 151 through 175 removed outlier: 5.678A pdb=" N ALA I 163 " --> pdb=" O ASP I 159 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N GLU I 164 " --> pdb=" O LYS I 160 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA I 167 " --> pdb=" O ALA I 163 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N LEU I 174 " --> pdb=" O GLN I 170 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N TYR I 175 " --> pdb=" O ALA I 171 " (cutoff:3.500A) Processing helix chain 'J' and resid 5 through 22 Processing helix chain 'J' and resid 26 through 47 removed outlier: 3.542A pdb=" N LEU J 31 " --> pdb=" O ILE J 27 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N PHE J 47 " --> pdb=" O ILE J 43 " (cutoff:3.500A) Processing helix chain 'J' and resid 50 through 59 Processing helix chain 'J' and resid 64 through 74 Processing helix chain 'J' and resid 138 through 147 removed outlier: 3.911A pdb=" N LEU J 146 " --> pdb=" O GLY J 142 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N TYR J 147 " --> pdb=" O ILE J 143 " (cutoff:3.500A) Processing helix chain 'J' and resid 151 through 173 Processing helix chain 'K' and resid 3 through 21 Processing helix chain 'K' and resid 26 through 50 Processing helix chain 'K' and resid 54 through 85 removed outlier: 3.840A pdb=" N MET K 58 " --> pdb=" O LEU K 55 " (cutoff:3.500A) Proline residue: K 60 - end of helix removed outlier: 3.571A pdb=" N PHE K 66 " --> pdb=" O LEU K 63 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA K 67 " --> pdb=" O LEU K 64 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU K 75 " --> pdb=" O ALA K 72 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ASN K 83 " --> pdb=" O MET K 80 " (cutoff:3.500A) Processing helix chain 'K' and resid 90 through 92 No H-bonds generated for 'chain 'K' and resid 90 through 92' Processing helix chain 'L' and resid 3 through 22 removed outlier: 3.739A pdb=" N LEU L 12 " --> pdb=" O SER L 8 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU L 15 " --> pdb=" O THR L 11 " (cutoff:3.500A) Proline residue: L 18 - end of helix removed outlier: 3.515A pdb=" N MET L 22 " --> pdb=" O PRO L 18 " (cutoff:3.500A) Processing helix chain 'L' and resid 29 through 57 Proline residue: L 33 - end of helix removed outlier: 3.539A pdb=" N PHE L 44 " --> pdb=" O SER L 41 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE L 49 " --> pdb=" O THR L 46 " (cutoff:3.500A) Proline residue: L 50 - end of helix removed outlier: 3.768A 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: 3.833A 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: 3.573A pdb=" N GLY L 148 " --> pdb=" O TRP L 144 " (cutoff:3.500A) Processing helix chain 'L' and resid 162 through 192 removed outlier: 4.193A pdb=" N GLY L 181 " --> pdb=" O ILE L 177 " (cutoff:3.500A) Processing helix chain 'L' and resid 198 through 204 Processing helix chain 'L' and resid 210 through 223 Processing helix chain 'L' and resid 231 through 238 removed outlier: 4.106A pdb=" N MET L 237 " --> pdb=" O LEU L 233 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N GLU L 238 " --> pdb=" O PRO L 234 " (cutoff:3.500A) Processing helix chain 'L' and resid 241 through 248 Processing helix chain 'L' and resid 252 through 262 removed outlier: 3.823A pdb=" N GLY L 256 " --> pdb=" O VAL L 253 " (cutoff:3.500A) Processing helix chain 'L' and resid 264 through 269 removed outlier: 4.758A pdb=" N ASN L 269 " --> pdb=" O PRO L 265 " (cutoff:3.500A) Processing helix chain 'L' and resid 271 through 293 removed outlier: 3.546A pdb=" N LEU L 293 " --> pdb=" O ALA L 289 " (cutoff:3.500A) Processing helix chain 'L' and resid 298 through 318 Processing helix chain 'L' and resid 322 through 349 removed outlier: 3.875A pdb=" N PHE L 334 " --> pdb=" O CYS L 330 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N PHE L 335 " --> pdb=" O THR L 331 " (cutoff:3.500A) Processing helix chain 'L' and resid 356 through 358 No H-bonds generated for 'chain 'L' and resid 356 through 358' Processing helix chain 'L' and resid 367 through 380 Processing helix chain 'L' and resid 387 through 400 removed outlier: 4.047A pdb=" N LYS L 392 " --> pdb=" O PHE L 389 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N ASP L 393 " --> pdb=" O TYR L 390 " (cutoff:3.500A) Processing helix chain 'L' and resid 406 through 431 removed outlier: 3.572A pdb=" N ALA L 420 " --> pdb=" O THR L 416 " (cutoff:3.500A) Processing helix chain 'L' and resid 448 through 469 removed outlier: 6.242A pdb=" N GLY L 465 " --> pdb=" O SER L 461 " (cutoff:3.500A) removed outlier: 5.226A 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: 3.569A pdb=" N THR L 508 " --> pdb=" O ILE L 504 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N LYS L 509 " --> pdb=" O SER L 505 " (cutoff:3.500A) Processing helix chain 'L' and resid 518 through 524 Processing helix chain 'L' and resid 526 through 546 Proline residue: L 530 - end of helix removed outlier: 3.609A pdb=" N MET L 533 " --> pdb=" O PRO L 530 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N HIS L 534 " --> pdb=" O THR L 531 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG L 535 " --> pdb=" O ILE L 532 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU L 536 " --> pdb=" O MET L 533 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N ALA L 537 " --> pdb=" O HIS L 534 " (cutoff:3.500A) Proline residue: L 538 - end of helix removed outlier: 3.650A pdb=" N ASN L 541 " --> pdb=" O PRO L 538 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N SER L 543 " --> pdb=" O MET L 540 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLN L 546 " --> pdb=" O SER L 543 " (cutoff:3.500A) Processing helix chain 'M' and resid 5 through 16 removed outlier: 4.170A pdb=" N MET M 12 " --> pdb=" O THR M 8 " (cutoff:3.500A) Proline residue: M 13 - end of helix Processing helix chain 'M' and resid 20 through 42 removed outlier: 4.236A pdb=" N ILE M 23 " --> pdb=" O ASN M 20 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N TRP M 24 " --> pdb=" O ASN M 21 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ASN M 26 " --> pdb=" O ILE M 23 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N SER M 27 " --> pdb=" O TRP M 24 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N THR M 28 " --> pdb=" O VAL M 25 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N HIS M 30 " --> pdb=" O SER M 27 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER M 31 " --> pdb=" O THR M 28 " (cutoff:3.500A) Processing helix chain 'M' and resid 60 through 80 Proline residue: M 64 - end of helix removed outlier: 3.607A pdb=" N LEU M 73 " --> pdb=" O THR M 69 " (cutoff:3.500A) Proline residue: M 74 - end of helix Processing helix chain 'M' and resid 89 through 111 Processing helix chain 'M' and resid 115 through 135 removed outlier: 4.750A pdb=" N LEU M 126 " --> pdb=" O PHE M 122 " (cutoff:3.500A) removed outlier: 4.189A 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 147 through 155 Processing helix chain 'M' and resid 157 through 171 Processing helix chain 'M' and resid 176 through 182 removed outlier: 3.875A pdb=" N TYR M 181 " --> pdb=" O LEU M 177 " (cutoff:3.500A) Processing helix chain 'M' and resid 190 through 206 removed outlier: 5.101A pdb=" N ALA M 202 " --> pdb=" O ALA M 198 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N PHE M 203 " --> pdb=" O CYS M 199 " (cutoff:3.500A) Processing helix chain 'M' and resid 214 through 222 removed outlier: 3.770A pdb=" N LYS M 218 " --> pdb=" O LEU M 214 " (cutoff:3.500A) Processing helix chain 'M' and resid 225 through 233 Processing helix chain 'M' and resid 235 through 249 removed outlier: 4.126A pdb=" N GLY M 239 " --> pdb=" O LEU M 235 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLY M 240 " --> pdb=" O LEU M 236 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N LEU M 248 " --> pdb=" O LEU M 244 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N ILE M 249 " --> pdb=" O ARG M 245 " (cutoff:3.500A) Processing helix chain 'M' and resid 253 through 278 removed outlier: 3.730A pdb=" N MET M 257 " --> pdb=" O THR M 254 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N ALA M 258 " --> pdb=" O ASP M 255 " (cutoff:3.500A) Proline residue: M 260 - end of helix removed outlier: 3.569A pdb=" N LEU M 264 " --> pdb=" O PHE M 261 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N TRP M 267 " --> pdb=" O LEU M 264 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N MET M 269 " --> pdb=" O LEU M 266 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N THR M 272 " --> pdb=" O MET M 269 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER M 273 " --> pdb=" O ILE M 270 " (cutoff:3.500A) Processing helix chain 'M' and resid 282 through 303 removed outlier: 3.666A pdb=" N LEU M 296 " --> pdb=" O SER M 292 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL M 297 " --> pdb=" O HIS M 293 " (cutoff:3.500A) Processing helix chain 'M' and resid 306 through 337 removed outlier: 3.863A 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: 3.526A pdb=" N THR M 403 " --> pdb=" O MET M 400 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N SER M 407 " --> pdb=" O ALA M 404 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU M 408 " --> pdb=" O LEU M 405 " (cutoff:3.500A) removed outlier: 3.508A 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: 3.702A pdb=" N THR M 414 " --> pdb=" O LEU M 411 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLN M 415 " --> pdb=" O ILE M 412 " (cutoff:3.500A) Processing helix chain 'M' and resid 431 through 448 removed outlier: 3.504A pdb=" N HIS M 440 " --> pdb=" O LEU M 436 " (cutoff:3.500A) Proline residue: M 443 - end of helix removed outlier: 3.957A pdb=" N THR M 448 " --> pdb=" O LEU M 444 " (cutoff:3.500A) Processing helix chain 'M' and resid 451 through 454 Processing helix chain 'N' and resid 3 through 22 Processing helix chain 'N' and resid 26 through 44 Proline residue: N 42 - end of helix Processing helix chain 'N' and resid 50 through 81 Processing helix chain 'N' and resid 92 through 106 Processing helix chain 'N' and resid 113 through 120 removed outlier: 3.882A 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: 4.376A pdb=" N ALA N 137 " --> pdb=" O GLN N 134 " (cutoff:3.500A) Proline residue: N 138 - end of helix removed outlier: 3.871A pdb=" N TYR N 143 " --> pdb=" O SER N 140 " (cutoff:3.500A) removed outlier: 4.501A 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 169 Processing helix chain 'N' and resid 175 through 194 Processing helix chain 'N' and resid 198 through 222 Processing helix chain 'N' and resid 227 through 233 removed outlier: 3.571A pdb=" N SER N 231 " --> pdb=" O THR N 227 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N HIS N 232 " --> pdb=" O LEU N 228 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N THR N 233 " --> pdb=" O SER N 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 227 through 233' Processing helix chain 'N' and resid 238 through 252 Processing helix chain 'N' and resid 258 through 273 Proline residue: N 262 - end of helix Processing helix chain 'N' and resid 277 through 302 Processing helix chain 'N' and resid 309 through 316 Processing helix chain 'N' and resid 326 through 332 removed outlier: 3.574A pdb=" N VAL N 331 " --> pdb=" O PRO N 327 " (cutoff:3.500A) Processing helix chain 'N' and resid 337 through 346 Proline residue: N 341 - end of helix Processing helix chain 'O' and resid 5 through 9 Processing helix chain 'O' and resid 14 through 16 No H-bonds generated for 'chain 'O' and resid 14 through 16' Processing helix chain 'O' and resid 35 through 46 removed outlier: 3.678A pdb=" N LYS O 40 " --> pdb=" O SER O 36 " (cutoff:3.500A) Processing helix chain 'O' and resid 56 through 62 removed outlier: 4.464A pdb=" N VAL O 59 " --> pdb=" O ILE O 56 " (cutoff:3.500A) Processing helix chain 'O' and resid 72 through 74 No H-bonds generated for 'chain 'O' and resid 72 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 132 through 140 Processing helix chain 'O' and resid 146 through 159 Processing helix chain 'O' and resid 176 through 186 removed outlier: 3.554A pdb=" N SER O 181 " --> pdb=" O PRO O 177 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLN O 184 " --> pdb=" O GLN O 180 " (cutoff:3.500A) Processing helix chain 'O' and resid 189 through 193 removed outlier: 3.578A pdb=" N LYS O 193 " --> pdb=" O PRO O 189 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 189 through 193' Processing helix chain 'O' and resid 196 through 208 Processing helix chain 'O' and resid 210 through 217 removed outlier: 4.097A pdb=" N GLU O 216 " --> pdb=" O PRO O 212 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N LYS O 217 " --> pdb=" O GLU O 213 " (cutoff:3.500A) Processing helix chain 'O' and resid 225 through 229 removed outlier: 3.545A pdb=" N GLN O 229 " --> pdb=" O ALA O 225 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 225 through 229' Processing helix chain 'O' and resid 231 through 239 Processing helix chain 'O' and resid 247 through 250 Processing helix chain 'O' and resid 253 through 264 Processing helix chain 'O' and resid 266 through 274 removed outlier: 5.070A pdb=" N TYR O 272 " --> pdb=" O GLU O 268 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N THR O 273 " --> pdb=" O VAL O 269 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N SER O 274 " --> pdb=" O LEU O 270 " (cutoff:3.500A) Processing helix chain 'O' and resid 286 through 298 removed outlier: 3.557A pdb=" N GLU O 298 " --> pdb=" O GLN O 294 " (cutoff:3.500A) 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: 4.082A pdb=" N TYR P 33 " --> pdb=" O PHE P 29 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N MET P 41 " --> pdb=" O HIS P 37 " (cutoff:3.500A) Processing helix chain 'P' and resid 53 through 62 removed outlier: 4.977A 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 184 Processing helix chain 'P' and resid 207 through 219 Processing helix chain 'P' and resid 221 through 223 No H-bonds generated for 'chain 'P' and resid 221 through 223' Processing helix chain 'P' and resid 238 through 248 Processing helix chain 'P' and resid 281 through 287 Processing helix chain 'P' and resid 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: 4.814A pdb=" N ILE P 315 " --> pdb=" O GLU P 311 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N GLU P 316 " --> pdb=" O LEU P 312 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N ARG P 320 " --> pdb=" O GLU P 316 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N HIS P 321 " --> pdb=" O VAL P 317 " (cutoff:3.500A) Processing helix chain 'Q' and resid 20 through 22 No H-bonds generated for 'chain 'Q' and resid 20 through 22' Processing helix chain 'Q' and resid 27 through 31 removed outlier: 4.080A 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 98 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: 3.520A pdb=" N ALA R 45 " --> pdb=" O ILE R 41 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU R 46 " --> pdb=" O ASP R 42 " (cutoff:3.500A) Processing helix chain 'R' and resid 64 through 66 No H-bonds generated for 'chain 'R' and resid 64 through 66' Processing helix chain 'S' and resid 27 through 38 removed outlier: 4.825A pdb=" N GLY S 31 " --> pdb=" O GLY S 28 " (cutoff:3.500A) Processing helix chain 'S' and resid 40 through 46 Processing helix chain 'S' and resid 69 through 71 No H-bonds generated for 'chain 'S' and resid 69 through 71' Processing helix chain 'S' and resid 83 through 94 Processing helix chain 'T' and resid 12 through 21 Processing helix chain 'T' and resid 44A through 57 Processing helix chain 'T' and resid 64 through 67 No H-bonds generated for 'chain 'T' and resid 64 through 67' Processing helix chain 'T' and resid 73 through 81 Processing helix chain 'U' and resid 8 through 21 Processing helix chain 'U' and resid 44A through 58 Processing helix chain 'U' and resid 64 through 69 removed outlier: 4.629A pdb=" N LYS U 69 " --> pdb=" O ILE U 65 " (cutoff:3.500A) Processing helix chain 'U' and resid 73 through 84 Processing helix chain 'V' and resid 19 through 36 removed outlier: 4.257A pdb=" N HIS V 36 " --> pdb=" O ASP V 32 " (cutoff:3.500A) Processing helix chain 'V' and resid 42 through 60 Processing helix chain 'V' and resid 64 through 71 Processing helix chain 'V' and resid 76 through 96 removed outlier: 3.894A pdb=" N GLN V 95 " --> pdb=" O ARG V 91 " (cutoff:3.500A) Processing helix chain 'W' and resid 25 through 49 removed outlier: 3.607A pdb=" N ARG W 31 " --> pdb=" O GLU W 27 " (cutoff:3.500A) Proline residue: W 44 - end of helix Processing helix chain 'W' and resid 56 through 70 removed outlier: 4.069A 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: 4.444A pdb=" N PHE W 106 " --> pdb=" O HIS W 102 " (cutoff:3.500A) Processing helix chain 'W' and resid 118 through 124 Processing helix chain 'X' and resid 9 through 12 No H-bonds generated for 'chain 'X' and resid 9 through 12' Processing helix chain 'X' and resid 21 through 26 Processing helix chain 'X' and resid 28 through 34 removed outlier: 3.554A pdb=" N ALA X 33 " --> pdb=" O HIS X 29 " (cutoff:3.500A) Processing helix chain 'X' and resid 36 through 49 Processing helix chain 'X' and resid 52 through 76 removed outlier: 3.912A pdb=" N LEU X 56 " --> pdb=" O ARG X 53 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N GLU X 57 " --> pdb=" O ARG X 54 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N CYS X 65 " --> pdb=" O VAL X 62 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE X 73 " --> pdb=" O PHE X 70 " (cutoff:3.500A) Processing helix chain 'X' and resid 78 through 90 Processing helix chain 'X' and resid 97 through 114 removed outlier: 4.266A pdb=" N ARG X 100 " --> pdb=" O ARG X 97 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N LYS X 101 " --> pdb=" O ARG X 98 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLN X 103 " --> pdb=" O ARG X 100 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN X 105 " --> pdb=" O GLN X 102 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL X 110 " --> pdb=" O ASP X 107 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU X 111 " --> pdb=" O GLU X 108 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS X 113 " --> pdb=" O VAL X 110 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N LEU X 114 " --> pdb=" O LEU X 111 " (cutoff:3.500A) Processing helix chain 'Y' and resid 122 through 130 Processing helix chain 'Z' and resid 32 through 97 Proline residue: Z 73 - end of helix Processing helix chain 'Z' and resid 121 through 125 Processing helix chain 'Z' and resid 130 through 143 removed outlier: 5.340A pdb=" N PHE Z 140 " --> pdb=" O ALA Z 136 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N ILE Z 141 " --> pdb=" O THR Z 137 " (cutoff:3.500A) Processing helix chain 'a' and resid 2 through 30 Proline residue: a 7 - end of helix removed outlier: 3.704A pdb=" N ILE a 18 " --> pdb=" O CYS a 15 " (cutoff:3.500A) Proline residue: a 19 - end of helix removed outlier: 3.561A pdb=" N ALA a 22 " --> pdb=" O PRO a 19 " (cutoff:3.500A) removed outlier: 3.579A 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 3 through 14 Processing helix chain 'b' and resid 16 through 34 Proline residue: b 32 - end of helix Processing helix chain 'b' and resid 37 through 47 removed outlier: 3.710A pdb=" N ILE b 44 " --> pdb=" O SER b 41 " (cutoff:3.500A) Processing helix chain 'b' and resid 78 through 82 Processing helix chain 'c' and resid 14 through 46 Processing helix chain 'd' and resid 16 through 20 Processing helix chain 'd' and resid 29 through 49 Processing helix chain 'd' and resid 58 through 96 removed outlier: 3.590A 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: 4.140A pdb=" N LYS e 53 " --> pdb=" O ILE e 49 " (cutoff:3.500A) Processing helix chain 'e' and resid 56 through 67 Processing helix chain 'e' and resid 69 through 88 Processing helix chain 'f' and resid 7 through 33 removed outlier: 6.516A pdb=" N VAL f 12 " --> pdb=" O ARG f 8 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N HIS f 13 " --> pdb=" O ASP f 9 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N VAL f 14 " --> pdb=" O HIS f 10 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N LEU f 15 " --> pdb=" O TRP f 11 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N VAL f 16 " --> pdb=" O VAL f 12 " (cutoff:3.500A) Proline residue: f 17 - end of helix removed outlier: 3.587A pdb=" N GLU f 32 " --> pdb=" O ARG f 28 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS f 33 " --> pdb=" O LYS f 29 " (cutoff:3.500A) Processing helix chain 'g' and resid 37 through 40 No H-bonds generated for 'chain 'g' and resid 37 through 40' Processing helix chain 'g' and resid 51 through 65 Processing helix chain 'g' and resid 69 through 79 Processing helix chain 'g' and resid 83 through 103 removed outlier: 3.899A pdb=" N GLN g 86 " --> pdb=" O TYR g 83 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N GLU g 87 " --> pdb=" O ARG g 84 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS g 98 " --> pdb=" O ARG g 95 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU g 101 " --> pdb=" O LYS g 98 " (cutoff:3.500A) Processing helix chain 'g' and resid 115 through 117 No H-bonds generated for 'chain 'g' and resid 115 through 117' Processing helix chain 'h' and resid 16 through 46 removed outlier: 4.115A 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: 3.670A pdb=" N TYR h 66 " --> pdb=" O HIS h 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 63 through 66' Processing helix chain 'h' and resid 70 through 79 Processing helix chain 'h' and resid 83 through 117 Processing helix chain 'h' and resid 130 through 132 No H-bonds generated for 'chain 'h' and resid 130 through 132' Processing helix chain 'i' and resid 5 through 25 Processing helix chain 'i' and resid 60 through 73 removed outlier: 3.581A pdb=" N HIS i 66 " --> pdb=" O LYS i 62 " (cutoff:3.500A) Processing helix chain 'i' and resid 75 through 87 Processing helix chain 'j' and resid 19 through 48 removed outlier: 7.366A pdb=" N ASP j 45 " --> pdb=" O TRP j 41 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ALA j 46 " --> pdb=" O HIS j 42 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N VAL j 47 " --> pdb=" O ASP j 43 " (cutoff:3.500A) Processing helix chain 'j' and resid 56 through 58 No H-bonds generated for 'chain 'j' and resid 56 through 58' Processing helix chain 'j' and resid 61 through 64 No H-bonds generated for 'chain 'j' and resid 61 through 64' Processing helix chain 'k' and resid 27 through 38 removed outlier: 3.717A pdb=" N ARG k 38 " --> pdb=" O LYS k 34 " (cutoff:3.500A) Processing helix chain 'k' and resid 45 through 52 removed outlier: 4.887A pdb=" N TRP k 50 " --> pdb=" O ASN k 47 " (cutoff:3.500A) Processing helix chain 'k' and resid 62 through 66 Processing helix chain 'k' and resid 70 through 89 Processing helix chain 'l' and resid 6 through 8 No H-bonds generated for 'chain 'l' and resid 6 through 8' Processing helix chain 'l' and resid 17 through 26 Processing helix chain 'l' and resid 55 through 57 No H-bonds generated for 'chain 'l' and resid 55 through 57' Processing helix chain 'l' and resid 81 through 84 No H-bonds generated for 'chain 'l' and resid 81 through 84' Processing helix chain 'l' and resid 98 through 121 Processing helix chain 'l' and resid 134 through 138 Processing helix chain 'm' and resid 15 through 17 No H-bonds generated for 'chain 'm' and resid 15 through 17' Processing helix chain 'm' and resid 19 through 21 No H-bonds generated for 'chain 'm' and resid 19 through 21' Processing helix chain 'm' and resid 26 through 50 removed outlier: 3.724A pdb=" N GLN m 49 " --> pdb=" O GLU m 45 " (cutoff:3.500A) Processing helix chain 'm' and resid 62 through 72 Processing helix chain 'm' and resid 95 through 117 Processing helix chain 'n' and resid 11 through 30 Processing helix chain 'n' and resid 33 through 49 Processing helix chain 'n' and resid 56 through 73 Processing helix chain 'n' and resid 94 through 96 No H-bonds generated for 'chain 'n' and resid 94 through 96' Processing helix chain 'n' and resid 100 through 105 Processing helix chain 'n' and resid 108 through 113 removed outlier: 3.987A pdb=" N MET n 113 " --> pdb=" O SER n 109 " (cutoff:3.500A) Processing helix chain 'n' and resid 115 through 142 removed outlier: 4.723A pdb=" N GLU n 133 " --> pdb=" O ARG n 129 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N ARG n 134 " --> pdb=" O GLU n 130 " (cutoff:3.500A) Processing helix chain 'n' and resid 167 through 170 No H-bonds generated for 'chain 'n' and resid 167 through 170' Processing helix chain 'o' and resid 2 through 9 Processing helix chain 'o' and resid 12 through 14 No H-bonds generated for 'chain 'o' and resid 12 through 14' Processing helix chain 'o' and resid 42 through 47 Processing helix chain 'o' and resid 52 through 54 No H-bonds generated for 'chain 'o' and resid 52 through 54' Processing helix chain 'o' and resid 59 through 71 Processing helix chain 'o' and resid 80 through 118 Processing helix chain 'p' and resid 28 through 39 Processing helix chain 'p' and resid 41 through 57 Processing helix chain 'p' and resid 73 through 75 No H-bonds generated for 'chain 'p' and resid 73 through 75' Processing helix chain 'p' and resid 81 through 123 removed outlier: 3.585A pdb=" N GLU p 86 " --> pdb=" O LEU p 82 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N GLU p 118 " --> pdb=" O GLN p 114 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N SER p 119 " --> pdb=" O ARG p 115 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N HIS p 120 " --> pdb=" O GLU p 116 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N ARG p 121 " --> pdb=" O GLY p 117 " (cutoff:3.500A) removed outlier: 6.459A 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 4 through 17 removed outlier: 3.665A pdb=" N VAL q 14 " --> pdb=" O GLY q 10 " (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: 4.395A pdb=" N TRP q 89 " --> pdb=" O GLU q 85 " (cutoff:3.500A) Processing helix chain 'r' and resid 5 through 15 Processing helix chain 'r' and resid 19 through 22 Processing helix chain 'r' and resid 53 through 55 No H-bonds generated for 'chain 'r' and resid 53 through 55' Processing helix chain 'r' and resid 58 through 61 No H-bonds generated for 'chain 'r' and resid 58 through 61' Processing helix chain 's' and resid 42 through 45 Processing helix chain 's' and resid 50 through 61 removed outlier: 4.648A pdb=" N LYS s 60 " --> pdb=" O LEU s 56 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N PHE s 61 " --> pdb=" O ASP s 57 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.365A pdb=" N VAL B 85 " --> pdb=" O MET B 48 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N PHE B 50 " --> pdb=" O VAL B 85 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ILE B 87 " --> pdb=" O PHE B 50 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N TYR B 112 " --> pdb=" O MET B 86 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N VAL B 88 " --> pdb=" O TYR B 112 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N VAL B 114 " --> pdb=" O VAL B 88 " (cutoff:3.500A) removed outlier: 6.256A 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: 6.663A pdb=" N ASN C 95 " --> pdb=" O ALA C 76 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N LEU C 78 " --> pdb=" O VAL C 93 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N VAL C 93 " --> pdb=" O LEU C 78 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ALA C 80 " --> pdb=" O GLU C 91 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N GLU C 91 " --> pdb=" O ALA C 80 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N LEU C 48 " --> pdb=" O ARG C 104 " (cutoff:3.500A) removed outlier: 4.816A 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 46 through 48 removed outlier: 6.484A pdb=" N SER D 69 " --> pdb=" O VAL D 73 " (cutoff:3.500A) removed outlier: 5.553A 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: 6.449A pdb=" N TYR E 98 " --> pdb=" O THR E 138 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N ILE E 140 " --> pdb=" O TYR E 98 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ILE E 100 " --> pdb=" O ILE E 140 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N VAL E 142 " --> pdb=" O ILE E 100 " (cutoff:3.500A) removed outlier: 6.040A 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: 6.985A pdb=" N TYR F 92 " --> pdb=" O THR F 221 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N ALA F 223 " --> pdb=" O TYR F 92 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N VAL F 94 " --> pdb=" O ALA F 223 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ALA F 133 " --> pdb=" O LEU F 93 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N VAL F 95 " --> pdb=" O ALA F 133 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N TYR F 135 " --> pdb=" O VAL F 95 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ALA F 97 " --> pdb=" O TYR F 135 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N TYR F 137 " --> pdb=" O ALA F 97 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ASP F 174 " --> pdb=" O ALA F 134 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N ILE F 136 " --> pdb=" O ASP F 174 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N PHE F 176 " --> pdb=" O ILE F 136 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N ILE F 138 " --> pdb=" O PHE F 176 " (cutoff:3.500A) removed outlier: 6.123A 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: 6.314A pdb=" N ARG G 243 " --> pdb=" O VAL G 247 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N VAL G 247 " --> pdb=" O ARG G 243 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'G' and resid 283 through 285 Processing sheet with id= N, first strand: chain 'G' and resid 343 through 345 removed outlier: 8.416A pdb=" N CYS G 344 " --> pdb=" O VAL G 315 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ALA G 317 " --> pdb=" O CYS G 344 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N MET G 521 " --> pdb=" O ALA G 316 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N ILE G 318 " --> pdb=" O MET G 521 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N PHE G 523 " --> pdb=" O ILE G 318 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N PHE G 542 " --> pdb=" O LEU G 522 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N LEU G 524 " --> pdb=" O PHE G 542 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N VAL G 544 " --> pdb=" O LEU G 524 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N VAL G 559 " --> pdb=" O TYR G 545 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N GLY G 547 " --> pdb=" O VAL G 559 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N LEU G 561 " --> pdb=" O GLY G 547 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'G' and resid 405 through 409 Processing sheet with id= P, first strand: chain 'G' and resid 572 through 574 Processing sheet with id= Q, first strand: chain 'I' and resid 65 through 67 Processing sheet with id= R, first strand: chain 'I' and resid 92 through 98 removed outlier: 5.994A pdb=" N GLU I 97 " --> pdb=" O THR I 106 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N THR I 106 " --> pdb=" O GLU I 97 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'L' and resid 69 through 71 Processing sheet with id= T, first strand: chain 'L' and resid 61 through 67 removed outlier: 6.719A pdb=" N LEU L 78 " --> pdb=" O ASN L 65 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'O' and resid 219 through 224 removed outlier: 6.300A pdb=" N VAL O 122 " --> pdb=" O ILE O 25 " (cutoff:3.500A) removed outlier: 8.005A pdb=" N VAL O 27 " --> pdb=" O VAL O 122 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N LEU O 124 " --> pdb=" O VAL O 27 " (cutoff:3.500A) removed outlier: 8.614A pdb=" N GLY O 29 " --> pdb=" O LEU O 124 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N LYS O 49 " --> pdb=" O VAL O 123 " (cutoff:3.500A) removed outlier: 8.325A pdb=" N GLU O 125 " --> pdb=" O LYS O 49 " (cutoff:3.500A) removed outlier: 8.216A pdb=" N PHE O 51 " --> pdb=" O GLU O 125 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'P' and resid 227 through 230 removed outlier: 6.637A pdb=" N ILE P 165 " --> pdb=" O PHE P 228 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N PHE P 230 " --> pdb=" O ILE P 165 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N LYS P 167 " --> pdb=" O PHE P 230 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N GLN P 44 " --> pdb=" O ALA P 21 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N VAL P 23 " --> pdb=" O GLN P 44 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ILE P 46 " --> pdb=" O VAL P 23 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'Q' and resid 102 through 105 Processing sheet with id= X, first strand: chain 'Q' and resid 64 through 66 Processing sheet with id= Y, first strand: chain 'R' and resid 50 through 52 Processing sheet with id= Z, first strand: chain 'R' and resid 56 through 59 Processing sheet with id= AA, first strand: chain 'S' and resid 52 through 56 removed outlier: 8.536A pdb=" N LEU S 53 " --> pdb=" O ARG S 16 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ILE S 18 " --> pdb=" O LEU S 53 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N ARG S 55 " --> pdb=" O ILE S 18 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ILE S 20 " --> pdb=" O ARG S 55 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ARG S 67 " --> pdb=" O ARG S 16 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ILE S 18 " --> pdb=" O TRP S 65 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N TRP S 65 " --> pdb=" O ILE S 18 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N ILE S 20 " --> pdb=" O LYS S 63 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N LYS S 63 " --> pdb=" O ILE S 20 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLN S 72 " --> pdb=" O TYR S 68 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'q' and resid 60 through 63 removed outlier: 6.414A pdb=" N GLU q 50 " --> pdb=" O LEU q 38 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N LEU q 38 " --> pdb=" O GLU q 50 " (cutoff:3.500A) 2772 hydrogen bonds defined for protein. 7446 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 22.24 Time building geometry restraints manager: 24.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.40: 26454 1.40 - 1.63: 38337 1.63 - 1.85: 802 1.85 - 2.08: 0 2.08 - 2.30: 81 Bond restraints: 65674 Sorted by residual: bond pdb=" C5 GTP O 401 " pdb=" N7 GTP O 401 " ideal model delta sigma weight residual 1.350 1.519 -0.169 2.00e-02 2.50e+03 7.14e+01 bond pdb=" C6 GTP O 401 " pdb=" O6 GTP O 401 " ideal model delta sigma weight residual 1.230 1.398 -0.168 2.00e-02 2.50e+03 7.04e+01 bond pdb=" CB7 CDL d1202 " pdb=" OB8 CDL d1202 " ideal model delta sigma weight residual 1.334 1.405 -0.071 1.10e-02 8.26e+03 4.18e+01 bond pdb=" C SAC i 1 " pdb=" O SAC i 1 " ideal model delta sigma weight residual 1.231 1.360 -0.129 2.00e-02 2.50e+03 4.17e+01 bond pdb=" CB7 CDL r 201 " pdb=" OB8 CDL r 201 " ideal model delta sigma weight residual 1.334 1.402 -0.068 1.10e-02 8.26e+03 3.85e+01 ... (remaining 65669 not shown) Histogram of bond angle deviations from ideal: 72.60 - 84.91: 76 84.91 - 97.22: 2 97.22 - 109.53: 7188 109.53 - 121.84: 69093 121.84 - 134.15: 12503 Bond angle restraints: 88862 Sorted by residual: angle pdb=" O SAC i 1 " pdb=" C SAC i 1 " pdb=" N GLY i 2 " ideal model delta sigma weight residual 123.00 87.85 35.15 1.60e+00 3.91e-01 4.83e+02 angle pdb=" C51 CDL h1001 " pdb=" CB5 CDL h1001 " pdb=" OB6 CDL h1001 " ideal model delta sigma weight residual 111.33 122.22 -10.89 1.32e+00 5.72e-01 6.78e+01 angle pdb=" C51 CDL X 201 " pdb=" CB5 CDL X 201 " pdb=" OB6 CDL X 201 " ideal model delta sigma weight residual 111.33 120.40 -9.07 1.32e+00 5.72e-01 4.71e+01 angle pdb=" C11 CDL X 201 " pdb=" CA5 CDL X 201 " pdb=" OA6 CDL X 201 " ideal model delta sigma weight residual 111.33 120.28 -8.95 1.32e+00 5.72e-01 4.59e+01 angle pdb=" C11 CDL r 201 " pdb=" CA5 CDL r 201 " pdb=" OA6 CDL r 201 " ideal model delta sigma weight residual 111.33 120.26 -8.93 1.32e+00 5.72e-01 4.56e+01 ... (remaining 88857 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.89: 38204 34.89 - 69.79: 1535 69.79 - 104.68: 219 104.68 - 139.57: 40 139.57 - 174.46: 5 Dihedral angle restraints: 40003 sinusoidal: 17299 harmonic: 22704 Sorted by residual: dihedral pdb=" C10 FMN F 501 " pdb=" C1' FMN F 501 " pdb=" N10 FMN F 501 " pdb=" C2' FMN F 501 " ideal model delta sinusoidal sigma weight residual 257.59 83.13 174.46 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" C8 GTP O 401 " pdb=" C1' GTP O 401 " pdb=" N9 GTP O 401 " pdb=" O4' GTP O 401 " ideal model delta sinusoidal sigma weight residual 104.59 -41.55 146.14 1 2.00e+01 2.50e-03 4.39e+01 dihedral pdb=" C5' FMN F 501 " pdb=" O5' FMN F 501 " pdb=" P FMN F 501 " pdb=" O1P FMN F 501 " ideal model delta sinusoidal sigma weight residual 75.26 -66.34 141.59 1 2.00e+01 2.50e-03 4.28e+01 ... (remaining 40000 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.274: 9676 4.274 - 8.547: 0 8.547 - 12.821: 0 12.821 - 17.094: 0 17.094 - 21.368: 16 Chirality restraints: 9692 Sorted by residual: chirality pdb="FE1 SF4 I 202 " pdb=" S2 SF4 I 202 " pdb=" S3 SF4 I 202 " pdb=" S4 SF4 I 202 " both_signs ideal model delta sigma weight residual False -10.55 10.81 -21.37 2.00e-01 2.50e+01 1.14e+04 chirality pdb="FE4 SF4 F 502 " pdb=" S1 SF4 F 502 " pdb=" S2 SF4 F 502 " pdb=" S3 SF4 F 502 " both_signs ideal model delta sigma weight residual False 10.55 -10.80 21.35 2.00e-01 2.50e+01 1.14e+04 chirality pdb="FE2 SF4 I 202 " pdb=" S1 SF4 I 202 " pdb=" S3 SF4 I 202 " pdb=" S4 SF4 I 202 " both_signs ideal model delta sigma weight residual False 10.55 -10.79 21.34 2.00e-01 2.50e+01 1.14e+04 ... (remaining 9689 not shown) Planarity restraints: 11096 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C08 I49 N1102 " 0.407 2.00e-02 2.50e+03 4.81e-01 4.63e+03 pdb=" C14 I49 N1102 " -0.154 2.00e-02 2.50e+03 pdb=" C15 I49 N1102 " -0.063 2.00e-02 2.50e+03 pdb=" N01 I49 N1102 " 0.028 2.00e-02 2.50e+03 pdb=" N02 I49 N1102 " -0.508 2.00e-02 2.50e+03 pdb=" N03 I49 N1102 " -0.040 2.00e-02 2.50e+03 pdb=" N04 I49 N1102 " -0.654 2.00e-02 2.50e+03 pdb=" N05 I49 N1102 " 0.985 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SAC i 1 " 0.146 2.00e-02 2.50e+03 2.32e-01 5.40e+02 pdb=" C SAC i 1 " -0.402 2.00e-02 2.50e+03 pdb=" O SAC i 1 " 0.118 2.00e-02 2.50e+03 pdb=" N GLY i 2 " 0.138 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA 2MR D 85 " 0.078 2.00e-02 2.50e+03 1.47e-01 2.16e+02 pdb=" C 2MR D 85 " -0.254 2.00e-02 2.50e+03 pdb=" O 2MR D 85 " 0.085 2.00e-02 2.50e+03 pdb=" N GLY D 86 " 0.091 2.00e-02 2.50e+03 ... (remaining 11093 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.55: 675 2.55 - 3.20: 61789 3.20 - 3.85: 140473 3.85 - 4.49: 202269 4.49 - 5.14: 305307 Nonbonded interactions: 710513 Sorted by model distance: nonbonded pdb=" O4' LMT p 201 " pdb=" O6' LMT p 201 " model vdw 1.904 2.440 nonbonded pdb=" O HOH a 103 " pdb=" O HOH a 112 " model vdw 1.908 2.440 nonbonded pdb=" O PRO h 141 " pdb=" O HOH h1101 " model vdw 1.909 2.440 nonbonded pdb=" O HOH X 309 " pdb=" O HOH X 324 " model vdw 1.935 2.440 nonbonded pdb=" OE1 GLU H 204 " pdb=" O HOH H1001 " model vdw 1.948 2.440 ... (remaining 710508 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 11 through 82 or resid 101)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 13.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.060 Extract box with map and model: 57.230 Check model and map are aligned: 0.730 Set scattering table: 0.470 Process input model: 160.340 Find NCS groups from input model: 1.970 Set up NCS constraints: 0.270 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:12.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 247.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.169 65674 Z= 0.463 Angle : 0.790 35.149 88862 Z= 0.372 Chirality : 0.866 21.368 9692 Planarity : 0.006 0.481 11096 Dihedral : 18.773 174.464 25343 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.46 % Favored : 97.52 % Rotamer: Outliers : 1.29 % Allowed : 12.03 % Favored : 86.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.09), residues: 7669 helix: 0.83 (0.08), residues: 4109 sheet: -0.00 (0.25), residues: 420 loop : 0.17 (0.11), residues: 3140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP X 85 HIS 0.006 0.001 HIS C 160 PHE 0.025 0.002 PHE M 122 TYR 0.021 0.002 TYR I 118 ARG 0.013 0.000 ARG m 9 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15338 Ramachandran restraints generated. 7669 Oldfield, 0 Emsley, 7669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15338 Ramachandran restraints generated. 7669 Oldfield, 0 Emsley, 7669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1054 residues out of total 6807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 966 time to evaluate : 5.814 Fit side-chains revert: symmetry clash REVERT: E 204 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7654 (mm-30) REVERT: H 212 ASN cc_start: 0.6224 (OUTLIER) cc_final: 0.5970 (m110) REVERT: H 220 PHE cc_start: 0.7676 (t80) cc_final: 0.7393 (t80) REVERT: K 24 SER cc_start: 0.8740 (t) cc_final: 0.8474 (p) REVERT: O 21 LYS cc_start: 0.7501 (ptmm) cc_final: 0.7205 (ttpp) REVERT: O 139 TYR cc_start: 0.7837 (t80) cc_final: 0.7521 (t80) REVERT: S 39 ARG cc_start: 0.8158 (mmt90) cc_final: 0.7796 (mmt90) REVERT: b 30 ILE cc_start: 0.8607 (mt) cc_final: 0.8283 (mm) REVERT: o 17 ASP cc_start: 0.8575 (t70) cc_final: 0.8329 (t70) REVERT: s 35 ASN cc_start: 0.8400 (t0) cc_final: 0.7981 (t0) outliers start: 88 outliers final: 68 residues processed: 1042 average time/residue: 1.7602 time to fit residues: 2284.2272 Evaluate side-chains 980 residues out of total 6807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 910 time to evaluate : 5.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain D residue 331 SER Chi-restraints excluded: chain E residue 162 GLU Chi-restraints excluded: chain E residue 204 GLU Chi-restraints excluded: chain F residue 84 LYS Chi-restraints excluded: chain F residue 310 SER Chi-restraints excluded: chain G residue 17 SER Chi-restraints excluded: chain G residue 137 VAL Chi-restraints excluded: chain G residue 193 SER Chi-restraints excluded: chain G residue 309 SER Chi-restraints excluded: chain G residue 480 SER Chi-restraints excluded: chain G residue 484 THR Chi-restraints excluded: chain G residue 646 SER Chi-restraints excluded: chain G residue 657 LEU Chi-restraints excluded: chain H residue 212 ASN Chi-restraints excluded: chain H residue 259 PHE Chi-restraints excluded: chain J residue 168 ILE Chi-restraints excluded: chain L residue 6 SER Chi-restraints excluded: chain L residue 79 SER Chi-restraints excluded: chain L residue 393 ASP Chi-restraints excluded: chain L residue 461 SER Chi-restraints excluded: chain M residue 116 ILE Chi-restraints excluded: chain M residue 189 SER Chi-restraints excluded: chain M residue 387 SER Chi-restraints excluded: chain N residue 237 THR Chi-restraints excluded: chain N residue 303 THR Chi-restraints excluded: chain N residue 307 SER Chi-restraints excluded: chain N residue 319 LEU Chi-restraints excluded: chain N residue 324 THR Chi-restraints excluded: chain O residue 19 THR Chi-restraints excluded: chain O residue 26 THR Chi-restraints excluded: chain O residue 135 LEU Chi-restraints excluded: chain O residue 194 ILE Chi-restraints excluded: chain O residue 215 SER Chi-restraints excluded: chain O residue 269 VAL Chi-restraints excluded: chain O residue 282 VAL Chi-restraints excluded: chain O residue 295 GLU Chi-restraints excluded: chain P residue 199 LYS Chi-restraints excluded: chain P residue 234 SER Chi-restraints excluded: chain R residue 4 THR Chi-restraints excluded: chain S residue 82 SER Chi-restraints excluded: chain S residue 93 VAL Chi-restraints excluded: chain T residue 31 SER Chi-restraints excluded: chain T residue 44 SER Chi-restraints excluded: chain T residue 82 ASP Chi-restraints excluded: chain W residue 22 SER Chi-restraints excluded: chain W residue 68 LYS Chi-restraints excluded: chain X residue 14 VAL Chi-restraints excluded: chain X residue 109 CYS Chi-restraints excluded: chain X residue 130 VAL Chi-restraints excluded: chain Z residue 128 ARG Chi-restraints excluded: chain a residue 12 MET Chi-restraints excluded: chain e residue 92 THR Chi-restraints excluded: chain f residue 6 VAL Chi-restraints excluded: chain f residue 7 VAL Chi-restraints excluded: chain f residue 47 GLU Chi-restraints excluded: chain f residue 57 LYS Chi-restraints excluded: chain g residue 110 SER Chi-restraints excluded: chain g residue 112 CYS Chi-restraints excluded: chain g residue 122 GLU Chi-restraints excluded: chain l residue 42 THR Chi-restraints excluded: chain l residue 153 VAL Chi-restraints excluded: chain m residue 119 LYS Chi-restraints excluded: chain o residue 30 PHE Chi-restraints excluded: chain p residue 3 SER Chi-restraints excluded: chain p residue 16 THR Chi-restraints excluded: chain p residue 171 GLU Chi-restraints excluded: chain q residue 15 SER Chi-restraints excluded: chain s residue 59 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 757 random chunks: chunk 639 optimal weight: 6.9990 chunk 573 optimal weight: 0.6980 chunk 318 optimal weight: 0.8980 chunk 195 optimal weight: 5.9990 chunk 387 optimal weight: 0.6980 chunk 306 optimal weight: 0.7980 chunk 593 optimal weight: 0.9990 chunk 229 optimal weight: 0.8980 chunk 360 optimal weight: 0.9980 chunk 441 optimal weight: 6.9990 chunk 687 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 ASN A 85 ASN B 106 GLN C 211 GLN D 55 HIS D 114 ASN F 436 GLN H 5 ASN H 212 ASN H 287 HIS H 317 GLN L 170 GLN L 541 ASN M 366 ASN M 390 ASN ** N 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 92 ASN O 153 ASN P 87 HIS S 30 GLN S 75 ASN W 26 ASN X 15 GLN Z 85 GLN n 12 GLN n 159 GLN q 5 GLN r 24 GLN s 40 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.0986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.264 65674 Z= 0.441 Angle : 1.329 50.433 88862 Z= 0.854 Chirality : 0.265 6.568 9692 Planarity : 0.004 0.044 11096 Dihedral : 14.171 173.402 10028 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.37 % Favored : 98.62 % Rotamer: Outliers : 1.94 % Allowed : 11.50 % Favored : 86.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.09), residues: 7669 helix: 1.55 (0.08), residues: 4099 sheet: -0.02 (0.25), residues: 410 loop : 0.30 (0.11), residues: 3160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP j 38 HIS 0.006 0.001 HIS G 101 PHE 0.021 0.001 PHE M 122 TYR 0.021 0.001 TYR L 422 ARG 0.007 0.000 ARG B 174 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15338 Ramachandran restraints generated. 7669 Oldfield, 0 Emsley, 7669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15338 Ramachandran restraints generated. 7669 Oldfield, 0 Emsley, 7669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1093 residues out of total 6807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 961 time to evaluate : 5.838 Fit side-chains revert: symmetry clash REVERT: G 444 GLN cc_start: 0.7518 (OUTLIER) cc_final: 0.7184 (tt0) REVERT: G 596 ASP cc_start: 0.8285 (m-30) cc_final: 0.8024 (m-30) REVERT: H 176 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8676 (mm) REVERT: H 220 PHE cc_start: 0.7484 (t80) cc_final: 0.7122 (t80) REVERT: L 515 TYR cc_start: 0.4966 (OUTLIER) cc_final: 0.4442 (p90) REVERT: O 2 GLN cc_start: 0.7738 (OUTLIER) cc_final: 0.7430 (tp40) REVERT: O 21 LYS cc_start: 0.7490 (ptmm) cc_final: 0.7148 (ttpp) REVERT: P 306 GLU cc_start: 0.7404 (OUTLIER) cc_final: 0.7188 (mt-10) REVERT: Q 107 GLU cc_start: 0.8362 (mm-30) cc_final: 0.7963 (mm-30) REVERT: S 45 LYS cc_start: 0.8672 (mtmt) cc_final: 0.8351 (mtmt) REVERT: U 37 MET cc_start: 0.8577 (OUTLIER) cc_final: 0.7282 (mmm) REVERT: a 52 ARG cc_start: 0.8275 (OUTLIER) cc_final: 0.7583 (ttp-110) REVERT: a 59 ARG cc_start: 0.8074 (OUTLIER) cc_final: 0.7496 (mmp80) REVERT: b 30 ILE cc_start: 0.8560 (mt) cc_final: 0.8293 (mm) REVERT: c 37 GLU cc_start: 0.7506 (OUTLIER) cc_final: 0.7244 (mt-10) REVERT: d 25 LYS cc_start: 0.8395 (OUTLIER) cc_final: 0.8032 (mtmt) REVERT: i 16 GLU cc_start: 0.7701 (OUTLIER) cc_final: 0.7314 (tt0) REVERT: m 21 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.6957 (mt-10) REVERT: m 92 PHE cc_start: 0.4093 (OUTLIER) cc_final: 0.3817 (t80) REVERT: r 72 GLN cc_start: 0.6789 (OUTLIER) cc_final: 0.6448 (pp30) REVERT: s 35 ASN cc_start: 0.8561 (t0) cc_final: 0.8162 (t0) outliers start: 132 outliers final: 44 residues processed: 1042 average time/residue: 1.7218 time to fit residues: 2245.4527 Evaluate side-chains 983 residues out of total 6807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 925 time to evaluate : 5.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 118 GLU Chi-restraints excluded: chain F residue 105 CYS Chi-restraints excluded: chain F residue 310 SER Chi-restraints excluded: chain G residue 137 VAL Chi-restraints excluded: chain G residue 444 GLN Chi-restraints excluded: chain H residue 176 LEU Chi-restraints excluded: chain H residue 259 PHE Chi-restraints excluded: chain J residue 50 SER Chi-restraints excluded: chain K residue 98 CYS Chi-restraints excluded: chain L residue 515 TYR Chi-restraints excluded: chain M residue 126 LEU Chi-restraints excluded: chain N residue 237 THR Chi-restraints excluded: chain O residue 1 LEU Chi-restraints excluded: chain O residue 2 GLN Chi-restraints excluded: chain O residue 19 THR Chi-restraints excluded: chain O residue 30 ASN Chi-restraints excluded: chain O residue 135 LEU Chi-restraints excluded: chain O residue 194 ILE Chi-restraints excluded: chain O residue 269 VAL Chi-restraints excluded: chain P residue 306 GLU Chi-restraints excluded: chain R residue 4 THR Chi-restraints excluded: chain T residue 31 SER Chi-restraints excluded: chain T residue 32 VAL Chi-restraints excluded: chain T residue 44 SER Chi-restraints excluded: chain U residue 37 MET Chi-restraints excluded: chain W residue 49 LEU Chi-restraints excluded: chain W residue 68 LYS Chi-restraints excluded: chain X residue 109 CYS Chi-restraints excluded: chain X residue 130 VAL Chi-restraints excluded: chain Z residue 128 ARG Chi-restraints excluded: chain Z residue 144 THR Chi-restraints excluded: chain a residue 52 ARG Chi-restraints excluded: chain a residue 59 ARG Chi-restraints excluded: chain b residue 42 LEU Chi-restraints excluded: chain c residue 6 GLU Chi-restraints excluded: chain c residue 24 SER Chi-restraints excluded: chain c residue 37 GLU Chi-restraints excluded: chain d residue 25 LYS Chi-restraints excluded: chain d residue 111 GLU Chi-restraints excluded: chain f residue 6 VAL Chi-restraints excluded: chain g residue 122 GLU Chi-restraints excluded: chain i residue 16 GLU Chi-restraints excluded: chain l residue 153 VAL Chi-restraints excluded: chain m residue 21 GLU Chi-restraints excluded: chain m residue 92 PHE Chi-restraints excluded: chain m residue 116 GLN Chi-restraints excluded: chain o residue 30 PHE Chi-restraints excluded: chain o residue 116 GLN Chi-restraints excluded: chain p residue 3 SER Chi-restraints excluded: chain p residue 171 GLU Chi-restraints excluded: chain q residue 15 SER Chi-restraints excluded: chain r residue 72 GLN Chi-restraints excluded: chain s residue 48 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 757 random chunks: chunk 382 optimal weight: 2.9990 chunk 213 optimal weight: 3.9990 chunk 572 optimal weight: 5.9990 chunk 468 optimal weight: 9.9990 chunk 189 optimal weight: 1.9990 chunk 688 optimal weight: 4.9990 chunk 743 optimal weight: 9.9990 chunk 613 optimal weight: 6.9990 chunk 682 optimal weight: 10.0000 chunk 234 optimal weight: 5.9990 chunk 552 optimal weight: 9.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 ASN B 106 GLN C 211 GLN D 55 HIS D 59 HIS D 157 HIS F 436 GLN H 287 HIS ** H 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 170 GLN M 88 ASN M 366 ASN M 390 ASN ** N 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 76 ASN O 114 HIS O 153 ASN O 180 GLN O 252 ASN S 30 GLN S 75 ASN V 95 GLN W 26 ASN X 15 GLN Z 24 ASN Z 85 GLN f 30 ASN g 86 GLN n 12 GLN n 52 ASN ** n 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 5 GLN r 24 GLN r 28 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.0869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.247 65674 Z= 0.562 Angle : 1.365 50.473 88862 Z= 0.868 Chirality : 0.268 6.697 9692 Planarity : 0.005 0.052 11096 Dihedral : 12.991 175.283 9951 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.11 % Favored : 97.87 % Rotamer: Outliers : 2.25 % Allowed : 11.92 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.09), residues: 7669 helix: 1.39 (0.08), residues: 4118 sheet: -0.06 (0.25), residues: 406 loop : 0.23 (0.11), residues: 3145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP X 85 HIS 0.008 0.001 HIS o 84 PHE 0.030 0.002 PHE M 122 TYR 0.026 0.002 TYR I 118 ARG 0.008 0.001 ARG B 174 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15338 Ramachandran restraints generated. 7669 Oldfield, 0 Emsley, 7669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15338 Ramachandran restraints generated. 7669 Oldfield, 0 Emsley, 7669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1087 residues out of total 6807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 934 time to evaluate : 5.804 Fit side-chains REVERT: B 178 ARG cc_start: 0.8025 (mtt180) cc_final: 0.7758 (mtt90) REVERT: E 32 GLU cc_start: 0.7815 (tt0) cc_final: 0.7603 (tt0) REVERT: E 118 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.6727 (mp0) REVERT: G 444 GLN cc_start: 0.7521 (OUTLIER) cc_final: 0.7195 (tt0) REVERT: G 596 ASP cc_start: 0.8348 (m-30) cc_final: 0.8061 (m-30) REVERT: H 176 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8673 (mm) REVERT: L 140 LEU cc_start: 0.9211 (OUTLIER) cc_final: 0.8995 (tt) REVERT: L 515 TYR cc_start: 0.4981 (OUTLIER) cc_final: 0.4433 (p90) REVERT: M 195 MET cc_start: 0.8514 (OUTLIER) cc_final: 0.8184 (ttm) REVERT: M 396 MET cc_start: 0.8867 (mmt) cc_final: 0.8484 (mmt) REVERT: N 305 PHE cc_start: 0.6246 (OUTLIER) cc_final: 0.5965 (m-80) REVERT: O 2 GLN cc_start: 0.7762 (OUTLIER) cc_final: 0.7430 (tp40) REVERT: O 206 TYR cc_start: 0.7631 (OUTLIER) cc_final: 0.5822 (m-10) REVERT: P 306 GLU cc_start: 0.7414 (OUTLIER) cc_final: 0.7189 (mt-10) REVERT: S 45 LYS cc_start: 0.8709 (mtmt) cc_final: 0.8321 (mtmt) REVERT: U 37 MET cc_start: 0.8665 (OUTLIER) cc_final: 0.7383 (mmm) REVERT: a 59 ARG cc_start: 0.8104 (OUTLIER) cc_final: 0.7493 (mmp80) REVERT: b 30 ILE cc_start: 0.8533 (mt) cc_final: 0.8261 (mm) REVERT: d 25 LYS cc_start: 0.8460 (OUTLIER) cc_final: 0.8088 (mtmt) REVERT: d 55 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8286 (tm) REVERT: i 16 GLU cc_start: 0.7770 (OUTLIER) cc_final: 0.7399 (tt0) REVERT: j 40 PHE cc_start: 0.8590 (OUTLIER) cc_final: 0.8115 (t80) REVERT: l 49 LYS cc_start: 0.8781 (tttm) cc_final: 0.8491 (tttt) REVERT: m 21 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.7033 (mt-10) REVERT: m 29 ARG cc_start: 0.7892 (OUTLIER) cc_final: 0.6836 (mmp80) REVERT: m 92 PHE cc_start: 0.4202 (OUTLIER) cc_final: 0.3908 (t80) REVERT: o 112 LYS cc_start: 0.8539 (OUTLIER) cc_final: 0.8218 (ttmm) REVERT: p 68 ARG cc_start: 0.8760 (OUTLIER) cc_final: 0.8366 (ttm110) REVERT: r 72 GLN cc_start: 0.6799 (OUTLIER) cc_final: 0.6444 (pp30) REVERT: s 35 ASN cc_start: 0.8569 (t0) cc_final: 0.8172 (t0) outliers start: 153 outliers final: 65 residues processed: 1025 average time/residue: 1.7371 time to fit residues: 2223.5508 Evaluate side-chains 1000 residues out of total 6807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 913 time to evaluate : 5.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 77 ARG Chi-restraints excluded: chain B residue 125 TYR Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 340 THR Chi-restraints excluded: chain D residue 420 THR Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 118 GLU Chi-restraints excluded: chain F residue 10 THR Chi-restraints excluded: chain F residue 105 CYS Chi-restraints excluded: chain F residue 310 SER Chi-restraints excluded: chain G residue 137 VAL Chi-restraints excluded: chain G residue 351 THR Chi-restraints excluded: chain G residue 444 GLN Chi-restraints excluded: chain G residue 657 LEU Chi-restraints excluded: chain H residue 176 LEU Chi-restraints excluded: chain H residue 259 PHE Chi-restraints excluded: chain I residue 11 SER Chi-restraints excluded: chain J residue 50 SER Chi-restraints excluded: chain K residue 15 SER Chi-restraints excluded: chain K residue 98 CYS Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain L residue 515 TYR Chi-restraints excluded: chain M residue 86 LYS Chi-restraints excluded: chain M residue 116 ILE Chi-restraints excluded: chain M residue 126 LEU Chi-restraints excluded: chain M residue 195 MET Chi-restraints excluded: chain N residue 237 THR Chi-restraints excluded: chain N residue 305 PHE Chi-restraints excluded: chain O residue 1 LEU Chi-restraints excluded: chain O residue 2 GLN Chi-restraints excluded: chain O residue 19 THR Chi-restraints excluded: chain O residue 26 THR Chi-restraints excluded: chain O residue 30 ASN Chi-restraints excluded: chain O residue 194 ILE Chi-restraints excluded: chain O residue 206 TYR Chi-restraints excluded: chain O residue 269 VAL Chi-restraints excluded: chain O residue 282 VAL Chi-restraints excluded: chain P residue 199 LYS Chi-restraints excluded: chain P residue 222 ASP Chi-restraints excluded: chain P residue 306 GLU Chi-restraints excluded: chain R residue 4 THR Chi-restraints excluded: chain S residue 93 VAL Chi-restraints excluded: chain T residue 23 ASP Chi-restraints excluded: chain T residue 31 SER Chi-restraints excluded: chain T residue 32 VAL Chi-restraints excluded: chain T residue 44 SER Chi-restraints excluded: chain U residue 37 MET Chi-restraints excluded: chain W residue 49 LEU Chi-restraints excluded: chain X residue 108 GLU Chi-restraints excluded: chain X residue 109 CYS Chi-restraints excluded: chain X residue 130 VAL Chi-restraints excluded: chain Z residue 128 ARG Chi-restraints excluded: chain Z residue 144 THR Chi-restraints excluded: chain a residue 12 MET Chi-restraints excluded: chain a residue 59 ARG Chi-restraints excluded: chain b residue 42 LEU Chi-restraints excluded: chain c residue 6 GLU Chi-restraints excluded: chain c residue 29 ILE Chi-restraints excluded: chain d residue 25 LYS Chi-restraints excluded: chain d residue 55 LEU Chi-restraints excluded: chain d residue 106 LYS Chi-restraints excluded: chain d residue 111 GLU Chi-restraints excluded: chain e residue 69 GLN Chi-restraints excluded: chain f residue 6 VAL Chi-restraints excluded: chain f residue 47 GLU Chi-restraints excluded: chain g residue 122 GLU Chi-restraints excluded: chain i residue 16 GLU Chi-restraints excluded: chain i residue 78 VAL Chi-restraints excluded: chain j residue 40 PHE Chi-restraints excluded: chain l residue 153 VAL Chi-restraints excluded: chain m residue 21 GLU Chi-restraints excluded: chain m residue 29 ARG Chi-restraints excluded: chain m residue 92 PHE Chi-restraints excluded: chain o residue 30 PHE Chi-restraints excluded: chain o residue 112 LYS Chi-restraints excluded: chain o residue 116 GLN Chi-restraints excluded: chain p residue 16 THR Chi-restraints excluded: chain p residue 68 ARG Chi-restraints excluded: chain p residue 171 GLU Chi-restraints excluded: chain q residue 15 SER Chi-restraints excluded: chain q residue 134 ILE Chi-restraints excluded: chain r residue 72 GLN Chi-restraints excluded: chain r residue 91 LYS Chi-restraints excluded: chain s residue 48 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 757 random chunks: chunk 680 optimal weight: 0.0270 chunk 517 optimal weight: 2.9990 chunk 357 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 328 optimal weight: 0.0470 chunk 462 optimal weight: 2.9990 chunk 691 optimal weight: 2.9990 chunk 731 optimal weight: 7.9990 chunk 361 optimal weight: 0.5980 chunk 655 optimal weight: 7.9990 chunk 197 optimal weight: 0.9990 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 ASN B 106 GLN C 211 GLN D 55 HIS D 157 HIS F 436 GLN H 287 HIS H 317 GLN M 88 ASN M 366 ASN M 390 ASN P 93 ASN S 30 GLN V 95 GLN W 26 ASN X 15 GLN X 63 ASN Z 24 ASN Z 85 GLN ** f 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 12 GLN n 52 ASN ** n 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 5 GLN r 24 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.1359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.247 65674 Z= 0.433 Angle : 1.311 50.560 88862 Z= 0.849 Chirality : 0.260 6.422 9692 Planarity : 0.004 0.049 11096 Dihedral : 11.605 174.509 9944 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.42 % Favored : 98.57 % Rotamer: Outliers : 1.53 % Allowed : 13.04 % Favored : 85.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.10), residues: 7669 helix: 1.73 (0.08), residues: 4106 sheet: -0.02 (0.25), residues: 397 loop : 0.32 (0.11), residues: 3166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP X 85 HIS 0.005 0.001 HIS G 101 PHE 0.021 0.001 PHE M 122 TYR 0.021 0.001 TYR L 422 ARG 0.007 0.000 ARG B 174 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15338 Ramachandran restraints generated. 7669 Oldfield, 0 Emsley, 7669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15338 Ramachandran restraints generated. 7669 Oldfield, 0 Emsley, 7669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1077 residues out of total 6807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 973 time to evaluate : 5.966 Fit side-chains revert: symmetry clash REVERT: A 112 GLU cc_start: 0.8163 (mm-30) cc_final: 0.7863 (mm-30) REVERT: E 118 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.6638 (mp0) REVERT: G 150 MET cc_start: 0.9313 (mmm) cc_final: 0.9018 (mmm) REVERT: G 444 GLN cc_start: 0.7518 (OUTLIER) cc_final: 0.7178 (tt0) REVERT: G 596 ASP cc_start: 0.8239 (m-30) cc_final: 0.7991 (m-30) REVERT: H 126 LYS cc_start: 0.7429 (mttt) cc_final: 0.7075 (mtpp) REVERT: H 176 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8629 (mm) REVERT: I 11 SER cc_start: 0.8604 (m) cc_final: 0.8209 (t) REVERT: L 515 TYR cc_start: 0.4837 (OUTLIER) cc_final: 0.4305 (p90) REVERT: M 396 MET cc_start: 0.8614 (mmt) cc_final: 0.8403 (mmt) REVERT: O 2 GLN cc_start: 0.7696 (OUTLIER) cc_final: 0.7383 (tp40) REVERT: O 18 MET cc_start: 0.7620 (mmm) cc_final: 0.7399 (mtm) REVERT: O 182 ARG cc_start: 0.7146 (OUTLIER) cc_final: 0.6189 (mpt-90) REVERT: O 252 ASN cc_start: 0.7723 (p0) cc_final: 0.7283 (p0) REVERT: S 45 LYS cc_start: 0.8731 (mtmt) cc_final: 0.8364 (mtmt) REVERT: S 84 ASP cc_start: 0.7967 (m-30) cc_final: 0.7758 (m-30) REVERT: Y 129 LEU cc_start: 0.8799 (mt) cc_final: 0.8516 (mp) REVERT: Z 24 ASN cc_start: 0.8770 (t0) cc_final: 0.8493 (t0) REVERT: a 52 ARG cc_start: 0.8259 (OUTLIER) cc_final: 0.7841 (ttp-170) REVERT: b 30 ILE cc_start: 0.8411 (mt) cc_final: 0.8154 (mm) REVERT: b 82 ARG cc_start: 0.7259 (mtm110) cc_final: 0.6524 (ptp-170) REVERT: c 37 GLU cc_start: 0.7507 (OUTLIER) cc_final: 0.7238 (mt-10) REVERT: d 25 LYS cc_start: 0.8415 (OUTLIER) cc_final: 0.8051 (mtmt) REVERT: d 55 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8234 (tm) REVERT: m 92 PHE cc_start: 0.4069 (OUTLIER) cc_final: 0.3867 (t80) REVERT: m 119 LYS cc_start: 0.8419 (mptp) cc_final: 0.8178 (mmtt) REVERT: s 35 ASN cc_start: 0.8556 (t0) cc_final: 0.8162 (t0) outliers start: 104 outliers final: 39 residues processed: 1042 average time/residue: 1.7180 time to fit residues: 2249.5791 Evaluate side-chains 977 residues out of total 6807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 927 time to evaluate : 5.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 420 THR Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 118 GLU Chi-restraints excluded: chain F residue 105 CYS Chi-restraints excluded: chain F residue 227 THR Chi-restraints excluded: chain F residue 310 SER Chi-restraints excluded: chain G residue 444 GLN Chi-restraints excluded: chain H residue 176 LEU Chi-restraints excluded: chain H residue 259 PHE Chi-restraints excluded: chain I residue 37 THR Chi-restraints excluded: chain J residue 50 SER Chi-restraints excluded: chain K residue 15 SER Chi-restraints excluded: chain K residue 98 CYS Chi-restraints excluded: chain L residue 515 TYR Chi-restraints excluded: chain M residue 116 ILE Chi-restraints excluded: chain M residue 126 LEU Chi-restraints excluded: chain N residue 237 THR Chi-restraints excluded: chain O residue 1 LEU Chi-restraints excluded: chain O residue 2 GLN Chi-restraints excluded: chain O residue 19 THR Chi-restraints excluded: chain O residue 182 ARG Chi-restraints excluded: chain O residue 194 ILE Chi-restraints excluded: chain O residue 269 VAL Chi-restraints excluded: chain Q residue 27 GLU Chi-restraints excluded: chain T residue 23 ASP Chi-restraints excluded: chain T residue 44 SER Chi-restraints excluded: chain X residue 108 GLU Chi-restraints excluded: chain X residue 130 VAL Chi-restraints excluded: chain Z residue 144 THR Chi-restraints excluded: chain a residue 52 ARG Chi-restraints excluded: chain b residue 42 LEU Chi-restraints excluded: chain c residue 37 GLU Chi-restraints excluded: chain d residue 25 LYS Chi-restraints excluded: chain d residue 55 LEU Chi-restraints excluded: chain d residue 106 LYS Chi-restraints excluded: chain d residue 111 GLU Chi-restraints excluded: chain e residue 86 ILE Chi-restraints excluded: chain g residue 122 GLU Chi-restraints excluded: chain i residue 78 VAL Chi-restraints excluded: chain l residue 153 VAL Chi-restraints excluded: chain m residue 92 PHE Chi-restraints excluded: chain o residue 30 PHE Chi-restraints excluded: chain o residue 116 GLN Chi-restraints excluded: chain p residue 16 THR Chi-restraints excluded: chain p residue 171 GLU Chi-restraints excluded: chain s residue 48 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 757 random chunks: chunk 609 optimal weight: 0.9980 chunk 415 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 544 optimal weight: 1.9990 chunk 301 optimal weight: 6.9990 chunk 624 optimal weight: 1.9990 chunk 505 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 373 optimal weight: 4.9990 chunk 656 optimal weight: 2.9990 chunk 184 optimal weight: 6.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 ASN B 106 GLN C 211 GLN D 55 HIS D 59 HIS F 436 GLN H 287 HIS ** H 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 23 GLN M 88 ASN S 30 GLN S 75 ASN S 92 ASN W 26 ASN X 15 GLN a 58 ASN ** f 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 86 GLN n 12 GLN n 52 ASN ** n 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 43 GLN q 5 GLN r 24 GLN r 28 GLN s 40 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.1230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.245 65674 Z= 0.465 Angle : 1.324 50.557 88862 Z= 0.853 Chirality : 0.263 6.527 9692 Planarity : 0.004 0.051 11096 Dihedral : 11.469 176.622 9934 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.76 % Favored : 98.23 % Rotamer: Outliers : 1.62 % Allowed : 13.32 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.10), residues: 7669 helix: 1.72 (0.08), residues: 4107 sheet: -0.02 (0.25), residues: 399 loop : 0.33 (0.11), residues: 3163 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP O 318 HIS 0.007 0.001 HIS G 101 PHE 0.025 0.002 PHE M 122 TYR 0.020 0.001 TYR k 86 ARG 0.007 0.000 ARG B 174 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15338 Ramachandran restraints generated. 7669 Oldfield, 0 Emsley, 7669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15338 Ramachandran restraints generated. 7669 Oldfield, 0 Emsley, 7669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1048 residues out of total 6807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 938 time to evaluate : 5.922 Fit side-chains revert: symmetry clash REVERT: A 112 GLU cc_start: 0.8198 (mm-30) cc_final: 0.7926 (mm-30) REVERT: B 59 MET cc_start: 0.7882 (tpt) cc_final: 0.7625 (tpt) REVERT: E 118 GLU cc_start: 0.7611 (OUTLIER) cc_final: 0.6646 (mp0) REVERT: G 444 GLN cc_start: 0.7530 (OUTLIER) cc_final: 0.7203 (tt0) REVERT: G 596 ASP cc_start: 0.8295 (m-30) cc_final: 0.8034 (m-30) REVERT: H 49 ILE cc_start: 0.9155 (OUTLIER) cc_final: 0.8879 (mt) REVERT: H 126 LYS cc_start: 0.7494 (mttt) cc_final: 0.7131 (mtpp) REVERT: H 176 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8662 (mm) REVERT: I 11 SER cc_start: 0.8646 (m) cc_final: 0.8297 (t) REVERT: L 140 LEU cc_start: 0.9144 (OUTLIER) cc_final: 0.8924 (tt) REVERT: L 512 LYS cc_start: 0.8451 (OUTLIER) cc_final: 0.8175 (ttmm) REVERT: L 515 TYR cc_start: 0.4900 (OUTLIER) cc_final: 0.4373 (p90) REVERT: M 396 MET cc_start: 0.8801 (mmt) cc_final: 0.8446 (mmt) REVERT: N 305 PHE cc_start: 0.6247 (OUTLIER) cc_final: 0.5989 (m-80) REVERT: O 2 GLN cc_start: 0.7721 (OUTLIER) cc_final: 0.7392 (tp40) REVERT: O 18 MET cc_start: 0.7631 (mmm) cc_final: 0.7430 (mtm) REVERT: O 153 ASN cc_start: 0.8541 (m-40) cc_final: 0.8291 (m-40) REVERT: O 182 ARG cc_start: 0.7181 (OUTLIER) cc_final: 0.6232 (mpt-90) REVERT: O 252 ASN cc_start: 0.7747 (p0) cc_final: 0.7368 (p0) REVERT: S 45 LYS cc_start: 0.8716 (mtmt) cc_final: 0.8325 (mtmt) REVERT: S 84 ASP cc_start: 0.7987 (m-30) cc_final: 0.7775 (m-30) REVERT: U 37 MET cc_start: 0.8634 (OUTLIER) cc_final: 0.7379 (mmm) REVERT: V 17 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.6938 (mp0) REVERT: Y 129 LEU cc_start: 0.8791 (mt) cc_final: 0.8518 (mp) REVERT: Z 24 ASN cc_start: 0.8811 (t0) cc_final: 0.8498 (t0) REVERT: a 52 ARG cc_start: 0.8420 (OUTLIER) cc_final: 0.7895 (ttp-170) REVERT: b 30 ILE cc_start: 0.8421 (mt) cc_final: 0.8153 (mm) REVERT: b 82 ARG cc_start: 0.7286 (mtm110) cc_final: 0.6526 (ptp-170) REVERT: c 37 GLU cc_start: 0.7518 (OUTLIER) cc_final: 0.7239 (mt-10) REVERT: d 25 LYS cc_start: 0.8456 (OUTLIER) cc_final: 0.8084 (mtmt) REVERT: d 55 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8250 (tm) REVERT: f 47 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.7531 (mp0) REVERT: i 16 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.7340 (tt0) REVERT: m 21 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.6971 (mt-10) REVERT: m 27 GLU cc_start: 0.7802 (mp0) cc_final: 0.7573 (mp0) REVERT: m 92 PHE cc_start: 0.4137 (OUTLIER) cc_final: 0.3907 (t80) REVERT: m 119 LYS cc_start: 0.8443 (mptp) cc_final: 0.8132 (mptt) REVERT: r 72 GLN cc_start: 0.6702 (OUTLIER) cc_final: 0.6374 (pp30) REVERT: s 35 ASN cc_start: 0.8575 (t0) cc_final: 0.8169 (t0) outliers start: 110 outliers final: 48 residues processed: 1008 average time/residue: 1.7280 time to fit residues: 2177.1174 Evaluate side-chains 993 residues out of total 6807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 924 time to evaluate : 5.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 420 THR Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 118 GLU Chi-restraints excluded: chain F residue 105 CYS Chi-restraints excluded: chain F residue 310 SER Chi-restraints excluded: chain G residue 444 GLN Chi-restraints excluded: chain H residue 49 ILE Chi-restraints excluded: chain H residue 176 LEU Chi-restraints excluded: chain H residue 259 PHE Chi-restraints excluded: chain I residue 37 THR Chi-restraints excluded: chain J residue 50 SER Chi-restraints excluded: chain K residue 9 MET Chi-restraints excluded: chain K residue 15 SER Chi-restraints excluded: chain K residue 98 CYS Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain L residue 149 ILE Chi-restraints excluded: chain L residue 512 LYS Chi-restraints excluded: chain L residue 515 TYR Chi-restraints excluded: chain M residue 116 ILE Chi-restraints excluded: chain M residue 269 MET Chi-restraints excluded: chain N residue 237 THR Chi-restraints excluded: chain N residue 305 PHE Chi-restraints excluded: chain O residue 1 LEU Chi-restraints excluded: chain O residue 2 GLN Chi-restraints excluded: chain O residue 135 LEU Chi-restraints excluded: chain O residue 182 ARG Chi-restraints excluded: chain O residue 194 ILE Chi-restraints excluded: chain O residue 269 VAL Chi-restraints excluded: chain P residue 199 LYS Chi-restraints excluded: chain P residue 222 ASP Chi-restraints excluded: chain Q residue 27 GLU Chi-restraints excluded: chain S residue 93 VAL Chi-restraints excluded: chain T residue 23 ASP Chi-restraints excluded: chain T residue 32 VAL Chi-restraints excluded: chain T residue 44 SER Chi-restraints excluded: chain U residue 37 MET Chi-restraints excluded: chain V residue 17 GLU Chi-restraints excluded: chain W residue 49 LEU Chi-restraints excluded: chain X residue 108 GLU Chi-restraints excluded: chain X residue 130 VAL Chi-restraints excluded: chain Z residue 144 THR Chi-restraints excluded: chain a residue 52 ARG Chi-restraints excluded: chain b residue 42 LEU Chi-restraints excluded: chain c residue 6 GLU Chi-restraints excluded: chain c residue 37 GLU Chi-restraints excluded: chain d residue 25 LYS Chi-restraints excluded: chain d residue 55 LEU Chi-restraints excluded: chain d residue 106 LYS Chi-restraints excluded: chain d residue 111 GLU Chi-restraints excluded: chain f residue 6 VAL Chi-restraints excluded: chain f residue 47 GLU Chi-restraints excluded: chain g residue 122 GLU Chi-restraints excluded: chain i residue 16 GLU Chi-restraints excluded: chain i residue 78 VAL Chi-restraints excluded: chain l residue 153 VAL Chi-restraints excluded: chain m residue 21 GLU Chi-restraints excluded: chain m residue 92 PHE Chi-restraints excluded: chain o residue 30 PHE Chi-restraints excluded: chain o residue 116 GLN Chi-restraints excluded: chain p residue 3 SER Chi-restraints excluded: chain p residue 16 THR Chi-restraints excluded: chain p residue 171 GLU Chi-restraints excluded: chain r residue 72 GLN Chi-restraints excluded: chain s residue 48 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 757 random chunks: chunk 246 optimal weight: 0.7980 chunk 658 optimal weight: 5.9990 chunk 144 optimal weight: 3.9990 chunk 429 optimal weight: 6.9990 chunk 180 optimal weight: 6.9990 chunk 732 optimal weight: 0.9980 chunk 608 optimal weight: 2.9990 chunk 339 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 242 optimal weight: 1.9990 chunk 384 optimal weight: 0.9980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 ASN B 106 GLN C 211 GLN D 55 HIS D 59 HIS F 436 GLN H 194 ASN H 287 HIS H 317 GLN M 88 ASN S 30 GLN S 75 ASN S 92 ASN W 26 ASN X 15 GLN a 58 ASN ** f 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 12 GLN ** n 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 5 GLN r 24 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.1302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.246 65674 Z= 0.451 Angle : 1.319 50.565 88862 Z= 0.851 Chirality : 0.262 6.496 9692 Planarity : 0.004 0.051 11096 Dihedral : 11.200 172.891 9933 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.64 % Favored : 98.34 % Rotamer: Outliers : 1.76 % Allowed : 13.35 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.10), residues: 7669 helix: 1.73 (0.08), residues: 4118 sheet: 0.00 (0.25), residues: 400 loop : 0.34 (0.11), residues: 3151 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 0.024 0.001 PHE M 122 TYR 0.020 0.001 TYR k 86 ARG 0.009 0.000 ARG B 174 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15338 Ramachandran restraints generated. 7669 Oldfield, 0 Emsley, 7669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15338 Ramachandran restraints generated. 7669 Oldfield, 0 Emsley, 7669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1059 residues out of total 6807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 939 time to evaluate : 5.958 Fit side-chains revert: symmetry clash REVERT: A 112 GLU cc_start: 0.8142 (mm-30) cc_final: 0.7858 (mm-30) REVERT: B 59 MET cc_start: 0.7883 (tpt) cc_final: 0.7631 (tpt) REVERT: E 118 GLU cc_start: 0.7602 (OUTLIER) cc_final: 0.6641 (mp0) REVERT: G 337 ARG cc_start: 0.8384 (OUTLIER) cc_final: 0.8020 (mtt90) REVERT: G 444 GLN cc_start: 0.7527 (OUTLIER) cc_final: 0.7199 (tt0) REVERT: G 596 ASP cc_start: 0.8273 (m-30) cc_final: 0.8019 (m-30) REVERT: G 673 MET cc_start: 0.8740 (OUTLIER) cc_final: 0.8075 (mtt) REVERT: H 126 LYS cc_start: 0.7429 (mttt) cc_final: 0.7076 (mtpp) REVERT: I 11 SER cc_start: 0.8528 (OUTLIER) cc_final: 0.8238 (t) REVERT: L 140 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8933 (tt) REVERT: L 512 LYS cc_start: 0.8451 (OUTLIER) cc_final: 0.8173 (ttmm) REVERT: L 515 TYR cc_start: 0.4878 (OUTLIER) cc_final: 0.4357 (p90) REVERT: N 305 PHE cc_start: 0.6230 (OUTLIER) cc_final: 0.5986 (m-80) REVERT: O 2 GLN cc_start: 0.7732 (OUTLIER) cc_final: 0.7406 (tp40) REVERT: O 153 ASN cc_start: 0.8548 (m-40) cc_final: 0.8295 (m-40) REVERT: O 206 TYR cc_start: 0.7611 (OUTLIER) cc_final: 0.6017 (m-80) REVERT: O 252 ASN cc_start: 0.7712 (p0) cc_final: 0.7295 (p0) REVERT: S 45 LYS cc_start: 0.8738 (mtmt) cc_final: 0.8358 (mtmt) REVERT: S 84 ASP cc_start: 0.7982 (m-30) cc_final: 0.7771 (m-30) REVERT: U 37 MET cc_start: 0.8632 (OUTLIER) cc_final: 0.7344 (mmm) REVERT: V 17 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.6938 (mp0) REVERT: Z 24 ASN cc_start: 0.8804 (t0) cc_final: 0.8494 (t0) REVERT: a 52 ARG cc_start: 0.8419 (OUTLIER) cc_final: 0.7912 (ttp-170) REVERT: b 30 ILE cc_start: 0.8397 (mt) cc_final: 0.8140 (mm) REVERT: b 39 LYS cc_start: 0.8293 (pttp) cc_final: 0.8057 (pttm) REVERT: b 82 ARG cc_start: 0.7277 (mtm110) cc_final: 0.6602 (ptp-170) REVERT: c 37 GLU cc_start: 0.7508 (OUTLIER) cc_final: 0.7228 (mt-10) REVERT: d 25 LYS cc_start: 0.8440 (OUTLIER) cc_final: 0.8069 (mtmt) REVERT: d 55 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8233 (tm) REVERT: f 47 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.7505 (mp0) REVERT: i 16 GLU cc_start: 0.7703 (OUTLIER) cc_final: 0.7334 (tt0) REVERT: m 21 GLU cc_start: 0.7608 (OUTLIER) cc_final: 0.6976 (mt-10) REVERT: m 92 PHE cc_start: 0.4061 (OUTLIER) cc_final: 0.3858 (t80) REVERT: m 119 LYS cc_start: 0.8411 (mptp) cc_final: 0.8115 (mptt) REVERT: s 35 ASN cc_start: 0.8568 (t0) cc_final: 0.8161 (t0) outliers start: 120 outliers final: 59 residues processed: 1018 average time/residue: 1.7114 time to fit residues: 2179.5548 Evaluate side-chains 1003 residues out of total 6807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 923 time to evaluate : 6.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 MET Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain B residue 125 TYR Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 420 THR Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 118 GLU Chi-restraints excluded: chain F residue 105 CYS Chi-restraints excluded: chain F residue 227 THR Chi-restraints excluded: chain F residue 310 SER Chi-restraints excluded: chain G residue 337 ARG Chi-restraints excluded: chain G residue 351 THR Chi-restraints excluded: chain G residue 444 GLN Chi-restraints excluded: chain G residue 673 MET Chi-restraints excluded: chain H residue 259 PHE Chi-restraints excluded: chain I residue 11 SER Chi-restraints excluded: chain I residue 37 THR Chi-restraints excluded: chain J residue 50 SER Chi-restraints excluded: chain K residue 9 MET Chi-restraints excluded: chain K residue 15 SER Chi-restraints excluded: chain K residue 79 VAL Chi-restraints excluded: chain K residue 98 CYS Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain L residue 149 ILE Chi-restraints excluded: chain L residue 512 LYS Chi-restraints excluded: chain L residue 515 TYR Chi-restraints excluded: chain M residue 116 ILE Chi-restraints excluded: chain M residue 126 LEU Chi-restraints excluded: chain M residue 400 MET Chi-restraints excluded: chain N residue 209 ILE Chi-restraints excluded: chain N residue 237 THR Chi-restraints excluded: chain N residue 305 PHE Chi-restraints excluded: chain O residue 1 LEU Chi-restraints excluded: chain O residue 2 GLN Chi-restraints excluded: chain O residue 135 LEU Chi-restraints excluded: chain O residue 194 ILE Chi-restraints excluded: chain O residue 206 TYR Chi-restraints excluded: chain O residue 269 VAL Chi-restraints excluded: chain O residue 282 VAL Chi-restraints excluded: chain P residue 199 LYS Chi-restraints excluded: chain P residue 222 ASP Chi-restraints excluded: chain Q residue 27 GLU Chi-restraints excluded: chain T residue 23 ASP Chi-restraints excluded: chain T residue 32 VAL Chi-restraints excluded: chain T residue 44 SER Chi-restraints excluded: chain U residue 37 MET Chi-restraints excluded: chain V residue 17 GLU Chi-restraints excluded: chain W residue 49 LEU Chi-restraints excluded: chain X residue 108 GLU Chi-restraints excluded: chain X residue 109 CYS Chi-restraints excluded: chain X residue 130 VAL Chi-restraints excluded: chain Z residue 128 ARG Chi-restraints excluded: chain Z residue 144 THR Chi-restraints excluded: chain a residue 12 MET Chi-restraints excluded: chain a residue 52 ARG Chi-restraints excluded: chain b residue 42 LEU Chi-restraints excluded: chain c residue 6 GLU Chi-restraints excluded: chain c residue 37 GLU Chi-restraints excluded: chain d residue 25 LYS Chi-restraints excluded: chain d residue 55 LEU Chi-restraints excluded: chain d residue 106 LYS Chi-restraints excluded: chain d residue 111 GLU Chi-restraints excluded: chain f residue 6 VAL Chi-restraints excluded: chain f residue 47 GLU Chi-restraints excluded: chain g residue 122 GLU Chi-restraints excluded: chain i residue 16 GLU Chi-restraints excluded: chain i residue 78 VAL Chi-restraints excluded: chain i residue 98 GLU Chi-restraints excluded: chain l residue 153 VAL Chi-restraints excluded: chain m residue 21 GLU Chi-restraints excluded: chain m residue 92 PHE Chi-restraints excluded: chain o residue 30 PHE Chi-restraints excluded: chain o residue 34 LYS Chi-restraints excluded: chain o residue 116 GLN Chi-restraints excluded: chain p residue 3 SER Chi-restraints excluded: chain p residue 16 THR Chi-restraints excluded: chain p residue 171 GLU Chi-restraints excluded: chain s residue 48 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 757 random chunks: chunk 706 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 417 optimal weight: 5.9990 chunk 534 optimal weight: 5.9990 chunk 414 optimal weight: 9.9990 chunk 616 optimal weight: 0.0970 chunk 408 optimal weight: 4.9990 chunk 729 optimal weight: 0.8980 chunk 456 optimal weight: 4.9990 chunk 444 optimal weight: 7.9990 chunk 336 optimal weight: 4.9990 overall best weight: 2.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 ASN B 106 GLN C 211 GLN D 55 HIS D 59 HIS F 436 GLN G 313 ASN H 287 HIS H 317 GLN M 88 ASN S 30 GLN S 75 ASN S 92 ASN W 26 ASN X 15 GLN a 58 ASN ** f 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 86 GLN n 12 GLN n 159 GLN q 5 GLN q 52 ASN r 24 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.1213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.244 65674 Z= 0.483 Angle : 1.332 50.554 88862 Z= 0.856 Chirality : 0.264 6.565 9692 Planarity : 0.004 0.051 11096 Dihedral : 11.189 173.717 9933 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.89 % Favored : 98.10 % Rotamer: Outliers : 1.93 % Allowed : 13.29 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.09), residues: 7669 helix: 1.66 (0.08), residues: 4118 sheet: -0.04 (0.25), residues: 402 loop : 0.32 (0.11), residues: 3149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP O 318 HIS 0.007 0.001 HIS G 101 PHE 0.027 0.002 PHE M 122 TYR 0.021 0.002 TYR M 406 ARG 0.009 0.000 ARG B 174 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15338 Ramachandran restraints generated. 7669 Oldfield, 0 Emsley, 7669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15338 Ramachandran restraints generated. 7669 Oldfield, 0 Emsley, 7669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1071 residues out of total 6807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 940 time to evaluate : 5.911 Fit side-chains REVERT: A 112 GLU cc_start: 0.8185 (mm-30) cc_final: 0.7908 (mm-30) REVERT: B 59 MET cc_start: 0.7874 (tpt) cc_final: 0.7631 (tpt) REVERT: E 118 GLU cc_start: 0.7616 (OUTLIER) cc_final: 0.6671 (mp0) REVERT: G 444 GLN cc_start: 0.7507 (OUTLIER) cc_final: 0.7176 (tt0) REVERT: G 596 ASP cc_start: 0.8314 (m-30) cc_final: 0.8045 (m-30) REVERT: G 673 MET cc_start: 0.8777 (OUTLIER) cc_final: 0.8133 (mtt) REVERT: H 126 LYS cc_start: 0.7472 (mttt) cc_final: 0.7071 (mtpp) REVERT: I 11 SER cc_start: 0.8536 (OUTLIER) cc_final: 0.8219 (t) REVERT: L 140 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8968 (tt) REVERT: L 515 TYR cc_start: 0.4895 (OUTLIER) cc_final: 0.4364 (p90) REVERT: M 396 MET cc_start: 0.8754 (mmt) cc_final: 0.8511 (mmt) REVERT: N 305 PHE cc_start: 0.6216 (OUTLIER) cc_final: 0.5968 (m-80) REVERT: O 2 GLN cc_start: 0.7742 (OUTLIER) cc_final: 0.7413 (tp40) REVERT: O 153 ASN cc_start: 0.8538 (m-40) cc_final: 0.8239 (t0) REVERT: O 252 ASN cc_start: 0.7761 (p0) cc_final: 0.7388 (p0) REVERT: R 10 LYS cc_start: 0.8701 (OUTLIER) cc_final: 0.8495 (mttt) REVERT: S 45 LYS cc_start: 0.8737 (mtmt) cc_final: 0.8365 (mtmt) REVERT: S 84 ASP cc_start: 0.7957 (m-30) cc_final: 0.7739 (m-30) REVERT: U 37 MET cc_start: 0.8658 (OUTLIER) cc_final: 0.7340 (mmm) REVERT: V 17 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.6957 (mp0) REVERT: Z 24 ASN cc_start: 0.8816 (t0) cc_final: 0.8502 (t0) REVERT: a 52 ARG cc_start: 0.8427 (OUTLIER) cc_final: 0.7921 (ttp-170) REVERT: a 59 ARG cc_start: 0.8081 (OUTLIER) cc_final: 0.7493 (mmp80) REVERT: b 30 ILE cc_start: 0.8433 (mt) cc_final: 0.8173 (mm) REVERT: b 39 LYS cc_start: 0.8328 (pttp) cc_final: 0.8090 (pttm) REVERT: b 82 ARG cc_start: 0.7250 (mtm110) cc_final: 0.6605 (ptp-170) REVERT: c 37 GLU cc_start: 0.7513 (OUTLIER) cc_final: 0.7234 (mt-10) REVERT: d 25 LYS cc_start: 0.8458 (OUTLIER) cc_final: 0.8084 (mtmt) REVERT: d 55 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8250 (tm) REVERT: i 16 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.7348 (tt0) REVERT: j 40 PHE cc_start: 0.8596 (OUTLIER) cc_final: 0.8103 (t80) REVERT: m 21 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.6986 (mt-10) REVERT: m 92 PHE cc_start: 0.4155 (OUTLIER) cc_final: 0.3946 (t80) REVERT: o 112 LYS cc_start: 0.8540 (OUTLIER) cc_final: 0.8168 (ttmm) REVERT: r 72 GLN cc_start: 0.6710 (OUTLIER) cc_final: 0.6373 (pp30) REVERT: s 35 ASN cc_start: 0.8582 (t0) cc_final: 0.8176 (t0) outliers start: 131 outliers final: 59 residues processed: 1025 average time/residue: 1.7430 time to fit residues: 2232.4283 Evaluate side-chains 1009 residues out of total 6807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 928 time to evaluate : 5.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 MET Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 125 TYR Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 420 THR Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 118 GLU Chi-restraints excluded: chain F residue 105 CYS Chi-restraints excluded: chain F residue 227 THR Chi-restraints excluded: chain F residue 310 SER Chi-restraints excluded: chain G residue 351 THR Chi-restraints excluded: chain G residue 444 GLN Chi-restraints excluded: chain G residue 657 LEU Chi-restraints excluded: chain G residue 673 MET Chi-restraints excluded: chain H residue 259 PHE Chi-restraints excluded: chain I residue 11 SER Chi-restraints excluded: chain I residue 37 THR Chi-restraints excluded: chain J residue 50 SER Chi-restraints excluded: chain K residue 15 SER Chi-restraints excluded: chain K residue 98 CYS Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain L residue 515 TYR Chi-restraints excluded: chain M residue 86 LYS Chi-restraints excluded: chain M residue 116 ILE Chi-restraints excluded: chain M residue 126 LEU Chi-restraints excluded: chain N residue 209 ILE Chi-restraints excluded: chain N residue 237 THR Chi-restraints excluded: chain N residue 305 PHE Chi-restraints excluded: chain O residue 1 LEU Chi-restraints excluded: chain O residue 2 GLN Chi-restraints excluded: chain O residue 135 LEU Chi-restraints excluded: chain O residue 194 ILE Chi-restraints excluded: chain O residue 269 VAL Chi-restraints excluded: chain O residue 282 VAL Chi-restraints excluded: chain P residue 199 LYS Chi-restraints excluded: chain P residue 222 ASP Chi-restraints excluded: chain Q residue 27 GLU Chi-restraints excluded: chain R residue 7 THR Chi-restraints excluded: chain R residue 10 LYS Chi-restraints excluded: chain S residue 93 VAL Chi-restraints excluded: chain T residue 23 ASP Chi-restraints excluded: chain T residue 32 VAL Chi-restraints excluded: chain T residue 44 SER Chi-restraints excluded: chain U residue 37 MET Chi-restraints excluded: chain V residue 17 GLU Chi-restraints excluded: chain W residue 49 LEU Chi-restraints excluded: chain X residue 108 GLU Chi-restraints excluded: chain X residue 109 CYS Chi-restraints excluded: chain X residue 130 VAL Chi-restraints excluded: chain Z residue 128 ARG Chi-restraints excluded: chain Z residue 144 THR Chi-restraints excluded: chain a residue 12 MET Chi-restraints excluded: chain a residue 52 ARG Chi-restraints excluded: chain a residue 59 ARG Chi-restraints excluded: chain b residue 42 LEU Chi-restraints excluded: chain c residue 6 GLU Chi-restraints excluded: chain c residue 37 GLU Chi-restraints excluded: chain d residue 25 LYS Chi-restraints excluded: chain d residue 55 LEU Chi-restraints excluded: chain d residue 106 LYS Chi-restraints excluded: chain d residue 111 GLU Chi-restraints excluded: chain e residue 69 GLN Chi-restraints excluded: chain f residue 6 VAL Chi-restraints excluded: chain g residue 122 GLU Chi-restraints excluded: chain i residue 16 GLU Chi-restraints excluded: chain i residue 78 VAL Chi-restraints excluded: chain j residue 40 PHE Chi-restraints excluded: chain l residue 31 VAL Chi-restraints excluded: chain l residue 153 VAL Chi-restraints excluded: chain m residue 21 GLU Chi-restraints excluded: chain m residue 92 PHE Chi-restraints excluded: chain o residue 30 PHE Chi-restraints excluded: chain o residue 34 LYS Chi-restraints excluded: chain o residue 112 LYS Chi-restraints excluded: chain o residue 116 GLN Chi-restraints excluded: chain p residue 3 SER Chi-restraints excluded: chain p residue 16 THR Chi-restraints excluded: chain p residue 171 GLU Chi-restraints excluded: chain r residue 72 GLN Chi-restraints excluded: chain s residue 48 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 757 random chunks: chunk 451 optimal weight: 5.9990 chunk 291 optimal weight: 0.9980 chunk 435 optimal weight: 9.9990 chunk 219 optimal weight: 7.9990 chunk 143 optimal weight: 3.9990 chunk 141 optimal weight: 4.9990 chunk 463 optimal weight: 1.9990 chunk 497 optimal weight: 0.9980 chunk 360 optimal weight: 0.3980 chunk 67 optimal weight: 3.9990 chunk 573 optimal weight: 0.5980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 ASN B 106 GLN C 211 GLN D 55 HIS D 59 HIS F 436 GLN H 287 HIS H 317 GLN M 88 ASN S 30 GLN S 75 ASN S 92 ASN W 26 ASN X 15 GLN a 58 ASN ** f 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 12 GLN n 159 GLN q 5 GLN q 52 ASN r 24 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.1404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.246 65674 Z= 0.439 Angle : 1.314 50.719 88862 Z= 0.850 Chirality : 0.261 6.471 9692 Planarity : 0.004 0.052 11096 Dihedral : 10.777 172.682 9933 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.62 % Favored : 98.37 % Rotamer: Outliers : 1.48 % Allowed : 13.91 % Favored : 84.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.10), residues: 7669 helix: 1.78 (0.08), residues: 4123 sheet: 0.03 (0.25), residues: 397 loop : 0.37 (0.11), residues: 3149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP X 85 HIS 0.006 0.001 HIS G 101 PHE 0.023 0.001 PHE M 122 TYR 0.020 0.001 TYR L 422 ARG 0.009 0.000 ARG B 174 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15338 Ramachandran restraints generated. 7669 Oldfield, 0 Emsley, 7669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15338 Ramachandran restraints generated. 7669 Oldfield, 0 Emsley, 7669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1051 residues out of total 6807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 950 time to evaluate : 5.926 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 112 GLU cc_start: 0.8100 (mm-30) cc_final: 0.7769 (mm-30) REVERT: B 59 MET cc_start: 0.7789 (tpt) cc_final: 0.7566 (tpt) REVERT: E 118 GLU cc_start: 0.7591 (OUTLIER) cc_final: 0.6637 (mp0) REVERT: G 337 ARG cc_start: 0.8395 (OUTLIER) cc_final: 0.8018 (mtt90) REVERT: G 444 GLN cc_start: 0.7523 (OUTLIER) cc_final: 0.7192 (tt0) REVERT: G 596 ASP cc_start: 0.8273 (m-30) cc_final: 0.8022 (m-30) REVERT: G 613 TYR cc_start: 0.9049 (OUTLIER) cc_final: 0.7977 (p90) REVERT: G 673 MET cc_start: 0.8694 (OUTLIER) cc_final: 0.7398 (mtm) REVERT: H 126 LYS cc_start: 0.7429 (mttt) cc_final: 0.7023 (mtpp) REVERT: I 11 SER cc_start: 0.8486 (m) cc_final: 0.8217 (t) REVERT: L 515 TYR cc_start: 0.4859 (OUTLIER) cc_final: 0.4360 (p90) REVERT: M 396 MET cc_start: 0.8667 (mmt) cc_final: 0.8413 (mmt) REVERT: O 2 GLN cc_start: 0.7714 (OUTLIER) cc_final: 0.7399 (tp40) REVERT: O 252 ASN cc_start: 0.7659 (p0) cc_final: 0.7270 (p0) REVERT: S 45 LYS cc_start: 0.8741 (mtmt) cc_final: 0.8371 (mtmt) REVERT: S 84 ASP cc_start: 0.7971 (m-30) cc_final: 0.7757 (m-30) REVERT: U 37 MET cc_start: 0.8622 (OUTLIER) cc_final: 0.7333 (mmm) REVERT: W 109 GLU cc_start: 0.8306 (mt-10) cc_final: 0.8072 (mt-10) REVERT: Z 24 ASN cc_start: 0.8798 (t0) cc_final: 0.8492 (t0) REVERT: b 82 ARG cc_start: 0.7256 (mtm110) cc_final: 0.6487 (ptp-170) REVERT: c 37 GLU cc_start: 0.7501 (OUTLIER) cc_final: 0.7223 (mt-10) REVERT: d 25 LYS cc_start: 0.8444 (OUTLIER) cc_final: 0.8076 (mtmt) REVERT: d 55 LEU cc_start: 0.8635 (OUTLIER) cc_final: 0.8210 (tm) REVERT: i 16 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.7320 (tt0) REVERT: m 21 GLU cc_start: 0.7548 (OUTLIER) cc_final: 0.6899 (mt-10) REVERT: m 119 LYS cc_start: 0.8392 (OUTLIER) cc_final: 0.8118 (mptt) REVERT: r 39 LYS cc_start: 0.8857 (OUTLIER) cc_final: 0.7824 (tmtp) REVERT: r 72 GLN cc_start: 0.6662 (OUTLIER) cc_final: 0.6331 (pp30) REVERT: s 35 ASN cc_start: 0.8552 (t0) cc_final: 0.8142 (t0) outliers start: 101 outliers final: 51 residues processed: 1014 average time/residue: 1.7421 time to fit residues: 2209.3915 Evaluate side-chains 996 residues out of total 6807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 929 time to evaluate : 7.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 420 THR Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 118 GLU Chi-restraints excluded: chain F residue 105 CYS Chi-restraints excluded: chain F residue 227 THR Chi-restraints excluded: chain F residue 310 SER Chi-restraints excluded: chain G residue 337 ARG Chi-restraints excluded: chain G residue 351 THR Chi-restraints excluded: chain G residue 444 GLN Chi-restraints excluded: chain G residue 613 TYR Chi-restraints excluded: chain G residue 657 LEU Chi-restraints excluded: chain G residue 673 MET Chi-restraints excluded: chain H residue 259 PHE Chi-restraints excluded: chain I residue 37 THR Chi-restraints excluded: chain J residue 3 LEU Chi-restraints excluded: chain J residue 50 SER Chi-restraints excluded: chain K residue 15 SER Chi-restraints excluded: chain K residue 79 VAL Chi-restraints excluded: chain K residue 98 CYS Chi-restraints excluded: chain L residue 149 ILE Chi-restraints excluded: chain L residue 515 TYR Chi-restraints excluded: chain M residue 116 ILE Chi-restraints excluded: chain M residue 126 LEU Chi-restraints excluded: chain N residue 237 THR Chi-restraints excluded: chain O residue 1 LEU Chi-restraints excluded: chain O residue 2 GLN Chi-restraints excluded: chain O residue 135 LEU Chi-restraints excluded: chain O residue 269 VAL Chi-restraints excluded: chain P residue 222 ASP Chi-restraints excluded: chain Q residue 27 GLU Chi-restraints excluded: chain R residue 7 THR Chi-restraints excluded: chain T residue 23 ASP Chi-restraints excluded: chain T residue 32 VAL Chi-restraints excluded: chain T residue 44 SER Chi-restraints excluded: chain U residue 37 MET Chi-restraints excluded: chain W residue 49 LEU Chi-restraints excluded: chain W residue 101 THR Chi-restraints excluded: chain X residue 109 CYS Chi-restraints excluded: chain X residue 130 VAL Chi-restraints excluded: chain Z residue 128 ARG Chi-restraints excluded: chain Z residue 144 THR Chi-restraints excluded: chain b residue 42 LEU Chi-restraints excluded: chain c residue 6 GLU Chi-restraints excluded: chain c residue 37 GLU Chi-restraints excluded: chain d residue 25 LYS Chi-restraints excluded: chain d residue 55 LEU Chi-restraints excluded: chain d residue 106 LYS Chi-restraints excluded: chain d residue 111 GLU Chi-restraints excluded: chain e residue 69 GLN Chi-restraints excluded: chain g residue 122 GLU Chi-restraints excluded: chain i residue 16 GLU Chi-restraints excluded: chain i residue 78 VAL Chi-restraints excluded: chain i residue 98 GLU Chi-restraints excluded: chain l residue 153 VAL Chi-restraints excluded: chain m residue 21 GLU Chi-restraints excluded: chain m residue 119 LYS Chi-restraints excluded: chain o residue 30 PHE Chi-restraints excluded: chain o residue 116 GLN Chi-restraints excluded: chain p residue 3 SER Chi-restraints excluded: chain p residue 16 THR Chi-restraints excluded: chain p residue 171 GLU Chi-restraints excluded: chain r residue 39 LYS Chi-restraints excluded: chain r residue 72 GLN Chi-restraints excluded: chain s residue 48 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 757 random chunks: chunk 663 optimal weight: 0.7980 chunk 698 optimal weight: 0.4980 chunk 637 optimal weight: 3.9990 chunk 679 optimal weight: 2.9990 chunk 409 optimal weight: 9.9990 chunk 296 optimal weight: 0.8980 chunk 533 optimal weight: 2.9990 chunk 208 optimal weight: 0.9990 chunk 614 optimal weight: 5.9990 chunk 643 optimal weight: 4.9990 chunk 677 optimal weight: 4.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 ASN B 106 GLN C 211 GLN D 55 HIS D 59 HIS F 436 GLN G 313 ASN H 287 HIS ** H 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 88 ASN S 30 GLN S 75 ASN S 92 ASN W 26 ASN X 15 GLN a 58 ASN ** f 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 86 GLN n 12 GLN n 159 GLN q 5 GLN q 52 ASN r 24 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.1428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.246 65674 Z= 0.444 Angle : 1.317 50.584 88862 Z= 0.850 Chirality : 0.262 6.499 9692 Planarity : 0.004 0.057 11096 Dihedral : 10.554 172.766 9931 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.80 % Favored : 98.19 % Rotamer: Outliers : 1.25 % Allowed : 14.23 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.10), residues: 7669 helix: 1.79 (0.08), residues: 4123 sheet: 0.03 (0.25), residues: 400 loop : 0.39 (0.11), residues: 3146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP X 85 HIS 0.006 0.001 HIS G 101 PHE 0.024 0.001 PHE M 122 TYR 0.019 0.001 TYR L 422 ARG 0.010 0.000 ARG B 174 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15338 Ramachandran restraints generated. 7669 Oldfield, 0 Emsley, 7669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15338 Ramachandran restraints generated. 7669 Oldfield, 0 Emsley, 7669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1025 residues out of total 6807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 940 time to evaluate : 6.088 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 112 GLU cc_start: 0.8104 (mm-30) cc_final: 0.7761 (mm-30) REVERT: B 59 MET cc_start: 0.7811 (tpt) cc_final: 0.7573 (tpt) REVERT: E 118 GLU cc_start: 0.7596 (OUTLIER) cc_final: 0.6636 (mp0) REVERT: F 310 SER cc_start: 0.8586 (OUTLIER) cc_final: 0.8362 (p) REVERT: G 337 ARG cc_start: 0.8394 (OUTLIER) cc_final: 0.8011 (mtt90) REVERT: G 444 GLN cc_start: 0.7519 (OUTLIER) cc_final: 0.7189 (tt0) REVERT: G 596 ASP cc_start: 0.8268 (m-30) cc_final: 0.8016 (m-30) REVERT: G 673 MET cc_start: 0.8678 (OUTLIER) cc_final: 0.7392 (mtm) REVERT: H 126 LYS cc_start: 0.7410 (mttt) cc_final: 0.7000 (mtpp) REVERT: I 11 SER cc_start: 0.8461 (m) cc_final: 0.8220 (t) REVERT: L 515 TYR cc_start: 0.4811 (OUTLIER) cc_final: 0.4302 (p90) REVERT: M 396 MET cc_start: 0.8674 (mmt) cc_final: 0.8414 (mmt) REVERT: O 2 GLN cc_start: 0.7749 (OUTLIER) cc_final: 0.7421 (tp40) REVERT: O 252 ASN cc_start: 0.7639 (p0) cc_final: 0.7234 (p0) REVERT: S 45 LYS cc_start: 0.8738 (mtmt) cc_final: 0.8352 (mtmt) REVERT: S 84 ASP cc_start: 0.7964 (m-30) cc_final: 0.7750 (m-30) REVERT: U 37 MET cc_start: 0.8624 (OUTLIER) cc_final: 0.7339 (mmm) REVERT: W 109 GLU cc_start: 0.8313 (mt-10) cc_final: 0.8090 (mt-10) REVERT: Z 24 ASN cc_start: 0.8816 (t0) cc_final: 0.8495 (t0) REVERT: a 59 ARG cc_start: 0.8079 (OUTLIER) cc_final: 0.7518 (mmp80) REVERT: b 82 ARG cc_start: 0.7265 (mtm110) cc_final: 0.6554 (ptp-170) REVERT: c 37 GLU cc_start: 0.7502 (OUTLIER) cc_final: 0.7223 (mt-10) REVERT: d 25 LYS cc_start: 0.8460 (OUTLIER) cc_final: 0.8087 (mtmt) REVERT: d 55 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8208 (tm) REVERT: i 16 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.7335 (tt0) REVERT: l 49 LYS cc_start: 0.8761 (tttm) cc_final: 0.8477 (tttt) REVERT: m 119 LYS cc_start: 0.8393 (OUTLIER) cc_final: 0.8119 (mptt) REVERT: o 112 LYS cc_start: 0.8542 (OUTLIER) cc_final: 0.8164 (ttmm) REVERT: s 35 ASN cc_start: 0.8551 (t0) cc_final: 0.8151 (t0) outliers start: 85 outliers final: 53 residues processed: 994 average time/residue: 1.7635 time to fit residues: 2195.6379 Evaluate side-chains 1002 residues out of total 6807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 934 time to evaluate : 5.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 77 ARG Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 420 THR Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 118 GLU Chi-restraints excluded: chain F residue 105 CYS Chi-restraints excluded: chain F residue 227 THR Chi-restraints excluded: chain F residue 310 SER Chi-restraints excluded: chain G residue 337 ARG Chi-restraints excluded: chain G residue 351 THR Chi-restraints excluded: chain G residue 444 GLN Chi-restraints excluded: chain G residue 657 LEU Chi-restraints excluded: chain G residue 673 MET Chi-restraints excluded: chain H residue 259 PHE Chi-restraints excluded: chain I residue 37 THR Chi-restraints excluded: chain J residue 3 LEU Chi-restraints excluded: chain J residue 50 SER Chi-restraints excluded: chain K residue 15 SER Chi-restraints excluded: chain K residue 79 VAL Chi-restraints excluded: chain K residue 98 CYS Chi-restraints excluded: chain L residue 515 TYR Chi-restraints excluded: chain M residue 116 ILE Chi-restraints excluded: chain M residue 126 LEU Chi-restraints excluded: chain N residue 237 THR Chi-restraints excluded: chain O residue 1 LEU Chi-restraints excluded: chain O residue 2 GLN Chi-restraints excluded: chain O residue 269 VAL Chi-restraints excluded: chain P residue 222 ASP Chi-restraints excluded: chain Q residue 27 GLU Chi-restraints excluded: chain Q residue 66 GLU Chi-restraints excluded: chain R residue 7 THR Chi-restraints excluded: chain T residue 23 ASP Chi-restraints excluded: chain T residue 32 VAL Chi-restraints excluded: chain T residue 44 SER Chi-restraints excluded: chain U residue 37 MET Chi-restraints excluded: chain W residue 49 LEU Chi-restraints excluded: chain W residue 101 THR Chi-restraints excluded: chain X residue 108 GLU Chi-restraints excluded: chain X residue 109 CYS Chi-restraints excluded: chain X residue 130 VAL Chi-restraints excluded: chain Z residue 128 ARG Chi-restraints excluded: chain Z residue 144 THR Chi-restraints excluded: chain a residue 59 ARG Chi-restraints excluded: chain b residue 42 LEU Chi-restraints excluded: chain c residue 6 GLU Chi-restraints excluded: chain c residue 37 GLU Chi-restraints excluded: chain d residue 25 LYS Chi-restraints excluded: chain d residue 55 LEU Chi-restraints excluded: chain d residue 106 LYS Chi-restraints excluded: chain d residue 111 GLU Chi-restraints excluded: chain e residue 69 GLN Chi-restraints excluded: chain f residue 47 GLU Chi-restraints excluded: chain g residue 122 GLU Chi-restraints excluded: chain i residue 16 GLU Chi-restraints excluded: chain i residue 78 VAL Chi-restraints excluded: chain i residue 98 GLU Chi-restraints excluded: chain l residue 31 VAL Chi-restraints excluded: chain l residue 153 VAL Chi-restraints excluded: chain m residue 119 LYS Chi-restraints excluded: chain o residue 30 PHE Chi-restraints excluded: chain o residue 112 LYS Chi-restraints excluded: chain o residue 116 GLN Chi-restraints excluded: chain p residue 3 SER Chi-restraints excluded: chain p residue 16 THR Chi-restraints excluded: chain p residue 171 GLU Chi-restraints excluded: chain s residue 48 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 757 random chunks: chunk 446 optimal weight: 4.9990 chunk 718 optimal weight: 5.9990 chunk 438 optimal weight: 10.0000 chunk 341 optimal weight: 0.9990 chunk 499 optimal weight: 7.9990 chunk 754 optimal weight: 4.9990 chunk 694 optimal weight: 2.9990 chunk 600 optimal weight: 0.4980 chunk 62 optimal weight: 10.0000 chunk 463 optimal weight: 2.9990 chunk 368 optimal weight: 0.0010 overall best weight: 1.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 ASN B 106 GLN C 211 GLN D 55 HIS D 59 HIS F 436 GLN G 313 ASN H 287 HIS ** H 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 88 ASN S 30 GLN S 75 ASN S 92 ASN W 26 ASN X 15 GLN Y 128 GLN a 58 ASN ** f 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 86 GLN n 12 GLN n 159 GLN q 5 GLN q 52 ASN r 24 GLN r 28 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.1402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.245 65674 Z= 0.450 Angle : 1.320 50.568 88862 Z= 0.851 Chirality : 0.262 6.503 9692 Planarity : 0.004 0.056 11096 Dihedral : 10.454 173.904 9931 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.83 % Favored : 98.16 % Rotamer: Outliers : 1.31 % Allowed : 14.30 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.10), residues: 7669 helix: 1.77 (0.08), residues: 4121 sheet: 0.03 (0.25), residues: 400 loop : 0.39 (0.11), residues: 3148 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 0.024 0.001 PHE M 122 TYR 0.020 0.001 TYR m 69 ARG 0.010 0.000 ARG B 174 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15338 Ramachandran restraints generated. 7669 Oldfield, 0 Emsley, 7669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15338 Ramachandran restraints generated. 7669 Oldfield, 0 Emsley, 7669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1026 residues out of total 6807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 937 time to evaluate : 5.910 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 112 GLU cc_start: 0.8099 (mm-30) cc_final: 0.7749 (mm-30) REVERT: B 59 MET cc_start: 0.7818 (tpt) cc_final: 0.7586 (tpt) REVERT: E 118 GLU cc_start: 0.7600 (OUTLIER) cc_final: 0.6636 (mp0) REVERT: G 337 ARG cc_start: 0.8385 (OUTLIER) cc_final: 0.8012 (mtt90) REVERT: G 444 GLN cc_start: 0.7517 (OUTLIER) cc_final: 0.7189 (tt0) REVERT: G 596 ASP cc_start: 0.8274 (m-30) cc_final: 0.8025 (m-30) REVERT: G 673 MET cc_start: 0.8692 (OUTLIER) cc_final: 0.7420 (mtm) REVERT: H 126 LYS cc_start: 0.7423 (mttt) cc_final: 0.7008 (mtpp) REVERT: H 176 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8631 (mm) REVERT: I 11 SER cc_start: 0.8465 (m) cc_final: 0.8223 (t) REVERT: L 515 TYR cc_start: 0.4834 (OUTLIER) cc_final: 0.4310 (p90) REVERT: M 396 MET cc_start: 0.8694 (mmt) cc_final: 0.8422 (mmt) REVERT: O 2 GLN cc_start: 0.7746 (OUTLIER) cc_final: 0.7418 (tp40) REVERT: O 21 LYS cc_start: 0.7530 (OUTLIER) cc_final: 0.7189 (ttpp) REVERT: O 252 ASN cc_start: 0.7653 (p0) cc_final: 0.7271 (p0) REVERT: S 45 LYS cc_start: 0.8737 (mtmt) cc_final: 0.8346 (mtmt) REVERT: S 84 ASP cc_start: 0.7973 (m-30) cc_final: 0.7757 (m-30) REVERT: U 37 MET cc_start: 0.8632 (OUTLIER) cc_final: 0.7305 (mmm) REVERT: W 109 GLU cc_start: 0.8293 (mt-10) cc_final: 0.8087 (mt-10) REVERT: Z 24 ASN cc_start: 0.8816 (t0) cc_final: 0.8494 (t0) REVERT: a 59 ARG cc_start: 0.8080 (OUTLIER) cc_final: 0.7515 (mmp80) REVERT: b 82 ARG cc_start: 0.7224 (mtm110) cc_final: 0.6542 (ptp-170) REVERT: c 37 GLU cc_start: 0.7502 (OUTLIER) cc_final: 0.7222 (mt-10) REVERT: d 25 LYS cc_start: 0.8458 (OUTLIER) cc_final: 0.8085 (mtmt) REVERT: d 55 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8200 (tm) REVERT: i 16 GLU cc_start: 0.7703 (OUTLIER) cc_final: 0.7341 (tt0) REVERT: j 40 PHE cc_start: 0.8583 (OUTLIER) cc_final: 0.8072 (t80) REVERT: l 49 LYS cc_start: 0.8761 (tttm) cc_final: 0.8475 (tttt) REVERT: m 119 LYS cc_start: 0.8401 (OUTLIER) cc_final: 0.8120 (mptt) REVERT: o 112 LYS cc_start: 0.8538 (OUTLIER) cc_final: 0.8156 (ttmm) REVERT: r 39 LYS cc_start: 0.8877 (OUTLIER) cc_final: 0.7875 (tmtp) REVERT: s 35 ASN cc_start: 0.8553 (t0) cc_final: 0.8150 (t0) outliers start: 89 outliers final: 55 residues processed: 988 average time/residue: 1.7596 time to fit residues: 2181.3270 Evaluate side-chains 1005 residues out of total 6807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 932 time to evaluate : 5.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 MET Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 77 ARG Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 420 THR Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 118 GLU Chi-restraints excluded: chain F residue 105 CYS Chi-restraints excluded: chain F residue 227 THR Chi-restraints excluded: chain G residue 337 ARG Chi-restraints excluded: chain G residue 351 THR Chi-restraints excluded: chain G residue 444 GLN Chi-restraints excluded: chain G residue 657 LEU Chi-restraints excluded: chain G residue 673 MET Chi-restraints excluded: chain H residue 176 LEU Chi-restraints excluded: chain H residue 259 PHE Chi-restraints excluded: chain I residue 37 THR Chi-restraints excluded: chain J residue 3 LEU Chi-restraints excluded: chain J residue 50 SER Chi-restraints excluded: chain K residue 15 SER Chi-restraints excluded: chain K residue 79 VAL Chi-restraints excluded: chain K residue 98 CYS Chi-restraints excluded: chain L residue 515 TYR Chi-restraints excluded: chain M residue 116 ILE Chi-restraints excluded: chain M residue 126 LEU Chi-restraints excluded: chain N residue 237 THR Chi-restraints excluded: chain O residue 1 LEU Chi-restraints excluded: chain O residue 2 GLN Chi-restraints excluded: chain O residue 21 LYS Chi-restraints excluded: chain O residue 269 VAL Chi-restraints excluded: chain P residue 222 ASP Chi-restraints excluded: chain Q residue 27 GLU Chi-restraints excluded: chain R residue 7 THR Chi-restraints excluded: chain S residue 93 VAL Chi-restraints excluded: chain T residue 23 ASP Chi-restraints excluded: chain T residue 32 VAL Chi-restraints excluded: chain T residue 44 SER Chi-restraints excluded: chain U residue 37 MET Chi-restraints excluded: chain W residue 49 LEU Chi-restraints excluded: chain X residue 108 GLU Chi-restraints excluded: chain X residue 109 CYS Chi-restraints excluded: chain X residue 130 VAL Chi-restraints excluded: chain Z residue 128 ARG Chi-restraints excluded: chain Z residue 144 THR Chi-restraints excluded: chain a residue 59 ARG Chi-restraints excluded: chain b residue 42 LEU Chi-restraints excluded: chain c residue 6 GLU Chi-restraints excluded: chain c residue 37 GLU Chi-restraints excluded: chain d residue 25 LYS Chi-restraints excluded: chain d residue 55 LEU Chi-restraints excluded: chain d residue 106 LYS Chi-restraints excluded: chain d residue 111 GLU Chi-restraints excluded: chain e residue 69 GLN Chi-restraints excluded: chain f residue 47 GLU Chi-restraints excluded: chain g residue 107 ILE Chi-restraints excluded: chain g residue 122 GLU Chi-restraints excluded: chain i residue 16 GLU Chi-restraints excluded: chain i residue 78 VAL Chi-restraints excluded: chain i residue 98 GLU Chi-restraints excluded: chain j residue 40 PHE Chi-restraints excluded: chain l residue 31 VAL Chi-restraints excluded: chain l residue 153 VAL Chi-restraints excluded: chain m residue 119 LYS Chi-restraints excluded: chain o residue 30 PHE Chi-restraints excluded: chain o residue 34 LYS Chi-restraints excluded: chain o residue 112 LYS Chi-restraints excluded: chain o residue 116 GLN Chi-restraints excluded: chain p residue 3 SER Chi-restraints excluded: chain p residue 16 THR Chi-restraints excluded: chain p residue 171 GLU Chi-restraints excluded: chain r residue 39 LYS Chi-restraints excluded: chain s residue 48 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 757 random chunks: chunk 477 optimal weight: 3.9990 chunk 639 optimal weight: 0.8980 chunk 183 optimal weight: 0.9990 chunk 553 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 166 optimal weight: 2.9990 chunk 601 optimal weight: 7.9990 chunk 251 optimal weight: 0.9990 chunk 617 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 chunk 110 optimal weight: 4.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 ASN B 106 GLN C 211 GLN D 55 HIS D 59 HIS F 436 GLN G 313 ASN H 287 HIS ** H 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 88 ASN S 30 GLN S 75 ASN S 92 ASN W 26 ASN X 15 GLN a 58 ASN ** f 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 86 GLN n 12 GLN n 159 GLN q 5 GLN q 52 ASN r 24 GLN r 28 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.096514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.075384 restraints weight = 66247.587| |-----------------------------------------------------------------------------| r_work (start): 0.2865 rms_B_bonded: 1.11 r_work: 0.2767 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.2664 rms_B_bonded: 2.53 restraints_weight: 0.2500 r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8931 moved from start: 0.1367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.245 65674 Z= 0.459 Angle : 1.325 50.565 88862 Z= 0.853 Chirality : 0.263 6.519 9692 Planarity : 0.004 0.056 11096 Dihedral : 10.435 174.618 9930 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.81 % Favored : 98.17 % Rotamer: Outliers : 1.37 % Allowed : 14.30 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.10), residues: 7669 helix: 1.74 (0.08), residues: 4119 sheet: 0.01 (0.25), residues: 400 loop : 0.38 (0.11), residues: 3150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP X 85 HIS 0.007 0.001 HIS G 101 PHE 0.025 0.001 PHE M 122 TYR 0.021 0.001 TYR k 86 ARG 0.007 0.000 ARG m 9 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 32273.31 seconds wall clock time: 558 minutes 7.23 seconds (33487.23 seconds total)