Starting phenix.real_space_refine on Tue Mar 12 22:52:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r4g_14307/03_2024/7r4g_14307_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r4g_14307/03_2024/7r4g_14307.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r4g_14307/03_2024/7r4g_14307_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r4g_14307/03_2024/7r4g_14307_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r4g_14307/03_2024/7r4g_14307_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r4g_14307/03_2024/7r4g_14307.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r4g_14307/03_2024/7r4g_14307.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r4g_14307/03_2024/7r4g_14307_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r4g_14307/03_2024/7r4g_14307_updated.pdb" } resolution = 2.5 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= 1.066 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 2 10.91 5 K 1 8.98 5 Fe 28 7.16 5 Zn 1 6.06 5 P 33 5.49 5 Mg 1 5.21 5 S 454 5.16 5 Cl 2 4.86 5 C 41554 2.51 5 N 10657 2.21 5 O 12420 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 112": "OE1" <-> "OE2" Residue "B ARG 71": "NH1" <-> "NH2" Residue "B ARG 77": "NH1" <-> "NH2" Residue "B GLU 109": "OE1" <-> "OE2" Residue "B ARG 111": "NH1" <-> "NH2" Residue "B TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 143": "OD1" <-> "OD2" Residue "B GLU 154": "OE1" <-> "OE2" Residue "B TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 8": "NH1" <-> "NH2" Residue "C ARG 12": "NH1" <-> "NH2" Residue "C GLU 31": "OE1" <-> "OE2" Residue "C PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 149": "NH1" <-> "NH2" Residue "C GLU 158": "OE1" <-> "OE2" Residue "C GLU 173": "OE1" <-> "OE2" Residue "C GLU 179": "OE1" <-> "OE2" Residue "C GLU 186": "OE1" <-> "OE2" Residue "C GLU 193": "OE1" <-> "OE2" Residue "D GLU 67": "OE1" <-> "OE2" Residue "D GLU 123": "OE1" <-> "OE2" Residue "D ASP 160": "OD1" <-> "OD2" Residue "D PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 179": "OE1" <-> "OE2" Residue "D PHE 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 221": "NH1" <-> "NH2" Residue "D ARG 233": "NH1" <-> "NH2" Residue "D ASP 249": "OD1" <-> "OD2" Residue "D TYR 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 337": "OE1" <-> "OE2" Residue "D GLU 343": "OE1" <-> "OE2" Residue "D ASP 422": "OD1" <-> "OD2" Residue "E GLU 14": "OE1" <-> "OE2" Residue "E ASP 22": "OD1" <-> "OD2" Residue "E GLU 40": "OE1" <-> "OE2" Residue "E GLU 82": "OE1" <-> "OE2" Residue "E PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 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 PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 226": "OE1" <-> "OE2" Residue "F ARG 249": "NH1" <-> "NH2" Residue "F PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 269": "OE1" <-> "OE2" Residue "F GLU 270": "OE1" <-> "OE2" Residue "F GLU 278": "OE1" <-> "OE2" Residue "F ASP 292": "OD1" <-> "OD2" Residue "F ARG 349": "NH1" <-> "NH2" Residue "F GLU 367": "OE1" <-> "OE2" Residue "F GLU 394": "OE1" <-> "OE2" Residue "F PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 429": "NH1" <-> "NH2" Residue "F PHE 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 12": "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 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 ARG 218": "NH1" <-> "NH2" Residue "G GLU 226": "OE1" <-> "OE2" Residue "G ASP 232": "OD1" <-> "OD2" Residue "G ARG 243": "NH1" <-> "NH2" Residue "G ARG 253": "NH1" <-> "NH2" Residue "G GLU 260": "OE1" <-> "OE2" Residue "G GLU 261": "OE1" <-> "OE2" Residue "G ASP 265": "OD1" <-> "OD2" Residue "G GLU 281": "OE1" <-> "OE2" Residue "G ARG 285": "NH1" <-> "NH2" Residue "G ASP 298": "OD1" <-> "OD2" Residue "G ARG 302": "NH1" <-> "NH2" Residue "G ASP 341": "OD1" <-> "OD2" Residue "G GLU 347": "OE1" <-> "OE2" Residue "G GLU 372": "OE1" <-> "OE2" Residue "G ARG 385": "NH1" <-> "NH2" Residue "G ARG 418": "NH1" <-> "NH2" Residue "G TYR 419": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 486": "OD1" <-> "OD2" Residue "G TYR 573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 577": "OE1" <-> "OE2" Residue "G GLU 624": "OE1" <-> "OE2" Residue "G GLU 625": "OE1" <-> "OE2" Residue "G GLU 637": "OE1" <-> "OE2" Residue "G ASP 675": "OD1" <-> "OD2" Residue "H PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 24": "OE1" <-> "OE2" Residue "H ARG 25": "NH1" <-> "NH2" Residue "H ARG 34": "NH1" <-> "NH2" Residue "H PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 62": "NH1" <-> "NH2" Residue "H GLU 170": "OE1" <-> "OE2" Residue "H GLU 206": "OE1" <-> "OE2" Residue "H PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 8": "NH1" <-> "NH2" Residue "I GLU 74": "OE1" <-> "OE2" Residue "I GLU 95": "OE1" <-> "OE2" Residue "I ARG 108": "NH1" <-> "NH2" Residue "I PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 152": "OE1" <-> "OE2" Residue "J PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 132": "OD1" <-> "OD2" Residue "J PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 138": "OE1" <-> "OE2" Residue "J GLU 139": "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 GLU 34": "OE1" <-> "OE2" Residue "K GLU 70": "OE1" <-> "OE2" Residue "K ASP 88": "OD1" <-> "OD2" Residue "L PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 102": "OE1" <-> "OE2" Residue "L PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 145": "OE1" <-> "OE2" Residue "L PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 161": "NH1" <-> "NH2" Residue "L GLU 238": "OE1" <-> "OE2" Residue "L PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 262": "NH1" <-> "NH2" Residue "L TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 397": "OE1" <-> "OE2" Residue "L TYR 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 456": "NH1" <-> "NH2" Residue "L PHE 463": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 466": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 503": "OE1" <-> "OE2" Residue "L PHE 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 123": "OE1" <-> "OE2" Residue "M TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 281": "OD1" <-> "OD2" Residue "M GLU 335": "OE1" <-> "OE2" Residue "M ARG 346": "NH1" <-> "NH2" Residue "M TYR 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 432": "NH1" <-> "NH2" Residue "N GLU 34": "OE1" <-> "OE2" Residue "N PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 269": "OE1" <-> "OE2" Residue "N TYR 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 295": "NH1" <-> "NH2" Residue "N PHE 325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 44": "OE1" <-> "OE2" Residue "O PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 80": "OE1" <-> "OE2" Residue "O PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 104": "NH1" <-> "NH2" Residue "O GLU 113": "OE1" <-> "OE2" Residue "O ARG 126": "NH1" <-> "NH2" Residue "O PHE 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 219": "OE1" <-> "OE2" Residue "O TYR 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 230": "OD1" <-> "OD2" Residue "O TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 268": "OE1" <-> "OE2" Residue "O TYR 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 281": "OE1" <-> "OE2" Residue "O ARG 302": "NH1" <-> "NH2" Residue "O ARG 305": "NH1" <-> "NH2" Residue "O GLU 310": "OE1" <-> "OE2" 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 ASP 72": "OD1" <-> "OD2" Residue "P ARG 82": "NH1" <-> "NH2" Residue "P ARG 97": "NH1" <-> "NH2" Residue "P ASP 105": "OD1" <-> "OD2" Residue "P GLU 123": "OE1" <-> "OE2" Residue "P GLU 127": "OE1" <-> "OE2" Residue "P PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 147": "NH1" <-> "NH2" Residue "P GLU 153": "OE1" <-> "OE2" Residue "P ARG 157": "NH1" <-> "NH2" Residue "P PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 162": "OE1" <-> "OE2" Residue "P PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 175": "OE1" <-> "OE2" Residue "P TYR 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 235": "NH1" <-> "NH2" Residue "P TYR 236": "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 ASP 14": "OD1" <-> "OD2" Residue "Q GLU 58": "OE1" <-> "OE2" Residue "Q PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 31": "NH1" <-> "NH2" Residue "R GLU 37": "OE1" <-> "OE2" Residue "S ASP 34": "OD1" <-> "OD2" Residue "S GLU 37": "OE1" <-> "OE2" Residue "S ASP 84": "OD1" <-> "OD2" Residue "S GLU 91": "OE1" <-> "OE2" Residue "T ASP 13": "OD1" <-> "OD2" Residue "T TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 39": "OD1" <-> "OD2" Residue "T ASP 46": "OD1" <-> "OD2" Residue "T GLU 55": "OE1" <-> "OE2" Residue "T GLU 57": "OE1" <-> "OE2" Residue "T ASP 66": "OD1" <-> "OD2" 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 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 68": "OE1" <-> "OE2" Residue "U TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 22": "NH1" <-> "NH2" Residue "V GLU 53": "OE1" <-> "OE2" Residue "V GLU 61": "OE1" <-> "OE2" Residue "V GLU 68": "OE1" <-> "OE2" Residue "V GLU 77": "OE1" <-> "OE2" Residue "V GLU 78": "OE1" <-> "OE2" Residue "V GLU 86": "OE1" <-> "OE2" Residue "V GLU 104": "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 GLU 65": "OE1" <-> "OE2" Residue "W GLU 91": "OE1" <-> "OE2" Residue "W PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 117": "OD1" <-> "OD2" Residue "W ASP 127": "OD1" <-> "OD2" Residue "X GLU 10": "OE1" <-> "OE2" 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 ARG 97": "NH1" <-> "NH2" Residue "X ASP 112": "OD1" <-> "OD2" Residue "X ARG 118": "NH1" <-> "NH2" Residue "X ARG 134": "NH1" <-> "NH2" Residue "X TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 144": "NH1" <-> "NH2" Residue "X ARG 146": "NH1" <-> "NH2" Residue "X GLU 148": "OE1" <-> "OE2" Residue "X GLU 154": "OE1" <-> "OE2" Residue "Z GLU 56": "OE1" <-> "OE2" Residue "Z ARG 82": "NH1" <-> "NH2" Residue "Z ASP 100": "OD1" <-> "OD2" Residue "Z GLU 108": "OE1" <-> "OE2" Residue "Z TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 128": "NH1" <-> "NH2" Residue "Z TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 51": "OD1" <-> "OD2" Residue "a ARG 59": "NH1" <-> "NH2" Residue "b TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 57": "NH1" <-> "NH2" Residue "b ASP 58": "OD1" <-> "OD2" Residue "b ASP 64": "OD1" <-> "OD2" Residue "b ASP 71": "OD1" <-> "OD2" Residue "b GLU 78": "OE1" <-> "OE2" Residue "c GLU 37": "OE1" <-> "OE2" Residue "c GLU 41": "OE1" <-> "OE2" Residue "c ARG 44": "NH1" <-> "NH2" Residue "d ASP 16": "OD1" <-> "OD2" Residue "d ASP 28": "OD1" <-> "OD2" Residue "d TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 45": "OD1" <-> "OD2" Residue "d ARG 51": "NH1" <-> "NH2" Residue "d PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 86": "NH1" <-> "NH2" Residue "d GLU 111": "OE1" <-> "OE2" Residue "e ARG 8": "NH1" <-> "NH2" Residue "e GLU 38": "OE1" <-> "OE2" Residue "e GLU 41": "OE1" <-> "OE2" Residue "e ARG 50": "NH1" <-> "NH2" Residue "e GLU 54": "OE1" <-> "OE2" Residue "e GLU 58": "OE1" <-> "OE2" Residue "e GLU 60": "OE1" <-> "OE2" Residue "f TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ARG 28": "NH1" <-> "NH2" Residue "f ARG 46": "NH1" <-> "NH2" Residue "f GLU 52": "OE1" <-> "OE2" Residue "g GLU 39": "OE1" <-> "OE2" Residue "g ASP 43": "OD1" <-> "OD2" Residue "g ASP 50": "OD1" <-> "OD2" Residue "g GLU 92": "OE1" <-> "OE2" Residue "g GLU 94": "OE1" <-> "OE2" Residue "g GLU 101": "OE1" <-> "OE2" Residue "g GLU 109": "OE1" <-> "OE2" Residue "h PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ARG 20": "NH1" <-> "NH2" Residue "h GLU 49": "OE1" <-> "OE2" Residue "h ARG 77": "NH1" <-> "NH2" Residue "h GLU 84": "OE1" <-> "OE2" Residue "h 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 ARG 18": "NH1" <-> "NH2" Residue "i GLU 26": "OE1" <-> "OE2" Residue "i TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i GLU 111": "OE1" <-> "OE2" Residue "i GLU 121": "OE1" <-> "OE2" Residue "i ASP 124": "OD1" <-> "OD2" Residue "j PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ASP 55": "OD1" <-> "OD2" Residue "j GLU 63": "OE1" <-> "OE2" Residue "j ASP 69": "OD1" <-> "OD2" Residue "j GLU 71": "OE1" <-> "OE2" Residue "k GLU 14": "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 "l ASP 7": "OD1" <-> "OD2" Residue "l TYR 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ARG 30": "NH1" <-> "NH2" Residue "l GLU 32": "OE1" <-> "OE2" Residue "l GLU 35": "OE1" <-> "OE2" Residue "l TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ASP 52": "OD1" <-> "OD2" Residue "l ASP 59": "OD1" <-> "OD2" Residue "l GLU 75": "OE1" <-> "OE2" Residue "l PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ARG 142": "NH1" <-> "NH2" Residue "m GLU 6": "OE1" <-> "OE2" Residue "m TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m ASP 23": "OD1" <-> "OD2" Residue "m GLU 34": "OE1" <-> "OE2" Residue "m ARG 39": "NH1" <-> "NH2" Residue "m GLU 45": "OE1" <-> "OE2" Residue "m TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m ASP 52": "OD1" <-> "OD2" Residue "m ARG 55": "NH1" <-> "NH2" Residue "m ARG 71": "NH1" <-> "NH2" Residue "m TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m GLU 112": "OE1" <-> "OE2" Residue "m GLU 117": "OE1" <-> "OE2" Residue "m ASP 121": "OD1" <-> "OD2" Residue "n TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 55": "OD1" <-> "OD2" Residue "n ARG 64": "NH1" <-> "NH2" Residue "n GLU 68": "OE1" <-> "OE2" Residue "n TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n GLU 83": "OE1" <-> "OE2" Residue "n ARG 92": "NH1" <-> "NH2" Residue "n TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n GLU 122": "OE1" <-> "OE2" Residue "n GLU 133": "OE1" <-> "OE2" Residue "n ARG 149": "NH1" <-> "NH2" Residue "o ARG 6": "NH1" <-> "NH2" Residue "o GLU 15": "OE1" <-> "OE2" Residue "o TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o GLU 35": "OE1" <-> "OE2" Residue "o ARG 36": "NH1" <-> "NH2" Residue "o GLU 44": "OE1" <-> "OE2" Residue "o ASP 47": "OD1" <-> "OD2" 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 102": "OE1" <-> "OE2" Residue "o ARG 103": "NH1" <-> "NH2" Residue "o ARG 105": "NH1" <-> "NH2" Residue "o ARG 106": "NH1" <-> "NH2" Residue "o GLU 118": "OE1" <-> "OE2" Residue "p ASP 5": "OD1" <-> "OD2" Residue "p TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p ARG 15": "NH1" <-> "NH2" Residue "p PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p ASP 37": "OD1" <-> "OD2" Residue "p ASP 41": "OD1" <-> "OD2" Residue "p TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p GLU 66": "OE1" <-> "OE2" Residue "p PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p GLU 78": "OE1" <-> "OE2" Residue "p GLU 88": "OE1" <-> "OE2" Residue "p GLU 100": "OE1" <-> "OE2" Residue "p GLU 116": "OE1" <-> "OE2" Residue "p GLU 127": "OE1" <-> "OE2" Residue "p GLU 129": "OE1" <-> "OE2" Residue "p ASP 140": "OD1" <-> "OD2" Residue "p TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ARG 21": "NH1" <-> "NH2" Residue "q TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ARG 29": "NH1" <-> "NH2" Residue "q ASP 32": "OD1" <-> "OD2" Residue "q GLU 41": "OE1" <-> "OE2" Residue "q TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q GLU 50": "OE1" <-> "OE2" Residue "q GLU 85": "OE1" <-> "OE2" Residue "q ARG 88": "NH1" <-> "NH2" Residue "q PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r GLU 29": "OE1" <-> "OE2" Residue "r TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r ARG 59": "NH1" <-> "NH2" Residue "r GLU 109": "OE1" <-> "OE2" Residue "r TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s ASP 34": "OD1" <-> "OD2" Residue "s GLU 71": "OE1" <-> "OE2" Time to flip residues: 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 65153 Number of models: 1 Model: "" Number of chains: 111 Chain: "A" Number of atoms: 748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 748 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 3, 'TRANS': 89} 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: 3310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3310 Classifications: {'peptide': 430} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 408} Chain: "G" Number of atoms: 5279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 688, 5279 Classifications: {'peptide': 688} Link IDs: {'PTRANS': 32, 'TRANS': 655} Chain: "H" Number of atoms: 2468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2468 Classifications: {'peptide': 313} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 290} 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: "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: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 946 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 3, 'TRANS': 123} 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: 4318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 547, 4318 Classifications: {'peptide': 547} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 26, 'TRANS': 520} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'FME:plan-2': 1, 'TYR:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "M" Number of atoms: 3632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3632 Classifications: {'peptide': 459} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 3, 'PTRANS': 17, 'TRANS': 438} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'FME:plan-2': 1, 'GLN:plan1': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 17 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: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 612 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "U" Number of atoms: 681 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 681 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 3, 'TRANS': 80} Chain: "V" Number of atoms: 911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 911 Classifications: {'peptide': 112} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 103} Chain: "W" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 971 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 6, 'TRANS': 107} Chain: "X" Number of atoms: 1402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1402 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 12, 'TRANS': 158} Chain: "Y" Number of atoms: 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: 1145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1145 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 7, 'TRANS': 132} 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: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 892 Classifications: {'peptide': 104} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 91} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'SAC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "j" Number of atoms: 580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 580 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 7, 'TRANS': 59} Chain: "k" Number of atoms: 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: 1035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 1035 Classifications: {'peptide': 120} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 112} Chain: "p" Number of atoms: 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: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 92 Unusual residues: {'3PE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 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: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 86 Unusual residues: {'3PE': 1, 'I49': 1, 'LMT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'3PE:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "I" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 100 Unusual residues: {'3PE': 2, 'SF4': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 18 Chain: "J" Number of atoms: 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: 198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 198 Unusual residues: {'3PE': 2, 'CDL': 1, 'LMT': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 39 Chain: "M" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 92 Unusual residues: {'3PE': 1, 'PC1': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Chain: "N" Number of atoms: 235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 235 Unusual residues: {'3PE': 1, 'CDL': 2, 'I49': 1, 'LMT': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 68 Chain: "O" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 84 Unusual residues: {' MG': 1, '3PE': 1, 'GTP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: "b" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'LMT': 1} Classifications: {'undetermined': 1} Chain: "g" 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: "q" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 76 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 24 Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "B" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 36 Classifications: {'water': 36} Link IDs: {None: 35} Chain: "C" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 55 Classifications: {'water': 55} Link IDs: {None: 54} Chain: "D" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 104 Classifications: {'water': 104} Link IDs: {None: 103} Chain: "E" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "F" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "G" Number of atoms: 139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 139 Classifications: {'water': 139} Link IDs: {None: 138} Chain: "H" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 25 Classifications: {'water': 25} Link IDs: {None: 24} Chain: "I" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 76 Classifications: {'water': 76} Link IDs: {None: 75} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "L" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 32 Classifications: {'water': 32} Link IDs: {None: 31} Chain: "M" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 25 Classifications: {'water': 25} Link IDs: {None: 24} Chain: "N" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "P" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 25 Classifications: {'water': 25} Link IDs: {None: 24} Chain: "Q" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 54 Classifications: {'water': 54} Link IDs: {None: 53} Chain: "R" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 25 Classifications: {'water': 25} Link IDs: {None: 24} Chain: "U" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "V" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "W" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "X" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "Y" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "Z" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "a" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "b" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "d" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "e" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "f" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "g" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "h" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "i" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "j" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "k" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "l" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} 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: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "o" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "p" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "q" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "r" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 26 Classifications: {'water': 26} Link IDs: {None: 25} Chain: "s" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1484 SG CYS B 119 97.154 92.857 209.396 1.00 32.49 S ATOM 1714 SG CYS B 149 94.810 90.644 214.159 1.00 30.49 S ATOM 980 SG CYS B 54 91.504 89.277 208.626 1.00 36.00 S ATOM 986 SG CYS B 55 91.258 95.105 211.258 1.00 36.04 S ATOM 7591 SG CYS E 103 112.971 45.524 266.687 1.00 50.67 S ATOM 7625 SG CYS E 108 111.362 43.009 268.709 1.00 51.13 S ATOM 7905 SG CYS E 144 115.178 42.066 263.417 1.00 49.15 S ATOM 7928 SG CYS E 148 113.795 39.428 264.474 1.00 52.55 S ATOM 11137 SG CYS F 362 118.457 51.374 242.902 1.00 33.53 S ATOM 11157 SG CYS F 365 115.525 50.929 247.738 1.00 35.49 S ATOM 11481 SG CYS F 405 119.968 46.407 247.079 1.00 37.65 S ATOM 11118 SG CYS F 359 122.073 52.173 248.392 1.00 37.95 S ATOM 12578 SG CYS G 114 115.498 69.665 232.996 1.00 30.89 S ATOM 12517 SG CYS G 105 109.701 72.350 234.707 1.00 29.50 S ATOM 12538 SG CYS G 108 115.303 74.725 236.842 1.00 29.82 S ATOM 12910 SG CYS G 156 123.802 63.588 238.236 1.00 32.78 S ATOM 12887 SG CYS G 153 120.915 66.059 243.695 1.00 32.04 S ATOM 12934 SG CYS G 159 127.102 66.872 242.372 1.00 35.14 S ATOM 13264 SG CYS G 203 122.681 69.608 238.367 1.00 33.09 S ATOM 12023 SG CYS G 41 123.986 56.758 236.163 1.00 32.71 S ATOM 12109 SG CYS G 52 120.163 57.256 235.088 1.00 32.72 S ATOM 12134 SG CYS G 55 121.682 52.663 231.991 1.00 34.71 S ATOM 12235 SG CYS G 69 124.891 53.322 233.121 1.00 35.42 S ATOM 20453 SG CYS I 119 97.605 84.856 220.398 1.00 27.74 S ATOM 20427 SG CYS I 116 98.049 91.395 220.990 1.00 28.26 S ATOM 20474 SG CYS I 122 99.241 87.144 225.879 1.00 27.85 S ATOM 20201 SG CYS I 87 103.305 87.659 220.763 1.00 27.23 S ATOM 20503 SG CYS I 126 101.577 84.067 233.431 1.00 29.32 S ATOM 20132 SG CYS I 77 106.544 88.262 234.452 1.00 30.96 S ATOM 20174 SG CYS I 83 105.099 86.382 228.498 1.00 28.46 S ATOM 20151 SG CYS I 80 107.067 81.851 232.232 1.00 29.06 S ATOM 39640 SG CYS R 59 102.922 80.033 248.767 1.00 36.64 S ATOM 39818 SG CYS R 84 105.998 80.578 246.712 1.00 36.03 S ATOM 39840 SG CYS R 87 103.750 83.334 247.372 1.00 35.09 S Time building chain proxies: 27.14, per 1000 atoms: 0.42 Number of scatterers: 65153 At special positions: 0 Unit cell: (185.674, 198.101, 298.248, 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 2 52.95 Zn 1 29.99 Fe 28 26.01 K 1 19.00 Cl 2 17.00 S 454 16.00 P 33 15.00 Mg 1 11.99 O 12420 8.00 N 10657 7.00 C 41554 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS X 45 " - pdb=" SG CYS X 55 " distance=2.04 Simple disulfide: pdb=" SG CYS X 87 " - pdb=" SG CYS X 99 " distance=2.04 Simple disulfide: pdb=" SG CYS e 32 " - pdb=" SG CYS e 65 " distance=2.04 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: 21.53 Conformation dependent library (CDL) restraints added in 8.3 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 148 " pdb="FE2 FES E 301 " - pdb=" SG CYS E 144 " pdb=" FES G 803 " pdb="FE2 FES G 803 " - pdb=" SG CYS G 69 " 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=" SF4 B 201 " pdb="FE1 SF4 B 201 " - pdb=" SG CYS B 119 " pdb="FE2 SF4 B 201 " - pdb=" SG CYS B 149 " pdb="FE4 SF4 B 201 " - pdb=" SG CYS B 55 " pdb="FE3 SF4 B 201 " - pdb=" SG CYS B 54 " pdb=" SF4 F 502 " pdb="FE4 SF4 F 502 " - pdb=" SG CYS F 359 " pdb="FE2 SF4 F 502 " - pdb=" SG CYS F 365 " pdb="FE3 SF4 F 502 " - pdb=" SG CYS F 405 " pdb="FE1 SF4 F 502 " - pdb=" SG CYS F 362 " pdb=" SF4 G 801 " pdb="FE3 SF4 G 801 " - pdb=" NE2 HIS G 101 " pdb="FE4 SF4 G 801 " - pdb=" SG CYS G 108 " pdb="FE1 SF4 G 801 " - pdb=" SG CYS G 114 " pdb="FE2 SF4 G 801 " - pdb=" SG CYS G 105 " pdb=" SF4 G 802 " pdb="FE2 SF4 G 802 " - pdb=" SG CYS G 153 " pdb="FE4 SF4 G 802 " - pdb=" SG CYS G 203 " pdb="FE1 SF4 G 802 " - pdb=" SG CYS G 156 " pdb="FE3 SF4 G 802 " - pdb=" SG CYS G 159 " pdb=" SF4 I 202 " pdb="FE4 SF4 I 202 " - pdb=" SG CYS I 87 " pdb="FE2 SF4 I 202 " - pdb=" SG CYS I 116 " pdb="FE3 SF4 I 202 " - pdb=" SG CYS I 122 " pdb="FE1 SF4 I 202 " - pdb=" SG CYS I 119 " pdb=" SF4 I 203 " pdb="FE3 SF4 I 203 " - pdb=" SG CYS I 83 " pdb="FE2 SF4 I 203 " - pdb=" SG CYS I 77 " pdb="FE4 SF4 I 203 " - pdb=" SG CYS I 80 " pdb="FE1 SF4 I 203 " - pdb=" SG CYS I 126 " 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 15366 Ramachandran restraints generated. 7683 Oldfield, 0 Emsley, 7683 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14674 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 345 helices and 28 sheets defined 53.5% alpha, 4.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.71 Creating SS restraints... Processing helix chain 'A' and resid 3 through 22 Processing helix chain 'A' and resid 53 through 80 removed outlier: 3.581A pdb=" N LEU A 71 " --> pdb=" O LEU A 67 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU A 72 " --> pdb=" O GLU A 68 " (cutoff:3.500A) Proline residue: A 74 - end of helix removed outlier: 5.473A pdb=" N TRP A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 5.072A 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 42 Processing helix chain 'B' and resid 54 through 63 Processing helix chain 'B' and resid 69 through 72 Processing helix chain 'B' and resid 80 through 82 No H-bonds generated for 'chain 'B' and resid 80 through 82' Processing helix chain 'B' and resid 94 through 106 Proline residue: B 98 - end of helix Processing helix chain 'B' and resid 117 through 122 Processing helix chain 'B' and resid 124 through 126 No H-bonds generated for 'chain 'B' and resid 124 through 126' Processing helix chain 'B' and resid 136 through 138 No H-bonds generated for 'chain 'B' and resid 136 through 138' Processing helix chain 'B' and resid 153 through 168 Processing helix chain 'B' and resid 172 through 178 Processing helix chain 'C' and resid 16 through 32 Processing helix chain 'C' and resid 54 through 66 removed outlier: 4.774A pdb=" N ILE C 58 " --> pdb=" O ASP C 55 " (cutoff:3.500A) Proline residue: C 59 - end of helix removed outlier: 3.525A pdb=" N THR C 62 " --> pdb=" O PRO C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 138 removed outlier: 3.927A pdb=" N TRP C 129 " --> pdb=" O ALA C 126 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU C 131 " --> pdb=" O ASN C 128 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TRP C 135 " --> pdb=" O ARG C 132 " (cutoff:3.500A) removed outlier: 3.857A 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: 3.780A pdb=" N GLU D 92 " --> pdb=" O GLU D 88 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N TYR D 93 " --> pdb=" O LYS D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 104 Processing helix chain 'D' and resid 111 through 126 Processing helix chain 'D' and resid 132 through 161 Processing helix chain 'D' and resid 165 through 185 removed outlier: 3.603A pdb=" N GLU D 172 " --> pdb=" O PHE D 168 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLU D 173 " --> pdb=" O TRP D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 229 removed outlier: 3.782A pdb=" N ASN D 217 " --> pdb=" O GLU D 213 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N SER D 219 " --> pdb=" O SER D 215 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N LEU D 220 " --> pdb=" O LYS D 216 " (cutoff:3.500A) removed outlier: 3.630A 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: 4.476A pdb=" N GLY D 262 " --> pdb=" O MET D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 272 No H-bonds generated for 'chain 'D' and resid 269 through 272' Processing helix chain 'D' and resid 278 through 280 No H-bonds generated for 'chain 'D' and resid 278 through 280' Processing helix chain 'D' and resid 293 through 317 Processing helix chain 'D' and resid 335 through 338 No H-bonds generated for 'chain 'D' and resid 335 through 338' Processing helix chain 'D' and resid 342 through 351 Processing helix chain 'D' and resid 394 through 405 removed outlier: 3.527A pdb=" N LEU D 402 " --> pdb=" O HIS D 398 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N ASP D 403 " --> pdb=" O LEU D 399 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N LYS D 404 " --> pdb=" O ALA D 400 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 421 removed outlier: 4.119A pdb=" N VAL D 415 " --> pdb=" O LEU D 411 " (cutoff:3.500A) removed outlier: 3.605A 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: 3.557A pdb=" N ASN E 37 " --> pdb=" O ALA E 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 58 removed outlier: 4.512A pdb=" N LEU E 48 " --> pdb=" O ALA E 45 " (cutoff:3.500A) Proline residue: E 49 - end of helix removed outlier: 3.529A pdb=" N ASP E 52 " --> pdb=" O PRO E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 73 Processing helix chain 'E' and resid 77 through 86 removed outlier: 3.584A pdb=" N VAL E 83 " --> pdb=" O ARG E 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 111 removed outlier: 3.516A pdb=" N ARG E 111 " --> pdb=" O PRO E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 113 through 124 Processing helix chain 'E' and resid 148 through 150 No H-bonds generated for 'chain 'E' and resid 148 through 150' Processing helix chain 'E' and resid 166 through 177 Processing helix chain 'F' and resid 17 through 19 No H-bonds generated for 'chain 'F' and resid 17 through 19' Processing helix chain 'F' and resid 33 through 39 Processing helix chain 'F' and resid 45 through 51 Processing helix chain 'F' and resid 53 through 63 Processing helix chain 'F' and resid 75 through 82 removed outlier: 3.633A pdb=" N PHE F 81 " --> pdb=" O LEU F 77 " (cutoff:3.500A) removed outlier: 4.597A 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 283 Processing helix chain 'F' and resid 291 through 293 No H-bonds generated for 'chain 'F' and resid 291 through 293' Processing helix chain 'F' and resid 309 through 312 No H-bonds generated for 'chain 'F' and resid 309 through 312' Processing helix chain 'F' and resid 319 through 324 Processing helix chain 'F' and resid 343 through 357 Processing helix chain 'F' and resid 363 through 381 removed outlier: 4.282A pdb=" N ASP F 370 " --> pdb=" O ARG F 366 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ARG F 381 " --> pdb=" O ALA F 377 " (cutoff:3.500A) Processing helix chain 'F' and resid 386 through 399 removed outlier: 3.606A pdb=" N ASP F 390 " --> pdb=" O ALA F 387 " (cutoff:3.500A) Processing helix chain 'F' and resid 407 through 436 Proline residue: F 414 - end of helix removed outlier: 3.570A 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 32 removed outlier: 3.572A pdb=" N LYS G 32 " --> pdb=" O GLN G 28 " (cutoff:3.500A) Processing helix chain 'G' and resid 84 through 99 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: 3.589A 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: 5.070A pdb=" N TYR G 271 " --> pdb=" O THR G 267 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ASP G 272 " --> pdb=" O ARG G 268 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N GLY G 273 " --> pdb=" O PHE G 269 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N LEU G 274 " --> pdb=" O ALA G 270 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N LYS G 275 " --> pdb=" O TYR G 271 " (cutoff:3.500A) Processing helix chain 'G' and resid 296 through 309 removed outlier: 3.685A pdb=" N SER G 309 " --> pdb=" O GLY G 305 " (cutoff:3.500A) Processing helix chain 'G' and resid 312 through 314 No H-bonds generated for 'chain 'G' and resid 312 through 314' Processing helix chain 'G' and resid 325 through 337 Processing helix chain 'G' and resid 359 through 362 Processing helix chain 'G' and resid 369 through 373 Processing helix chain 'G' and resid 384 through 387 No H-bonds generated for 'chain 'G' and resid 384 through 387' Processing helix chain 'G' and resid 389 through 401 Processing helix chain 'G' and resid 426 through 434 Processing helix chain 'G' and resid 438 through 445 Processing helix chain 'G' and resid 457 through 459 No H-bonds generated for 'chain 'G' and resid 457 through 459' Processing helix chain 'G' and resid 463 through 479 Processing helix chain 'G' and resid 499 through 504 Processing helix chain 'G' and resid 512 through 516 Processing helix chain 'G' and resid 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 650 Processing helix chain 'G' and resid 668 through 670 No H-bonds generated for 'chain 'G' and resid 668 through 670' Processing helix chain 'G' and resid 676 through 680 Processing helix chain 'G' and resid 682 through 692 Processing helix chain 'H' and resid 3 through 32 Proline residue: H 12 - end of helix removed outlier: 3.924A pdb=" N LEU H 22 " --> pdb=" O ALA H 18 " (cutoff:3.500A) Processing helix chain 'H' and resid 42 through 44 No H-bonds generated for 'chain 'H' and resid 42 through 44' Processing helix chain 'H' and resid 47 through 56 Processing helix chain 'H' and resid 68 through 86 removed outlier: 3.611A pdb=" N LEU H 73 " --> pdb=" O SER H 69 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA H 74 " --> pdb=" O MET H 70 " (cutoff:3.500A) Proline residue: H 75 - end of helix removed outlier: 4.258A pdb=" N TRP H 86 " --> pdb=" O ALA H 82 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 123 removed outlier: 3.709A pdb=" N LEU H 111 " --> pdb=" O ALA H 107 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA H 112 " --> pdb=" O MET H 108 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N VAL H 113 " --> pdb=" O SER H 109 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N TYR H 114 " --> pdb=" O SER H 110 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N SER H 115 " --> pdb=" O LEU H 111 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ILE H 116 " --> pdb=" O ALA H 112 " (cutoff:3.500A) Processing helix chain 'H' and resid 126 through 157 removed outlier: 4.058A pdb=" N THR H 145 " --> pdb=" O SER H 141 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU H 146 " --> pdb=" O TYR H 142 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N MET H 156 " --> pdb=" O SER H 152 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER H 157 " --> pdb=" O VAL H 153 " (cutoff:3.500A) Processing helix chain 'H' and resid 162 through 168 removed outlier: 3.935A pdb=" N ILE H 166 " --> pdb=" O LEU H 162 " (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 removed outlier: 3.570A pdb=" N MET H 184 " --> pdb=" O PRO H 180 " (cutoff:3.500A) Processing helix chain 'H' and resid 200 through 205 Processing helix chain 'H' and resid 218 through 242 Processing helix chain 'H' and resid 252 through 274 removed outlier: 3.614A pdb=" N LEU H 271 " --> pdb=" O THR H 267 " (cutoff:3.500A) Processing helix chain 'H' and resid 282 through 290 removed outlier: 3.535A pdb=" N LEU H 289 " --> pdb=" O LEU H 285 " (cutoff:3.500A) 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 41 Processing helix chain 'I' and resid 82 through 86 Processing helix chain 'I' and resid 121 through 125 Processing helix chain 'I' and resid 145 through 147 No H-bonds generated for 'chain 'I' and resid 145 through 147' Processing helix chain 'I' and resid 151 through 175 removed outlier: 5.538A pdb=" N ALA I 163 " --> pdb=" O ASP I 159 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N GLU I 164 " --> pdb=" O LYS I 160 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA I 167 " --> pdb=" O ALA I 163 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N LEU I 174 " --> pdb=" O GLN I 170 " (cutoff:3.500A) removed outlier: 6.142A 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: 3.814A pdb=" N PHE J 47 " --> pdb=" O ILE J 43 " (cutoff:3.500A) Processing helix chain 'J' and resid 50 through 59 removed outlier: 3.568A pdb=" N PHE J 57 " --> pdb=" O GLY J 53 " (cutoff:3.500A) Processing helix chain 'J' and resid 64 through 74 Processing helix chain 'J' and resid 138 through 147 removed outlier: 3.954A pdb=" N LEU J 146 " --> pdb=" O GLY J 142 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N TYR J 147 " --> pdb=" O ILE J 143 " (cutoff:3.500A) Processing helix chain 'J' and resid 151 through 171 Processing helix chain 'K' and resid 3 through 21 Processing helix chain 'K' and resid 26 through 51 Processing helix chain 'K' and resid 54 through 85 removed outlier: 3.820A pdb=" N MET K 58 " --> pdb=" O LEU K 55 " (cutoff:3.500A) Proline residue: K 60 - end of helix removed outlier: 3.615A pdb=" N PHE K 66 " --> pdb=" O LEU K 63 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU K 70 " --> pdb=" O ALA K 67 " (cutoff:3.500A) Processing helix chain 'L' and resid 3 through 23 removed outlier: 3.674A pdb=" N THR L 11 " --> pdb=" O LEU L 7 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LEU L 12 " --> pdb=" O SER L 8 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR L 16 " --> pdb=" O LEU L 12 " (cutoff:3.500A) Proline residue: L 18 - end of helix removed outlier: 3.512A pdb=" N MET L 22 " --> pdb=" O PRO L 18 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N SER L 23 " --> pdb=" O ILE L 19 " (cutoff:3.500A) Processing helix chain 'L' and resid 29 through 57 removed outlier: 3.953A pdb=" N TYR L 32 " --> pdb=" O PRO L 29 " (cutoff:3.500A) Proline residue: L 33 - end of helix removed outlier: 3.647A pdb=" N THR L 46 " --> pdb=" O ALA L 43 " (cutoff:3.500A) Proline residue: L 50 - end of helix removed outlier: 3.745A 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: 3.763A pdb=" N TRP L 106 " --> pdb=" O GLU L 102 " (cutoff:3.500A) Processing helix chain 'L' and resid 114 through 133 removed outlier: 3.566A pdb=" N MET L 128 " --> pdb=" O PHE L 124 " (cutoff:3.500A) Processing helix chain 'L' and resid 137 through 155 removed outlier: 3.705A pdb=" N GLY L 148 " --> pdb=" O TRP L 144 " (cutoff:3.500A) Processing helix chain 'L' and resid 162 through 192 removed outlier: 4.131A 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: 4.155A pdb=" N MET L 237 " --> pdb=" O LEU L 233 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N GLU L 238 " --> pdb=" O PRO L 234 " (cutoff:3.500A) Processing helix chain 'L' and resid 241 through 247 Processing helix chain 'L' and resid 252 through 262 removed outlier: 4.332A pdb=" N GLY L 256 " --> pdb=" O MET L 252 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ILE L 257 " --> pdb=" O VAL L 253 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU L 260 " --> pdb=" O GLY L 256 " (cutoff:3.500A) Processing helix chain 'L' and resid 264 through 269 removed outlier: 4.658A pdb=" N ASN L 269 " --> pdb=" O PRO L 265 " (cutoff:3.500A) Processing helix chain 'L' and resid 271 through 294 removed outlier: 3.502A pdb=" N LEU L 293 " --> pdb=" O ALA L 289 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N THR L 294 " --> pdb=" O MET L 290 " (cutoff:3.500A) Processing helix chain 'L' and resid 298 through 318 Processing helix chain 'L' and resid 322 through 349 removed outlier: 3.889A pdb=" N PHE L 334 " --> pdb=" O CYS L 330 " (cutoff:3.500A) removed outlier: 3.757A 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: 3.710A pdb=" N TYR L 390 " --> pdb=" O THR L 387 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER L 391 " --> pdb=" O GLY L 388 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LYS L 392 " --> pdb=" O PHE L 389 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N ASP L 393 " --> pdb=" O TYR L 390 " (cutoff:3.500A) Processing helix chain 'L' and resid 406 through 431 removed outlier: 3.599A pdb=" N ALA L 420 " --> pdb=" O THR L 416 " (cutoff:3.500A) Processing helix chain 'L' and resid 448 through 469 removed outlier: 3.578A pdb=" N LEU L 457 " --> pdb=" O SER L 453 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N GLY L 465 " --> pdb=" O SER L 461 " (cutoff:3.500A) removed outlier: 5.247A 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: 3.568A pdb=" N GLU L 503 " --> pdb=" O ILE L 499 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE L 504 " --> pdb=" O LEU L 500 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR L 508 " --> pdb=" O ILE L 504 " (cutoff:3.500A) removed outlier: 4.238A 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: 3.540A pdb=" N MET L 533 " --> pdb=" O PRO L 530 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N HIS L 534 " --> pdb=" O THR L 531 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU L 536 " --> pdb=" O MET L 533 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N ALA L 537 " --> pdb=" O HIS L 534 " (cutoff:3.500A) Proline residue: L 538 - end of helix removed outlier: 3.934A pdb=" N SER L 543 " --> pdb=" O MET L 540 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLN L 546 " --> pdb=" O SER L 543 " (cutoff:3.500A) Processing helix chain 'M' and resid 5 through 17 removed outlier: 4.205A 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: 4.090A pdb=" N ILE M 23 " --> pdb=" O ASN M 20 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N TRP M 24 " --> pdb=" O ASN M 21 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASN M 26 " --> pdb=" O ILE M 23 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N SER M 27 " --> pdb=" O TRP M 24 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N THR M 28 " --> pdb=" O VAL M 25 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N HIS M 30 " --> pdb=" O SER M 27 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER M 31 " --> pdb=" O THR M 28 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE M 34 " --> pdb=" O SER M 31 " (cutoff:3.500A) Processing helix chain 'M' and resid 60 through 80 Proline residue: M 64 - end of helix removed outlier: 3.658A pdb=" N LEU M 73 " --> pdb=" O THR M 69 " (cutoff:3.500A) Proline residue: M 74 - end of helix Processing helix chain 'M' and resid 89 through 111 removed outlier: 3.560A pdb=" N THR M 111 " --> pdb=" O ILE M 107 " (cutoff:3.500A) Processing helix chain 'M' and resid 115 through 135 removed outlier: 4.821A pdb=" N LEU M 126 " --> pdb=" O PHE M 122 " (cutoff:3.500A) removed outlier: 4.164A 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: 3.844A pdb=" N TYR M 181 " --> pdb=" O LEU M 177 " (cutoff:3.500A) Processing helix chain 'M' and resid 190 through 206 removed outlier: 4.692A pdb=" N ALA M 202 " --> pdb=" O ALA M 198 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N PHE M 203 " --> pdb=" O CYS M 199 " (cutoff:3.500A) Processing helix chain 'M' and resid 214 through 222 removed outlier: 3.767A 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: 4.087A pdb=" N GLY M 239 " --> pdb=" O LEU M 235 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N LEU M 248 " --> pdb=" O LEU M 244 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N ILE M 249 " --> pdb=" O ARG M 245 " (cutoff:3.500A) Processing helix chain 'M' and resid 253 through 257 removed outlier: 3.860A pdb=" N MET M 257 " --> pdb=" O THR M 254 " (cutoff:3.500A) Processing helix chain 'M' and resid 259 through 278 removed outlier: 3.804A pdb=" N ILE M 270 " --> pdb=" O LEU M 266 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER M 273 " --> pdb=" O MET M 269 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU M 277 " --> pdb=" O SER M 273 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ARG M 278 " --> pdb=" O SER M 274 " (cutoff:3.500A) Processing helix chain 'M' and resid 282 through 303 removed outlier: 3.793A pdb=" N LEU M 296 " --> pdb=" O SER M 292 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL M 297 " --> pdb=" O HIS M 293 " (cutoff:3.500A) Processing helix chain 'M' and resid 306 through 337 removed outlier: 3.512A pdb=" N ASN M 333 " --> pdb=" O LEU M 329 " (cutoff:3.500A) removed outlier: 3.683A 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 removed outlier: 3.613A pdb=" N SER M 387 " --> pdb=" O MET M 383 " (cutoff:3.500A) Processing helix chain 'M' and resid 390 through 415 removed outlier: 3.543A pdb=" N MET M 396 " --> pdb=" O ILE M 393 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR M 403 " --> pdb=" O MET M 400 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N TYR M 406 " --> pdb=" O THR M 403 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER M 407 " --> pdb=" O ALA M 404 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU M 408 " --> pdb=" O LEU M 405 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N TYR M 409 " --> pdb=" O TYR M 406 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N MET M 413 " --> pdb=" O MET M 410 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N THR M 414 " --> pdb=" O LEU M 411 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLN M 415 " --> pdb=" O ILE M 412 " (cutoff:3.500A) Processing helix chain 'M' and resid 431 through 448 removed outlier: 3.519A pdb=" N HIS M 440 " --> pdb=" O LEU M 436 " (cutoff:3.500A) Proline residue: M 443 - end of helix removed outlier: 4.074A 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 45 removed outlier: 3.558A pdb=" N ILE N 41 " --> pdb=" O MET N 37 " (cutoff:3.500A) Proline residue: N 42 - end of helix Processing helix chain 'N' and resid 50 through 81 Processing helix chain 'N' and resid 92 through 106 Processing helix chain 'N' and resid 113 through 120 removed outlier: 3.923A 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: 4.430A pdb=" N ALA N 137 " --> pdb=" O GLN N 134 " (cutoff:3.500A) Proline residue: N 138 - end of helix removed outlier: 3.839A pdb=" N TYR N 143 " --> pdb=" O SER N 140 " (cutoff:3.500A) removed outlier: 4.726A 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 192 Processing helix chain 'N' and resid 198 through 222 Processing helix chain 'N' and resid 227 through 236 removed outlier: 3.556A pdb=" N SER N 231 " --> pdb=" O THR N 227 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N HIS N 232 " --> pdb=" O LEU N 228 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N THR N 233 " --> pdb=" O SER N 229 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N TRP N 234 " --> pdb=" O LEU N 230 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N ASN N 235 " --> pdb=" O SER N 231 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LYS N 236 " --> pdb=" O HIS N 232 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 227 through 236' Processing helix chain 'N' and resid 238 through 252 Processing helix chain 'N' and resid 258 through 272 Proline residue: N 262 - end of helix Processing helix chain 'N' and resid 277 through 301 Processing helix chain 'N' and resid 309 through 316 Processing helix chain 'N' and resid 326 through 332 Processing helix chain 'N' and resid 337 through 346 Proline residue: N 341 - end of helix Processing helix chain 'O' and resid 5 through 10 Processing helix chain 'O' and resid 14 through 16 No H-bonds generated for 'chain 'O' and resid 14 through 16' Processing helix chain 'O' and resid 35 through 46 Processing helix chain 'O' and resid 72 through 74 No H-bonds generated for 'chain 'O' and resid 72 through 74' Processing helix chain 'O' and resid 81 through 84 No H-bonds generated for 'chain 'O' and resid 81 through 84' Processing helix chain 'O' and resid 92 through 117 Processing helix chain 'O' and resid 131 through 140 removed outlier: 3.977A pdb=" N GLU O 136 " --> pdb=" O VAL O 133 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG O 140 " --> pdb=" O ALA O 137 " (cutoff:3.500A) Processing helix chain 'O' and resid 146 through 159 removed outlier: 3.557A pdb=" N ASP O 150 " --> pdb=" O LYS O 146 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASN O 153 " --> pdb=" O VAL O 149 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL O 155 " --> pdb=" O HIS O 151 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL O 158 " --> pdb=" O GLN O 154 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR O 159 " --> pdb=" O VAL O 155 " (cutoff:3.500A) Processing helix chain 'O' and resid 176 through 186 Processing helix chain 'O' and resid 191 through 193 No H-bonds generated for 'chain 'O' and resid 191 through 193' Processing helix chain 'O' and resid 196 through 207 Processing helix chain 'O' and resid 209 through 217 removed outlier: 3.750A pdb=" N GLU O 213 " --> pdb=" O THR O 209 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N MET O 214 " --> pdb=" O PHE O 210 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU O 216 " --> pdb=" O PRO O 212 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS O 217 " --> pdb=" O GLU O 213 " (cutoff:3.500A) Processing helix chain 'O' and resid 225 through 229 removed outlier: 3.955A pdb=" N GLN O 229 " --> pdb=" O ALA O 225 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 225 through 229' Processing helix chain 'O' and resid 231 through 240 removed outlier: 4.110A pdb=" N ILE O 238 " --> pdb=" O VAL O 234 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TYR O 240 " --> pdb=" O GLU O 236 " (cutoff:3.500A) Processing helix chain 'O' and resid 247 through 250 Processing helix chain 'O' and resid 253 through 263 removed outlier: 3.572A pdb=" N LEU O 259 " --> pdb=" O LYS O 255 " (cutoff:3.500A) Processing helix chain 'O' and resid 266 through 269 No H-bonds generated for 'chain 'O' and resid 266 through 269' Processing helix chain 'O' and resid 272 through 274 No H-bonds generated for 'chain 'O' and resid 272 through 274' Processing helix chain 'O' and resid 286 through 298 removed outlier: 3.981A 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 40 removed outlier: 3.923A pdb=" N TYR P 33 " --> pdb=" O PHE P 29 " (cutoff:3.500A) Processing helix chain 'P' and resid 53 through 62 removed outlier: 5.099A pdb=" N HIS P 58 " --> pdb=" O ASP P 55 " (cutoff:3.500A) Proline residue: P 61 - end of helix Processing helix chain 'P' and resid 78 through 85 removed outlier: 3.753A pdb=" N ALA P 84 " --> pdb=" O SER P 80 " (cutoff:3.500A) Processing helix chain 'P' and resid 106 through 109 No H-bonds generated for 'chain 'P' and resid 106 through 109' Processing helix chain 'P' and resid 112 through 124 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 238 through 248 removed outlier: 3.514A pdb=" N PHE P 246 " --> pdb=" O VAL P 242 " (cutoff:3.500A) Processing helix chain 'P' and resid 281 through 287 Processing helix chain 'P' and resid 300 through 303 Processing helix chain 'P' and resid 310 through 321 removed outlier: 4.958A pdb=" N ILE P 315 " --> pdb=" O GLU P 311 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N GLU P 316 " --> pdb=" O LEU P 312 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N ARG P 320 " --> pdb=" O GLU P 316 " (cutoff:3.500A) removed outlier: 5.586A 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: 3.933A pdb=" N LYS Q 31 " --> pdb=" O GLU Q 28 " (cutoff:3.500A) Processing helix chain 'Q' and resid 50 through 52 No H-bonds generated for 'chain 'Q' and resid 50 through 52' Processing helix chain 'Q' and resid 89 through 99 Processing helix chain 'Q' and resid 118 through 122 Processing helix chain 'R' and resid 23 through 28 Processing helix chain 'R' and resid 40 through 46 removed outlier: 3.543A pdb=" N ALA R 45 " --> pdb=" O ILE R 41 " (cutoff:3.500A) Processing helix chain 'R' and resid 64 through 66 No H-bonds generated for 'chain 'R' and resid 64 through 66' Processing helix chain 'S' and resid 27 through 38 removed outlier: 4.893A 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 8 through 21 removed outlier: 3.535A pdb=" N LYS T 12 " --> pdb=" O LEU T 8 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASP T 13 " --> pdb=" O GLU T 9 " (cutoff:3.500A) Processing helix chain 'T' and resid 27 through 29 No H-bonds generated for 'chain 'T' and resid 27 through 29' Processing helix chain 'T' and resid 44A through 58 Processing helix chain 'T' and resid 64 through 69 removed outlier: 4.539A pdb=" N LYS T 69 " --> pdb=" O ILE T 65 " (cutoff:3.500A) Processing helix chain 'T' and resid 73 through 81 Processing helix chain 'U' and resid 8 through 20 Processing helix chain 'U' and resid 44A through 58 Processing helix chain 'U' and resid 64 through 69 removed outlier: 4.577A pdb=" N LYS U 69 " --> pdb=" O ILE U 65 " (cutoff:3.500A) Processing helix chain 'U' and resid 73 through 83 Processing helix chain 'V' and resid 19 through 36 removed outlier: 4.161A 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: 3.792A pdb=" N GLN V 95 " --> pdb=" O ARG V 91 " (cutoff:3.500A) Processing helix chain 'W' and resid 25 through 49 removed outlier: 3.504A 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: 4.137A 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: 4.675A 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 11 No H-bonds generated for 'chain 'X' and resid 9 through 11' Processing helix chain 'X' and resid 21 through 26 Processing helix chain 'X' and resid 36 through 49 Processing helix chain 'X' and resid 52 through 76 removed outlier: 3.569A pdb=" N CYS X 55 " --> pdb=" O PRO X 52 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU X 56 " --> pdb=" O ARG X 53 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N GLU X 57 " --> pdb=" O ARG X 54 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL X 62 " --> pdb=" O GLY X 59 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLN X 64 " --> pdb=" O LEU X 61 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA X 66 " --> pdb=" O ASN X 63 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N PHE X 69 " --> pdb=" O ALA X 66 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLN X 72 " --> pdb=" O PHE X 69 " (cutoff:3.500A) removed outlier: 4.155A 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 100 through 114 removed outlier: 3.626A pdb=" N ASP X 112 " --> pdb=" O GLU X 108 " (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 124 No H-bonds generated for 'chain 'Z' and resid 121 through 124' Processing helix chain 'Z' and resid 132 through 142 removed outlier: 5.389A pdb=" N PHE Z 140 " --> pdb=" O ALA Z 136 " (cutoff:3.500A) removed outlier: 5.161A 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: 3.579A pdb=" N VAL a 11 " --> pdb=" O GLY a 8 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ILE a 18 " --> pdb=" O CYS a 15 " (cutoff:3.500A) Proline residue: a 19 - end of helix removed outlier: 3.770A pdb=" N THR a 23 " --> pdb=" O GLY a 20 " (cutoff:3.500A) Processing helix chain 'a' and resid 42 through 55 Processing helix chain 'a' and resid 66 through 68 No H-bonds generated for 'chain 'a' and resid 66 through 68' Processing helix chain 'b' and resid 2 through 14 Processing helix chain 'b' and resid 16 through 34 Proline residue: b 32 - end of helix Processing helix chain 'b' and resid 38 through 47 removed outlier: 3.825A pdb=" N LEU b 42 " --> pdb=" O THR b 38 " (cutoff:3.500A) Processing helix chain 'b' and resid 78 through 82 Processing helix chain 'c' and resid 14 through 46 Processing helix chain 'd' and resid 16 through 20 Processing helix chain 'd' and resid 29 through 48 Processing helix chain 'd' and resid 58 through 96 removed outlier: 3.689A pdb=" N TYR d 74 " --> pdb=" O PHE d 70 " (cutoff:3.500A) Processing helix chain 'd' and resid 98 through 100 No H-bonds generated for 'chain 'd' and resid 98 through 100' Processing helix chain 'e' and resid 5 through 9 Processing helix chain 'e' and resid 15 through 17 No H-bonds generated for 'chain 'e' and resid 15 through 17' Processing helix chain 'e' and resid 25 through 27 No H-bonds generated for 'chain 'e' and resid 25 through 27' Processing helix chain 'e' and resid 33 through 42 Processing helix chain 'e' and resid 48 through 54 removed outlier: 4.164A pdb=" N LYS e 53 " --> pdb=" O ILE e 49 " (cutoff:3.500A) Processing helix chain 'e' and resid 56 through 67 Processing helix chain 'e' and resid 69 through 87 Processing helix chain 'f' and resid 7 through 33 removed outlier: 6.605A pdb=" N VAL f 12 " --> pdb=" O ARG f 8 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N HIS f 13 " --> pdb=" O ASP f 9 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N VAL f 14 " --> pdb=" O HIS f 10 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N LEU f 15 " --> pdb=" O TRP f 11 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N VAL f 16 " --> pdb=" O VAL f 12 " (cutoff:3.500A) Proline residue: f 17 - end of helix removed outlier: 3.568A pdb=" N ASP f 31 " --> pdb=" O ASP f 27 " (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 removed outlier: 3.586A pdb=" N MET g 58 " --> pdb=" O ASP g 54 " (cutoff:3.500A) Processing helix chain 'g' and resid 69 through 78 Processing helix chain 'g' and resid 83 through 103 removed outlier: 3.792A pdb=" N GLN g 86 " --> pdb=" O TYR g 83 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N GLU g 87 " --> pdb=" O ARG g 84 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL g 97 " --> pdb=" O GLU g 94 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS g 98 " --> pdb=" O ARG g 95 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG g 100 " --> pdb=" O VAL g 97 " (cutoff:3.500A) removed outlier: 3.686A 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: 4.167A 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: 3.844A pdb=" N TYR h 66 " --> pdb=" O HIS h 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 63 through 66' Processing helix chain 'h' and resid 70 through 79 Processing helix chain 'h' and resid 83 through 117 Processing helix chain 'h' and resid 130 through 132 No H-bonds generated for 'chain 'h' and resid 130 through 132' Processing helix chain 'i' and resid 5 through 25 removed outlier: 3.511A pdb=" N LEU i 17 " --> pdb=" O GLN i 13 " (cutoff:3.500A) Processing helix chain 'i' and resid 59 through 73 Processing helix chain 'i' and resid 75 through 87 Processing helix chain 'j' and resid 19 through 42 Processing helix chain 'j' and resid 44 through 48 Processing helix chain 'j' and resid 56 through 58 No H-bonds generated for 'chain 'j' and resid 56 through 58' Processing helix chain 'j' and resid 61 through 64 No H-bonds generated for 'chain 'j' and resid 61 through 64' Processing helix chain 'k' and resid 18 through 20 No H-bonds generated for 'chain 'k' and resid 18 through 20' Processing helix chain 'k' and resid 27 through 38 removed outlier: 3.933A pdb=" N ARG k 38 " --> pdb=" O LYS k 34 " (cutoff:3.500A) Processing helix chain 'k' and resid 49 through 52 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 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: 3.639A 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 116 Processing helix chain 'n' and resid 11 through 30 removed outlier: 3.509A pdb=" N LEU n 16 " --> pdb=" O GLN n 12 " (cutoff:3.500A) Processing helix chain 'n' and resid 33 through 50 removed outlier: 3.520A pdb=" N CYS n 41 " --> pdb=" O ARG n 37 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N HIS n 50 " --> pdb=" O ARG n 46 " (cutoff:3.500A) Processing helix chain 'n' and resid 56 through 73 Processing helix chain 'n' and resid 94 through 96 No H-bonds generated for 'chain 'n' and resid 94 through 96' Processing helix chain 'n' and resid 100 through 105 Processing helix chain 'n' and resid 108 through 113 removed outlier: 3.941A pdb=" N MET n 113 " --> pdb=" O SER n 109 " (cutoff:3.500A) Processing helix chain 'n' and resid 115 through 142 removed outlier: 4.450A pdb=" N GLU n 133 " --> pdb=" O ARG n 129 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N ARG n 134 " --> pdb=" O GLU n 130 " (cutoff:3.500A) Processing helix chain 'n' and resid 167 through 170 No H-bonds generated for 'chain 'n' and resid 167 through 170' Processing helix chain 'o' and resid 2 through 8 Processing helix chain 'o' and resid 12 through 14 No H-bonds generated for 'chain 'o' and resid 12 through 14' Processing helix chain 'o' and resid 42 through 48 Processing helix chain 'o' and resid 52 through 54 No H-bonds generated for 'chain 'o' and resid 52 through 54' Processing helix chain 'o' and resid 59 through 72 Processing helix chain 'o' and resid 80 through 119 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: 3.746A pdb=" N GLU p 86 " --> pdb=" O LEU p 82 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N GLU p 118 " --> pdb=" O GLN p 114 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N SER p 119 " --> pdb=" O ARG p 115 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N HIS p 120 " --> pdb=" O GLU p 116 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N ARG p 121 " --> pdb=" O GLY p 117 " (cutoff:3.500A) removed outlier: 6.349A 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 removed outlier: 3.503A pdb=" N LYS p 170 " --> pdb=" O ARG p 166 " (cutoff:3.500A) Processing helix chain 'q' and resid 4 through 17 removed outlier: 3.758A pdb=" N VAL q 14 " --> pdb=" O GLY q 10 " (cutoff:3.500A) Processing helix chain 'q' and resid 20 through 30 Processing helix chain 'q' and resid 79 through 81 No H-bonds generated for 'chain 'q' and resid 79 through 81' Processing helix chain 'q' and resid 84 through 90 removed outlier: 4.234A pdb=" N TRP q 89 " --> pdb=" O GLU q 85 " (cutoff:3.500A) Processing helix chain 'r' and resid 5 through 15 Processing helix chain 'r' and resid 19 through 22 Processing helix chain 'r' and resid 53 through 55 No H-bonds generated for 'chain 'r' and resid 53 through 55' Processing helix chain 'r' and resid 59 through 61 No H-bonds generated for 'chain 'r' and resid 59 through 61' Processing helix chain 's' and resid 42 through 44 No H-bonds generated for 'chain 's' and resid 42 through 44' Processing helix chain 's' and resid 50 through 60 removed outlier: 4.666A pdb=" N LYS s 60 " --> pdb=" O LEU s 56 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.273A pdb=" N VAL B 85 " --> pdb=" O MET B 48 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N PHE B 50 " --> pdb=" O VAL B 85 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ILE B 87 " --> pdb=" O PHE B 50 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N TYR B 112 " --> pdb=" O MET B 86 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N VAL B 88 " --> pdb=" O TYR B 112 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N VAL B 114 " --> pdb=" O VAL B 88 " (cutoff:3.500A) removed outlier: 6.352A 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: 6.692A 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: 6.663A pdb=" N VAL C 93 " --> pdb=" O LEU C 78 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ALA C 80 " --> pdb=" O GLU C 91 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N GLU C 91 " --> pdb=" O ALA C 80 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N LEU C 48 " --> pdb=" O ARG C 104 " (cutoff:3.500A) removed outlier: 4.827A 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 49 removed outlier: 4.273A pdb=" N LEU D 64 " --> pdb=" O LEU D 49 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N SER D 69 " --> pdb=" O VAL D 73 " (cutoff:3.500A) removed outlier: 5.495A 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: 6.655A pdb=" N TYR E 98 " --> pdb=" O THR E 138 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N ILE E 140 " --> pdb=" O TYR E 98 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ILE E 100 " --> pdb=" O ILE E 140 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N VAL E 142 " --> pdb=" O ILE E 100 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N VAL E 102 " --> pdb=" O VAL E 142 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'F' and resid 220 through 224 removed outlier: 7.010A pdb=" N TYR F 92 " --> pdb=" O THR F 221 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N ALA F 223 " --> pdb=" O TYR F 92 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N VAL F 94 " --> pdb=" O ALA F 223 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ALA F 133 " --> pdb=" O LEU F 93 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N VAL F 95 " --> pdb=" O ALA F 133 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N TYR F 135 " --> pdb=" O VAL F 95 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N ALA F 97 " --> pdb=" O TYR F 135 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N TYR F 137 " --> pdb=" O ALA F 97 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N ASP F 174 " --> pdb=" O ALA F 134 " (cutoff:3.500A) removed outlier: 7.456A 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: 7.556A pdb=" N ILE F 138 " --> pdb=" O PHE F 176 " (cutoff:3.500A) removed outlier: 6.281A 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 8 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: 3.550A pdb=" N ARG G 249 " --> pdb=" O SER G 241 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ARG G 243 " --> pdb=" O VAL G 247 " (cutoff:3.500A) removed outlier: 5.496A 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: 8.501A pdb=" N CYS G 344 " --> pdb=" O VAL G 315 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ALA G 317 " --> pdb=" O CYS G 344 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N MET G 521 " --> pdb=" O ALA G 316 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N ILE G 318 " --> pdb=" O MET G 521 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N PHE G 523 " --> pdb=" O ILE G 318 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N PHE G 542 " --> pdb=" O LEU G 522 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N LEU G 524 " --> pdb=" O PHE G 542 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N VAL G 544 " --> pdb=" O LEU G 524 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N VAL G 559 " --> pdb=" O TYR G 545 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N GLY G 547 " --> pdb=" O VAL G 559 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N LEU G 561 " --> pdb=" O GLY G 547 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'G' and resid 490 through 493 removed outlier: 8.103A pdb=" N ASN G 491 " --> pdb=" O PRO G 449 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N VAL G 451 " --> pdb=" O ASN G 491 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N LEU G 493 " --> pdb=" O VAL G 451 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LEU G 453 " --> pdb=" O LEU G 493 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N VAL G 376 " --> pdb=" O MET G 450 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N ILE G 452 " --> pdb=" O VAL G 376 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N LEU G 378 " --> pdb=" O ILE G 452 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N GLY G 454 " --> pdb=" O LEU G 378 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N VAL G 380 " --> pdb=" O GLY G 454 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N LYS G 405 " --> pdb=" O VAL G 377 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N LEU G 379 " --> pdb=" O LYS G 405 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ALA G 407 " --> pdb=" O LEU G 379 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ASP G 420 " --> pdb=" O LEU G 408 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'G' and resid 572 through 574 Processing sheet with id= Q, first strand: chain 'I' and resid 65 through 67 Processing sheet with id= R, first strand: chain 'I' and resid 92 through 98 removed outlier: 5.961A pdb=" N GLU I 97 " --> pdb=" O THR I 106 " (cutoff:3.500A) removed outlier: 5.284A 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: 6.607A 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: 6.308A pdb=" N VAL O 122 " --> pdb=" O ILE O 25 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N VAL O 27 " --> pdb=" O VAL O 122 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N LEU O 124 " --> pdb=" O VAL O 27 " (cutoff:3.500A) removed outlier: 8.646A pdb=" N GLY O 29 " --> pdb=" O LEU O 124 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N LYS O 49 " --> pdb=" O VAL O 123 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N GLU O 125 " --> pdb=" O LYS O 49 " (cutoff:3.500A) removed outlier: 8.109A 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: 6.560A pdb=" N ILE P 165 " --> pdb=" O PHE P 228 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N PHE P 230 " --> pdb=" O ILE P 165 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N LYS P 167 " --> pdb=" O PHE P 230 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE P 132 " --> pdb=" O ASN P 93 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N GLN P 44 " --> pdb=" O ALA P 21 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N VAL P 23 " --> pdb=" O GLN P 44 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ILE P 46 " --> pdb=" O VAL P 23 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'Q' and resid 102 through 105 Processing sheet with id= X, first strand: chain 'Q' and resid 64 through 66 Processing sheet with id= Y, first strand: chain 'R' and resid 50 through 52 Processing sheet with id= Z, first strand: chain 'R' and resid 56 through 59 Processing sheet with id= AA, first strand: chain 'S' and resid 51 through 56 removed outlier: 3.538A pdb=" N LEU S 22 " --> pdb=" O ARG S 55 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ARG S 67 " --> pdb=" O ARG S 16 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ILE S 18 " --> pdb=" O TRP S 65 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N TRP S 65 " --> pdb=" O ILE S 18 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ILE S 20 " --> pdb=" O LYS S 63 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N LYS S 63 " --> pdb=" O ILE S 20 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'q' and resid 60 through 63 removed outlier: 6.655A pdb=" N GLU q 50 " --> pdb=" O LEU q 38 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N LEU q 38 " --> pdb=" O GLU q 50 " (cutoff:3.500A) 2710 hydrogen bonds defined for protein. 7329 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: 21.95 Time building geometry restraints manager: 23.29 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: 26528 1.40 - 1.63: 38490 1.63 - 1.85: 801 1.85 - 2.08: 0 2.08 - 2.31: 82 Bond restraints: 65901 Sorted by residual: bond pdb=" C5 GTP O1202 " pdb=" N7 GTP O1202 " ideal model delta sigma weight residual 1.350 1.520 -0.170 2.00e-02 2.50e+03 7.23e+01 bond pdb=" C6 GTP O1202 " pdb=" O6 GTP O1202 " ideal model delta sigma weight residual 1.230 1.396 -0.166 2.00e-02 2.50e+03 6.91e+01 bond pdb=" C SAC i 1 " pdb=" O SAC i 1 " ideal model delta sigma weight residual 1.231 1.364 -0.133 2.00e-02 2.50e+03 4.40e+01 bond pdb=" CB7 CDL q 201 " pdb=" OB8 CDL q 201 " ideal model delta sigma weight residual 1.334 1.404 -0.070 1.10e-02 8.26e+03 4.08e+01 bond pdb=" C 2MR D 85 " pdb=" O 2MR D 85 " ideal model delta sigma weight residual 1.231 1.353 -0.122 2.00e-02 2.50e+03 3.73e+01 ... (remaining 65896 not shown) Histogram of bond angle deviations from ideal: 72.63 - 84.92: 76 84.92 - 97.21: 1 97.21 - 109.51: 7368 109.51 - 121.80: 69083 121.80 - 134.10: 12624 Bond angle restraints: 89152 Sorted by residual: angle pdb=" C51 CDL h1001 " pdb=" CB5 CDL h1001 " pdb=" OB6 CDL h1001 " ideal model delta sigma weight residual 111.33 121.90 -10.57 1.32e+00 5.72e-01 6.40e+01 angle pdb=" C51 CDL X 201 " pdb=" CB5 CDL X 201 " pdb=" OB6 CDL X 201 " ideal model delta sigma weight residual 111.33 120.72 -9.39 1.32e+00 5.72e-01 5.05e+01 angle pdb=" C11 CDL h1001 " pdb=" CA5 CDL h1001 " pdb=" OA6 CDL h1001 " ideal model delta sigma weight residual 111.33 120.27 -8.94 1.32e+00 5.72e-01 4.57e+01 angle pdb=" C51 CDL N1302 " pdb=" CB5 CDL N1302 " pdb=" OB6 CDL N1302 " ideal model delta sigma weight residual 111.33 120.26 -8.93 1.32e+00 5.72e-01 4.57e+01 angle pdb=" C11 CDL q 201 " pdb=" CA5 CDL q 201 " pdb=" OA6 CDL q 201 " ideal model delta sigma weight residual 111.33 120.17 -8.84 1.32e+00 5.72e-01 4.47e+01 ... (remaining 89147 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.64: 39007 34.64 - 69.29: 1048 69.29 - 103.93: 167 103.93 - 138.57: 38 138.57 - 173.21: 5 Dihedral angle restraints: 40265 sinusoidal: 17522 harmonic: 22743 Sorted by residual: dihedral pdb=" C10 FMN F 501 " pdb=" C1' FMN F 501 " pdb=" N10 FMN F 501 " pdb=" C2' FMN F 501 " ideal model delta sinusoidal sigma weight residual 257.59 84.38 173.21 1 2.00e+01 2.50e-03 4.78e+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 -82.56 157.82 1 2.00e+01 2.50e-03 4.62e+01 dihedral pdb=" C8 GTP O1202 " pdb=" C1' GTP O1202 " pdb=" N9 GTP O1202 " pdb=" O4' GTP O1202 " ideal model delta sinusoidal sigma weight residual 104.59 -29.24 133.83 1 2.00e+01 2.50e-03 4.06e+01 ... (remaining 40262 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.268: 9720 4.268 - 8.535: 0 8.535 - 12.803: 0 12.803 - 17.071: 0 17.071 - 21.338: 16 Chirality restraints: 9736 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 10.78 -21.34 2.00e-01 2.50e+01 1.14e+04 chirality pdb="FE2 SF4 G 801 " pdb=" S1 SF4 G 801 " pdb=" S3 SF4 G 801 " pdb=" S4 SF4 G 801 " both_signs ideal model delta sigma weight residual False 10.55 -10.74 21.29 2.00e-01 2.50e+01 1.13e+04 chirality pdb="FE3 SF4 I 202 " pdb=" S1 SF4 I 202 " pdb=" S2 SF4 I 202 " pdb=" S4 SF4 I 202 " both_signs ideal model delta sigma weight residual False -10.55 10.73 -21.29 2.00e-01 2.50e+01 1.13e+04 ... (remaining 9733 not shown) Planarity restraints: 11115 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C08 I49 N1305 " 0.147 2.00e-02 2.50e+03 5.69e-01 6.47e+03 pdb=" C14 I49 N1305 " -0.070 2.00e-02 2.50e+03 pdb=" C15 I49 N1305 " -0.007 2.00e-02 2.50e+03 pdb=" N01 I49 N1305 " -0.017 2.00e-02 2.50e+03 pdb=" N02 I49 N1305 " -0.230 2.00e-02 2.50e+03 pdb=" N03 I49 N1305 " 0.007 2.00e-02 2.50e+03 pdb=" N04 I49 N1305 " -1.031 2.00e-02 2.50e+03 pdb=" N05 I49 N1305 " 1.202 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C08 I49 H 403 " 0.493 2.00e-02 2.50e+03 5.33e-01 5.68e+03 pdb=" C14 I49 H 403 " -0.259 2.00e-02 2.50e+03 pdb=" C15 I49 H 403 " -0.049 2.00e-02 2.50e+03 pdb=" N01 I49 H 403 " -0.035 2.00e-02 2.50e+03 pdb=" N02 I49 H 403 " -0.759 2.00e-02 2.50e+03 pdb=" N03 I49 H 403 " -0.071 2.00e-02 2.50e+03 pdb=" N04 I49 H 403 " -0.417 2.00e-02 2.50e+03 pdb=" N05 I49 H 403 " 1.097 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SAC i 1 " 0.071 2.00e-02 2.50e+03 1.37e-01 1.87e+02 pdb=" C SAC i 1 " -0.236 2.00e-02 2.50e+03 pdb=" O SAC i 1 " 0.080 2.00e-02 2.50e+03 pdb=" N GLY i 2 " 0.086 2.00e-02 2.50e+03 ... (remaining 11112 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.52: 573 2.52 - 3.18: 58862 3.18 - 3.83: 134437 3.83 - 4.49: 199672 4.49 - 5.14: 303923 Nonbonded interactions: 697467 Sorted by model distance: nonbonded pdb=" O HOH H 518 " pdb=" O HOH q 322 " model vdw 1.869 2.440 nonbonded pdb=" OE2 GLU I 75 " pdb=" O HOH I 301 " model vdw 1.910 2.440 nonbonded pdb=" O GLN l 132 " pdb=" O HOH l 301 " model vdw 1.932 2.440 nonbonded pdb=" O SER C 201 " pdb=" O HOH C 301 " model vdw 1.944 2.440 nonbonded pdb=" OH TYR O 108 " pdb=" O LEU O 164 " model vdw 1.946 2.440 ... (remaining 697462 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'T' selection = (chain 'U' and (resid 7 through 82 or resid 101)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 13.610 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: 58.200 Check model and map are aligned: 0.760 Set scattering table: 0.540 Process input model: 158.470 Find NCS groups from input model: 2.260 Set up NCS constraints: 0.280 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:12.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 247.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.170 65901 Z= 0.511 Angle : 0.808 16.873 89152 Z= 0.380 Chirality : 0.863 21.338 9736 Planarity : 0.008 0.569 11115 Dihedral : 16.789 173.213 25576 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.19 % Favored : 96.80 % Rotamer: Outliers : 0.03 % Allowed : 0.10 % Favored : 99.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.68 % 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: -0.01 (0.09), residues: 7683 helix: 0.18 (0.08), residues: 4088 sheet: -0.00 (0.25), residues: 416 loop : -0.04 (0.11), residues: 3179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.002 TRP P 73 HIS 0.010 0.001 HIS D 59 PHE 0.079 0.002 PHE D 171 TYR 0.074 0.002 TYR B 125 ARG 0.017 0.001 ARG r 102 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15366 Ramachandran restraints generated. 7683 Oldfield, 0 Emsley, 7683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15366 Ramachandran restraints generated. 7683 Oldfield, 0 Emsley, 7683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1081 residues out of total 6819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1079 time to evaluate : 5.879 Fit side-chains REVERT: C 137 MET cc_start: 0.8968 (mmm) cc_final: 0.8673 (mmm) REVERT: E 93 LYS cc_start: 0.8582 (mtpp) cc_final: 0.8272 (mtpt) REVERT: E 114 ASP cc_start: 0.7557 (m-30) cc_final: 0.7328 (m-30) REVERT: G 297 GLU cc_start: 0.7128 (mm-30) cc_final: 0.6677 (mp0) REVERT: G 517 ASN cc_start: 0.8343 (m110) cc_final: 0.8014 (m110) REVERT: J 79 TYR cc_start: 0.6095 (t80) cc_final: 0.5827 (t80) REVERT: L 108 MET cc_start: 0.8771 (mmm) cc_final: 0.8459 (mmm) REVERT: O 32 CYS cc_start: 0.6349 (m) cc_final: 0.5991 (t) REVERT: O 82 PHE cc_start: 0.7621 (t80) cc_final: 0.7337 (t80) REVERT: O 192 MET cc_start: 0.5801 (mpp) cc_final: 0.5126 (pmm) REVERT: P 199 LYS cc_start: 0.5290 (ptpt) cc_final: 0.4813 (pmtt) REVERT: P 338 LYS cc_start: 0.7734 (ptpp) cc_final: 0.7414 (ptmm) REVERT: S 39 ARG cc_start: 0.7987 (mmt90) cc_final: 0.7549 (mmt90) REVERT: a 67 GLU cc_start: 0.8143 (pm20) cc_final: 0.7882 (pm20) REVERT: b 30 ILE cc_start: 0.8730 (mt) cc_final: 0.8506 (mm) outliers start: 2 outliers final: 1 residues processed: 1081 average time/residue: 1.7534 time to fit residues: 2361.0462 Evaluate side-chains 939 residues out of total 6819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 938 time to evaluate : 5.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain T residue 44 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 760 random chunks: chunk 641 optimal weight: 4.9990 chunk 576 optimal weight: 1.9990 chunk 319 optimal weight: 1.9990 chunk 196 optimal weight: 7.9990 chunk 388 optimal weight: 2.9990 chunk 307 optimal weight: 0.6980 chunk 595 optimal weight: 2.9990 chunk 230 optimal weight: 3.9990 chunk 362 optimal weight: 2.9990 chunk 443 optimal weight: 9.9990 chunk 690 optimal weight: 0.9980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 106 GLN C 211 GLN D 55 HIS D 114 ASN E 121 GLN F 257 ASN F 431 GLN F 435 GLN F 436 GLN G 7 ASN G 237 ASN G 475 GLN G 643 GLN L 135 ASN L 479 GLN L 541 ASN M 44 GLN M 82 HIS M 138 ASN M 168 GLN N 172 GLN N 316 GLN ** O 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 252 ASN P 87 HIS P 119 GLN Z 85 GLN Z 90 ASN a 58 ASN ** a 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 36 ASN g 86 GLN g 119 GLN j 6 HIS j 24 GLN l 104 HIS n 140 GLN n 159 GLN q 112 ASN r 8 GLN r 50 ASN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.1085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.261 65901 Z= 0.463 Angle : 1.346 50.758 89152 Z= 0.861 Chirality : 0.262 6.495 9736 Planarity : 0.004 0.051 11115 Dihedral : 13.928 179.301 10130 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.03 % Favored : 97.96 % Rotamer: Outliers : 1.12 % Allowed : 6.11 % Favored : 92.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.68 % 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: 0.92 (0.09), residues: 7683 helix: 1.12 (0.08), residues: 4092 sheet: 0.06 (0.25), residues: 397 loop : 0.17 (0.11), residues: 3194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP P 73 HIS 0.006 0.001 HIS G 101 PHE 0.033 0.001 PHE D 171 TYR 0.037 0.001 TYR B 125 ARG 0.008 0.000 ARG b 46 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15366 Ramachandran restraints generated. 7683 Oldfield, 0 Emsley, 7683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15366 Ramachandran restraints generated. 7683 Oldfield, 0 Emsley, 7683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1081 residues out of total 6819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 1005 time to evaluate : 5.978 Fit side-chains REVERT: A 16 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7790 (tp) REVERT: B 77 ARG cc_start: 0.7512 (OUTLIER) cc_final: 0.7092 (ptm160) REVERT: F 248 GLU cc_start: 0.7169 (OUTLIER) cc_final: 0.6934 (mp0) REVERT: G 297 GLU cc_start: 0.7050 (mm-30) cc_final: 0.6710 (mp0) REVERT: G 517 ASN cc_start: 0.8188 (m110) cc_final: 0.7836 (m110) REVERT: G 651 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.8241 (mm) REVERT: J 79 TYR cc_start: 0.6049 (t80) cc_final: 0.5814 (t80) REVERT: L 82 MET cc_start: 0.8426 (OUTLIER) cc_final: 0.8094 (mmm) REVERT: L 108 MET cc_start: 0.8724 (mmm) cc_final: 0.8449 (mmm) REVERT: M 114 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.7361 (tm-30) REVERT: O 32 CYS cc_start: 0.6522 (m) cc_final: 0.6031 (t) REVERT: O 37 LYS cc_start: 0.7036 (OUTLIER) cc_final: 0.6784 (ptpt) REVERT: O 82 PHE cc_start: 0.7612 (t80) cc_final: 0.7379 (t80) REVERT: O 192 MET cc_start: 0.5884 (mpp) cc_final: 0.5136 (pmm) REVERT: P 170 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7678 (mp0) REVERT: P 199 LYS cc_start: 0.5280 (ptpt) cc_final: 0.4800 (pmtt) REVERT: P 338 LYS cc_start: 0.7707 (ptpp) cc_final: 0.7316 (ptmm) REVERT: S 39 ARG cc_start: 0.8002 (mmt90) cc_final: 0.7603 (mmm-85) REVERT: U 29 LYS cc_start: 0.7913 (OUTLIER) cc_final: 0.7588 (mptt) REVERT: V 63 ASP cc_start: 0.7989 (t0) cc_final: 0.7691 (t70) REVERT: V 65 LYS cc_start: 0.7809 (mtmm) cc_final: 0.7467 (mtmm) REVERT: c 33 LYS cc_start: 0.7913 (OUTLIER) cc_final: 0.7166 (mmpt) REVERT: e 31 ARG cc_start: 0.7845 (mtm110) cc_final: 0.7618 (mtp180) REVERT: n 134 ARG cc_start: 0.8102 (OUTLIER) cc_final: 0.7634 (tpt-90) REVERT: r 66 SER cc_start: 0.8798 (m) cc_final: 0.8520 (p) outliers start: 76 outliers final: 20 residues processed: 1030 average time/residue: 1.6933 time to fit residues: 2186.2733 Evaluate side-chains 978 residues out of total 6819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 947 time to evaluate : 5.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain B residue 77 ARG Chi-restraints excluded: chain D residue 279 ASP Chi-restraints excluded: chain F residue 248 GLU Chi-restraints excluded: chain G residue 651 LEU Chi-restraints excluded: chain H residue 8 MET Chi-restraints excluded: chain H residue 207 LEU Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain L residue 82 MET Chi-restraints excluded: chain L residue 496 LEU Chi-restraints excluded: chain M residue 94 LEU Chi-restraints excluded: chain M residue 114 GLU Chi-restraints excluded: chain M residue 157 SER Chi-restraints excluded: chain N residue 45 MET Chi-restraints excluded: chain N residue 223 SER Chi-restraints excluded: chain O residue 37 LYS Chi-restraints excluded: chain O residue 146 LYS Chi-restraints excluded: chain P residue 170 GLU Chi-restraints excluded: chain Q residue 28 GLU Chi-restraints excluded: chain R residue 79 THR Chi-restraints excluded: chain T residue 44 SER Chi-restraints excluded: chain U residue 29 LYS Chi-restraints excluded: chain X residue 63 ASN Chi-restraints excluded: chain a residue 60 SER Chi-restraints excluded: chain c residue 33 LYS Chi-restraints excluded: chain l residue 5 THR Chi-restraints excluded: chain n residue 134 ARG Chi-restraints excluded: chain o residue 120 ASP Chi-restraints excluded: chain p residue 77 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 760 random chunks: chunk 383 optimal weight: 2.9990 chunk 214 optimal weight: 0.7980 chunk 574 optimal weight: 0.7980 chunk 469 optimal weight: 5.9990 chunk 190 optimal weight: 8.9990 chunk 691 optimal weight: 8.9990 chunk 746 optimal weight: 20.0000 chunk 615 optimal weight: 6.9990 chunk 685 optimal weight: 4.9990 chunk 235 optimal weight: 6.9990 chunk 554 optimal weight: 10.0000 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 106 GLN F 435 GLN F 436 GLN G 7 ASN G 237 ASN L 479 GLN N 316 GLN O 76 ASN O 153 ASN ** O 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 252 ASN P 119 GLN V 75 GLN Z 85 GLN Z 90 ASN a 58 ASN ** a 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 36 ASN g 119 GLN n 74 GLN n 140 GLN n 159 GLN q 13 GLN r 50 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.1170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.243 65901 Z= 0.509 Angle : 1.350 50.583 89152 Z= 0.861 Chirality : 0.264 6.647 9736 Planarity : 0.004 0.050 11115 Dihedral : 12.759 170.624 10130 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.47 % Favored : 97.51 % Rotamer: Outliers : 1.53 % Allowed : 7.58 % Favored : 90.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.09), residues: 7683 helix: 1.22 (0.08), residues: 4109 sheet: 0.06 (0.25), residues: 402 loop : 0.16 (0.11), residues: 3172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP N 84 HIS 0.009 0.001 HIS D 59 PHE 0.031 0.002 PHE D 171 TYR 0.025 0.002 TYR I 118 ARG 0.009 0.000 ARG b 46 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15366 Ramachandran restraints generated. 7683 Oldfield, 0 Emsley, 7683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15366 Ramachandran restraints generated. 7683 Oldfield, 0 Emsley, 7683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1066 residues out of total 6819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 962 time to evaluate : 5.966 Fit side-chains REVERT: A 16 LEU cc_start: 0.8219 (OUTLIER) cc_final: 0.7804 (tp) REVERT: B 77 ARG cc_start: 0.7485 (OUTLIER) cc_final: 0.7162 (ptm160) REVERT: B 170 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7737 (mt-10) REVERT: C 87 GLN cc_start: 0.8241 (tt0) cc_final: 0.8009 (tt0) REVERT: G 297 GLU cc_start: 0.7105 (mm-30) cc_final: 0.6754 (mp0) REVERT: G 517 ASN cc_start: 0.8227 (m110) cc_final: 0.7882 (m110) REVERT: G 651 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.8143 (mm) REVERT: J 79 TYR cc_start: 0.6002 (t80) cc_final: 0.5728 (t80) REVERT: L 82 MET cc_start: 0.8453 (OUTLIER) cc_final: 0.8142 (mmm) REVERT: L 479 GLN cc_start: 0.8263 (OUTLIER) cc_final: 0.7422 (tm130) REVERT: M 114 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.7294 (tm-30) REVERT: M 168 GLN cc_start: 0.9043 (OUTLIER) cc_final: 0.8034 (tt0) REVERT: N 336 MET cc_start: 0.7824 (mmm) cc_final: 0.7609 (tpp) REVERT: O 82 PHE cc_start: 0.7582 (t80) cc_final: 0.7268 (t80) REVERT: O 192 MET cc_start: 0.6065 (mpp) cc_final: 0.5262 (pmm) REVERT: O 236 GLU cc_start: 0.7060 (tp30) cc_final: 0.6791 (tp30) REVERT: P 170 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7605 (mp0) REVERT: P 199 LYS cc_start: 0.5313 (ptpt) cc_final: 0.4836 (pmtt) REVERT: P 338 LYS cc_start: 0.7695 (ptpp) cc_final: 0.7334 (ptmm) REVERT: Q 15 GLU cc_start: 0.6958 (OUTLIER) cc_final: 0.6442 (mm-30) REVERT: S 39 ARG cc_start: 0.7984 (mmt90) cc_final: 0.7604 (mmm-85) REVERT: T 74 GLN cc_start: 0.7123 (OUTLIER) cc_final: 0.6066 (tm-30) REVERT: T 78 ASP cc_start: 0.7611 (m-30) cc_final: 0.7139 (m-30) REVERT: U 29 LYS cc_start: 0.7927 (OUTLIER) cc_final: 0.7595 (mptt) REVERT: U 88 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.7147 (pp20) REVERT: V 63 ASP cc_start: 0.7997 (t0) cc_final: 0.7685 (t70) REVERT: V 65 LYS cc_start: 0.7873 (OUTLIER) cc_final: 0.7495 (mtmm) REVERT: b 15 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.7658 (mm-30) REVERT: n 72 HIS cc_start: 0.8220 (t-90) cc_final: 0.7827 (t-90) REVERT: n 134 ARG cc_start: 0.8152 (OUTLIER) cc_final: 0.7594 (tpt-90) outliers start: 104 outliers final: 36 residues processed: 1007 average time/residue: 1.7024 time to fit residues: 2149.8452 Evaluate side-chains 986 residues out of total 6819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 934 time to evaluate : 5.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 77 ARG Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain D residue 279 ASP Chi-restraints excluded: chain G residue 471 SER Chi-restraints excluded: chain G residue 475 GLN Chi-restraints excluded: chain G residue 651 LEU Chi-restraints excluded: chain H residue 8 MET Chi-restraints excluded: chain J residue 136 PHE Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain L residue 82 MET Chi-restraints excluded: chain L residue 479 GLN Chi-restraints excluded: chain L residue 496 LEU Chi-restraints excluded: chain M residue 114 GLU Chi-restraints excluded: chain M residue 157 SER Chi-restraints excluded: chain M residue 168 GLN Chi-restraints excluded: chain M residue 378 GLU Chi-restraints excluded: chain N residue 43 ILE Chi-restraints excluded: chain N residue 45 MET Chi-restraints excluded: chain N residue 223 SER Chi-restraints excluded: chain O residue 146 LYS Chi-restraints excluded: chain P residue 170 GLU Chi-restraints excluded: chain Q residue 15 GLU Chi-restraints excluded: chain Q residue 28 GLU Chi-restraints excluded: chain Q residue 115 SER Chi-restraints excluded: chain R residue 79 THR Chi-restraints excluded: chain S residue 90 LEU Chi-restraints excluded: chain T residue 44 SER Chi-restraints excluded: chain T residue 74 GLN Chi-restraints excluded: chain U residue 29 LYS Chi-restraints excluded: chain U residue 88 GLU Chi-restraints excluded: chain V residue 65 LYS Chi-restraints excluded: chain X residue 63 ASN Chi-restraints excluded: chain Z residue 97 VAL Chi-restraints excluded: chain a residue 60 SER Chi-restraints excluded: chain b residue 15 GLU Chi-restraints excluded: chain c residue 40 LEU Chi-restraints excluded: chain f residue 7 VAL Chi-restraints excluded: chain h residue 60 VAL Chi-restraints excluded: chain j residue 45 ASP Chi-restraints excluded: chain k residue 87 LEU Chi-restraints excluded: chain l residue 5 THR Chi-restraints excluded: chain l residue 42 THR Chi-restraints excluded: chain m residue 15 THR Chi-restraints excluded: chain m residue 30 LYS Chi-restraints excluded: chain n residue 134 ARG Chi-restraints excluded: chain p residue 77 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 760 random chunks: chunk 683 optimal weight: 0.9980 chunk 519 optimal weight: 2.9990 chunk 358 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 329 optimal weight: 7.9990 chunk 464 optimal weight: 9.9990 chunk 693 optimal weight: 4.9990 chunk 734 optimal weight: 0.9990 chunk 362 optimal weight: 3.9990 chunk 657 optimal weight: 0.9990 chunk 197 optimal weight: 1.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 106 GLN C 192 GLN F 435 GLN F 436 GLN G 7 ASN G 237 ASN H 194 ASN K 83 ASN L 59 GLN ** L 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 316 GLN O 76 ASN O 153 ASN ** O 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 252 ASN P 119 GLN V 75 GLN W 26 ASN Y 128 GLN Z 85 GLN Z 90 ASN a 58 ASN a 68 ASN c 36 ASN g 86 GLN g 119 GLN j 6 HIS ** o 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 58 ASN r 50 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.1471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.246 65901 Z= 0.442 Angle : 1.319 50.552 89152 Z= 0.850 Chirality : 0.260 6.445 9736 Planarity : 0.004 0.049 11115 Dihedral : 11.718 171.746 10130 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.99 % Favored : 98.00 % Rotamer: Outliers : 1.32 % Allowed : 8.71 % Favored : 89.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.68 % 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: 1.30 (0.10), residues: 7683 helix: 1.48 (0.08), residues: 4094 sheet: 0.16 (0.25), residues: 402 loop : 0.28 (0.11), residues: 3187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP X 85 HIS 0.005 0.001 HIS O 190 PHE 0.025 0.001 PHE O 132 TYR 0.021 0.001 TYR L 422 ARG 0.008 0.000 ARG X 98 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15366 Ramachandran restraints generated. 7683 Oldfield, 0 Emsley, 7683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15366 Ramachandran restraints generated. 7683 Oldfield, 0 Emsley, 7683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1080 residues out of total 6819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 990 time to evaluate : 5.987 Fit side-chains REVERT: A 53 MET cc_start: 0.8332 (OUTLIER) cc_final: 0.7594 (tpp) REVERT: B 77 ARG cc_start: 0.7380 (OUTLIER) cc_final: 0.7081 (ptm160) REVERT: B 170 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7698 (mt-10) REVERT: D 75 LYS cc_start: 0.8375 (ttpp) cc_final: 0.8117 (ttpm) REVERT: G 297 GLU cc_start: 0.7037 (mm-30) cc_final: 0.6775 (mp0) REVERT: G 517 ASN cc_start: 0.8125 (m110) cc_final: 0.7768 (m110) REVERT: G 651 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.8158 (mm) REVERT: J 20 PHE cc_start: 0.8083 (OUTLIER) cc_final: 0.6709 (t80) REVERT: J 79 TYR cc_start: 0.5849 (t80) cc_final: 0.5609 (t80) REVERT: L 82 MET cc_start: 0.8415 (OUTLIER) cc_final: 0.8128 (mmm) REVERT: L 393 ASP cc_start: 0.7074 (OUTLIER) cc_final: 0.6799 (m-30) REVERT: M 114 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.7228 (tm-30) REVERT: O 82 PHE cc_start: 0.7526 (t80) cc_final: 0.7273 (t80) REVERT: O 192 MET cc_start: 0.6231 (mpp) cc_final: 0.5292 (pmm) REVERT: O 210 PHE cc_start: 0.7428 (t80) cc_final: 0.6999 (t80) REVERT: O 214 MET cc_start: 0.5226 (mpt) cc_final: 0.4681 (mmt) REVERT: O 295 GLU cc_start: 0.7797 (OUTLIER) cc_final: 0.7552 (mp0) REVERT: P 170 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7540 (mp0) REVERT: P 199 LYS cc_start: 0.5262 (ptpt) cc_final: 0.4783 (pmtt) REVERT: P 338 LYS cc_start: 0.7642 (ptpp) cc_final: 0.7244 (ptmm) REVERT: Q 15 GLU cc_start: 0.6857 (OUTLIER) cc_final: 0.6348 (mm-30) REVERT: S 39 ARG cc_start: 0.7970 (mmt90) cc_final: 0.7581 (mmm-85) REVERT: T 74 GLN cc_start: 0.7131 (OUTLIER) cc_final: 0.6124 (tm-30) REVERT: U 29 LYS cc_start: 0.7930 (OUTLIER) cc_final: 0.7595 (mptt) REVERT: V 63 ASP cc_start: 0.7899 (t0) cc_final: 0.7604 (t70) REVERT: V 65 LYS cc_start: 0.7855 (mtmm) cc_final: 0.7434 (mtmm) REVERT: W 68 LYS cc_start: 0.8431 (tptm) cc_final: 0.8034 (ttpp) REVERT: e 84 LYS cc_start: 0.7903 (ttmm) cc_final: 0.7523 (ttmt) REVERT: m 18 ASP cc_start: 0.7926 (t0) cc_final: 0.7716 (t0) REVERT: n 72 HIS cc_start: 0.8165 (t-90) cc_final: 0.7839 (t-90) REVERT: n 134 ARG cc_start: 0.8093 (OUTLIER) cc_final: 0.7545 (tpt170) REVERT: q 54 GLN cc_start: 0.8994 (mm-40) cc_final: 0.8642 (mm-40) REVERT: r 66 SER cc_start: 0.8834 (m) cc_final: 0.8545 (p) REVERT: r 69 MET cc_start: 0.8572 (tmt) cc_final: 0.8220 (tmt) REVERT: s 71 GLU cc_start: 0.7824 (tp30) cc_final: 0.7382 (tp30) outliers start: 90 outliers final: 26 residues processed: 1025 average time/residue: 1.7120 time to fit residues: 2197.5717 Evaluate side-chains 983 residues out of total 6819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 943 time to evaluate : 5.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain B residue 77 ARG Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain D residue 279 ASP Chi-restraints excluded: chain G residue 471 SER Chi-restraints excluded: chain G residue 475 GLN Chi-restraints excluded: chain G residue 651 LEU Chi-restraints excluded: chain J residue 20 PHE Chi-restraints excluded: chain J residue 136 PHE Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain L residue 82 MET Chi-restraints excluded: chain L residue 393 ASP Chi-restraints excluded: chain L residue 496 LEU Chi-restraints excluded: chain M residue 114 GLU Chi-restraints excluded: chain M residue 157 SER Chi-restraints excluded: chain N residue 43 ILE Chi-restraints excluded: chain N residue 45 MET Chi-restraints excluded: chain N residue 319 LEU Chi-restraints excluded: chain O residue 146 LYS Chi-restraints excluded: chain O residue 295 GLU Chi-restraints excluded: chain P residue 170 GLU Chi-restraints excluded: chain Q residue 15 GLU Chi-restraints excluded: chain Q residue 28 GLU Chi-restraints excluded: chain Q residue 115 SER Chi-restraints excluded: chain R residue 79 THR Chi-restraints excluded: chain T residue 44 SER Chi-restraints excluded: chain T residue 74 GLN Chi-restraints excluded: chain U residue 29 LYS Chi-restraints excluded: chain W residue 49 LEU Chi-restraints excluded: chain Z residue 96 THR Chi-restraints excluded: chain a residue 60 SER Chi-restraints excluded: chain g residue 70 LEU Chi-restraints excluded: chain j residue 45 ASP Chi-restraints excluded: chain k residue 87 LEU Chi-restraints excluded: chain l residue 5 THR Chi-restraints excluded: chain m residue 30 LYS Chi-restraints excluded: chain n residue 134 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 760 random chunks: chunk 611 optimal weight: 10.0000 chunk 417 optimal weight: 10.0000 chunk 10 optimal weight: 3.9990 chunk 546 optimal weight: 6.9990 chunk 303 optimal weight: 3.9990 chunk 626 optimal weight: 6.9990 chunk 507 optimal weight: 0.0870 chunk 0 optimal weight: 10.0000 chunk 375 optimal weight: 1.9990 chunk 659 optimal weight: 6.9990 chunk 185 optimal weight: 0.9980 overall best weight: 2.2164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 106 GLN E 74 GLN F 435 GLN G 7 ASN G 237 ASN G 308 GLN G 655 GLN L 479 GLN O 76 ASN O 153 ASN O 200 GLN P 119 GLN V 75 GLN W 26 ASN X 63 ASN Z 85 GLN Z 90 ASN a 58 ASN c 36 ASN g 86 GLN g 119 GLN j 6 HIS n 74 GLN r 50 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.1446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.244 65901 Z= 0.473 Angle : 1.327 50.532 89152 Z= 0.853 Chirality : 0.262 6.521 9736 Planarity : 0.004 0.056 11115 Dihedral : 11.415 179.524 10130 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.28 % Favored : 97.71 % Rotamer: Outliers : 1.45 % Allowed : 9.49 % Favored : 89.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.68 % 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: 1.31 (0.10), residues: 7683 helix: 1.48 (0.08), residues: 4096 sheet: 0.22 (0.25), residues: 397 loop : 0.28 (0.11), residues: 3190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP O 318 HIS 0.007 0.001 HIS D 59 PHE 0.025 0.001 PHE M 122 TYR 0.021 0.001 TYR I 118 ARG 0.009 0.000 ARG W 100 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15366 Ramachandran restraints generated. 7683 Oldfield, 0 Emsley, 7683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15366 Ramachandran restraints generated. 7683 Oldfield, 0 Emsley, 7683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1047 residues out of total 6819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 948 time to evaluate : 6.954 Fit side-chains REVERT: A 53 MET cc_start: 0.8361 (OUTLIER) cc_final: 0.7731 (tpp) REVERT: B 77 ARG cc_start: 0.7401 (OUTLIER) cc_final: 0.7084 (ptm160) REVERT: B 170 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7726 (mt-10) REVERT: D 75 LYS cc_start: 0.8382 (ttpp) cc_final: 0.8126 (ttpm) REVERT: G 297 GLU cc_start: 0.7119 (mm-30) cc_final: 0.6833 (mp0) REVERT: G 517 ASN cc_start: 0.8151 (m110) cc_final: 0.7812 (m110) REVERT: G 643 GLN cc_start: 0.7614 (OUTLIER) cc_final: 0.7251 (tp-100) REVERT: G 651 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.8174 (mm) REVERT: J 2 MET cc_start: 0.5695 (OUTLIER) cc_final: 0.5385 (ttm) REVERT: J 20 PHE cc_start: 0.8142 (OUTLIER) cc_final: 0.6782 (t80) REVERT: J 79 TYR cc_start: 0.5857 (t80) cc_final: 0.5545 (t80) REVERT: L 82 MET cc_start: 0.8423 (OUTLIER) cc_final: 0.8162 (mmm) REVERT: L 393 ASP cc_start: 0.7107 (OUTLIER) cc_final: 0.6828 (m-30) REVERT: M 19 LYS cc_start: 0.8003 (OUTLIER) cc_final: 0.7519 (mtpt) REVERT: M 114 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.7269 (tm-30) REVERT: N 336 MET cc_start: 0.7791 (mmm) cc_final: 0.7556 (tpp) REVERT: O 82 PHE cc_start: 0.7525 (t80) cc_final: 0.7255 (t80) REVERT: O 192 MET cc_start: 0.6209 (mpp) cc_final: 0.5288 (pmm) REVERT: O 295 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.7549 (mp0) REVERT: P 170 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7538 (mp0) REVERT: P 199 LYS cc_start: 0.5306 (ptpt) cc_final: 0.4839 (pmtt) REVERT: P 338 LYS cc_start: 0.7632 (ptpp) cc_final: 0.7249 (ptmm) REVERT: Q 15 GLU cc_start: 0.6925 (OUTLIER) cc_final: 0.6370 (mm-30) REVERT: S 39 ARG cc_start: 0.7984 (mmt90) cc_final: 0.7586 (mmm-85) REVERT: T 74 GLN cc_start: 0.7123 (OUTLIER) cc_final: 0.6141 (tm-30) REVERT: T 78 ASP cc_start: 0.7574 (m-30) cc_final: 0.7127 (m-30) REVERT: U 29 LYS cc_start: 0.7949 (OUTLIER) cc_final: 0.7579 (mptt) REVERT: U 88 GLU cc_start: 0.7598 (OUTLIER) cc_final: 0.7157 (pp20) REVERT: V 63 ASP cc_start: 0.7924 (t0) cc_final: 0.7663 (t70) REVERT: V 65 LYS cc_start: 0.7831 (OUTLIER) cc_final: 0.7444 (mtmm) REVERT: W 68 LYS cc_start: 0.8416 (tptm) cc_final: 0.7938 (ttmt) REVERT: a 64 LYS cc_start: 0.8406 (mmtm) cc_final: 0.8162 (mmtm) REVERT: b 15 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.7613 (mm-30) REVERT: e 84 LYS cc_start: 0.7915 (OUTLIER) cc_final: 0.7522 (ttmt) REVERT: m 18 ASP cc_start: 0.7933 (t0) cc_final: 0.7731 (t0) REVERT: n 72 HIS cc_start: 0.8155 (t-90) cc_final: 0.7846 (t-90) REVERT: n 134 ARG cc_start: 0.8125 (OUTLIER) cc_final: 0.7588 (tpt170) REVERT: r 69 MET cc_start: 0.8606 (tmt) cc_final: 0.8237 (tmt) REVERT: s 71 GLU cc_start: 0.7825 (tp30) cc_final: 0.7387 (tp30) outliers start: 99 outliers final: 44 residues processed: 991 average time/residue: 1.6844 time to fit residues: 2097.5871 Evaluate side-chains 992 residues out of total 6819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 927 time to evaluate : 6.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 77 ARG Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 49 GLU Chi-restraints excluded: chain D residue 279 ASP Chi-restraints excluded: chain D residue 407 LYS Chi-restraints excluded: chain G residue 471 SER Chi-restraints excluded: chain G residue 475 GLN Chi-restraints excluded: chain G residue 643 GLN Chi-restraints excluded: chain G residue 651 LEU Chi-restraints excluded: chain H residue 70 MET Chi-restraints excluded: chain H residue 121 TRP Chi-restraints excluded: chain J residue 2 MET Chi-restraints excluded: chain J residue 20 PHE Chi-restraints excluded: chain J residue 136 PHE Chi-restraints excluded: chain K residue 15 SER Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain L residue 82 MET Chi-restraints excluded: chain L residue 393 ASP Chi-restraints excluded: chain L residue 496 LEU Chi-restraints excluded: chain M residue 19 LYS Chi-restraints excluded: chain M residue 114 GLU Chi-restraints excluded: chain N residue 43 ILE Chi-restraints excluded: chain N residue 45 MET Chi-restraints excluded: chain N residue 223 SER Chi-restraints excluded: chain N residue 237 THR Chi-restraints excluded: chain N residue 319 LEU Chi-restraints excluded: chain O residue 146 LYS Chi-restraints excluded: chain O residue 295 GLU Chi-restraints excluded: chain P residue 170 GLU Chi-restraints excluded: chain Q residue 15 GLU Chi-restraints excluded: chain Q residue 28 GLU Chi-restraints excluded: chain Q residue 115 SER Chi-restraints excluded: chain R residue 79 THR Chi-restraints excluded: chain T residue 30 LEU Chi-restraints excluded: chain T residue 74 GLN Chi-restraints excluded: chain U residue 29 LYS Chi-restraints excluded: chain U residue 88 GLU Chi-restraints excluded: chain V residue 65 LYS Chi-restraints excluded: chain W residue 49 LEU Chi-restraints excluded: chain X residue 63 ASN Chi-restraints excluded: chain Z residue 96 THR Chi-restraints excluded: chain Z residue 97 VAL Chi-restraints excluded: chain a residue 60 SER Chi-restraints excluded: chain b residue 15 GLU Chi-restraints excluded: chain c residue 40 LEU Chi-restraints excluded: chain d residue 67 SER Chi-restraints excluded: chain e residue 84 LYS Chi-restraints excluded: chain f residue 7 VAL Chi-restraints excluded: chain g residue 70 LEU Chi-restraints excluded: chain g residue 85 MET Chi-restraints excluded: chain j residue 45 ASP Chi-restraints excluded: chain k residue 87 LEU Chi-restraints excluded: chain l residue 5 THR Chi-restraints excluded: chain l residue 148 LYS Chi-restraints excluded: chain m residue 15 THR Chi-restraints excluded: chain m residue 30 LYS Chi-restraints excluded: chain n residue 134 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 760 random chunks: chunk 247 optimal weight: 0.9980 chunk 661 optimal weight: 0.9980 chunk 145 optimal weight: 2.9990 chunk 431 optimal weight: 6.9990 chunk 181 optimal weight: 8.9990 chunk 735 optimal weight: 0.9980 chunk 610 optimal weight: 3.9990 chunk 340 optimal weight: 0.9990 chunk 61 optimal weight: 0.8980 chunk 243 optimal weight: 3.9990 chunk 386 optimal weight: 0.9980 overall best weight: 0.9780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 74 GLN F 435 GLN G 7 ASN G 237 ASN L 479 GLN O 76 ASN O 153 ASN ** O 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 119 GLN W 26 ASN Y 128 GLN Z 85 GLN Z 90 ASN a 58 ASN c 36 ASN g 86 GLN g 119 GLN j 6 HIS r 50 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.247 65901 Z= 0.437 Angle : 1.309 50.861 89152 Z= 0.847 Chirality : 0.260 6.422 9736 Planarity : 0.004 0.051 11115 Dihedral : 10.932 170.268 10129 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.99 % Favored : 97.98 % Rotamer: Outliers : 1.26 % Allowed : 10.07 % Favored : 88.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.68 % 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 (0.10), residues: 7683 helix: 1.62 (0.08), residues: 4100 sheet: 0.15 (0.25), residues: 405 loop : 0.37 (0.11), residues: 3178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP O 318 HIS 0.006 0.001 HIS O 190 PHE 0.023 0.001 PHE O 132 TYR 0.022 0.001 TYR L 422 ARG 0.010 0.000 ARG X 98 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15366 Ramachandran restraints generated. 7683 Oldfield, 0 Emsley, 7683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15366 Ramachandran restraints generated. 7683 Oldfield, 0 Emsley, 7683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1050 residues out of total 6819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 964 time to evaluate : 5.914 Fit side-chains revert: symmetry clash REVERT: B 77 ARG cc_start: 0.7310 (OUTLIER) cc_final: 0.6990 (ptm160) REVERT: B 170 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7675 (mt-10) REVERT: D 75 LYS cc_start: 0.8379 (ttpp) cc_final: 0.7872 (tttm) REVERT: G 297 GLU cc_start: 0.7112 (mm-30) cc_final: 0.6848 (mp0) REVERT: G 517 ASN cc_start: 0.8115 (m110) cc_final: 0.7778 (m-40) REVERT: G 643 GLN cc_start: 0.7566 (OUTLIER) cc_final: 0.7216 (tp-100) REVERT: G 651 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.8179 (mm) REVERT: J 20 PHE cc_start: 0.8149 (OUTLIER) cc_final: 0.6754 (t80) REVERT: L 82 MET cc_start: 0.8364 (OUTLIER) cc_final: 0.8156 (mmm) REVERT: L 108 MET cc_start: 0.8681 (mmm) cc_final: 0.8458 (mmm) REVERT: L 341 MET cc_start: 0.8759 (mtp) cc_final: 0.8527 (mtp) REVERT: L 393 ASP cc_start: 0.7089 (t70) cc_final: 0.6827 (m-30) REVERT: M 114 GLU cc_start: 0.8303 (OUTLIER) cc_final: 0.7214 (tm-30) REVERT: N 336 MET cc_start: 0.7775 (mmm) cc_final: 0.7546 (tpp) REVERT: O 192 MET cc_start: 0.6223 (mpp) cc_final: 0.5291 (pmm) REVERT: O 209 THR cc_start: 0.6618 (p) cc_final: 0.6034 (m) REVERT: O 210 PHE cc_start: 0.7446 (t80) cc_final: 0.7126 (t80) REVERT: O 214 MET cc_start: 0.5103 (mpt) cc_final: 0.4680 (mmt) REVERT: O 295 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.7540 (mp0) REVERT: P 170 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.7520 (mp0) REVERT: P 199 LYS cc_start: 0.5257 (ptpt) cc_final: 0.4779 (pmtt) REVERT: Q 106 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7687 (mt-10) REVERT: T 74 GLN cc_start: 0.7170 (OUTLIER) cc_final: 0.6208 (tm-30) REVERT: U 29 LYS cc_start: 0.7925 (OUTLIER) cc_final: 0.7570 (mptt) REVERT: V 63 ASP cc_start: 0.7885 (t0) cc_final: 0.7595 (t70) REVERT: V 65 LYS cc_start: 0.7811 (OUTLIER) cc_final: 0.7468 (mtmm) REVERT: W 68 LYS cc_start: 0.8440 (tptm) cc_final: 0.7975 (ttmt) REVERT: Z 93 GLU cc_start: 0.7360 (OUTLIER) cc_final: 0.7054 (tp30) REVERT: a 64 LYS cc_start: 0.8401 (mmtm) cc_final: 0.8160 (mmtm) REVERT: e 84 LYS cc_start: 0.7903 (OUTLIER) cc_final: 0.7529 (ttmt) REVERT: n 72 HIS cc_start: 0.8133 (t-90) cc_final: 0.7876 (t-90) REVERT: n 134 ARG cc_start: 0.8085 (OUTLIER) cc_final: 0.7571 (tpt170) REVERT: o 116 GLN cc_start: 0.7708 (tm-30) cc_final: 0.7252 (tm-30) REVERT: r 66 SER cc_start: 0.8809 (m) cc_final: 0.8525 (p) REVERT: r 69 MET cc_start: 0.8582 (tmt) cc_final: 0.8224 (tmt) REVERT: s 71 GLU cc_start: 0.7813 (tp30) cc_final: 0.7396 (tp30) outliers start: 86 outliers final: 34 residues processed: 1001 average time/residue: 1.6553 time to fit residues: 2086.2760 Evaluate side-chains 973 residues out of total 6819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 923 time to evaluate : 5.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 PHE Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain B residue 77 ARG Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 125 TYR Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain D residue 279 ASP Chi-restraints excluded: chain G residue 471 SER Chi-restraints excluded: chain G residue 475 GLN Chi-restraints excluded: chain G residue 643 GLN Chi-restraints excluded: chain G residue 651 LEU Chi-restraints excluded: chain H residue 121 TRP Chi-restraints excluded: chain J residue 20 PHE Chi-restraints excluded: chain J residue 136 PHE Chi-restraints excluded: chain K residue 15 SER Chi-restraints excluded: chain K residue 24 SER Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain L residue 82 MET Chi-restraints excluded: chain L residue 496 LEU Chi-restraints excluded: chain M residue 114 GLU Chi-restraints excluded: chain N residue 43 ILE Chi-restraints excluded: chain N residue 45 MET Chi-restraints excluded: chain N residue 223 SER Chi-restraints excluded: chain N residue 237 THR Chi-restraints excluded: chain N residue 319 LEU Chi-restraints excluded: chain O residue 1 LEU Chi-restraints excluded: chain O residue 146 LYS Chi-restraints excluded: chain O residue 295 GLU Chi-restraints excluded: chain P residue 170 GLU Chi-restraints excluded: chain Q residue 28 GLU Chi-restraints excluded: chain Q residue 106 GLU Chi-restraints excluded: chain Q residue 115 SER Chi-restraints excluded: chain R residue 79 THR Chi-restraints excluded: chain R residue 94 GLN Chi-restraints excluded: chain S residue 93 VAL Chi-restraints excluded: chain T residue 74 GLN Chi-restraints excluded: chain U residue 29 LYS Chi-restraints excluded: chain V residue 65 LYS Chi-restraints excluded: chain V residue 94 ILE Chi-restraints excluded: chain Z residue 93 GLU Chi-restraints excluded: chain c residue 40 LEU Chi-restraints excluded: chain d residue 67 SER Chi-restraints excluded: chain e residue 84 LYS Chi-restraints excluded: chain k residue 87 LEU Chi-restraints excluded: chain l residue 5 THR Chi-restraints excluded: chain l residue 16 THR Chi-restraints excluded: chain m residue 30 LYS Chi-restraints excluded: chain n residue 134 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 760 random chunks: chunk 708 optimal weight: 6.9990 chunk 82 optimal weight: 10.0000 chunk 418 optimal weight: 9.9990 chunk 536 optimal weight: 7.9990 chunk 416 optimal weight: 9.9990 chunk 618 optimal weight: 8.9990 chunk 410 optimal weight: 5.9990 chunk 732 optimal weight: 1.9990 chunk 458 optimal weight: 5.9990 chunk 446 optimal weight: 9.9990 chunk 338 optimal weight: 6.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN B 106 GLN E 74 GLN F 435 GLN G 7 ASN G 237 ASN K 52 HIS K 83 ASN L 328 HIS L 479 GLN O 76 ASN O 153 ASN O 190 HIS P 119 GLN S 30 GLN W 26 ASN X 63 ASN Y 128 GLN Z 85 GLN Z 90 ASN g 86 GLN g 119 GLN o 116 GLN r 50 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.1306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.244 65901 Z= 0.642 Angle : 1.384 50.481 89152 Z= 0.875 Chirality : 0.267 6.712 9736 Planarity : 0.005 0.061 11115 Dihedral : 11.589 170.162 10129 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.43 % Favored : 97.55 % Rotamer: Outliers : 1.81 % Allowed : 10.18 % Favored : 88.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.68 % 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: 1.01 (0.09), residues: 7683 helix: 1.20 (0.08), residues: 4107 sheet: 0.14 (0.25), residues: 393 loop : 0.19 (0.11), residues: 3183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP O 318 HIS 0.012 0.002 HIS D 59 PHE 0.035 0.002 PHE M 122 TYR 0.028 0.002 TYR I 118 ARG 0.010 0.001 ARG e 80 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15366 Ramachandran restraints generated. 7683 Oldfield, 0 Emsley, 7683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15366 Ramachandran restraints generated. 7683 Oldfield, 0 Emsley, 7683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1040 residues out of total 6819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 917 time to evaluate : 6.074 Fit side-chains REVERT: A 4 MET cc_start: 0.7367 (mmm) cc_final: 0.7148 (mmm) REVERT: A 16 LEU cc_start: 0.8269 (OUTLIER) cc_final: 0.7905 (tp) REVERT: B 77 ARG cc_start: 0.7542 (OUTLIER) cc_final: 0.7147 (ptm160) REVERT: B 170 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7797 (mt-10) REVERT: G 297 GLU cc_start: 0.7275 (mm-30) cc_final: 0.6973 (mp0) REVERT: G 372 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.8319 (mt-10) REVERT: G 444 GLN cc_start: 0.7700 (OUTLIER) cc_final: 0.7289 (tp40) REVERT: G 517 ASN cc_start: 0.8279 (m110) cc_final: 0.7955 (m110) REVERT: G 643 GLN cc_start: 0.7635 (OUTLIER) cc_final: 0.7285 (tp-100) REVERT: G 651 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8123 (mm) REVERT: I 29 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.7186 (pm20) REVERT: J 20 PHE cc_start: 0.8287 (OUTLIER) cc_final: 0.6967 (t80) REVERT: J 79 TYR cc_start: 0.6006 (t80) cc_final: 0.5697 (t80) REVERT: L 82 MET cc_start: 0.8503 (OUTLIER) cc_final: 0.8277 (mmm) REVERT: L 393 ASP cc_start: 0.7258 (OUTLIER) cc_final: 0.6946 (m-30) REVERT: M 114 GLU cc_start: 0.8434 (OUTLIER) cc_final: 0.7363 (tm-30) REVERT: M 168 GLN cc_start: 0.9048 (OUTLIER) cc_final: 0.7909 (tm-30) REVERT: N 336 MET cc_start: 0.7864 (OUTLIER) cc_final: 0.7659 (tpp) REVERT: O 82 PHE cc_start: 0.7527 (t80) cc_final: 0.7255 (t80) REVERT: O 192 MET cc_start: 0.6151 (mpp) cc_final: 0.5389 (pmm) REVERT: P 170 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.7570 (mp0) REVERT: P 199 LYS cc_start: 0.5343 (ptpt) cc_final: 0.4820 (pmtt) REVERT: R 55 ARG cc_start: 0.8614 (OUTLIER) cc_final: 0.7751 (mtm180) REVERT: S 39 ARG cc_start: 0.7995 (mmt90) cc_final: 0.7528 (mmm-85) REVERT: T 74 GLN cc_start: 0.7164 (OUTLIER) cc_final: 0.6199 (tm-30) REVERT: U 88 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.7218 (pp20) REVERT: a 64 LYS cc_start: 0.8440 (mmtm) cc_final: 0.8198 (mmtm) REVERT: b 15 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.7617 (mm-30) REVERT: b 42 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8717 (tm) REVERT: j 62 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7872 (tp30) REVERT: k 85 TYR cc_start: 0.7275 (t80) cc_final: 0.7061 (t80) REVERT: n 72 HIS cc_start: 0.8181 (t-90) cc_final: 0.7862 (t-90) REVERT: n 134 ARG cc_start: 0.8210 (OUTLIER) cc_final: 0.7665 (tpt170) REVERT: o 114 ARG cc_start: 0.7568 (OUTLIER) cc_final: 0.7083 (ttm170) REVERT: r 69 MET cc_start: 0.8684 (tmt) cc_final: 0.8328 (tmt) outliers start: 123 outliers final: 58 residues processed: 973 average time/residue: 1.6868 time to fit residues: 2060.5903 Evaluate side-chains 983 residues out of total 6819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 902 time to evaluate : 5.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 51 PHE Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 77 ARG Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 125 TYR Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 49 GLU Chi-restraints excluded: chain D residue 279 ASP Chi-restraints excluded: chain D residue 407 LYS Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 372 GLU Chi-restraints excluded: chain G residue 444 GLN Chi-restraints excluded: chain G residue 471 SER Chi-restraints excluded: chain G residue 475 GLN Chi-restraints excluded: chain G residue 643 GLN Chi-restraints excluded: chain G residue 651 LEU Chi-restraints excluded: chain H residue 70 MET Chi-restraints excluded: chain H residue 121 TRP Chi-restraints excluded: chain I residue 29 GLU Chi-restraints excluded: chain J residue 20 PHE Chi-restraints excluded: chain J residue 136 PHE Chi-restraints excluded: chain K residue 3 MET Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 15 SER Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain L residue 22 MET Chi-restraints excluded: chain L residue 82 MET Chi-restraints excluded: chain L residue 393 ASP Chi-restraints excluded: chain L residue 496 LEU Chi-restraints excluded: chain M residue 114 GLU Chi-restraints excluded: chain M residue 116 ILE Chi-restraints excluded: chain M residue 168 GLN Chi-restraints excluded: chain M residue 378 GLU Chi-restraints excluded: chain N residue 43 ILE Chi-restraints excluded: chain N residue 45 MET Chi-restraints excluded: chain N residue 223 SER Chi-restraints excluded: chain N residue 237 THR Chi-restraints excluded: chain N residue 319 LEU Chi-restraints excluded: chain N residue 336 MET Chi-restraints excluded: chain O residue 146 LYS Chi-restraints excluded: chain P residue 170 GLU Chi-restraints excluded: chain Q residue 28 GLU Chi-restraints excluded: chain Q residue 115 SER Chi-restraints excluded: chain R residue 55 ARG Chi-restraints excluded: chain R residue 79 THR Chi-restraints excluded: chain S residue 90 LEU Chi-restraints excluded: chain S residue 93 VAL Chi-restraints excluded: chain T residue 74 GLN Chi-restraints excluded: chain U residue 88 GLU Chi-restraints excluded: chain V residue 65 LYS Chi-restraints excluded: chain W residue 49 LEU Chi-restraints excluded: chain X residue 63 ASN Chi-restraints excluded: chain Z residue 96 THR Chi-restraints excluded: chain Z residue 97 VAL Chi-restraints excluded: chain a residue 60 SER Chi-restraints excluded: chain b residue 15 GLU Chi-restraints excluded: chain b residue 42 LEU Chi-restraints excluded: chain c residue 40 LEU Chi-restraints excluded: chain d residue 67 SER Chi-restraints excluded: chain f residue 7 VAL Chi-restraints excluded: chain g residue 85 MET Chi-restraints excluded: chain h residue 60 VAL Chi-restraints excluded: chain j residue 62 GLU Chi-restraints excluded: chain k residue 87 LEU Chi-restraints excluded: chain l residue 4 ILE Chi-restraints excluded: chain l residue 5 THR Chi-restraints excluded: chain l residue 16 THR Chi-restraints excluded: chain l residue 42 THR Chi-restraints excluded: chain l residue 148 LYS Chi-restraints excluded: chain m residue 15 THR Chi-restraints excluded: chain m residue 30 LYS Chi-restraints excluded: chain n residue 134 ARG Chi-restraints excluded: chain o residue 114 ARG Chi-restraints excluded: chain p residue 77 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 760 random chunks: chunk 453 optimal weight: 0.9980 chunk 292 optimal weight: 0.9980 chunk 437 optimal weight: 0.0370 chunk 220 optimal weight: 20.0000 chunk 143 optimal weight: 2.9990 chunk 141 optimal weight: 0.9980 chunk 465 optimal weight: 1.9990 chunk 499 optimal weight: 8.9990 chunk 362 optimal weight: 0.7980 chunk 68 optimal weight: 4.9990 chunk 575 optimal weight: 4.9990 overall best weight: 0.7658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 74 GLN F 435 GLN G 7 ASN G 237 ASN L 135 ASN L 199 GLN L 479 GLN O 76 ASN O 153 ASN O 252 ASN S 30 GLN W 26 ASN ** X 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 85 GLN Z 90 ASN g 86 GLN g 119 GLN j 6 HIS ** o 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 50 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.247 65901 Z= 0.437 Angle : 1.314 50.562 89152 Z= 0.849 Chirality : 0.259 6.408 9736 Planarity : 0.004 0.047 11115 Dihedral : 10.885 170.628 10129 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.85 % Favored : 98.13 % Rotamer: Outliers : 1.07 % Allowed : 11.13 % Favored : 87.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.10), residues: 7683 helix: 1.55 (0.08), residues: 4100 sheet: 0.15 (0.25), residues: 401 loop : 0.33 (0.11), residues: 3182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP O 318 HIS 0.004 0.001 HIS i 88 PHE 0.023 0.001 PHE O 132 TYR 0.024 0.001 TYR L 422 ARG 0.008 0.000 ARG D 290 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15366 Ramachandran restraints generated. 7683 Oldfield, 0 Emsley, 7683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15366 Ramachandran restraints generated. 7683 Oldfield, 0 Emsley, 7683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1012 residues out of total 6819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 939 time to evaluate : 5.972 Fit side-chains REVERT: A 4 MET cc_start: 0.7329 (mmm) cc_final: 0.7068 (mmm) REVERT: A 16 LEU cc_start: 0.8218 (OUTLIER) cc_final: 0.7852 (tp) REVERT: B 77 ARG cc_start: 0.7350 (OUTLIER) cc_final: 0.7015 (ptm160) REVERT: G 297 GLU cc_start: 0.7172 (mm-30) cc_final: 0.6928 (mp0) REVERT: G 517 ASN cc_start: 0.8099 (m110) cc_final: 0.7766 (m-40) REVERT: G 643 GLN cc_start: 0.7578 (OUTLIER) cc_final: 0.7227 (tp-100) REVERT: G 651 LEU cc_start: 0.8384 (OUTLIER) cc_final: 0.8146 (mm) REVERT: J 20 PHE cc_start: 0.8141 (OUTLIER) cc_final: 0.6731 (t80) REVERT: L 393 ASP cc_start: 0.7033 (t70) cc_final: 0.6763 (m-30) REVERT: L 515 TYR cc_start: 0.6222 (OUTLIER) cc_final: 0.5734 (m-80) REVERT: M 114 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.7252 (tm-30) REVERT: N 336 MET cc_start: 0.7800 (mmm) cc_final: 0.7574 (tpp) REVERT: O 192 MET cc_start: 0.6137 (mpp) cc_final: 0.5305 (pmm) REVERT: O 209 THR cc_start: 0.6608 (p) cc_final: 0.6039 (m) REVERT: O 210 PHE cc_start: 0.7467 (t80) cc_final: 0.7122 (t80) REVERT: O 214 MET cc_start: 0.5068 (mpt) cc_final: 0.4618 (mmt) REVERT: O 295 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.7520 (mp0) REVERT: P 154 LYS cc_start: 0.8233 (tptt) cc_final: 0.7999 (tptt) REVERT: P 170 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7515 (mp0) REVERT: P 199 LYS cc_start: 0.5306 (ptpt) cc_final: 0.4787 (pmtt) REVERT: R 55 ARG cc_start: 0.8617 (OUTLIER) cc_final: 0.7749 (mtm180) REVERT: T 74 GLN cc_start: 0.7180 (OUTLIER) cc_final: 0.6243 (tm-30) REVERT: V 65 LYS cc_start: 0.7794 (OUTLIER) cc_final: 0.7547 (mtmm) REVERT: W 68 LYS cc_start: 0.8390 (tptm) cc_final: 0.7977 (ttmt) REVERT: Z 93 GLU cc_start: 0.7412 (OUTLIER) cc_final: 0.7100 (tp30) REVERT: a 64 LYS cc_start: 0.8403 (mmtm) cc_final: 0.8163 (mmtm) REVERT: b 15 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7582 (mm-30) REVERT: e 7 LYS cc_start: 0.8594 (mtpt) cc_final: 0.8326 (tptp) REVERT: e 84 LYS cc_start: 0.7758 (ttmm) cc_final: 0.7558 (ttmt) REVERT: n 72 HIS cc_start: 0.8142 (t-90) cc_final: 0.7869 (t-90) REVERT: n 134 ARG cc_start: 0.8076 (OUTLIER) cc_final: 0.7537 (tpt170) REVERT: o 114 ARG cc_start: 0.7541 (OUTLIER) cc_final: 0.6967 (ttm170) REVERT: r 69 MET cc_start: 0.8592 (tmt) cc_final: 0.8243 (tmt) REVERT: s 71 GLU cc_start: 0.7787 (tp30) cc_final: 0.7359 (tp30) outliers start: 73 outliers final: 34 residues processed: 968 average time/residue: 1.7058 time to fit residues: 2073.8867 Evaluate side-chains 966 residues out of total 6819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 916 time to evaluate : 5.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 51 PHE Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain B residue 77 ARG Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 125 TYR Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain D residue 279 ASP Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain G residue 475 GLN Chi-restraints excluded: chain G residue 643 GLN Chi-restraints excluded: chain G residue 651 LEU Chi-restraints excluded: chain H residue 8 MET Chi-restraints excluded: chain H residue 121 TRP Chi-restraints excluded: chain H residue 207 LEU Chi-restraints excluded: chain J residue 20 PHE Chi-restraints excluded: chain J residue 136 PHE Chi-restraints excluded: chain K residue 15 SER Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain L residue 22 MET Chi-restraints excluded: chain L residue 496 LEU Chi-restraints excluded: chain L residue 515 TYR Chi-restraints excluded: chain M residue 86 LYS Chi-restraints excluded: chain M residue 114 GLU Chi-restraints excluded: chain N residue 45 MET Chi-restraints excluded: chain N residue 237 THR Chi-restraints excluded: chain N residue 319 LEU Chi-restraints excluded: chain O residue 146 LYS Chi-restraints excluded: chain O residue 206 TYR Chi-restraints excluded: chain O residue 295 GLU Chi-restraints excluded: chain P residue 170 GLU Chi-restraints excluded: chain Q residue 28 GLU Chi-restraints excluded: chain R residue 55 ARG Chi-restraints excluded: chain R residue 79 THR Chi-restraints excluded: chain S residue 93 VAL Chi-restraints excluded: chain T residue 74 GLN Chi-restraints excluded: chain V residue 65 LYS Chi-restraints excluded: chain Z residue 93 GLU Chi-restraints excluded: chain a residue 60 SER Chi-restraints excluded: chain b residue 15 GLU Chi-restraints excluded: chain c residue 40 LEU Chi-restraints excluded: chain l residue 5 THR Chi-restraints excluded: chain l residue 16 THR Chi-restraints excluded: chain l residue 148 LYS Chi-restraints excluded: chain n residue 134 ARG Chi-restraints excluded: chain o residue 114 ARG Chi-restraints excluded: chain p residue 77 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 760 random chunks: chunk 666 optimal weight: 6.9990 chunk 701 optimal weight: 3.9990 chunk 640 optimal weight: 0.6980 chunk 682 optimal weight: 9.9990 chunk 410 optimal weight: 2.9990 chunk 297 optimal weight: 0.9990 chunk 536 optimal weight: 6.9990 chunk 209 optimal weight: 6.9990 chunk 616 optimal weight: 6.9990 chunk 645 optimal weight: 4.9990 chunk 680 optimal weight: 9.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 106 GLN E 74 GLN F 435 GLN G 7 ASN G 237 ASN L 479 GLN O 76 ASN O 153 ASN W 26 ASN X 63 ASN Z 85 GLN Z 90 ASN g 86 GLN g 119 GLN j 6 HIS ** o 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 50 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.1540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.244 65901 Z= 0.491 Angle : 1.333 50.520 89152 Z= 0.855 Chirality : 0.263 6.543 9736 Planarity : 0.004 0.048 11115 Dihedral : 10.944 170.063 10129 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.30 % Favored : 97.68 % Rotamer: Outliers : 1.23 % Allowed : 11.35 % Favored : 87.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.68 % 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: 1.31 (0.10), residues: 7683 helix: 1.48 (0.08), residues: 4106 sheet: 0.22 (0.25), residues: 397 loop : 0.29 (0.11), residues: 3180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP O 318 HIS 0.006 0.001 HIS D 59 PHE 0.026 0.002 PHE M 122 TYR 0.022 0.002 TYR I 118 ARG 0.009 0.000 ARG e 80 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15366 Ramachandran restraints generated. 7683 Oldfield, 0 Emsley, 7683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15366 Ramachandran restraints generated. 7683 Oldfield, 0 Emsley, 7683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 999 residues out of total 6819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 915 time to evaluate : 6.060 Fit side-chains REVERT: A 16 LEU cc_start: 0.8241 (OUTLIER) cc_final: 0.7911 (tp) REVERT: B 77 ARG cc_start: 0.7430 (OUTLIER) cc_final: 0.7026 (ptm160) REVERT: D 164 MET cc_start: 0.8288 (ptt) cc_final: 0.8078 (ptt) REVERT: G 297 GLU cc_start: 0.7216 (mm-30) cc_final: 0.6967 (mp0) REVERT: G 517 ASN cc_start: 0.8173 (m110) cc_final: 0.7846 (m110) REVERT: G 643 GLN cc_start: 0.7583 (OUTLIER) cc_final: 0.7244 (tp-100) REVERT: G 651 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.8135 (mm) REVERT: J 2 MET cc_start: 0.5734 (OUTLIER) cc_final: 0.5485 (ttm) REVERT: J 20 PHE cc_start: 0.8215 (OUTLIER) cc_final: 0.6837 (t80) REVERT: L 393 ASP cc_start: 0.7101 (t70) cc_final: 0.6817 (m-30) REVERT: L 515 TYR cc_start: 0.6219 (OUTLIER) cc_final: 0.5713 (m-80) REVERT: M 114 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.7307 (tm-30) REVERT: N 96 MET cc_start: 0.7824 (tmm) cc_final: 0.7532 (tmt) REVERT: N 336 MET cc_start: 0.7848 (mmm) cc_final: 0.7598 (tpp) REVERT: O 186 LYS cc_start: 0.7333 (tptt) cc_final: 0.6546 (ttmm) REVERT: O 192 MET cc_start: 0.6246 (mpp) cc_final: 0.5414 (pmm) REVERT: O 209 THR cc_start: 0.6662 (p) cc_final: 0.6073 (m) REVERT: O 295 GLU cc_start: 0.7764 (OUTLIER) cc_final: 0.7527 (mp0) REVERT: P 154 LYS cc_start: 0.8244 (tptt) cc_final: 0.8006 (tptt) REVERT: P 170 GLU cc_start: 0.8101 (OUTLIER) cc_final: 0.7510 (mp0) REVERT: P 199 LYS cc_start: 0.5347 (ptpt) cc_final: 0.4824 (pmtt) REVERT: R 55 ARG cc_start: 0.8618 (OUTLIER) cc_final: 0.7768 (mtm180) REVERT: T 74 GLN cc_start: 0.7148 (OUTLIER) cc_final: 0.6229 (tm-30) REVERT: U 29 LYS cc_start: 0.7936 (OUTLIER) cc_final: 0.7622 (mptt) REVERT: V 65 LYS cc_start: 0.7805 (OUTLIER) cc_final: 0.7579 (mtmm) REVERT: Z 7 LYS cc_start: 0.8677 (OUTLIER) cc_final: 0.8347 (tptm) REVERT: Z 93 GLU cc_start: 0.7447 (OUTLIER) cc_final: 0.7130 (tp30) REVERT: a 64 LYS cc_start: 0.8408 (mmtm) cc_final: 0.8168 (mmtm) REVERT: b 15 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.7588 (mm-30) REVERT: b 46 ARG cc_start: 0.8042 (mtp-110) cc_final: 0.7816 (mtt-85) REVERT: j 62 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7872 (tp30) REVERT: n 72 HIS cc_start: 0.8162 (t-90) cc_final: 0.7892 (t-90) REVERT: n 134 ARG cc_start: 0.8150 (OUTLIER) cc_final: 0.7620 (tpt170) REVERT: o 114 ARG cc_start: 0.7560 (OUTLIER) cc_final: 0.7006 (ttm170) REVERT: r 69 MET cc_start: 0.8644 (tmt) cc_final: 0.8288 (tmt) REVERT: s 71 GLU cc_start: 0.7810 (tp30) cc_final: 0.7404 (tp30) outliers start: 84 outliers final: 40 residues processed: 952 average time/residue: 1.7142 time to fit residues: 2050.9737 Evaluate side-chains 965 residues out of total 6819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 905 time to evaluate : 5.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 51 PHE Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain B residue 77 ARG Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 279 ASP Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain G residue 471 SER Chi-restraints excluded: chain G residue 475 GLN Chi-restraints excluded: chain G residue 643 GLN Chi-restraints excluded: chain G residue 651 LEU Chi-restraints excluded: chain H residue 8 MET Chi-restraints excluded: chain H residue 121 TRP Chi-restraints excluded: chain J residue 2 MET Chi-restraints excluded: chain J residue 20 PHE Chi-restraints excluded: chain K residue 15 SER Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain L residue 22 MET Chi-restraints excluded: chain L residue 496 LEU Chi-restraints excluded: chain L residue 515 TYR Chi-restraints excluded: chain M residue 86 LYS Chi-restraints excluded: chain M residue 114 GLU Chi-restraints excluded: chain N residue 43 ILE Chi-restraints excluded: chain N residue 45 MET Chi-restraints excluded: chain N residue 223 SER Chi-restraints excluded: chain N residue 237 THR Chi-restraints excluded: chain N residue 319 LEU Chi-restraints excluded: chain O residue 146 LYS Chi-restraints excluded: chain O residue 206 TYR Chi-restraints excluded: chain O residue 295 GLU Chi-restraints excluded: chain P residue 170 GLU Chi-restraints excluded: chain Q residue 28 GLU Chi-restraints excluded: chain R residue 55 ARG Chi-restraints excluded: chain R residue 79 THR Chi-restraints excluded: chain S residue 93 VAL Chi-restraints excluded: chain S residue 95 SER Chi-restraints excluded: chain T residue 74 GLN Chi-restraints excluded: chain U residue 29 LYS Chi-restraints excluded: chain V residue 65 LYS Chi-restraints excluded: chain W residue 49 LEU Chi-restraints excluded: chain Z residue 7 LYS Chi-restraints excluded: chain Z residue 93 GLU Chi-restraints excluded: chain Z residue 97 VAL Chi-restraints excluded: chain a residue 60 SER Chi-restraints excluded: chain b residue 15 GLU Chi-restraints excluded: chain c residue 40 LEU Chi-restraints excluded: chain d residue 67 SER Chi-restraints excluded: chain j residue 62 GLU Chi-restraints excluded: chain l residue 5 THR Chi-restraints excluded: chain l residue 16 THR Chi-restraints excluded: chain l residue 148 LYS Chi-restraints excluded: chain n residue 134 ARG Chi-restraints excluded: chain o residue 114 ARG Chi-restraints excluded: chain o residue 120 ASP Chi-restraints excluded: chain p residue 77 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 760 random chunks: chunk 448 optimal weight: 8.9990 chunk 721 optimal weight: 9.9990 chunk 440 optimal weight: 0.9980 chunk 342 optimal weight: 3.9990 chunk 501 optimal weight: 3.9990 chunk 757 optimal weight: 5.9990 chunk 696 optimal weight: 1.9990 chunk 602 optimal weight: 6.9990 chunk 62 optimal weight: 4.9990 chunk 465 optimal weight: 2.9990 chunk 369 optimal weight: 3.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 106 GLN E 74 GLN F 435 GLN G 7 ASN G 237 ASN L 479 GLN O 76 ASN O 153 ASN W 26 ASN X 63 ASN Z 85 GLN Z 90 ASN g 86 GLN g 119 GLN j 6 HIS o 116 GLN r 50 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.1524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.243 65901 Z= 0.493 Angle : 1.337 50.525 89152 Z= 0.857 Chirality : 0.263 6.565 9736 Planarity : 0.004 0.048 11115 Dihedral : 10.989 170.510 10129 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.30 % Favored : 97.68 % Rotamer: Outliers : 1.23 % Allowed : 11.40 % Favored : 87.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.10), residues: 7683 helix: 1.42 (0.08), residues: 4104 sheet: 0.18 (0.25), residues: 397 loop : 0.26 (0.11), residues: 3182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP O 318 HIS 0.007 0.001 HIS D 59 PHE 0.027 0.002 PHE M 122 TYR 0.023 0.002 TYR I 118 ARG 0.010 0.000 ARG e 80 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15366 Ramachandran restraints generated. 7683 Oldfield, 0 Emsley, 7683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15366 Ramachandran restraints generated. 7683 Oldfield, 0 Emsley, 7683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1005 residues out of total 6819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 921 time to evaluate : 5.935 Fit side-chains REVERT: A 4 MET cc_start: 0.7380 (mmm) cc_final: 0.7095 (mmm) REVERT: A 16 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.7901 (tp) REVERT: B 77 ARG cc_start: 0.7453 (OUTLIER) cc_final: 0.7060 (ptm160) REVERT: G 297 GLU cc_start: 0.7236 (mm-30) cc_final: 0.6969 (mp0) REVERT: G 517 ASN cc_start: 0.8183 (m110) cc_final: 0.7861 (m110) REVERT: G 643 GLN cc_start: 0.7588 (OUTLIER) cc_final: 0.7248 (tp-100) REVERT: G 651 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.8131 (mm) REVERT: J 2 MET cc_start: 0.5739 (OUTLIER) cc_final: 0.5486 (ttm) REVERT: J 20 PHE cc_start: 0.8237 (OUTLIER) cc_final: 0.6843 (t80) REVERT: L 393 ASP cc_start: 0.7132 (t70) cc_final: 0.6840 (m-30) REVERT: L 515 TYR cc_start: 0.6233 (OUTLIER) cc_final: 0.5710 (m-80) REVERT: M 114 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.7334 (tm-30) REVERT: N 96 MET cc_start: 0.7834 (tmm) cc_final: 0.7539 (tmt) REVERT: N 336 MET cc_start: 0.7853 (mmm) cc_final: 0.7604 (tpp) REVERT: O 192 MET cc_start: 0.6207 (mpp) cc_final: 0.5411 (pmm) REVERT: O 209 THR cc_start: 0.6645 (p) cc_final: 0.6070 (m) REVERT: O 210 PHE cc_start: 0.7481 (t80) cc_final: 0.7067 (t80) REVERT: O 214 MET cc_start: 0.5034 (mpt) cc_final: 0.4627 (mmt) REVERT: O 295 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.7536 (mp0) REVERT: P 154 LYS cc_start: 0.8246 (tptt) cc_final: 0.8008 (tptt) REVERT: P 170 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7542 (mp0) REVERT: P 199 LYS cc_start: 0.5348 (ptpt) cc_final: 0.4819 (pmtt) REVERT: R 55 ARG cc_start: 0.8616 (OUTLIER) cc_final: 0.7761 (mtm180) REVERT: T 74 GLN cc_start: 0.7139 (OUTLIER) cc_final: 0.6225 (tm-30) REVERT: V 65 LYS cc_start: 0.7811 (OUTLIER) cc_final: 0.7589 (mtmm) REVERT: Z 7 LYS cc_start: 0.8666 (OUTLIER) cc_final: 0.8339 (tptm) REVERT: a 64 LYS cc_start: 0.8406 (mmtm) cc_final: 0.8166 (mmtm) REVERT: b 15 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7583 (mm-30) REVERT: j 62 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7867 (tp30) REVERT: n 72 HIS cc_start: 0.8172 (t-90) cc_final: 0.7874 (t-90) REVERT: n 134 ARG cc_start: 0.8164 (OUTLIER) cc_final: 0.7625 (tpt170) REVERT: o 114 ARG cc_start: 0.7594 (OUTLIER) cc_final: 0.7024 (ttm170) REVERT: r 69 MET cc_start: 0.8657 (tmt) cc_final: 0.8303 (tmt) REVERT: s 71 GLU cc_start: 0.7810 (tp30) cc_final: 0.7401 (tp30) outliers start: 84 outliers final: 40 residues processed: 954 average time/residue: 1.7042 time to fit residues: 2049.1304 Evaluate side-chains 965 residues out of total 6819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 907 time to evaluate : 5.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 51 PHE Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain B residue 77 ARG Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 279 ASP Chi-restraints excluded: chain D residue 407 LYS Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain G residue 475 GLN Chi-restraints excluded: chain G residue 643 GLN Chi-restraints excluded: chain G residue 651 LEU Chi-restraints excluded: chain H residue 8 MET Chi-restraints excluded: chain H residue 121 TRP Chi-restraints excluded: chain J residue 2 MET Chi-restraints excluded: chain J residue 20 PHE Chi-restraints excluded: chain J residue 136 PHE Chi-restraints excluded: chain K residue 15 SER Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain L residue 496 LEU Chi-restraints excluded: chain L residue 515 TYR Chi-restraints excluded: chain M residue 86 LYS Chi-restraints excluded: chain M residue 114 GLU Chi-restraints excluded: chain N residue 43 ILE Chi-restraints excluded: chain N residue 45 MET Chi-restraints excluded: chain N residue 223 SER Chi-restraints excluded: chain N residue 237 THR Chi-restraints excluded: chain N residue 319 LEU Chi-restraints excluded: chain O residue 146 LYS Chi-restraints excluded: chain O residue 295 GLU Chi-restraints excluded: chain P residue 170 GLU Chi-restraints excluded: chain Q residue 28 GLU Chi-restraints excluded: chain R residue 55 ARG Chi-restraints excluded: chain R residue 79 THR Chi-restraints excluded: chain R residue 94 GLN Chi-restraints excluded: chain S residue 93 VAL Chi-restraints excluded: chain S residue 95 SER Chi-restraints excluded: chain T residue 74 GLN Chi-restraints excluded: chain V residue 65 LYS Chi-restraints excluded: chain W residue 49 LEU Chi-restraints excluded: chain Z residue 7 LYS Chi-restraints excluded: chain Z residue 97 VAL Chi-restraints excluded: chain a residue 60 SER Chi-restraints excluded: chain b residue 15 GLU Chi-restraints excluded: chain c residue 40 LEU Chi-restraints excluded: chain d residue 67 SER Chi-restraints excluded: chain j residue 62 GLU Chi-restraints excluded: chain l residue 5 THR Chi-restraints excluded: chain l residue 16 THR Chi-restraints excluded: chain l residue 148 LYS Chi-restraints excluded: chain n residue 134 ARG Chi-restraints excluded: chain o residue 114 ARG Chi-restraints excluded: chain o residue 120 ASP Chi-restraints excluded: chain p residue 77 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 760 random chunks: chunk 478 optimal weight: 0.9990 chunk 642 optimal weight: 10.0000 chunk 184 optimal weight: 6.9990 chunk 555 optimal weight: 0.7980 chunk 89 optimal weight: 2.9990 chunk 167 optimal weight: 0.6980 chunk 603 optimal weight: 3.9990 chunk 252 optimal weight: 0.6980 chunk 620 optimal weight: 2.9990 chunk 76 optimal weight: 5.9990 chunk 111 optimal weight: 7.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 74 GLN F 435 GLN G 7 ASN G 237 ASN L 479 GLN O 76 ASN O 153 ASN W 26 ASN X 63 ASN Z 85 GLN Z 90 ASN g 86 GLN g 119 GLN j 6 HIS r 50 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.099654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.080149 restraints weight = 71564.820| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 1.18 r_work: 0.2908 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 2.72 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8803 moved from start: 0.1706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.246 65901 Z= 0.444 Angle : 1.316 50.570 89152 Z= 0.849 Chirality : 0.260 6.499 9736 Planarity : 0.004 0.047 11115 Dihedral : 10.628 170.305 10129 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.15 % Favored : 97.84 % Rotamer: Outliers : 0.98 % Allowed : 11.63 % Favored : 87.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.68 % 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: 1.43 (0.10), residues: 7683 helix: 1.59 (0.08), residues: 4097 sheet: 0.12 (0.25), residues: 404 loop : 0.35 (0.11), residues: 3182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP O 318 HIS 0.004 0.001 HIS N 112 PHE 0.023 0.001 PHE N 292 TYR 0.023 0.001 TYR T 17 ARG 0.009 0.000 ARG e 80 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 30751.61 seconds wall clock time: 532 minutes 11.49 seconds (31931.49 seconds total)