Starting phenix.real_space_refine on Sun Feb 25 21:27:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ylg_10838/02_2024/6ylg_10838_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ylg_10838/02_2024/6ylg_10838.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ylg_10838/02_2024/6ylg_10838.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ylg_10838/02_2024/6ylg_10838.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ylg_10838/02_2024/6ylg_10838_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ylg_10838/02_2024/6ylg_10838_updated.pdb" } resolution = 3.0 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= 0.000 sd= 0.007 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: 7 Type Number sf(0) Gaussians Zn 4 6.06 5 P 3316 5.49 5 Mg 2 5.21 5 S 209 5.16 5 C 79869 2.51 5 N 27005 2.21 5 O 36785 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "4 GLU 22": "OE1" <-> "OE2" Residue "4 ARG 29": "NH1" <-> "NH2" Residue "4 GLU 63": "OE1" <-> "OE2" Residue "4 ASP 69": "OD1" <-> "OD2" Residue "4 ARG 75": "NH1" <-> "NH2" Residue "4 ASP 109": "OD1" <-> "OD2" Residue "4 ARG 134": "NH1" <-> "NH2" Residue "4 ARG 224": "NH1" <-> "NH2" Residue "4 ASP 228": "OD1" <-> "OD2" Residue "4 ARG 232": "NH1" <-> "NH2" Residue "4 ARG 243": "NH1" <-> "NH2" Residue "4 GLU 263": "OE1" <-> "OE2" Residue "4 ARG 362": "NH1" <-> "NH2" Residue "4 PHE 364": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ASP 383": "OD1" <-> "OD2" Residue "4 TYR 388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 434": "OE1" <-> "OE2" Residue "4 ASP 461": "OD1" <-> "OD2" Residue "4 GLU 472": "OE1" <-> "OE2" Residue "4 GLU 503": "OE1" <-> "OE2" Residue "4 GLU 521": "OE1" <-> "OE2" Residue "5 GLU 81": "OE1" <-> "OE2" Residue "5 GLU 84": "OE1" <-> "OE2" Residue "5 ARG 94": "NH1" <-> "NH2" Residue "5 GLU 105": "OE1" <-> "OE2" Residue "5 ARG 110": "NH1" <-> "NH2" Residue "A ARG 9": "NH1" <-> "NH2" Residue "A ARG 37": "NH1" <-> "NH2" Residue "A TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 73": "OE1" <-> "OE2" Residue "A TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 122": "OD1" <-> "OD2" Residue "A TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 142": "OD1" <-> "OD2" Residue "A ARG 149": "NH1" <-> "NH2" Residue "A ARG 190": "NH1" <-> "NH2" Residue "A ARG 193": "NH1" <-> "NH2" Residue "A ARG 200": "NH1" <-> "NH2" Residue "B PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 62": "NH1" <-> "NH2" Residue "B GLU 71": "OE1" <-> "OE2" Residue "B GLU 74": "OE1" <-> "OE2" Residue "B TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 146": "NH1" <-> "NH2" Residue "B GLU 147": "OE1" <-> "OE2" Residue "B GLU 210": "OE1" <-> "OE2" Residue "B ASP 216": "OD1" <-> "OD2" Residue "B GLU 227": "OE1" <-> "OE2" Residue "B ARG 232": "NH1" <-> "NH2" Residue "B ASP 290": "OD1" <-> "OD2" Residue "B GLU 291": "OE1" <-> "OE2" Residue "B PHE 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 299": "OD1" <-> "OD2" Residue "B GLU 316": "OE1" <-> "OE2" Residue "B GLU 352": "OE1" <-> "OE2" Residue "B ARG 369": "NH1" <-> "NH2" Residue "C ARG 3": "NH1" <-> "NH2" Residue "C GLU 14": "OE1" <-> "OE2" Residue "C PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 69": "NH1" <-> "NH2" Residue "C TYR 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 147": "OE1" <-> "OE2" Residue "C TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 211": "OE1" <-> "OE2" Residue "C GLU 294": "OE1" <-> "OE2" Residue "C ARG 326": "NH1" <-> "NH2" Residue "C ASP 362": "OD1" <-> "OD2" Residue "D ARG 15": "NH1" <-> "NH2" Residue "D ARG 22": "NH1" <-> "NH2" Residue "D TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 168": "OD1" <-> "OD2" Residue "D TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 184": "OD1" <-> "OD2" Residue "D ASP 214": "OD1" <-> "OD2" Residue "D GLU 217": "OE1" <-> "OE2" Residue "D GLU 221": "OE1" <-> "OE2" Residue "D ASP 230": "OD1" <-> "OD2" Residue "D ASP 232": "OD1" <-> "OD2" Residue "D ASP 234": "OD1" <-> "OD2" Residue "D ASP 238": "OD1" <-> "OD2" Residue "D ASP 250": "OD1" <-> "OD2" Residue "D GLU 257": "OE1" <-> "OE2" Residue "D TYR 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 129": "OE1" <-> "OE2" Residue "E PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 30": "NH1" <-> "NH2" Residue "F GLU 46": "OE1" <-> "OE2" Residue "F TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 100": "NH1" <-> "NH2" Residue "F ARG 110": "NH1" <-> "NH2" Residue "F GLU 125": "OE1" <-> "OE2" Residue "F TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 165": "OD1" <-> "OD2" Residue "F GLU 170": "OE1" <-> "OE2" Residue "F GLU 187": "OE1" <-> "OE2" Residue "F PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 234": "OE1" <-> "OE2" Residue "F PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 54": "OE1" <-> "OE2" Residue "G TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 104": "OE1" <-> "OE2" Residue "G GLU 112": "OE1" <-> "OE2" Residue "G ASP 124": "OD1" <-> "OD2" Residue "G TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 204": "NH1" <-> "NH2" Residue "G GLU 228": "OE1" <-> "OE2" Residue "H ARG 23": "NH1" <-> "NH2" Residue "H ASP 42": "OD1" <-> "OD2" Residue "H ARG 62": "NH1" <-> "NH2" Residue "H TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 91": "NH1" <-> "NH2" Residue "H TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 130": "OD1" <-> "OD2" Residue "H ARG 166": "NH1" <-> "NH2" Residue "H ARG 168": "NH1" <-> "NH2" Residue "H ASP 171": "OD1" <-> "OD2" Residue "H ARG 173": "NH1" <-> "NH2" Residue "H PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 8": "NH1" <-> "NH2" Residue "I ASP 19": "OD1" <-> "OD2" Residue "I ASP 40": "OD1" <-> "OD2" Residue "I GLU 41": "OE1" <-> "OE2" Residue "I GLU 59": "OE1" <-> "OE2" Residue "I ARG 75": "NH1" <-> "NH2" Residue "I ASP 91": "OD1" <-> "OD2" Residue "I TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 104": "NH1" <-> "NH2" Residue "I GLU 107": "OE1" <-> "OE2" Residue "I GLU 115": "OE1" <-> "OE2" Residue "I GLU 125": "OE1" <-> "OE2" Residue "J ASP 11": "OD1" <-> "OD2" Residue "J GLU 38": "OE1" <-> "OE2" Residue "J ARG 51": "NH1" <-> "NH2" Residue "J ARG 55": "NH1" <-> "NH2" Residue "J ARG 61": "NH1" <-> "NH2" Residue "J PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 108": "OE1" <-> "OE2" Residue "J ASP 111": "OD1" <-> "OD2" Residue "J ASP 158": "OD1" <-> "OD2" Residue "K GLU 26": "OE1" <-> "OE2" Residue "K ARG 29": "NH1" <-> "NH2" Residue "K ASP 33": "OD1" <-> "OD2" Residue "K PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 44": "NH1" <-> "NH2" Residue "K ASP 54": "OD1" <-> "OD2" Residue "K GLU 72": "OE1" <-> "OE2" Residue "K ARG 88": "NH1" <-> "NH2" Residue "K ARG 109": "NH1" <-> "NH2" Residue "K PHE 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 170": "NH1" <-> "NH2" Residue "K TYR 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 317": "OE1" <-> "OE2" Residue "L GLU 20": "OE1" <-> "OE2" Residue "L ARG 42": "NH1" <-> "NH2" Residue "L ARG 49": "NH1" <-> "NH2" Residue "L ARG 73": "NH1" <-> "NH2" Residue "L TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 136": "OE1" <-> "OE2" Residue "L ASP 153": "OD1" <-> "OD2" Residue "L GLU 155": "OE1" <-> "OE2" Residue "L ARG 171": "NH1" <-> "NH2" Residue "M GLU 16": "OE1" <-> "OE2" Residue "M ARG 19": "NH1" <-> "NH2" Residue "M ASP 47": "OD1" <-> "OD2" Residue "M ARG 108": "NH1" <-> "NH2" Residue "N TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 20": "NH1" <-> "NH2" Residue "N GLU 29": "OE1" <-> "OE2" Residue "N TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 103": "OE1" <-> "OE2" Residue "N ASP 153": "OD1" <-> "OD2" Residue "N PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 40": "OE1" <-> "OE2" Residue "O PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 3": "NH1" <-> "NH2" Residue "P GLU 31": "OE1" <-> "OE2" Residue "P ARG 56": "NH1" <-> "NH2" Residue "P PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 126": "NH1" <-> "NH2" Residue "P GLU 140": "OE1" <-> "OE2" Residue "P ARG 181": "NH1" <-> "NH2" Residue "Q PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 92": "NH1" <-> "NH2" Residue "Q GLU 120": "OE1" <-> "OE2" Residue "R ARG 5": "NH1" <-> "NH2" Residue "R ARG 62": "NH1" <-> "NH2" Residue "R GLU 72": "OE1" <-> "OE2" Residue "R ARG 104": "NH1" <-> "NH2" Residue "R ARG 110": "NH1" <-> "NH2" Residue "R GLU 126": "OE1" <-> "OE2" Residue "S GLU 6": "OE1" <-> "OE2" Residue "S ARG 28": "NH1" <-> "NH2" Residue "S ARG 117": "NH1" <-> "NH2" Residue "S GLU 128": "OE1" <-> "OE2" Residue "S ASP 134": "OD1" <-> "OD2" Residue "T TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 38": "OD1" <-> "OD2" Residue "T ASP 41": "OD1" <-> "OD2" Residue "T TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 88": "NH1" <-> "NH2" Residue "T GLU 107": "OE1" <-> "OE2" Residue "T ARG 108": "NH1" <-> "NH2" Residue "T GLU 137": "OE1" <-> "OE2" Residue "T ARG 139": "NH1" <-> "NH2" Residue "U ASP 18": "OD1" <-> "OD2" Residue "U PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 58": "OE1" <-> "OE2" Residue "U PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 27": "OD1" <-> "OD2" Residue "V ARG 32": "NH1" <-> "NH2" Residue "V ARG 70": "NH1" <-> "NH2" Residue "V ARG 86": "NH1" <-> "NH2" Residue "V ASP 89": "OD1" <-> "OD2" Residue "V ASP 97": "OD1" <-> "OD2" Residue "W PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 31": "NH1" <-> "NH2" Residue "W ASP 35": "OD1" <-> "OD2" Residue "W TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 49": "NH1" <-> "NH2" Residue "W ARG 57": "NH1" <-> "NH2" Residue "W GLU 79": "OE1" <-> "OE2" Residue "W ARG 81": "NH1" <-> "NH2" Residue "W TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 166": "NH1" <-> "NH2" Residue "W GLU 170": "OE1" <-> "OE2" Residue "W TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 193": "OE1" <-> "OE2" Residue "W ARG 198": "NH1" <-> "NH2" Residue "W PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 78": "OD1" <-> "OD2" Residue "X GLU 101": "OE1" <-> "OE2" Residue "X GLU 104": "OE1" <-> "OE2" Residue "X TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 125": "NH1" <-> "NH2" Residue "X TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 138": "NH1" <-> "NH2" Residue "Y ASP 11": "OD1" <-> "OD2" Residue "Y ARG 52": "NH1" <-> "NH2" Residue "Y GLU 67": "OE1" <-> "OE2" Residue "Y TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 121": "NH1" <-> "NH2" Residue "Z GLU 47": "OE1" <-> "OE2" Residue "Z TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 84": "NH1" <-> "NH2" Residue "Z PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 102": "OE1" <-> "OE2" Residue "Z ARG 135": "NH1" <-> "NH2" Residue "a ARG 59": "NH1" <-> "NH2" Residue "a TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 85": "OD1" <-> "OD2" Residue "a GLU 135": "OE1" <-> "OE2" Residue "a GLU 136": "OE1" <-> "OE2" Residue "b ARG 24": "NH1" <-> "NH2" Residue "b ARG 27": "NH1" <-> "NH2" Residue "b ARG 34": "NH1" <-> "NH2" Residue "b ARG 43": "NH1" <-> "NH2" Residue "b ASP 63": "OD1" <-> "OD2" Residue "b ARG 79": "NH1" <-> "NH2" Residue "b GLU 87": "OE1" <-> "OE2" Residue "b GLU 106": "OE1" <-> "OE2" Residue "b ARG 110": "NH1" <-> "NH2" Residue "b ARG 114": "NH1" <-> "NH2" Residue "b PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 135": "NH1" <-> "NH2" Residue "b ARG 144": "NH1" <-> "NH2" Residue "b GLU 151": "OE1" <-> "OE2" Residue "b ARG 154": "NH1" <-> "NH2" Residue "b ASP 193": "OD1" <-> "OD2" Residue "b TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 210": "OD1" <-> "OD2" Residue "b ASP 220": "OD1" <-> "OD2" Residue "b GLU 231": "OE1" <-> "OE2" Residue "b TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 258": "OE1" <-> "OE2" Residue "b ARG 302": "NH1" <-> "NH2" Residue "b GLU 330": "OE1" <-> "OE2" Residue "b GLU 337": "OE1" <-> "OE2" Residue "b ASP 370": "OD1" <-> "OD2" Residue "b PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 380": "OE1" <-> "OE2" Residue "b TYR 420": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 425": "OD1" <-> "OD2" Residue "b GLU 434": "OE1" <-> "OE2" Residue "b PHE 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 448": "OE1" <-> "OE2" Residue "b GLU 464": "OE1" <-> "OE2" Residue "b GLU 506": "OE1" <-> "OE2" Residue "b ARG 510": "NH1" <-> "NH2" Residue "b TYR 558": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 560": "OE1" <-> "OE2" Residue "b ASP 564": "OD1" <-> "OD2" Residue "b GLU 578": "OE1" <-> "OE2" Residue "b ASP 587": "OD1" <-> "OD2" Residue "b ASP 603": "OD1" <-> "OD2" Residue "b GLU 612": "OE1" <-> "OE2" Residue "b ARG 613": "NH1" <-> "NH2" Residue "b ARG 615": "NH1" <-> "NH2" Residue "b ARG 624": "NH1" <-> "NH2" Residue "b ARG 647": "NH1" <-> "NH2" Residue "c ARG 99": "NH1" <-> "NH2" Residue "c ASP 152": "OD1" <-> "OD2" Residue "d GLU 54": "OE1" <-> "OE2" Residue "d GLU 68": "OE1" <-> "OE2" Residue "d ARG 70": "NH1" <-> "NH2" Residue "d GLU 83": "OE1" <-> "OE2" Residue "d ASP 84": "OD1" <-> "OD2" Residue "d GLU 94": "OE1" <-> "OE2" Residue "e TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ARG 48": "NH1" <-> "NH2" Residue "g GLU 87": "OE1" <-> "OE2" Residue "g GLU 97": "OE1" <-> "OE2" Residue "g GLU 107": "OE1" <-> "OE2" Residue "h GLU 30": "OE1" <-> "OE2" Residue "h ASP 79": "OD1" <-> "OD2" Residue "h GLU 102": "OE1" <-> "OE2" Residue "h ARG 105": "NH1" <-> "NH2" Residue "i GLU 66": "OE1" <-> "OE2" Residue "j ARG 63": "NH1" <-> "NH2" Residue "k GLU 4": "OE1" <-> "OE2" Residue "k GLU 13": "OE1" <-> "OE2" Residue "k PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m ARG 10": "NH1" <-> "NH2" Residue "m GLU 14": "OE1" <-> "OE2" Residue "m TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m ASP 32": "OD1" <-> "OD2" Residue "m ARG 49": "NH1" <-> "NH2" Residue "m ASP 68": "OD1" <-> "OD2" Residue "m ARG 76": "NH1" <-> "NH2" Residue "m ARG 82": "NH1" <-> "NH2" Residue "m ARG 110": "NH1" <-> "NH2" Residue "m ARG 130": "NH1" <-> "NH2" Residue "m ARG 147": "NH1" <-> "NH2" Residue "m ARG 149": "NH1" <-> "NH2" Residue "m ARG 151": "NH1" <-> "NH2" Residue "m ASP 178": "OD1" <-> "OD2" Residue "m ARG 238": "NH1" <-> "NH2" Residue "m GLU 243": "OE1" <-> "OE2" Residue "m ARG 304": "NH1" <-> "NH2" Residue "m ARG 361": "NH1" <-> "NH2" Residue "m GLU 417": "OE1" <-> "OE2" Residue "m ARG 437": "NH1" <-> "NH2" Residue "m GLU 443": "OE1" <-> "OE2" Residue "m ARG 459": "NH1" <-> "NH2" Residue "m PHE 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ARG 52": "NH1" <-> "NH2" Residue "n GLU 57": "OE1" <-> "OE2" Residue "n TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n GLU 94": "OE1" <-> "OE2" Residue "n ASP 97": "OD1" <-> "OD2" Residue "p ARG 36": "NH1" <-> "NH2" Residue "q GLU 52": "OE1" <-> "OE2" Residue "r TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r ARG 9": "NH1" <-> "NH2" Residue "r ASP 19": "OD1" <-> "OD2" Residue "r GLU 21": "OE1" <-> "OE2" Residue "r ARG 30": "NH1" <-> "NH2" Residue "r GLU 31": "OE1" <-> "OE2" Residue "r PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r ARG 126": "NH1" <-> "NH2" Residue "r ARG 149": "NH1" <-> "NH2" Residue "r ARG 164": "NH1" <-> "NH2" Residue "r GLU 188": "OE1" <-> "OE2" Residue "r GLU 227": "OE1" <-> "OE2" Residue "r ARG 251": "NH1" <-> "NH2" Residue "r ASP 252": "OD1" <-> "OD2" Residue "s ARG 2": "NH1" <-> "NH2" Residue "s ARG 6": "NH1" <-> "NH2" Residue "t ASP 24": "OD1" <-> "OD2" Residue "t GLU 30": "OE1" <-> "OE2" Residue "t PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t GLU 129": "OE1" <-> "OE2" Residue "t ASP 142": "OD1" <-> "OD2" Residue "t GLU 148": "OE1" <-> "OE2" Residue "t ASP 213": "OD1" <-> "OD2" Residue "t ASP 236": "OD1" <-> "OD2" Residue "t ASP 237": "OD1" <-> "OD2" Residue "t ASP 338": "OD1" <-> "OD2" Residue "t GLU 362": "OE1" <-> "OE2" Residue "t ARG 398": "NH1" <-> "NH2" Residue "t ASP 413": "OD1" <-> "OD2" Residue "t ASP 434": "OD1" <-> "OD2" Residue "t GLU 439": "OE1" <-> "OE2" Residue "t ARG 449": "NH1" <-> "NH2" Residue "t GLU 450": "OE1" <-> "OE2" Residue "t TYR 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t ASP 491": "OD1" <-> "OD2" Residue "t ARG 502": "NH1" <-> "NH2" Residue "u ARG 2": "NH1" <-> "NH2" Residue "u ARG 23": "NH1" <-> "NH2" Residue "u ASP 25": "OD1" <-> "OD2" Residue "u GLU 28": "OE1" <-> "OE2" Residue "u PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u ARG 33": "NH1" <-> "NH2" Residue "u ARG 43": "NH1" <-> "NH2" Residue "u ARG 44": "NH1" <-> "NH2" Residue "u ARG 56": "NH1" <-> "NH2" Residue "u ARG 75": "NH1" <-> "NH2" Residue "u ARG 83": "NH1" <-> "NH2" Residue "u GLU 104": "OE1" <-> "OE2" Residue "u ARG 105": "NH1" <-> "NH2" Residue "u PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u ARG 111": "NH1" <-> "NH2" Residue "u ARG 113": "NH1" <-> "NH2" Residue "u ARG 122": "NH1" <-> "NH2" Residue "u GLU 140": "OE1" <-> "OE2" Residue "x ASP 165": "OD1" <-> "OD2" Residue "x TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x GLU 199": "OE1" <-> "OE2" Residue "x ASP 264": "OD1" <-> "OD2" Residue "x TYR 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x TYR 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x ASP 331": "OD1" <-> "OD2" Residue "x ASP 340": "OD1" <-> "OD2" Residue "x GLU 350": "OE1" <-> "OE2" Residue "x GLU 351": "OE1" <-> "OE2" Residue "y ARG 61": "NH1" <-> "NH2" Residue "y ARG 68": "NH1" <-> "NH2" Residue "y GLU 80": "OE1" <-> "OE2" Residue "y ARG 96": "NH1" <-> "NH2" Residue "y GLU 98": "OE1" <-> "OE2" Residue "y ARG 100": "NH1" <-> "NH2" Residue "y GLU 124": "OE1" <-> "OE2" Residue "y GLU 126": "OE1" <-> "OE2" Residue "y ASP 131": "OD1" <-> "OD2" Residue "y GLU 136": "OE1" <-> "OE2" Residue "y TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y ASP 226": "OD1" <-> "OD2" Residue "z ARG 6": "NH1" <-> "NH2" Residue "z ARG 29": "NH1" <-> "NH2" Residue "z GLU 30": "OE1" <-> "OE2" Residue "z GLU 39": "OE1" <-> "OE2" Time to flip residues: 0.18s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 147190 Number of models: 1 Model: "" Number of chains: 61 Chain: "1" Number of atoms: 65028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3039, 65028 Classifications: {'RNA': 3039} Modifications used: {'rna2p_pur': 314, 'rna2p_pyr': 224, 'rna3p_pur': 1376, 'rna3p_pyr': 1125} Link IDs: {'rna2p': 538, 'rna3p': 2500} Chain breaks: 28 Chain: "2" Number of atoms: 3273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 3273 Classifications: {'RNA': 154} Modifications used: {'rna2p_pur': 16, 'rna2p_pyr': 12, 'rna3p_pur': 62, 'rna3p_pyr': 64} Link IDs: {'rna2p': 27, 'rna3p': 126} Chain breaks: 1 Chain: "3" Number of atoms: 2494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 2494 Classifications: {'RNA': 117} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 7, 'rna3p_pur': 55, 'rna3p_pyr': 49} Link IDs: {'rna2p': 12, 'rna3p': 104} Chain breaks: 1 Chain: "4" Number of atoms: 3945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 509, 3945 Classifications: {'peptide': 509} Link IDs: {'PTRANS': 26, 'TRANS': 482} Chain breaks: 6 Chain: "5" Number of atoms: 681 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 681 Classifications: {'peptide': 78} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 77} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 1863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1863 Classifications: {'peptide': 245} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 233} Chain: "B" Number of atoms: 3081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3081 Classifications: {'peptide': 386} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 371} Chain: "C" Number of atoms: 2749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2749 Classifications: {'peptide': 361} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 343} Chain: "D" Number of atoms: 1969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1969 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 8, 'TRANS': 234} Chain breaks: 1 Chain: "E" Number of atoms: 1239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1239 Classifications: {'peptide': 156} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 147} Chain breaks: 1 Chain: "F" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1744 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 10, 'TRANS': 205} Chain: "G" Number of atoms: 1784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1784 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 12, 'TRANS': 215} Chain: "H" Number of atoms: 1486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1486 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 4, 'TRANS': 182} Chain: "I" Number of atoms: 1051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1051 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 4, 'TRANS': 125} Chain: "J" Number of atoms: 1344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1344 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 5, 'TRANS': 162} Chain: "K" Number of atoms: 1875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1875 Classifications: {'peptide': 234} Link IDs: {'PTRANS': 6, 'TRANS': 227} Chain breaks: 3 Chain: "L" Number of atoms: 1456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1456 Classifications: {'peptide': 181} Link IDs: {'PTRANS': 8, 'TRANS': 172} Chain: "M" Number of atoms: 1040 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1040 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 4, 'TRANS': 129} Chain: "N" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1720 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 7, 'TRANS': 195} Chain: "O" Number of atoms: 1555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1555 Classifications: {'peptide': 197} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 188} Chain: "P" Number of atoms: 1360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1360 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 5, 'TRANS': 165} Chain breaks: 1 Chain: "Q" Number of atoms: 1110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1110 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 7, 'TRANS': 136} Chain: "R" Number of atoms: 1219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1219 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 2, 'TRANS': 148} Chain: "S" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1437 Classifications: {'peptide': 171} Link IDs: {'CIS': 1, 'PTRANS': 7, 'TRANS': 162} Chain: "T" Number of atoms: 983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 983 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 5, 'TRANS': 118} Chain breaks: 1 Chain: "U" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 800 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 3, 'TRANS': 97} Chain: "V" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 993 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 7, 'TRANS': 126} Chain: "W" Number of atoms: 1877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1877 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 9, 'TRANS': 223} Chain: "X" Number of atoms: 1092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1092 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 6, 'TRANS': 133} Chain: "Y" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 984 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 5, 'TRANS': 119} Chain: "Z" Number of atoms: 1092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1092 Classifications: {'peptide': 135} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 127} Chain: "a" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 735 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 5, 'TRANS': 87} Chain: "b" Number of atoms: 4953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 613, 4953 Classifications: {'peptide': 613} Link IDs: {'PTRANS': 23, 'TRANS': 589} Chain breaks: 6 Chain: "c" Number of atoms: 872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 872 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 2, 'TRANS': 106} Chain breaks: 2 Chain: "d" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 856 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 4, 'TRANS': 100} Chain: "e" Number of atoms: 1020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1020 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain: "f" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 850 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 101} Chain: "g" Number of atoms: 846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 846 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 4, 'TRANS': 102} Chain: "h" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 969 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "i" Number of atoms: 743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 743 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "j" Number of atoms: 665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 665 Classifications: {'peptide': 84} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 81} Chain: "k" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 612 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "l" Number of atoms: 428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 428 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain: "m" Number of atoms: 3546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3546 Classifications: {'peptide': 439} Link IDs: {'PTRANS': 21, 'TRANS': 417} Chain breaks: 3 Chain: "n" Number of atoms: 743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 743 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 95} Chain: "o" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 877 Classifications: {'peptide': 177} Incomplete info: {'truncation_to_alanine': 160} Link IDs: {'PTRANS': 8, 'TRANS': 168} Chain breaks: 4 Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 537 Unresolved non-hydrogen angles: 666 Unresolved non-hydrogen dihedrals: 447 Unresolved non-hydrogen chiralities: 51 Planarities with less than four sites: {'GLN:plan1': 7, 'ASP:plan': 8, 'TYR:plan': 3, 'ASN:plan1': 10, 'HIS:plan': 1, 'PHE:plan': 10, 'GLU:plan': 6, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 232 Chain: "p" Number of atoms: 680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 680 Classifications: {'peptide': 89} Link IDs: {'TRANS': 88} Chain: "q" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 120} Chain breaks: 2 Chain: "r" Number of atoms: 1818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1818 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 10, 'TRANS': 214} Chain breaks: 2 Chain: "s" Number of atoms: 463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 463 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 3, 'TRANS': 52} Chain breaks: 1 Chain: "t" Number of atoms: 3395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3395 Classifications: {'peptide': 431} Link IDs: {'PTRANS': 13, 'TRANS': 417} Chain breaks: 2 Chain: "u" Number of atoms: 1247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1247 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 5, 'TRANS': 142} Chain: "x" Number of atoms: 3033 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3033 Classifications: {'peptide': 388} Link IDs: {'PTRANS': 14, 'TRANS': 373} Chain: "y" Number of atoms: 1841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1841 Classifications: {'peptide': 243} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 233} Chain: "z" Number of atoms: 643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 643 Classifications: {'peptide': 77} Link IDs: {'TRANS': 76} Chain breaks: 1 Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "b" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "j" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "m" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "p" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "u" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 91752 SG CYS I 51 196.387 47.351 124.840 1.00 58.23 S ATOM 91776 SG CYS I 54 197.360 52.125 124.535 1.00 58.05 S ATOM A0KAO SG CYS j 19 141.197 110.970 78.964 1.00 23.91 S ATOM A0KBD SG CYS j 22 141.107 113.481 82.281 1.00 22.98 S ATOM A0KE5 SG CYS j 34 139.753 110.352 83.380 1.00 24.03 S ATOM A0KEN SG CYS j 37 138.294 112.094 80.718 1.00 23.04 S ATOM A0PQD SG CYS p 39 152.933 46.635 65.089 1.00 39.60 S ATOM A0PR0 SG CYS p 42 155.678 46.680 62.715 1.00 42.01 S ATOM A0PU1 SG CYS p 57 156.194 48.192 66.554 1.00 40.02 S ATOM A0V6I SG CYS u 6 207.404 69.345 140.831 1.00 42.13 S ATOM A0VCE SG CYS u 32 207.488 73.311 141.129 1.00 36.96 S ATOM A0VDA SG CYS u 36 206.289 71.933 138.158 1.00 37.25 S Residues with excluded nonbonded symmetry interactions: 197 residue: pdb=" N VAL O 3 " occ=0.50 ... (5 atoms not shown) pdb=" CG2 VAL O 3 " occ=0.50 residue: pdb=" N GLU O 4 " occ=0.50 ... (7 atoms not shown) pdb=" OE2 GLU O 4 " occ=0.50 residue: pdb=" N PRO O 5 " occ=0.50 ... (5 atoms not shown) pdb=" CD PRO O 5 " occ=0.50 residue: pdb=" N VAL O 6 " occ=0.50 ... (5 atoms not shown) pdb=" CG2 VAL O 6 " occ=0.50 residue: pdb=" N VAL O 7 " occ=0.50 ... (5 atoms not shown) pdb=" CG2 VAL O 7 " occ=0.50 residue: pdb=" N VAL O 8 " occ=0.50 ... (5 atoms not shown) pdb=" CG2 VAL O 8 " occ=0.50 residue: pdb=" N ILE O 9 " occ=0.50 ... (6 atoms not shown) pdb=" CD1 ILE O 9 " occ=0.50 residue: pdb=" N ASP O 10 " occ=0.50 ... (6 atoms not shown) pdb=" OD2 ASP O 10 " occ=0.50 residue: pdb=" N GLY O 11 " occ=0.50 ... (2 atoms not shown) pdb=" O GLY O 11 " occ=0.50 residue: pdb=" N LYS O 12 " occ=0.50 ... (7 atoms not shown) pdb=" NZ LYS O 12 " occ=0.50 residue: pdb=" N GLY O 13 " occ=0.50 ... (2 atoms not shown) pdb=" O GLY O 13 " occ=0.50 residue: pdb=" N HIS O 14 " occ=0.50 ... (8 atoms not shown) pdb=" NE2 HIS O 14 " occ=0.50 ... (remaining 185 not shown) Time building chain proxies: 55.11, per 1000 atoms: 0.37 Number of scatterers: 147190 At special positions: 0 Unit cell: (257.337, 203.328, 270.045, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 4 29.99 S 209 16.00 P 3316 15.00 Mg 2 11.99 O 36785 8.00 N 27005 7.00 C 79869 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS g 44 " - pdb=" SG CYS g 47 " distance=2.53 Simple disulfide: pdb=" SG CYS g 44 " - pdb=" SG CYS g 81 " distance=2.61 Simple disulfide: pdb=" SG CYS g 47 " - pdb=" SG CYS g 81 " distance=2.11 Simple disulfide: pdb=" SG CYS g 47 " - pdb=" SG CYS g 84 " distance=1.91 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 58.58 Conformation dependent library (CDL) restraints added in 10.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" NE2 HIS I 67 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 54 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 51 " pdb=" ZN j 100 " pdb="ZN ZN j 100 " - pdb=" SG CYS j 37 " pdb="ZN ZN j 100 " - pdb=" SG CYS j 22 " pdb="ZN ZN j 100 " - pdb=" SG CYS j 19 " pdb="ZN ZN j 100 " - pdb=" SG CYS j 34 " pdb=" ZN p 501 " pdb="ZN ZN p 501 " - pdb=" SG CYS p 42 " pdb="ZN ZN p 501 " - pdb=" SG CYS p 57 " pdb="ZN ZN p 501 " - pdb=" SG CYS p 39 " pdb=" ZN u 201 " pdb="ZN ZN u 201 " - pdb=" SG CYS u 32 " pdb="ZN ZN u 201 " - pdb=" SG CYS u 6 " pdb="ZN ZN u 201 " - pdb=" SG CYS u 36 " Number of angles added : 6 18982 Ramachandran restraints generated. 9491 Oldfield, 0 Emsley, 9491 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 18142 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 356 helices and 82 sheets defined 46.9% alpha, 12.6% beta 1006 base pairs and 1723 stacking pairs defined. Time for finding SS restraints: 78.92 Creating SS restraints... Processing helix chain '4' and resid 21 through 50 removed outlier: 3.887A pdb=" N ILE 4 34 " --> pdb=" O THR 4 30 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA 4 35 " --> pdb=" O ALA 4 31 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASN 4 47 " --> pdb=" O THR 4 43 " (cutoff:3.500A) Processing helix chain '4' and resid 60 through 80 removed outlier: 3.561A pdb=" N LEU 4 67 " --> pdb=" O GLU 4 63 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N GLN 4 78 " --> pdb=" O THR 4 74 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N TYR 4 79 " --> pdb=" O ARG 4 75 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N TYR 4 80 " --> pdb=" O LEU 4 76 " (cutoff:3.500A) Processing helix chain '4' and resid 110 through 119 Processing helix chain '4' and resid 125 through 131 Processing helix chain '4' and resid 178 through 204 removed outlier: 4.058A pdb=" N ASP 4 182 " --> pdb=" O GLY 4 178 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N LEU 4 202 " --> pdb=" O LEU 4 198 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N THR 4 203 " --> pdb=" O ALA 4 199 " (cutoff:3.500A) Proline residue: 4 204 - end of helix Processing helix chain '4' and resid 219 through 235 Processing helix chain '4' and resid 270 through 280 Processing helix chain '4' and resid 372 through 386 removed outlier: 4.258A pdb=" N GLY 4 386 " --> pdb=" O ILE 4 382 " (cutoff:3.500A) Processing helix chain '4' and resid 391 through 396 removed outlier: 3.988A pdb=" N LEU 4 395 " --> pdb=" O LYS 4 391 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N SER 4 396 " --> pdb=" O LEU 4 392 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 391 through 396' Processing helix chain '4' and resid 405 through 427 removed outlier: 3.846A pdb=" N LEU 4 409 " --> pdb=" O ASN 4 405 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU 4 421 " --> pdb=" O LYS 4 417 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU 4 425 " --> pdb=" O LEU 4 421 " (cutoff:3.500A) Processing helix chain '4' and resid 444 through 451 removed outlier: 3.839A pdb=" N ILE 4 448 " --> pdb=" O PRO 4 444 " (cutoff:3.500A) Processing helix chain '4' and resid 466 through 472 removed outlier: 6.096A pdb=" N GLY 4 470 " --> pdb=" O LEU 4 466 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLU 4 472 " --> pdb=" O LEU 4 468 " (cutoff:3.500A) Processing helix chain '4' and resid 481 through 492 removed outlier: 4.179A pdb=" N THR 4 492 " --> pdb=" O LEU 4 488 " (cutoff:3.500A) Processing helix chain '4' and resid 547 through 562 removed outlier: 4.062A pdb=" N LYS 4 561 " --> pdb=" O ALA 4 557 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N ASP 4 562 " --> pdb=" O THR 4 558 " (cutoff:3.500A) Processing helix chain '5' and resid 42 through 106 removed outlier: 4.378A pdb=" N LYS 5 47 " --> pdb=" O SER 5 43 " (cutoff:3.500A) Processing helix chain '5' and resid 107 through 112 removed outlier: 4.964A pdb=" N LYS 5 112 " --> pdb=" O ARG 5 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 5 through 13 removed outlier: 4.053A pdb=" N GLY A 11 " --> pdb=" O ASN A 7 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N ALA A 12 " --> pdb=" O GLN A 8 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N GLY A 13 " --> pdb=" O ARG A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 39 Processing helix chain 'A' and resid 103 through 108 removed outlier: 3.704A pdb=" N VAL A 107 " --> pdb=" O PRO A 103 " (cutoff:3.500A) Proline residue: A 108 - end of helix No H-bonds generated for 'chain 'A' and resid 103 through 108' Processing helix chain 'A' and resid 181 through 193 removed outlier: 3.874A pdb=" N ALA A 185 " --> pdb=" O LYS A 181 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU A 191 " --> pdb=" O HIS A 187 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS A 192 " --> pdb=" O LYS A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 205 removed outlier: 3.712A pdb=" N MET A 204 " --> pdb=" O ARG A 200 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N ASN A 205 " --> pdb=" O GLY A 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 200 through 205' Processing helix chain 'B' and resid 111 through 120 removed outlier: 4.612A pdb=" N LYS B 120 " --> pdb=" O ARG B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 138 removed outlier: 4.147A pdb=" N ALA B 138 " --> pdb=" O SER B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 154 Processing helix chain 'B' and resid 165 through 170 removed outlier: 4.002A pdb=" N THR B 169 " --> pdb=" O GLN B 165 " (cutoff:3.500A) Proline residue: B 170 - end of helix No H-bonds generated for 'chain 'B' and resid 165 through 170' Processing helix chain 'B' and resid 187 through 199 Processing helix chain 'B' and resid 204 through 209 removed outlier: 3.887A pdb=" N VAL B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 233 Processing helix chain 'B' and resid 347 through 352 removed outlier: 4.277A pdb=" N LEU B 351 " --> pdb=" O SER B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 381 Processing helix chain 'C' and resid 31 through 46 removed outlier: 3.792A pdb=" N SER C 41 " --> pdb=" O THR C 37 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LYS C 44 " --> pdb=" O THR C 40 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ASN C 45 " --> pdb=" O SER C 41 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N LYS C 46 " --> pdb=" O VAL C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 132 removed outlier: 4.081A pdb=" N ALA C 130 " --> pdb=" O ILE C 126 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N VAL C 131 " --> pdb=" O ALA C 127 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N ALA C 132 " --> pdb=" O ALA C 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 139 Processing helix chain 'C' and resid 154 through 159 removed outlier: 4.460A pdb=" N SER C 158 " --> pdb=" O THR C 154 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ILE C 159 " --> pdb=" O ASP C 155 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 154 through 159' Processing helix chain 'C' and resid 161 through 173 Processing helix chain 'C' and resid 174 through 185 removed outlier: 3.940A pdb=" N VAL C 181 " --> pdb=" O ASP C 177 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N LEU C 182 " --> pdb=" O LEU C 178 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LYS C 183 " --> pdb=" O LEU C 179 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N LYS C 185 " --> pdb=" O VAL C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 196 removed outlier: 4.864A pdb=" N TYR C 194 " --> pdb=" O GLY C 190 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ARG C 195 " --> pdb=" O LYS C 191 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASN C 196 " --> pdb=" O GLY C 192 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 190 through 196' Processing helix chain 'C' and resid 214 through 221 removed outlier: 5.023A pdb=" N ASN C 221 " --> pdb=" O LYS C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 240 Proline residue: C 240 - end of helix Processing helix chain 'C' and resid 251 through 261 removed outlier: 4.650A pdb=" N ASP C 259 " --> pdb=" O PHE C 255 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N GLN C 260 " --> pdb=" O THR C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 285 through 292 removed outlier: 3.732A pdb=" N ILE C 289 " --> pdb=" O ASP C 285 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N SER C 292 " --> pdb=" O ARG C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 300 removed outlier: 5.487A pdb=" N ARG C 300 " --> pdb=" O GLN C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 328 removed outlier: 3.598A pdb=" N LEU C 327 " --> pdb=" O VAL C 323 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ASN C 328 " --> pdb=" O LEU C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 338 removed outlier: 4.670A pdb=" N VAL C 333 " --> pdb=" O PRO C 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 through 361 Processing helix chain 'D' and resid 9 through 16 Processing helix chain 'D' and resid 20 through 26 removed outlier: 4.755A pdb=" N GLY D 26 " --> pdb=" O ARG D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 38 removed outlier: 3.756A pdb=" N ARG D 35 " --> pdb=" O TYR D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 87 removed outlier: 4.868A pdb=" N LEU D 83 " --> pdb=" O TYR D 79 " (cutoff:3.500A) Proline residue: D 84 - end of helix Processing helix chain 'D' and resid 94 through 114 Processing helix chain 'D' and resid 157 through 170 Processing helix chain 'D' and resid 191 through 201 removed outlier: 3.861A pdb=" N LEU D 195 " --> pdb=" O ASP D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 215 Processing helix chain 'D' and resid 216 through 223 Processing helix chain 'D' and resid 224 through 230 Processing helix chain 'D' and resid 232 through 251 Proline residue: D 251 - end of helix Processing helix chain 'D' and resid 261 through 274 removed outlier: 3.641A pdb=" N TYR D 265 " --> pdb=" O THR D 261 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N TYR D 272 " --> pdb=" O GLU D 268 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N GLN D 274 " --> pdb=" O LYS D 270 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 85 removed outlier: 4.344A pdb=" N VAL E 84 " --> pdb=" O ASN E 80 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N ILE E 85 " --> pdb=" O ALA E 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 80 through 85' Processing helix chain 'E' and resid 102 through 108 removed outlier: 4.146A pdb=" N PHE E 106 " --> pdb=" O ASN E 102 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ALA E 107 " --> pdb=" O VAL E 103 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N LYS E 108 " --> pdb=" O GLU E 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 102 through 108' Processing helix chain 'E' and resid 131 through 150 removed outlier: 4.133A pdb=" N ALA E 144 " --> pdb=" O VAL E 140 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLU E 148 " --> pdb=" O ALA E 144 " (cutoff:3.500A) Processing helix chain 'E' and resid 154 through 162 removed outlier: 5.155A pdb=" N SER E 162 " --> pdb=" O TYR E 158 " (cutoff:3.500A) Processing helix chain 'F' and resid 29 through 73 Processing helix chain 'F' and resid 96 through 107 Processing helix chain 'F' and resid 120 through 131 removed outlier: 3.692A pdb=" N LEU F 126 " --> pdb=" O ALA F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 140 through 151 Processing helix chain 'F' and resid 165 through 173 removed outlier: 4.215A pdb=" N ILE F 169 " --> pdb=" O ASP F 165 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASN F 172 " --> pdb=" O ILE F 168 " (cutoff:3.500A) Processing helix chain 'F' and resid 180 through 191 removed outlier: 4.298A pdb=" N VAL F 191 " --> pdb=" O GLU F 187 " (cutoff:3.500A) Processing helix chain 'F' and resid 194 through 203 removed outlier: 4.876A pdb=" N TRP F 203 " --> pdb=" O ASN F 199 " (cutoff:3.500A) Processing helix chain 'F' and resid 234 through 244 removed outlier: 4.543A pdb=" N LYS F 238 " --> pdb=" O GLU F 234 " (cutoff:3.500A) Processing helix chain 'G' and resid 53 through 69 Processing helix chain 'G' and resid 72 through 81 removed outlier: 4.426A pdb=" N ALA G 76 " --> pdb=" O PRO G 72 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLN G 77 " --> pdb=" O PRO G 73 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N PHE G 78 " --> pdb=" O THR G 74 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N GLN G 79 " --> pdb=" O ILE G 75 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N TYR G 80 " --> pdb=" O ALA G 76 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N THR G 81 " --> pdb=" O GLN G 77 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 72 through 81' Processing helix chain 'G' and resid 83 through 98 removed outlier: 3.885A pdb=" N LYS G 96 " --> pdb=" O LYS G 92 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TYR G 97 " --> pdb=" O LEU G 93 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ARG G 98 " --> pdb=" O PHE G 94 " (cutoff:3.500A) Processing helix chain 'G' and resid 101 through 116 Processing helix chain 'G' and resid 135 through 146 removed outlier: 4.381A pdb=" N GLU G 144 " --> pdb=" O VAL G 140 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ASN G 145 " --> pdb=" O ALA G 141 " (cutoff:3.500A) Processing helix chain 'G' and resid 159 through 174 removed outlier: 4.545A pdb=" N VAL G 163 " --> pdb=" O PRO G 159 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N PHE G 165 " --> pdb=" O GLU G 161 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N LEU G 166 " --> pdb=" O LEU G 162 " (cutoff:3.500A) Proline residue: G 167 - end of helix Processing helix chain 'G' and resid 182 through 191 removed outlier: 3.812A pdb=" N LEU G 186 " --> pdb=" O GLY G 182 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU G 189 " --> pdb=" O ARG G 185 " (cutoff:3.500A) Processing helix chain 'G' and resid 204 through 227 removed outlier: 4.408A pdb=" N ALA G 209 " --> pdb=" O ALA G 205 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N ALA G 210 " --> pdb=" O GLU G 206 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ASP G 224 " --> pdb=" O ALA G 220 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N LYS G 225 " --> pdb=" O ASN G 221 " (cutoff:3.500A) Processing helix chain 'G' and resid 228 through 233 removed outlier: 4.914A pdb=" N HIS G 232 " --> pdb=" O GLU G 228 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N TRP G 233 " --> pdb=" O VAL G 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 228 through 233' Processing helix chain 'G' and resid 239 through 251 Processing helix chain 'H' and resid 61 through 84 Processing helix chain 'H' and resid 150 through 166 removed outlier: 3.590A pdb=" N CYS H 165 " --> pdb=" O LEU H 161 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ARG H 166 " --> pdb=" O GLN H 162 " (cutoff:3.500A) Processing helix chain 'H' and resid 171 through 176 removed outlier: 4.673A pdb=" N LEU H 176 " --> pdb=" O ILE H 172 " (cutoff:3.500A) Processing helix chain 'I' and resid 2 through 9 Processing helix chain 'I' and resid 17 through 27 removed outlier: 3.960A pdb=" N ILE I 21 " --> pdb=" O ASP I 17 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N THR I 27 " --> pdb=" O ASN I 23 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 37 Processing helix chain 'I' and resid 60 through 71 removed outlier: 4.136A pdb=" N GLY I 70 " --> pdb=" O THR I 66 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N LYS I 71 " --> pdb=" O HIS I 67 " (cutoff:3.500A) Processing helix chain 'I' and resid 72 through 82 removed outlier: 3.664A pdb=" N ARG I 76 " --> pdb=" O VAL I 72 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG I 81 " --> pdb=" O VAL I 77 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N GLY I 82 " --> pdb=" O LYS I 78 " (cutoff:3.500A) Processing helix chain 'I' and resid 86 through 95 removed outlier: 4.032A pdb=" N ALA I 94 " --> pdb=" O SER I 90 " (cutoff:3.500A) Processing helix chain 'I' and resid 97 through 131 removed outlier: 3.689A pdb=" N VAL I 112 " --> pdb=" O ILE I 108 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N GLY I 113 " --> pdb=" O THR I 109 " (cutoff:3.500A) Proline residue: I 114 - end of helix Processing helix chain 'J' and resid 27 through 42 Processing helix chain 'J' and resid 73 through 88 removed outlier: 3.710A pdb=" N GLU J 77 " --> pdb=" O GLY J 73 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N VAL J 86 " --> pdb=" O ARG J 82 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LYS J 87 " --> pdb=" O GLY J 83 " (cutoff:3.500A) Processing helix chain 'J' and resid 136 through 141 removed outlier: 3.855A pdb=" N ARG J 140 " --> pdb=" O ALA J 136 " (cutoff:3.500A) Processing helix chain 'J' and resid 155 through 168 removed outlier: 4.732A pdb=" N TYR J 167 " --> pdb=" O PHE J 163 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N ASP J 168 " --> pdb=" O LYS J 164 " (cutoff:3.500A) Processing helix chain 'J' and resid 92 through 97 removed outlier: 4.901A pdb=" N ASN J 95 " --> pdb=" O ARG J 92 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N PHE J 96 " --> pdb=" O ASP J 93 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N SER J 97 " --> pdb=" O ARG J 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 92 through 97' Processing helix chain 'J' and resid 108 through 113 removed outlier: 4.227A pdb=" N GLY J 113 " --> pdb=" O ILE J 110 " (cutoff:3.500A) Processing helix chain 'K' and resid 53 through 65 removed outlier: 5.080A pdb=" N LYS K 57 " --> pdb=" O HIS K 53 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N THR K 60 " --> pdb=" O THR K 56 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N LEU K 61 " --> pdb=" O LYS K 57 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N LEU K 62 " --> pdb=" O ARG K 58 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N LYS K 63 " --> pdb=" O LEU K 59 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N HIS K 64 " --> pdb=" O THR K 60 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N HIS K 65 " --> pdb=" O LEU K 61 " (cutoff:3.500A) Processing helix chain 'K' and resid 66 through 85 removed outlier: 4.041A pdb=" N ARG K 70 " --> pdb=" O ASN K 66 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE K 81 " --> pdb=" O PHE K 77 " (cutoff:3.500A) Proline residue: K 82 - end of helix Processing helix chain 'K' and resid 89 through 104 Proline residue: K 99 - end of helix removed outlier: 5.031A pdb=" N CYS K 102 " --> pdb=" O ILE K 98 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ASP K 103 " --> pdb=" O PRO K 99 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N GLU K 104 " --> pdb=" O LEU K 100 " (cutoff:3.500A) Processing helix chain 'K' and resid 105 through 123 Processing helix chain 'K' and resid 124 through 131 Processing helix chain 'K' and resid 132 through 144 removed outlier: 3.509A pdb=" N THR K 143 " --> pdb=" O ASN K 139 " (cutoff:3.500A) Processing helix chain 'K' and resid 146 through 164 removed outlier: 3.608A pdb=" N ASP K 152 " --> pdb=" O GLN K 148 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N SER K 153 " --> pdb=" O ILE K 149 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N THR K 154 " --> pdb=" O GLN K 150 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N LYS K 155 " --> pdb=" O ALA K 151 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N PHE K 156 " --> pdb=" O ASP K 152 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N TYR K 163 " --> pdb=" O HIS K 159 " (cutoff:3.500A) Processing helix chain 'K' and resid 165 through 172 removed outlier: 4.087A pdb=" N VAL K 169 " --> pdb=" O GLY K 165 " (cutoff:3.500A) Processing helix chain 'K' and resid 173 through 185 removed outlier: 3.514A pdb=" N GLY K 185 " --> pdb=" O PHE K 181 " (cutoff:3.500A) Processing helix chain 'K' and resid 205 through 223 removed outlier: 4.393A pdb=" N THR K 209 " --> pdb=" O ALA K 205 " (cutoff:3.500A) Processing helix chain 'K' and resid 294 through 309 removed outlier: 4.552A pdb=" N GLN K 299 " --> pdb=" O VAL K 295 " (cutoff:3.500A) Proline residue: K 302 - end of helix removed outlier: 3.667A pdb=" N ILE K 308 " --> pdb=" O VAL K 304 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N GLU K 309 " --> pdb=" O ARG K 305 " (cutoff:3.500A) Processing helix chain 'K' and resid 317 through 328 removed outlier: 4.657A pdb=" N SER K 321 " --> pdb=" O GLU K 317 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N LYS K 326 " --> pdb=" O ALA K 322 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N THR K 327 " --> pdb=" O ASN K 323 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N LEU K 328 " --> pdb=" O LYS K 324 " (cutoff:3.500A) Processing helix chain 'L' and resid 17 through 22 removed outlier: 4.077A pdb=" N ARG L 21 " --> pdb=" O HIS L 17 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N VAL L 22 " --> pdb=" O TRP L 18 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 17 through 22' Processing helix chain 'L' and resid 27 through 47 Processing helix chain 'L' and resid 76 through 84 Processing helix chain 'L' and resid 86 through 94 Processing helix chain 'L' and resid 105 through 123 Processing helix chain 'L' and resid 140 through 146 Proline residue: L 146 - end of helix Processing helix chain 'L' and resid 165 through 180 Processing helix chain 'L' and resid 181 through 190 Processing helix chain 'M' and resid 59 through 64 removed outlier: 4.103A pdb=" N VAL M 63 " --> pdb=" O ASN M 59 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N VAL M 64 " --> pdb=" O LEU M 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 59 through 64' Processing helix chain 'M' and resid 77 through 89 Processing helix chain 'M' and resid 90 through 98 removed outlier: 5.427A pdb=" N SER M 98 " --> pdb=" O TRP M 94 " (cutoff:3.500A) Processing helix chain 'M' and resid 99 through 112 Processing helix chain 'M' and resid 113 through 135 removed outlier: 3.570A pdb=" N THR M 130 " --> pdb=" O GLN M 126 " (cutoff:3.500A) Processing helix chain 'N' and resid 2 through 14 removed outlier: 4.989A pdb=" N TYR N 6 " --> pdb=" O GLY N 2 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LYS N 13 " --> pdb=" O GLU N 9 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N LYS N 14 " --> pdb=" O LEU N 10 " (cutoff:3.500A) Processing helix chain 'N' and resid 16 through 34 removed outlier: 3.837A pdb=" N TRP N 28 " --> pdb=" O ARG N 24 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N ASN N 34 " --> pdb=" O TYR N 30 " (cutoff:3.500A) Processing helix chain 'N' and resid 44 through 52 Processing helix chain 'N' and resid 97 through 111 Processing helix chain 'N' and resid 139 through 146 removed outlier: 4.128A pdb=" N ASP N 145 " --> pdb=" O ALA N 141 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N ALA N 146 " --> pdb=" O ILE N 142 " (cutoff:3.500A) Processing helix chain 'N' and resid 147 through 153 removed outlier: 6.660A pdb=" N ILE N 151 " --> pdb=" O ARG N 147 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N CYS N 152 " --> pdb=" O TYR N 148 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ASP N 153 " --> pdb=" O ASN N 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 147 through 153' Processing helix chain 'N' and resid 158 through 163 Processing helix chain 'N' and resid 165 through 173 Processing helix chain 'N' and resid 186 through 196 removed outlier: 4.198A pdb=" N THR N 196 " --> pdb=" O LYS N 192 " (cutoff:3.500A) Processing helix chain 'O' and resid 15 through 30 Processing helix chain 'O' and resid 37 through 42 removed outlier: 3.899A pdb=" N LEU O 41 " --> pdb=" O ARG O 37 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N ASN O 42 " --> pdb=" O ALA O 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 37 through 42' Processing helix chain 'O' and resid 46 through 61 removed outlier: 4.094A pdb=" N LYS O 60 " --> pdb=" O ASP O 56 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N ALA O 61 " --> pdb=" O PHE O 57 " (cutoff:3.500A) Processing helix chain 'O' and resid 65 through 70 removed outlier: 4.382A pdb=" N GLY O 69 " --> pdb=" O ASN O 65 " (cutoff:3.500A) Proline residue: O 70 - end of helix No H-bonds generated for 'chain 'O' and resid 65 through 70' Processing helix chain 'O' and resid 75 through 89 removed outlier: 3.941A pdb=" N MET O 87 " --> pdb=" O ALA O 83 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N SER O 89 " --> pdb=" O ARG O 85 " (cutoff:3.500A) Processing helix chain 'O' and resid 92 through 103 removed outlier: 4.015A pdb=" N LEU O 102 " --> pdb=" O ALA O 98 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N LYS O 103 " --> pdb=" O LEU O 99 " (cutoff:3.500A) Processing helix chain 'O' and resid 110 through 116 removed outlier: 7.783A pdb=" N LYS O 114 " --> pdb=" O PRO O 110 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N LYS O 115 " --> pdb=" O PRO O 111 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N LYS O 116 " --> pdb=" O TYR O 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 110 through 116' Processing helix chain 'O' and resid 124 through 129 Processing helix chain 'O' and resid 137 through 146 Processing helix chain 'O' and resid 151 through 184 removed outlier: 3.618A pdb=" N LYS O 155 " --> pdb=" O ASP O 151 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LYS O 159 " --> pdb=" O LYS O 155 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL O 162 " --> pdb=" O ALA O 158 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA O 173 " --> pdb=" O ALA O 169 " (cutoff:3.500A) Processing helix chain 'O' and resid 188 through 198 Processing helix chain 'P' and resid 10 through 15 removed outlier: 4.070A pdb=" N SER P 14 " --> pdb=" O ASN P 10 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N ALA P 15 " --> pdb=" O PRO P 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 10 through 15' Processing helix chain 'P' and resid 25 through 37 removed outlier: 3.667A pdb=" N GLU P 31 " --> pdb=" O LYS P 27 " (cutoff:3.500A) Processing helix chain 'P' and resid 40 through 54 removed outlier: 3.569A pdb=" N LEU P 52 " --> pdb=" O LEU P 48 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASP P 53 " --> pdb=" O GLU P 49 " (cutoff:3.500A) Processing helix chain 'P' and resid 71 through 77 removed outlier: 4.673A pdb=" N GLU P 75 " --> pdb=" O ALA P 71 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N PHE P 76 " --> pdb=" O GLN P 72 " (cutoff:3.500A) Processing helix chain 'P' and resid 84 through 106 Processing helix chain 'P' and resid 169 through 182 Processing helix chain 'Q' and resid 23 through 40 removed outlier: 3.641A pdb=" N PHE Q 35 " --> pdb=" O LYS Q 31 " (cutoff:3.500A) Processing helix chain 'Q' and resid 42 through 55 removed outlier: 4.270A pdb=" N LYS Q 46 " --> pdb=" O ALA Q 42 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N PHE Q 53 " --> pdb=" O LEU Q 49 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LEU Q 54 " --> pdb=" O LYS Q 50 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N SER Q 55 " --> pdb=" O ALA Q 51 " (cutoff:3.500A) Processing helix chain 'Q' and resid 63 through 73 removed outlier: 3.672A pdb=" N GLN Q 73 " --> pdb=" O ARG Q 69 " (cutoff:3.500A) Processing helix chain 'Q' and resid 107 through 118 Processing helix chain 'Q' and resid 123 through 131 Processing helix chain 'R' and resid 4 through 16 Processing helix chain 'R' and resid 18 through 23 removed outlier: 3.608A pdb=" N VAL R 22 " --> pdb=" O GLY R 18 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N TRP R 23 " --> pdb=" O LYS R 19 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 18 through 23' Processing helix chain 'R' and resid 28 through 36 removed outlier: 3.847A pdb=" N ALA R 35 " --> pdb=" O GLU R 31 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N ASN R 36 " --> pdb=" O ILE R 32 " (cutoff:3.500A) Processing helix chain 'R' and resid 37 through 48 removed outlier: 3.516A pdb=" N GLY R 48 " --> pdb=" O LEU R 44 " (cutoff:3.500A) Processing helix chain 'R' and resid 60 through 73 Processing helix chain 'R' and resid 77 through 82 removed outlier: 5.399A pdb=" N LYS R 82 " --> pdb=" O TYR R 78 " (cutoff:3.500A) Processing helix chain 'R' and resid 84 through 113 Proline residue: R 90 - end of helix removed outlier: 6.587A pdb=" N VAL R 93 " --> pdb=" O LEU R 89 " (cutoff:3.500A) Processing helix chain 'R' and resid 116 through 130 removed outlier: 3.691A pdb=" N ASN R 130 " --> pdb=" O GLU R 126 " (cutoff:3.500A) Processing helix chain 'R' and resid 134 through 152 Processing helix chain 'S' and resid 33 through 49 removed outlier: 3.677A pdb=" N LYS S 47 " --> pdb=" O TYR S 43 " (cutoff:3.500A) Processing helix chain 'S' and resid 98 through 114 Processing helix chain 'S' and resid 137 through 145 removed outlier: 4.586A pdb=" N PHE S 143 " --> pdb=" O TYR S 139 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LEU S 144 " --> pdb=" O VAL S 140 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N THR S 145 " --> pdb=" O LYS S 141 " (cutoff:3.500A) Processing helix chain 'T' and resid 26 through 32 removed outlier: 4.662A pdb=" N TYR T 30 " --> pdb=" O HIS T 26 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU T 31 " --> pdb=" O LEU T 27 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N LYS T 32 " --> pdb=" O SER T 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 26 through 32' Processing helix chain 'T' and resid 92 through 97 removed outlier: 3.948A pdb=" N ILE T 96 " --> pdb=" O ARG T 92 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N LYS T 97 " --> pdb=" O VAL T 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 92 through 97' Processing helix chain 'T' and resid 102 through 121 Processing helix chain 'U' and resid 19 through 26 removed outlier: 3.613A pdb=" N ASN U 25 " --> pdb=" O SER U 21 " (cutoff:3.500A) Processing helix chain 'U' and resid 29 through 41 removed outlier: 3.928A pdb=" N ASP U 39 " --> pdb=" O LYS U 35 " (cutoff:3.500A) Processing helix chain 'U' and resid 72 through 88 Processing helix chain 'V' and resid 119 through 127 Proline residue: V 127 - end of helix Processing helix chain 'V' and resid 128 through 133 Processing helix chain 'W' and resid 19 through 37 removed outlier: 3.971A pdb=" N LYS W 23 " --> pdb=" O GLY W 19 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ASP W 35 " --> pdb=" O ARG W 31 " (cutoff:3.500A) Processing helix chain 'W' and resid 49 through 61 removed outlier: 4.184A pdb=" N TRP W 60 " --> pdb=" O ILE W 56 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ALA W 61 " --> pdb=" O ARG W 57 " (cutoff:3.500A) Processing helix chain 'W' and resid 69 through 78 Processing helix chain 'W' and resid 88 through 96 removed outlier: 4.333A pdb=" N LEU W 92 " --> pdb=" O ASN W 88 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N LEU W 95 " --> pdb=" O GLN W 91 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N CYS W 96 " --> pdb=" O LEU W 92 " (cutoff:3.500A) Processing helix chain 'W' and resid 108 through 119 removed outlier: 3.616A pdb=" N VAL W 112 " --> pdb=" O ASP W 108 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS W 117 " --> pdb=" O LYS W 113 " (cutoff:3.500A) Processing helix chain 'W' and resid 150 through 155 removed outlier: 3.685A pdb=" N ASP W 154 " --> pdb=" O PRO W 150 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N VAL W 155 " --> pdb=" O ALA W 151 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 150 through 155' Processing helix chain 'W' and resid 158 through 167 removed outlier: 4.484A pdb=" N GLU W 162 " --> pdb=" O ILE W 158 " (cutoff:3.500A) Proline residue: W 163 - end of helix Processing helix chain 'W' and resid 196 through 207 Processing helix chain 'X' and resid 4 through 16 Processing helix chain 'X' and resid 58 through 64 removed outlier: 4.349A pdb=" N GLU X 64 " --> pdb=" O TYR X 60 " (cutoff:3.500A) Processing helix chain 'X' and resid 69 through 79 removed outlier: 3.910A pdb=" N GLU X 77 " --> pdb=" O MET X 73 " (cutoff:3.500A) Processing helix chain 'X' and resid 91 through 103 Processing helix chain 'X' and resid 131 through 140 removed outlier: 3.746A pdb=" N ILE X 135 " --> pdb=" O ASP X 131 " (cutoff:3.500A) Processing helix chain 'Y' and resid 11 through 22 Processing helix chain 'Y' and resid 23 through 32 removed outlier: 4.130A pdb=" N VAL Y 29 " --> pdb=" O SER Y 25 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N SER Y 32 " --> pdb=" O ARG Y 28 " (cutoff:3.500A) Processing helix chain 'Y' and resid 36 through 44 Processing helix chain 'Y' and resid 100 through 105 removed outlier: 3.599A pdb=" N LEU Y 104 " --> pdb=" O HIS Y 100 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N VAL Y 105 " --> pdb=" O PRO Y 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 100 through 105' Processing helix chain 'Y' and resid 112 through 123 Processing helix chain 'Z' and resid 58 through 67 removed outlier: 5.199A pdb=" N VAL Z 62 " --> pdb=" O GLY Z 58 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LYS Z 67 " --> pdb=" O ALA Z 63 " (cutoff:3.500A) Processing helix chain 'Z' and resid 76 through 81 removed outlier: 4.895A pdb=" N LEU Z 81 " --> pdb=" O TYR Z 77 " (cutoff:3.500A) Processing helix chain 'Z' and resid 97 through 102 removed outlier: 4.458A pdb=" N GLU Z 102 " --> pdb=" O THR Z 98 " (cutoff:3.500A) Processing helix chain 'Z' and resid 104 through 125 removed outlier: 7.903A pdb=" N GLU Z 108 " --> pdb=" O PRO Z 104 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU Z 109 " --> pdb=" O SER Z 105 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ALA Z 124 " --> pdb=" O GLU Z 120 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N GLY Z 125 " --> pdb=" O ARG Z 121 " (cutoff:3.500A) Processing helix chain 'Z' and resid 127 through 133 removed outlier: 5.303A pdb=" N LYS Z 133 " --> pdb=" O TRP Z 129 " (cutoff:3.500A) Processing helix chain 'a' and resid 64 through 69 removed outlier: 4.607A pdb=" N PHE a 68 " --> pdb=" O GLN a 64 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N TRP a 69 " --> pdb=" O GLN a 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 64 through 69' Processing helix chain 'a' and resid 77 through 83 removed outlier: 6.119A pdb=" N LEU a 81 " --> pdb=" O LYS a 77 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N ILE a 82 " --> pdb=" O LEU a 78 " (cutoff:3.500A) Proline residue: a 83 - end of helix No H-bonds generated for 'chain 'a' and resid 77 through 83' Processing helix chain 'a' and resid 84 through 94 removed outlier: 3.986A pdb=" N ASP a 88 " --> pdb=" O GLU a 84 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N GLN a 89 " --> pdb=" O ASP a 85 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ALA a 94 " --> pdb=" O TYR a 90 " (cutoff:3.500A) Processing helix chain 'a' and resid 103 through 108 removed outlier: 3.730A pdb=" N ALA a 107 " --> pdb=" O ASP a 103 " (cutoff:3.500A) Processing helix chain 'a' and resid 131 through 142 Processing helix chain 'b' and resid 13 through 29 Processing helix chain 'b' and resid 38 through 66 Processing helix chain 'b' and resid 70 through 75 removed outlier: 4.125A pdb=" N VAL b 74 " --> pdb=" O ASN b 70 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N HIS b 75 " --> pdb=" O ILE b 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 70 through 75' Processing helix chain 'b' and resid 76 through 86 Processing helix chain 'b' and resid 87 through 102 Processing helix chain 'b' and resid 104 through 120 removed outlier: 4.561A pdb=" N PHE b 118 " --> pdb=" O ARG b 114 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLY b 119 " --> pdb=" O LEU b 115 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N GLN b 120 " --> pdb=" O LEU b 116 " (cutoff:3.500A) Processing helix chain 'b' and resid 121 through 144 removed outlier: 3.731A pdb=" N LEU b 143 " --> pdb=" O ILE b 139 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ARG b 144 " --> pdb=" O VAL b 140 " (cutoff:3.500A) Processing helix chain 'b' and resid 145 through 161 removed outlier: 3.606A pdb=" N GLN b 152 " --> pdb=" O ALA b 148 " (cutoff:3.500A) Proline residue: b 161 - end of helix Processing helix chain 'b' and resid 179 through 188 removed outlier: 3.544A pdb=" N LEU b 184 " --> pdb=" O LYS b 180 " (cutoff:3.500A) Processing helix chain 'b' and resid 233 through 246 removed outlier: 3.588A pdb=" N GLN b 238 " --> pdb=" O ASN b 234 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N SER b 239 " --> pdb=" O ILE b 235 " (cutoff:3.500A) Processing helix chain 'b' and resid 263 through 279 Proline residue: b 276 - end of helix removed outlier: 3.846A pdb=" N ALA b 279 " --> pdb=" O LYS b 275 " (cutoff:3.500A) Processing helix chain 'b' and resid 299 through 312 removed outlier: 4.684A pdb=" N ALA b 303 " --> pdb=" O ASP b 299 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU b 306 " --> pdb=" O ARG b 302 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N VAL b 309 " --> pdb=" O LEU b 305 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N VAL b 312 " --> pdb=" O SER b 308 " (cutoff:3.500A) Processing helix chain 'b' and resid 324 through 347 removed outlier: 4.629A pdb=" N VAL b 328 " --> pdb=" O LEU b 324 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N MET b 329 " --> pdb=" O GLU b 325 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N SER b 342 " --> pdb=" O LYS b 338 " (cutoff:3.500A) Processing helix chain 'b' and resid 379 through 385 removed outlier: 4.203A pdb=" N LYS b 383 " --> pdb=" O PRO b 379 " (cutoff:3.500A) Processing helix chain 'b' and resid 398 through 407 removed outlier: 4.446A pdb=" N ILE b 402 " --> pdb=" O LEU b 398 " (cutoff:3.500A) Processing helix chain 'b' and resid 440 through 445 removed outlier: 3.715A pdb=" N PHE b 444 " --> pdb=" O ASN b 440 " (cutoff:3.500A) Processing helix chain 'b' and resid 448 through 467 removed outlier: 4.743A pdb=" N LYS b 452 " --> pdb=" O GLU b 448 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLY b 467 " --> pdb=" O LEU b 463 " (cutoff:3.500A) Processing helix chain 'b' and resid 482 through 511 removed outlier: 5.990A pdb=" N VAL b 486 " --> pdb=" O GLU b 482 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASN b 509 " --> pdb=" O ALA b 505 " (cutoff:3.500A) Processing helix chain 'b' and resid 520 through 525 removed outlier: 3.878A pdb=" N LEU b 524 " --> pdb=" O PRO b 520 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N THR b 525 " --> pdb=" O ARG b 521 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 520 through 525' Processing helix chain 'b' and resid 527 through 539 removed outlier: 4.527A pdb=" N MET b 531 " --> pdb=" O SER b 527 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N GLU b 532 " --> pdb=" O PHE b 528 " (cutoff:3.500A) Processing helix chain 'b' and resid 542 through 557 removed outlier: 4.057A pdb=" N ASP b 547 " --> pdb=" O SER b 543 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N LYS b 548 " --> pdb=" O ALA b 544 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ARG b 557 " --> pdb=" O ALA b 553 " (cutoff:3.500A) Processing helix chain 'b' and resid 561 through 570 removed outlier: 5.920A pdb=" N ASP b 569 " --> pdb=" O VAL b 565 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N GLN b 570 " --> pdb=" O VAL b 566 " (cutoff:3.500A) Processing helix chain 'b' and resid 595 through 617 removed outlier: 4.250A pdb=" N ARG b 611 " --> pdb=" O LYS b 607 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N GLU b 612 " --> pdb=" O MET b 608 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N ARG b 613 " --> pdb=" O GLU b 609 " (cutoff:3.500A) Processing helix chain 'b' and resid 631 through 636 removed outlier: 4.738A pdb=" N PHE b 635 " --> pdb=" O SER b 631 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N SER b 636 " --> pdb=" O LYS b 632 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 631 through 636' Processing helix chain 'c' and resid 10 through 34 removed outlier: 5.112A pdb=" N SER c 14 " --> pdb=" O PRO c 10 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLY c 34 " --> pdb=" O ARG c 30 " (cutoff:3.500A) Processing helix chain 'c' and resid 52 through 64 Processing helix chain 'c' and resid 90 through 113 Processing helix chain 'c' and resid 138 through 153 removed outlier: 3.779A pdb=" N ASP c 153 " --> pdb=" O SER c 149 " (cutoff:3.500A) Processing helix chain 'd' and resid 15 through 21 removed outlier: 4.048A pdb=" N ARG d 19 " --> pdb=" O ASN d 15 " (cutoff:3.500A) Processing helix chain 'd' and resid 27 through 44 Processing helix chain 'd' and resid 52 through 61 Processing helix chain 'e' and resid 21 through 26 removed outlier: 5.186A pdb=" N HIS e 26 " --> pdb=" O SER e 22 " (cutoff:3.500A) Processing helix chain 'e' and resid 40 through 45 Processing helix chain 'e' and resid 54 through 59 removed outlier: 4.328A pdb=" N GLY e 58 " --> pdb=" O LYS e 54 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N SER e 59 " --> pdb=" O ILE e 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 54 through 59' Processing helix chain 'e' and resid 78 through 87 removed outlier: 4.463A pdb=" N LEU e 85 " --> pdb=" O ASP e 81 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N THR e 86 " --> pdb=" O LEU e 82 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N MET e 87 " --> pdb=" O GLU e 83 " (cutoff:3.500A) Processing helix chain 'e' and resid 101 through 116 removed outlier: 4.111A pdb=" N VAL e 107 " --> pdb=" O LYS e 103 " (cutoff:3.500A) Processing helix chain 'f' and resid 37 through 45 removed outlier: 4.635A pdb=" N PHE f 43 " --> pdb=" O GLN f 39 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N TYR f 44 " --> pdb=" O ASP f 40 " (cutoff:3.500A) Processing helix chain 'g' and resid 58 through 66 removed outlier: 4.081A pdb=" N TYR g 62 " --> pdb=" O ARG g 58 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ALA g 63 " --> pdb=" O PRO g 59 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N THR g 64 " --> pdb=" O ARG g 60 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL g 65 " --> pdb=" O GLN g 61 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N SER g 66 " --> pdb=" O TYR g 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 58 through 66' Processing helix chain 'g' and resid 81 through 108 removed outlier: 6.113A pdb=" N VAL g 85 " --> pdb=" O CYS g 81 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ARG g 88 " --> pdb=" O CYS g 84 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ILE g 100 " --> pdb=" O GLU g 96 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N VAL g 101 " --> pdb=" O GLU g 97 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLN g 108 " --> pdb=" O VAL g 104 " (cutoff:3.500A) Processing helix chain 'h' and resid 5 through 13 removed outlier: 4.034A pdb=" N THR h 11 " --> pdb=" O TYR h 7 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LYS h 12 " --> pdb=" O GLU h 8 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N SER h 13 " --> pdb=" O LEU h 9 " (cutoff:3.500A) Processing helix chain 'h' and resid 14 through 36 removed outlier: 3.565A pdb=" N VAL h 33 " --> pdb=" O ALA h 29 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLN h 34 " --> pdb=" O GLU h 30 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LEU h 36 " --> pdb=" O LYS h 32 " (cutoff:3.500A) Processing helix chain 'h' and resid 42 through 71 removed outlier: 4.004A pdb=" N THR h 46 " --> pdb=" O PRO h 42 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA h 52 " --> pdb=" O ARG h 48 " (cutoff:3.500A) Processing helix chain 'h' and resid 77 through 82 removed outlier: 5.255A pdb=" N ALA h 82 " --> pdb=" O LYS h 78 " (cutoff:3.500A) Processing helix chain 'h' and resid 85 through 91 Processing helix chain 'h' and resid 93 through 99 Processing helix chain 'h' and resid 101 through 111 Processing helix chain 'i' and resid 25 through 30 removed outlier: 4.447A pdb=" N LYS i 29 " --> pdb=" O LYS i 25 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N LYS i 30 " --> pdb=" O ILE i 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 25 through 30' Processing helix chain 'i' and resid 34 through 49 Processing helix chain 'i' and resid 51 through 64 removed outlier: 3.557A pdb=" N ARG i 62 " --> pdb=" O ILE i 58 " (cutoff:3.500A) Processing helix chain 'i' and resid 65 through 78 removed outlier: 3.732A pdb=" N ALA i 69 " --> pdb=" O GLY i 65 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N GLY i 78 " --> pdb=" O LYS i 74 " (cutoff:3.500A) Processing helix chain 'i' and resid 79 through 98 removed outlier: 3.721A pdb=" N ALA i 85 " --> pdb=" O THR i 81 " (cutoff:3.500A) Processing helix chain 'j' and resid 4 through 11 removed outlier: 4.081A pdb=" N GLY j 9 " --> pdb=" O THR j 5 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N LYS j 10 " --> pdb=" O PRO j 6 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N ARG j 11 " --> pdb=" O SER j 7 " (cutoff:3.500A) Processing helix chain 'j' and resid 50 through 58 removed outlier: 3.709A pdb=" N LYS j 54 " --> pdb=" O GLY j 50 " (cutoff:3.500A) Processing helix chain 'j' and resid 66 through 77 removed outlier: 4.098A pdb=" N VAL j 70 " --> pdb=" O TYR j 66 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N SER j 71 " --> pdb=" O LEU j 67 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N ARG j 72 " --> pdb=" O LYS j 68 " (cutoff:3.500A) Processing helix chain 'k' and resid 7 through 17 removed outlier: 4.283A pdb=" N PHE k 11 " --> pdb=" O ASP k 7 " (cutoff:3.500A) Processing helix chain 'k' and resid 58 through 69 Processing helix chain 'l' and resid 6 through 21 removed outlier: 5.066A pdb=" N ARG l 21 " --> pdb=" O LYS l 17 " (cutoff:3.500A) Processing helix chain 'l' and resid 24 through 30 removed outlier: 4.310A pdb=" N ARG l 28 " --> pdb=" O PRO l 24 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LEU l 29 " --> pdb=" O GLN l 25 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ARG l 30 " --> pdb=" O TRP l 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 24 through 30' Processing helix chain 'm' and resid 6 through 15 Processing helix chain 'm' and resid 32 through 44 removed outlier: 3.532A pdb=" N LYS m 37 " --> pdb=" O SER m 33 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N TYR m 42 " --> pdb=" O PHE m 38 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N THR m 43 " --> pdb=" O LEU m 39 " (cutoff:3.500A) Processing helix chain 'm' and resid 74 through 79 removed outlier: 5.390A pdb=" N PHE m 78 " --> pdb=" O ASP m 74 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N GLY m 79 " --> pdb=" O ARG m 75 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 74 through 79' Processing helix chain 'm' and resid 85 through 103 removed outlier: 3.941A pdb=" N LYS m 101 " --> pdb=" O GLY m 97 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ASP m 102 " --> pdb=" O GLU m 98 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N THR m 103 " --> pdb=" O THR m 99 " (cutoff:3.500A) Processing helix chain 'm' and resid 109 through 114 removed outlier: 6.457A pdb=" N LEU m 113 " --> pdb=" O ARG m 109 " (cutoff:3.500A) Proline residue: m 114 - end of helix No H-bonds generated for 'chain 'm' and resid 109 through 114' Processing helix chain 'm' and resid 131 through 136 removed outlier: 4.397A pdb=" N SER m 136 " --> pdb=" O LEU m 132 " (cutoff:3.500A) Processing helix chain 'm' and resid 156 through 179 removed outlier: 4.539A pdb=" N LEU m 160 " --> pdb=" O ASN m 156 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N VAL m 161 " --> pdb=" O LEU m 157 " (cutoff:3.500A) Processing helix chain 'm' and resid 200 through 206 removed outlier: 4.755A pdb=" N SER m 204 " --> pdb=" O GLU m 200 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N LYS m 205 " --> pdb=" O ALA m 201 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N GLY m 206 " --> pdb=" O ILE m 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 200 through 206' Processing helix chain 'm' and resid 208 through 222 Processing helix chain 'm' and resid 233 through 238 Processing helix chain 'm' and resid 239 through 249 removed outlier: 3.847A pdb=" N GLU m 243 " --> pdb=" O CYS m 239 " (cutoff:3.500A) Processing helix chain 'm' and resid 261 through 266 removed outlier: 4.245A pdb=" N VAL m 265 " --> pdb=" O LYS m 261 " (cutoff:3.500A) Proline residue: m 266 - end of helix No H-bonds generated for 'chain 'm' and resid 261 through 266' Processing helix chain 'm' and resid 267 through 281 removed outlier: 3.829A pdb=" N LYS m 279 " --> pdb=" O LYS m 275 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N GLU m 280 " --> pdb=" O HIS m 276 " (cutoff:3.500A) Processing helix chain 'm' and resid 295 through 311 removed outlier: 3.524A pdb=" N THR m 311 " --> pdb=" O SER m 307 " (cutoff:3.500A) Processing helix chain 'm' and resid 327 through 337 Processing helix chain 'm' and resid 378 through 386 removed outlier: 4.851A pdb=" N GLY m 386 " --> pdb=" O ILE m 382 " (cutoff:3.500A) Processing helix chain 'm' and resid 389 through 394 removed outlier: 4.337A pdb=" N VAL m 393 " --> pdb=" O ARG m 389 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N THR m 394 " --> pdb=" O VAL m 390 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 389 through 394' Processing helix chain 'm' and resid 396 through 407 removed outlier: 4.210A pdb=" N ILE m 400 " --> pdb=" O PRO m 396 " (cutoff:3.500A) Proline residue: m 401 - end of helix Processing helix chain 'm' and resid 408 through 417 removed outlier: 3.532A pdb=" N TYR m 416 " --> pdb=" O LEU m 412 " (cutoff:3.500A) Processing helix chain 'm' and resid 423 through 436 Processing helix chain 'm' and resid 445 through 460 removed outlier: 3.537A pdb=" N VAL m 449 " --> pdb=" O ASP m 445 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASN m 458 " --> pdb=" O LEU m 454 " (cutoff:3.500A) Processing helix chain 'n' and resid 9 through 20 Processing helix chain 'n' and resid 26 through 37 Processing helix chain 'n' and resid 49 through 64 Processing helix chain 'n' and resid 73 through 82 Processing helix chain 'n' and resid 99 through 104 removed outlier: 4.824A pdb=" N LEU n 104 " --> pdb=" O ILE n 100 " (cutoff:3.500A) Processing helix chain 'o' and resid 7 through 24 removed outlier: 3.682A pdb=" N HIS o 12 " --> pdb=" O GLN o 8 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ASN o 21 " --> pdb=" O LEU o 17 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR o 23 " --> pdb=" O TYR o 19 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N LYS o 24 " --> pdb=" O SER o 20 " (cutoff:3.500A) Processing helix chain 'o' and resid 70 through 79 removed outlier: 3.782A pdb=" N ASP o 75 " --> pdb=" O ALA o 71 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ARG o 76 " --> pdb=" O PHE o 72 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N SER o 79 " --> pdb=" O ASP o 75 " (cutoff:3.500A) Processing helix chain 'o' and resid 86 through 94 removed outlier: 4.153A pdb=" N LEU o 90 " --> pdb=" O SER o 86 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS o 92 " --> pdb=" O ASP o 88 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N LEU o 93 " --> pdb=" O ASP o 89 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ASN o 94 " --> pdb=" O LEU o 90 " (cutoff:3.500A) Processing helix chain 'o' and resid 96 through 107 removed outlier: 3.527A pdb=" N LEU o 103 " --> pdb=" O LEU o 99 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER o 104 " --> pdb=" O ILE o 100 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N TYR o 107 " --> pdb=" O LEU o 103 " (cutoff:3.500A) Processing helix chain 'o' and resid 115 through 124 removed outlier: 4.582A pdb=" N GLN o 119 " --> pdb=" O VAL o 115 " (cutoff:3.500A) Proline residue: o 121 - end of helix Processing helix chain 'o' and resid 125 through 132 removed outlier: 4.640A pdb=" N SER o 129 " --> pdb=" O GLY o 125 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N LYS o 130 " --> pdb=" O PRO o 126 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N ALA o 131 " --> pdb=" O GLN o 127 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N GLY o 132 " --> pdb=" O LEU o 128 " (cutoff:3.500A) No H-bonds generated for 'chain 'o' and resid 125 through 132' Processing helix chain 'o' and resid 179 through 194 removed outlier: 4.662A pdb=" N ILE o 183 " --> pdb=" O LEU o 179 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LEU o 184 " --> pdb=" O VAL o 180 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N PHE o 189 " --> pdb=" O MET o 185 " (cutoff:3.500A) Processing helix chain 'p' and resid 19 through 35 removed outlier: 3.747A pdb=" N LEU p 29 " --> pdb=" O GLN p 25 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLN p 32 " --> pdb=" O LYS p 28 " (cutoff:3.500A) Processing helix chain 'p' and resid 73 through 90 removed outlier: 3.736A pdb=" N MET p 89 " --> pdb=" O ARG p 85 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL p 90 " --> pdb=" O LEU p 86 " (cutoff:3.500A) Processing helix chain 'p' and resid 9 through 14 removed outlier: 3.754A pdb=" N LYS p 13 " --> pdb=" O ILE p 10 " (cutoff:3.500A) Processing helix chain 'q' and resid 38 through 51 removed outlier: 3.808A pdb=" N VAL q 42 " --> pdb=" O SER q 38 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N GLY q 43 " --> pdb=" O PRO q 39 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLU q 44 " --> pdb=" O LYS q 40 " (cutoff:3.500A) Processing helix chain 'q' and resid 76 through 85 Processing helix chain 'q' and resid 105 through 117 removed outlier: 6.533A pdb=" N ILE q 109 " --> pdb=" O GLN q 105 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ILE q 110 " --> pdb=" O LEU q 106 " (cutoff:3.500A) Processing helix chain 'q' and resid 124 through 140 removed outlier: 3.980A pdb=" N LYS q 130 " --> pdb=" O ALA q 126 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N THR q 135 " --> pdb=" O GLU q 131 " (cutoff:3.500A) Processing helix chain 'q' and resid 147 through 158 removed outlier: 3.590A pdb=" N ILE q 151 " --> pdb=" O ASN q 147 " (cutoff:3.500A) Processing helix chain 'r' and resid 5 through 14 Processing helix chain 'r' and resid 21 through 35 removed outlier: 4.450A pdb=" N SER r 32 " --> pdb=" O GLU r 28 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N HIS r 33 " --> pdb=" O ALA r 29 " (cutoff:3.500A) Processing helix chain 'r' and resid 44 through 72 Processing helix chain 'r' and resid 88 through 93 removed outlier: 5.237A pdb=" N ASP r 93 " --> pdb=" O THR r 89 " (cutoff:3.500A) Processing helix chain 'r' and resid 129 through 134 Processing helix chain 'r' and resid 174 through 179 removed outlier: 3.848A pdb=" N ARG r 178 " --> pdb=" O PRO r 174 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N GLN r 179 " --> pdb=" O SER r 175 " (cutoff:3.500A) No H-bonds generated for 'chain 'r' and resid 174 through 179' Processing helix chain 'r' and resid 206 through 213 removed outlier: 4.399A pdb=" N THR r 210 " --> pdb=" O SER r 206 " (cutoff:3.500A) Processing helix chain 'r' and resid 248 through 253 removed outlier: 3.544A pdb=" N ASP r 252 " --> pdb=" O GLU r 248 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N GLY r 253 " --> pdb=" O PRO r 249 " (cutoff:3.500A) No H-bonds generated for 'chain 'r' and resid 248 through 253' Processing helix chain 's' and resid 12 through 35 removed outlier: 4.305A pdb=" N LYS s 16 " --> pdb=" O SER s 12 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LYS s 28 " --> pdb=" O SER s 24 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LYS s 35 " --> pdb=" O LYS s 31 " (cutoff:3.500A) Processing helix chain 's' and resid 56 through 64 removed outlier: 4.669A pdb=" N ILE s 60 " --> pdb=" O TYR s 56 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N LEU s 61 " --> pdb=" O LYS s 57 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N GLU s 62 " --> pdb=" O ALA s 58 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N GLU s 63 " --> pdb=" O LYS s 59 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N ILE s 64 " --> pdb=" O ILE s 60 " (cutoff:3.500A) No H-bonds generated for 'chain 's' and resid 56 through 64' Processing helix chain 't' and resid 6 through 14 Proline residue: t 11 - end of helix removed outlier: 4.512A pdb=" N ILE t 14 " --> pdb=" O LEU t 10 " (cutoff:3.500A) Processing helix chain 't' and resid 15 through 25 removed outlier: 3.614A pdb=" N ASN t 19 " --> pdb=" O ILE t 15 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ARG t 23 " --> pdb=" O ASN t 19 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASP t 24 " --> pdb=" O LEU t 20 " (cutoff:3.500A) Proline residue: t 25 - end of helix Processing helix chain 't' and resid 26 through 48 removed outlier: 6.643A pdb=" N GLU t 30 " --> pdb=" O GLU t 26 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N GLU t 31 " --> pdb=" O SER t 27 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLN t 35 " --> pdb=" O GLU t 31 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N HIS t 38 " --> pdb=" O GLN t 34 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE t 45 " --> pdb=" O SER t 41 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LEU t 48 " --> pdb=" O ASP t 44 " (cutoff:3.500A) Processing helix chain 't' and resid 81 through 102 removed outlier: 3.692A pdb=" N GLU t 89 " --> pdb=" O SER t 85 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLY t 92 " --> pdb=" O ILE t 88 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N SER t 99 " --> pdb=" O SER t 95 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N CYS t 100 " --> pdb=" O GLN t 96 " (cutoff:3.500A) Proline residue: t 102 - end of helix Processing helix chain 't' and resid 103 through 118 removed outlier: 7.855A pdb=" N ASN t 107 " --> pdb=" O ARG t 103 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N PHE t 108 " --> pdb=" O GLU t 104 " (cutoff:3.500A) Proline residue: t 109 - end of helix removed outlier: 3.811A pdb=" N GLU t 118 " --> pdb=" O GLN t 114 " (cutoff:3.500A) Processing helix chain 't' and resid 124 through 142 removed outlier: 4.427A pdb=" N ASP t 142 " --> pdb=" O LEU t 138 " (cutoff:3.500A) Processing helix chain 't' and resid 145 through 162 removed outlier: 4.374A pdb=" N GLN t 151 " --> pdb=" O GLU t 147 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N SER t 152 " --> pdb=" O GLU t 148 " (cutoff:3.500A) Proline residue: t 155 - end of helix removed outlier: 3.708A pdb=" N VAL t 158 " --> pdb=" O PHE t 154 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N SER t 162 " --> pdb=" O VAL t 158 " (cutoff:3.500A) Processing helix chain 't' and resid 163 through 168 removed outlier: 4.678A pdb=" N LEU t 167 " --> pdb=" O HIS t 163 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N GLY t 168 " --> pdb=" O GLY t 164 " (cutoff:3.500A) No H-bonds generated for 'chain 't' and resid 163 through 168' Processing helix chain 't' and resid 172 through 193 removed outlier: 3.655A pdb=" N THR t 193 " --> pdb=" O LYS t 189 " (cutoff:3.500A) Processing helix chain 't' and resid 197 through 215 removed outlier: 3.706A pdb=" N SER t 203 " --> pdb=" O LYS t 199 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA t 206 " --> pdb=" O LYS t 202 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL t 207 " --> pdb=" O SER t 203 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N CYS t 208 " --> pdb=" O THR t 204 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N GLN t 214 " --> pdb=" O ASN t 210 " (cutoff:3.500A) Proline residue: t 215 - end of helix Processing helix chain 't' and resid 218 through 233 removed outlier: 4.451A pdb=" N ALA t 222 " --> pdb=" O GLN t 218 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LEU t 225 " --> pdb=" O TRP t 221 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU t 228 " --> pdb=" O LYS t 224 " (cutoff:3.500A) Processing helix chain 't' and resid 237 through 250 removed outlier: 3.799A pdb=" N VAL t 241 " --> pdb=" O ASP t 237 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLU t 242 " --> pdb=" O SER t 238 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ILE t 243 " --> pdb=" O ARG t 239 " (cutoff:3.500A) Processing helix chain 't' and resid 252 through 265 removed outlier: 3.575A pdb=" N SER t 258 " --> pdb=" O LYS t 254 " (cutoff:3.500A) Processing helix chain 't' and resid 331 through 336 removed outlier: 3.973A pdb=" N LEU t 335 " --> pdb=" O SER t 331 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU t 336 " --> pdb=" O ALA t 332 " (cutoff:3.500A) No H-bonds generated for 'chain 't' and resid 331 through 336' Processing helix chain 't' and resid 338 through 350 Processing helix chain 't' and resid 360 through 379 removed outlier: 3.743A pdb=" N SER t 366 " --> pdb=" O GLU t 362 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR t 377 " --> pdb=" O ARG t 373 " (cutoff:3.500A) Processing helix chain 't' and resid 383 through 393 removed outlier: 4.800A pdb=" N THR t 387 " --> pdb=" O LEU t 383 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N LEU t 390 " --> pdb=" O TYR t 386 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N LYS t 391 " --> pdb=" O THR t 387 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N TYR t 392 " --> pdb=" O PHE t 388 " (cutoff:3.500A) Processing helix chain 't' and resid 399 through 412 removed outlier: 4.161A pdb=" N ILE t 403 " --> pdb=" O ASP t 399 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA t 408 " --> pdb=" O MET t 404 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N GLN t 409 " --> pdb=" O SER t 405 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA t 410 " --> pdb=" O ALA t 406 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N CYS t 411 " --> pdb=" O CYS t 407 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N HIS t 412 " --> pdb=" O ALA t 408 " (cutoff:3.500A) Processing helix chain 't' and resid 416 through 431 removed outlier: 4.105A pdb=" N ILE t 420 " --> pdb=" O PRO t 416 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N MET t 423 " --> pdb=" O VAL t 419 " (cutoff:3.500A) Processing helix chain 't' and resid 437 through 456 removed outlier: 3.684A pdb=" N ILE t 451 " --> pdb=" O THR t 447 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ARG t 454 " --> pdb=" O GLU t 450 " (cutoff:3.500A) Proline residue: t 456 - end of helix Processing helix chain 't' and resid 460 through 471 removed outlier: 4.588A pdb=" N TYR t 470 " --> pdb=" O ASP t 466 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N LYS t 471 " --> pdb=" O LEU t 467 " (cutoff:3.500A) Processing helix chain 't' and resid 475 through 493 removed outlier: 6.428A pdb=" N ASN t 479 " --> pdb=" O ALA t 475 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N MET t 480 " --> pdb=" O LYS t 476 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ASP t 491 " --> pdb=" O ALA t 487 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N VAL t 492 " --> pdb=" O LEU t 488 " (cutoff:3.500A) Processing helix chain 't' and resid 498 through 503 removed outlier: 5.856A pdb=" N GLY t 503 " --> pdb=" O LYS t 499 " (cutoff:3.500A) Processing helix chain 't' and resid 504 through 515 removed outlier: 4.626A pdb=" N MET t 508 " --> pdb=" O LYS t 504 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N LYS t 515 " --> pdb=" O GLN t 511 " (cutoff:3.500A) Processing helix chain 'u' and resid 33 through 43 Processing helix chain 'u' and resid 45 through 50 removed outlier: 3.541A pdb=" N LEU u 49 " --> pdb=" O ASN u 45 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N LYS u 50 " --> pdb=" O PRO u 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'u' and resid 45 through 50' Processing helix chain 'u' and resid 52 through 60 removed outlier: 4.067A pdb=" N ARG u 56 " --> pdb=" O THR u 52 " (cutoff:3.500A) Processing helix chain 'u' and resid 66 through 71 removed outlier: 4.197A pdb=" N THR u 70 " --> pdb=" O ASP u 66 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N PHE u 71 " --> pdb=" O SER u 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'u' and resid 66 through 71' Processing helix chain 'u' and resid 82 through 131 removed outlier: 3.652A pdb=" N ALA u 94 " --> pdb=" O LEU u 90 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N GLY u 114 " --> pdb=" O ASN u 110 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ASN u 115 " --> pdb=" O ARG u 111 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N LYS u 116 " --> pdb=" O MET u 112 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N GLU u 117 " --> pdb=" O ARG u 113 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LYS u 118 " --> pdb=" O GLY u 114 " (cutoff:3.500A) Proline residue: u 131 - end of helix Processing helix chain 'u' and resid 132 through 148 removed outlier: 3.998A pdb=" N ILE u 136 " --> pdb=" O GLU u 132 " (cutoff:3.500A) Processing helix chain 'x' and resid 239 through 244 removed outlier: 3.580A pdb=" N VAL x 243 " --> pdb=" O PRO x 239 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N LYS x 244 " --> pdb=" O ILE x 240 " (cutoff:3.500A) No H-bonds generated for 'chain 'x' and resid 239 through 244' Processing helix chain 'x' and resid 330 through 337 Processing helix chain 'x' and resid 348 through 365 removed outlier: 3.816A pdb=" N LYS x 354 " --> pdb=" O GLU x 350 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASN x 359 " --> pdb=" O LYS x 355 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ILE x 363 " --> pdb=" O ASN x 359 " (cutoff:3.500A) Processing helix chain 'y' and resid 12 through 17 removed outlier: 4.851A pdb=" N PHE y 16 " --> pdb=" O GLU y 12 " (cutoff:3.500A) Processing helix chain 'y' and resid 32 through 43 removed outlier: 3.891A pdb=" N SER y 36 " --> pdb=" O GLU y 32 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLU y 41 " --> pdb=" O ALA y 37 " (cutoff:3.500A) Processing helix chain 'y' and resid 58 through 63 Processing helix chain 'y' and resid 77 through 88 Processing helix chain 'y' and resid 103 through 108 Processing helix chain 'y' and resid 123 through 132 removed outlier: 4.811A pdb=" N ASP y 131 " --> pdb=" O GLU y 127 " (cutoff:3.500A) Processing helix chain 'y' and resid 147 through 152 Processing helix chain 'y' and resid 166 through 178 removed outlier: 3.703A pdb=" N LEU y 176 " --> pdb=" O GLU y 172 " (cutoff:3.500A) Processing helix chain 'y' and resid 192 through 197 removed outlier: 3.726A pdb=" N GLY y 196 " --> pdb=" O VAL y 192 " (cutoff:3.500A) Processing helix chain 'y' and resid 211 through 223 Processing helix chain 'y' and resid 230 through 237 removed outlier: 5.281A pdb=" N GLY y 234 " --> pdb=" O GLU y 230 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ASN y 235 " --> pdb=" O SER y 231 " (cutoff:3.500A) Processing helix chain 'y' and resid 238 through 244 Processing helix chain 'z' and resid 7 through 21 removed outlier: 3.869A pdb=" N ARG z 19 " --> pdb=" O SER z 15 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLY z 20 " --> pdb=" O VAL z 16 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL z 21 " --> pdb=" O LYS z 17 " (cutoff:3.500A) Processing helix chain 'z' and resid 22 through 51 removed outlier: 3.613A pdb=" N ARG z 29 " --> pdb=" O ALA z 25 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLU z 30 " --> pdb=" O VAL z 26 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLN z 44 " --> pdb=" O ASP z 40 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS z 50 " --> pdb=" O LEU z 46 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N LYS z 51 " --> pdb=" O GLU z 47 " (cutoff:3.500A) Processing helix chain 'z' and resid 84 through 100 Processing sheet with id= 1, first strand: chain '4' and resid 93 through 97 removed outlier: 3.774A pdb=" N ASP 4 137 " --> pdb=" O ILE 4 160 " (cutoff:3.500A) removed outlier: 13.400A pdb=" N THR 4 151 " --> pdb=" O VAL 4 508 " (cutoff:3.500A) removed outlier: 9.063A pdb=" N VAL 4 508 " --> pdb=" O THR 4 151 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N GLU 4 153 " --> pdb=" O THR 4 506 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N THR 4 506 " --> pdb=" O GLU 4 153 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ARG 4 502 " --> pdb=" O THR 4 157 " (cutoff:3.500A) removed outlier: 9.553A pdb=" N VAL 4 159 " --> pdb=" O VAL 4 500 " (cutoff:3.500A) removed outlier: 13.859A pdb=" N VAL 4 500 " --> pdb=" O VAL 4 159 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N LYS 4 322 " --> pdb=" O VAL 4 239 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain '4' and resid 335 through 340 removed outlier: 4.971A pdb=" N ILE 4 437 " --> pdb=" O VAL 4 340 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain '4' and resid 568 through 572 removed outlier: 3.530A pdb=" N THR 4 572 " --> pdb=" O ARG 4 524 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain '4' and resid 242 through 246 Processing sheet with id= 5, first strand: chain '4' and resid 506 through 509 removed outlier: 6.235A pdb=" N THR 4 506 " --> pdb=" O LEU 4 525 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'A' and resid 47 through 50 removed outlier: 3.867A pdb=" N GLN A 47 " --> pdb=" O LYS A 60 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N LYS A 60 " --> pdb=" O LYS A 46 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N GLN A 86 " --> pdb=" O VAL A 45 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'A' and resid 146 through 149 Processing sheet with id= 8, first strand: chain 'A' and resid 58 through 64 Processing sheet with id= 9, first strand: chain 'B' and resid 45 through 50 removed outlier: 3.631A pdb=" N LYS B 50 " --> pdb=" O ARG B 334 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ARG B 334 " --> pdb=" O LYS B 50 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N ILE B 335 " --> pdb=" O VAL B 220 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N VAL B 220 " --> pdb=" O ILE B 335 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'B' and resid 53 through 59 removed outlier: 6.017A pdb=" N ASN B 319 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLY B 288 " --> pdb=" O ASN B 319 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG B 284 " --> pdb=" O MET B 323 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'B' and resid 98 through 101 removed outlier: 3.598A pdb=" N GLY B 98 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 8.289A pdb=" N VAL B 87 " --> pdb=" O ALA B 107 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N THR B 103 " --> pdb=" O GLY B 91 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'B' and resid 177 through 182 removed outlier: 5.695A pdb=" N HIS B 177 " --> pdb=" O THR B 164 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'B' and resid 84 through 90 removed outlier: 6.406A pdb=" N LEU B 161 " --> pdb=" O VAL B 87 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N VAL B 89 " --> pdb=" O ARG B 159 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ARG B 159 " --> pdb=" O VAL B 89 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'B' and resid 213 through 216 removed outlier: 4.416A pdb=" N GLU B 213 " --> pdb=" O ILE B 282 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'C' and resid 4 through 7 Processing sheet with id= 16, first strand: chain 'C' and resid 205 through 208 Processing sheet with id= 17, first strand: chain 'D' and resid 60 through 66 removed outlier: 4.046A pdb=" N VAL D 53 " --> pdb=" O ASP D 147 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'E' and resid 38 through 43 removed outlier: 3.967A pdb=" N THR E 38 " --> pdb=" O TYR E 54 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LYS E 50 " --> pdb=" O LEU E 42 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'F' and resid 133 through 138 removed outlier: 7.435A pdb=" N TYR F 133 " --> pdb=" O ILE F 89 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N SER F 113 " --> pdb=" O ARG F 88 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N ASN F 112 " --> pdb=" O LEU F 207 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU F 207 " --> pdb=" O ASN F 112 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'G' and resid 176 through 181 Processing sheet with id= 21, first strand: chain 'H' and resid 5 through 12 removed outlier: 4.746A pdb=" N GLN H 51 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N LEU H 52 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'H' and resid 17 through 20 removed outlier: 5.902A pdb=" N ARG H 23 " --> pdb=" O LEU H 38 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'H' and resid 100 through 105 removed outlier: 6.055A pdb=" N LYS H 110 " --> pdb=" O VAL H 128 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'H' and resid 132 through 137 removed outlier: 5.309A pdb=" N GLU H 143 " --> pdb=" O SER H 137 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N ASP H 142 " --> pdb=" O TYR H 92 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'I' and resid 49 through 52 removed outlier: 5.281A pdb=" N HIS I 49 " --> pdb=" O MET I 58 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'J' and resid 45 through 49 removed outlier: 6.011A pdb=" N ILE J 65 " --> pdb=" O VAL J 23 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS J 16 " --> pdb=" O VAL J 130 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N SER J 22 " --> pdb=" O GLY J 124 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N GLY J 124 " --> pdb=" O SER J 22 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'L' and resid 55 through 59 Processing sheet with id= 28, first strand: chain 'M' and resid 19 through 24 removed outlier: 4.436A pdb=" N ARG M 19 " --> pdb=" O ILE M 35 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LYS M 31 " --> pdb=" O ILE M 23 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LEU M 45 " --> pdb=" O VAL M 36 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'N' and resid 113 through 116 removed outlier: 6.740A pdb=" N ILE N 133 " --> pdb=" O LEU N 116 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N TYR N 129 " --> pdb=" O VAL N 121 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'O' and resid 6 through 10 Processing sheet with id= 31, first strand: chain 'P' and resid 16 through 20 removed outlier: 6.706A pdb=" N VAL P 149 " --> pdb=" O SER P 115 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'P' and resid 57 through 60 removed outlier: 3.616A pdb=" N PHE P 60 " --> pdb=" O LYS P 80 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N LYS P 80 " --> pdb=" O PHE P 60 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'P' and resid 116 through 122 removed outlier: 3.500A pdb=" N HIS P 116 " --> pdb=" O VAL P 149 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'P' and resid 124 through 131 removed outlier: 3.866A pdb=" N GLN P 125 " --> pdb=" O SER P 141 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER P 141 " --> pdb=" O GLN P 125 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ARG P 127 " --> pdb=" O TYR P 139 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG P 131 " --> pdb=" O ARG P 135 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ARG P 135 " --> pdb=" O ARG P 131 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'Q' and resid 119 through 122 removed outlier: 4.918A pdb=" N THR Q 100 " --> pdb=" O LYS Q 79 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'S' and resid 24 through 31 removed outlier: 6.854A pdb=" N ILE S 10 " --> pdb=" O VAL S 59 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N GLU S 57 " --> pdb=" O ARG S 12 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'S' and resid 87 through 96 removed outlier: 4.149A pdb=" N HIS S 88 " --> pdb=" O TYR S 81 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N TYR S 81 " --> pdb=" O HIS S 88 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N TRP S 78 " --> pdb=" O LEU S 124 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'S' and resid 6 through 10 removed outlier: 4.362A pdb=" N GLU S 6 " --> pdb=" O ILE S 64 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE S 10 " --> pdb=" O SER S 60 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N SER S 60 " --> pdb=" O ILE S 10 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'S' and resid 74 through 78 removed outlier: 4.988A pdb=" N ASN S 74 " --> pdb=" O ILE S 129 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LYS S 125 " --> pdb=" O TRP S 78 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'T' and resid 38 through 43 removed outlier: 4.910A pdb=" N ASP T 38 " --> pdb=" O VAL T 64 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LYS T 60 " --> pdb=" O ILE T 42 " (cutoff:3.500A) removed outlier: 15.699A pdb=" N GLY T 59 " --> pdb=" O MET T 79 " (cutoff:3.500A) removed outlier: 13.237A pdb=" N MET T 79 " --> pdb=" O GLY T 59 " (cutoff:3.500A) removed outlier: 8.418A pdb=" N THR T 61 " --> pdb=" O ASN T 77 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N ASN T 77 " --> pdb=" O THR T 61 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL T 63 " --> pdb=" O ILE T 75 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N TYR T 65 " --> pdb=" O GLY T 73 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N GLY T 73 " --> pdb=" O TYR T 65 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'U' and resid 54 through 58 removed outlier: 5.910A pdb=" N ASN U 101 " --> pdb=" O THR U 14 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N TRP U 92 " --> pdb=" O TYR U 108 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'V' and resid 58 through 61 Processing sheet with id= 43, first strand: chain 'V' and resid 84 through 87 removed outlier: 4.443A pdb=" N VAL V 91 " --> pdb=" O ARG V 87 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'W' and resid 63 through 67 removed outlier: 4.977A pdb=" N VAL W 99 " --> pdb=" O LEU W 45 " (cutoff:3.500A) removed outlier: 8.489A pdb=" N ARG W 38 " --> pdb=" O ASN W 223 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL W 42 " --> pdb=" O ALA W 219 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ALA W 219 " --> pdb=" O VAL W 42 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'W' and resid 120 through 124 removed outlier: 6.198A pdb=" N ARG W 121 " --> pdb=" O GLU W 212 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLU W 212 " --> pdb=" O ARG W 121 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ASP W 123 " --> pdb=" O ALA W 210 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'W' and resid 135 through 139 removed outlier: 6.869A pdb=" N PHE W 135 " --> pdb=" O VAL W 188 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N TYR W 186 " --> pdb=" O ILE W 137 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N GLU W 139 " --> pdb=" O SER W 184 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N SER W 184 " --> pdb=" O GLU W 139 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'W' and resid 173 through 176 Processing sheet with id= 48, first strand: chain 'X' and resid 81 through 86 removed outlier: 3.879A pdb=" N LYS X 120 " --> pdb=" O VAL X 86 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N THR X 119 " --> pdb=" O ARG X 115 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'Y' and resid 72 through 75 Processing sheet with id= 50, first strand: chain 'Z' and resid 9 through 13 removed outlier: 4.417A pdb=" N LYS Z 9 " --> pdb=" O ILE Z 25 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LYS Z 21 " --> pdb=" O VAL Z 13 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N LEU Z 42 " --> pdb=" O VAL Z 26 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N PHE Z 71 " --> pdb=" O GLY Z 45 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'a' and resid 71 through 74 Processing sheet with id= 52, first strand: chain 'a' and resid 99 through 102 removed outlier: 3.528A pdb=" N VAL a 144 " --> pdb=" O VAL a 123 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'b' and resid 203 through 210 removed outlier: 7.091A pdb=" N SER b 203 " --> pdb=" O PRO b 222 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N ARG b 168 " --> pdb=" O ARG b 215 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N THR b 221 " --> pdb=" O ILE b 172 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N GLY b 174 " --> pdb=" O THR b 221 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N SER b 282 " --> pdb=" O SER b 248 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N ASN b 288 " --> pdb=" O MET b 254 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLU b 316 " --> pdb=" O VAL b 283 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'd' and resid 7 through 14 removed outlier: 3.964A pdb=" N VAL d 8 " --> pdb=" O ARG d 77 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N ARG d 72 " --> pdb=" O VAL d 96 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N ASP d 48 " --> pdb=" O LEU d 89 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'e' and resid 71 through 77 Processing sheet with id= 56, first strand: chain 'f' and resid 10 through 15 removed outlier: 6.283A pdb=" N LYS f 10 " --> pdb=" O GLU f 33 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N LEU f 29 " --> pdb=" O LEU f 14 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N VAL f 80 " --> pdb=" O THR f 74 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N THR f 74 " --> pdb=" O VAL f 80 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ARG f 82 " --> pdb=" O THR f 72 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N LYS f 63 " --> pdb=" O ALA f 55 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N LYS f 47 " --> pdb=" O VAL f 71 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ARG f 48 " --> pdb=" O PHE f 101 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'f' and resid 8 through 14 removed outlier: 4.022A pdb=" N ALA f 96 " --> pdb=" O HIS f 13 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'g' and resid 19 through 24 removed outlier: 4.687A pdb=" N LYS g 19 " --> pdb=" O VAL g 35 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'k' and resid 2 through 5 removed outlier: 4.550A pdb=" N VAL k 55 " --> pdb=" O ILE k 5 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N THR k 22 " --> pdb=" O ARG k 46 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ILE k 27 " --> pdb=" O LEU k 78 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'm' and resid 282 through 286 removed outlier: 6.300A pdb=" N TYR m 257 " --> pdb=" O PRO m 282 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N HIS m 254 " --> pdb=" O ASP m 223 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N VAL m 225 " --> pdb=" O HIS m 254 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N CYS m 367 " --> pdb=" O PHE m 320 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N GLY m 322 " --> pdb=" O CYS m 367 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'n' and resid 22 through 25 removed outlier: 6.353A pdb=" N LYS n 22 " --> pdb=" O LEU n 93 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU n 41 " --> pdb=" O ILE n 92 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LYS n 66 " --> pdb=" O LYS n 40 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'o' and resid 64 through 69 removed outlier: 4.184A pdb=" N ALA o 109 " --> pdb=" O SER o 64 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N CYS o 66 " --> pdb=" O ALA o 109 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE o 111 " --> pdb=" O CYS o 66 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'o' and resid 165 through 170 removed outlier: 3.958A pdb=" N LEU o 165 " --> pdb=" O VAL o 36 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N VAL o 32 " --> pdb=" O VAL o 169 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'p' and resid 46 through 50 removed outlier: 8.954A pdb=" N THR p 46 " --> pdb=" O SER p 58 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ILE p 54 " --> pdb=" O GLY p 50 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N GLY p 53 " --> pdb=" O GLY p 66 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N LYS p 62 " --> pdb=" O CYS p 57 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'q' and resid 11 through 16 removed outlier: 3.696A pdb=" N LEU q 15 " --> pdb=" O VAL q 60 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N VAL q 60 " --> pdb=" O LEU q 15 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N THR q 59 " --> pdb=" O VAL q 74 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'r' and resid 148 through 151 Processing sheet with id= 67, first strand: chain 'r' and resid 191 through 195 removed outlier: 3.968A pdb=" N VAL r 191 " --> pdb=" O HIS r 186 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N ASN r 256 " --> pdb=" O THR r 246 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N TYR r 242 " --> pdb=" O LEU r 260 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N THR r 219 " --> pdb=" O VAL r 245 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'u' and resid 3 through 6 removed outlier: 4.377A pdb=" N SER u 11 " --> pdb=" O CYS u 6 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'u' and resid 18 through 23 removed outlier: 3.524A pdb=" N LYS u 27 " --> pdb=" O ARG u 23 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'x' and resid 148 through 152 removed outlier: 6.920A pdb=" N ARG x 158 " --> pdb=" O ALA x 152 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N SER x 157 " --> pdb=" O CYS x 173 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N MET x 159 " --> pdb=" O TRP x 171 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'x' and resid 190 through 195 removed outlier: 5.433A pdb=" N VAL x 200 " --> pdb=" O SER x 195 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N LEU x 212 " --> pdb=" O LEU x 221 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'x' and resid 233 through 238 removed outlier: 4.783A pdb=" N SER x 234 " --> pdb=" O SER x 254 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N ARG x 250 " --> pdb=" O GLU x 238 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N THR x 259 " --> pdb=" O SER x 255 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N TYR x 272 " --> pdb=" O ILE x 262 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'x' and resid 283 through 287 removed outlier: 4.773A pdb=" N LEU x 291 " --> pdb=" O GLY x 287 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ASN x 314 " --> pdb=" O VAL x 303 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 'x' and resid 324 through 329 removed outlier: 4.885A pdb=" N HIS x 325 " --> pdb=" O ALA x 377 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ALA x 377 " --> pdb=" O HIS x 325 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N MET x 373 " --> pdb=" O SER x 329 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N THR x 382 " --> pdb=" O SER x 378 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA x 396 " --> pdb=" O LEU x 385 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 'x' and resid 406 through 411 removed outlier: 3.616A pdb=" N HIS x 407 " --> pdb=" O ALA x 420 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N TYR x 416 " --> pdb=" O SER x 411 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N SER x 425 " --> pdb=" O SER x 421 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER x 438 " --> pdb=" O LEU x 428 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain 'x' and resid 448 through 453 removed outlier: 4.432A pdb=" N GLN x 449 " --> pdb=" O CYS x 462 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N LEU x 458 " --> pdb=" O SER x 453 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N ARG x 457 " --> pdb=" O VAL x 473 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N VAL x 470 " --> pdb=" O SER x 479 " (cutoff:3.500A) Processing sheet with id= 77, first strand: chain 'x' and resid 491 through 495 removed outlier: 6.226A pdb=" N ARG x 500 " --> pdb=" O SER x 495 " (cutoff:3.500A) Processing sheet with id= 78, first strand: chain 'x' and resid 167 through 170 removed outlier: 4.702A pdb=" N HIS x 180 " --> pdb=" O ILE x 170 " (cutoff:3.500A) Processing sheet with id= 79, first strand: chain 'x' and resid 467 through 470 removed outlier: 3.556A pdb=" N VAL x 480 " --> pdb=" O VAL x 470 " (cutoff:3.500A) Processing sheet with id= 80, first strand: chain 'y' and resid 23 through 27 Processing sheet with id= 81, first strand: chain 'y' and resid 114 through 117 Processing sheet with id= 82, first strand: chain 'y' and resid 158 through 161 3222 hydrogen bonds defined for protein. 9582 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2476 hydrogen bonds 3992 hydrogen bond angles 0 basepair planarities 1006 basepair parallelities 1723 stacking parallelities Total time for adding SS restraints: 195.63 Time building geometry restraints manager: 63.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 25868 1.33 - 1.46: 58674 1.46 - 1.58: 65431 1.58 - 1.71: 6596 1.71 - 1.83: 331 Bond restraints: 156900 Sorted by residual: bond pdb=" C1' U 12318 " pdb=" N1 U 12318 " ideal model delta sigma weight residual 1.470 1.571 -0.101 1.50e-02 4.44e+03 4.54e+01 bond pdb=" N1 C 13093 " pdb=" C2 C 13093 " ideal model delta sigma weight residual 1.397 1.491 -0.094 2.00e-02 2.50e+03 2.21e+01 bond pdb=" C4 C 13093 " pdb=" C5 C 13093 " ideal model delta sigma weight residual 1.425 1.511 -0.086 2.00e-02 2.50e+03 1.84e+01 bond pdb=" C VAL V 101 " pdb=" N ILE V 102 " ideal model delta sigma weight residual 1.327 1.440 -0.112 2.97e-02 1.13e+03 1.43e+01 bond pdb=" C GLN B 371 " pdb=" N THR B 372 " ideal model delta sigma weight residual 1.329 1.374 -0.045 1.21e-02 6.83e+03 1.41e+01 ... (remaining 156895 not shown) Histogram of bond angle deviations from ideal: 98.37 - 107.65: 26741 107.65 - 116.92: 106645 116.92 - 126.20: 83080 126.20 - 135.47: 11424 135.47 - 144.75: 6 Bond angle restraints: 227896 Sorted by residual: angle pdb=" C LEU b 385 " pdb=" N LYS b 386 " pdb=" CA LYS b 386 " ideal model delta sigma weight residual 122.19 144.75 -22.56 1.41e+00 5.03e-01 2.56e+02 angle pdb=" C MET V 23 " pdb=" N ASN V 24 " pdb=" CA ASN V 24 " ideal model delta sigma weight residual 120.71 138.55 -17.84 1.42e+00 4.96e-01 1.58e+02 angle pdb=" C ARG u 23 " pdb=" N ASN u 24 " pdb=" CA ASN u 24 " ideal model delta sigma weight residual 120.60 140.42 -19.82 1.60e+00 3.91e-01 1.53e+02 angle pdb=" C ALA y 54 " pdb=" N GLY y 55 " pdb=" CA GLY y 55 " ideal model delta sigma weight residual 120.77 142.20 -21.43 1.74e+00 3.30e-01 1.52e+02 angle pdb=" C ILE V 36 " pdb=" N ILE V 37 " pdb=" CA ILE V 37 " ideal model delta sigma weight residual 120.70 134.80 -14.10 1.25e+00 6.40e-01 1.27e+02 ... (remaining 227891 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.92: 89597 35.92 - 71.84: 8560 71.84 - 107.76: 812 107.76 - 143.68: 29 143.68 - 179.60: 80 Dihedral angle restraints: 99078 sinusoidal: 71062 harmonic: 28016 Sorted by residual: dihedral pdb=" CA GLY V 100 " pdb=" C GLY V 100 " pdb=" N VAL V 101 " pdb=" CA VAL V 101 " ideal model delta harmonic sigma weight residual -180.00 -107.85 -72.15 0 5.00e+00 4.00e-02 2.08e+02 dihedral pdb=" CA PHE y 7 " pdb=" C PHE y 7 " pdb=" N GLU y 8 " pdb=" CA GLU y 8 " ideal model delta harmonic sigma weight residual -180.00 -113.38 -66.62 0 5.00e+00 4.00e-02 1.78e+02 dihedral pdb=" CA ALA V 99 " pdb=" C ALA V 99 " pdb=" N GLY V 100 " pdb=" CA GLY V 100 " ideal model delta harmonic sigma weight residual -180.00 -122.87 -57.13 0 5.00e+00 4.00e-02 1.31e+02 ... (remaining 99075 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.347: 28138 0.347 - 0.694: 60 0.694 - 1.040: 19 1.040 - 1.387: 6 1.387 - 1.734: 34 Chirality restraints: 28257 Sorted by residual: chirality pdb=" CB ILE u 19 " pdb=" CA ILE u 19 " pdb=" CG1 ILE u 19 " pdb=" CG2 ILE u 19 " both_signs ideal model delta sigma weight residual False 2.64 0.91 1.73 2.00e-01 2.50e+01 7.52e+01 chirality pdb=" CG LEU V 17 " pdb=" CB LEU V 17 " pdb=" CD1 LEU V 17 " pdb=" CD2 LEU V 17 " both_signs ideal model delta sigma weight residual False -2.59 -0.88 -1.71 2.00e-01 2.50e+01 7.33e+01 chirality pdb=" CG LEU V 49 " pdb=" CB LEU V 49 " pdb=" CD1 LEU V 49 " pdb=" CD2 LEU V 49 " both_signs ideal model delta sigma weight residual False -2.59 -0.88 -1.71 2.00e-01 2.50e+01 7.31e+01 ... (remaining 28254 not shown) Planarity restraints: 16563 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU o 15 " -0.039 2.00e-02 2.50e+03 7.36e-02 5.42e+01 pdb=" C GLU o 15 " 0.127 2.00e-02 2.50e+03 pdb=" O GLU o 15 " -0.046 2.00e-02 2.50e+03 pdb=" N LEU o 16 " -0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER o 20 " 0.035 2.00e-02 2.50e+03 7.19e-02 5.16e+01 pdb=" C SER o 20 " -0.124 2.00e-02 2.50e+03 pdb=" O SER o 20 " 0.047 2.00e-02 2.50e+03 pdb=" N ASN o 21 " 0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER b 342 " 0.037 2.00e-02 2.50e+03 7.03e-02 4.95e+01 pdb=" C SER b 342 " -0.122 2.00e-02 2.50e+03 pdb=" O SER b 342 " 0.044 2.00e-02 2.50e+03 pdb=" N ARG b 343 " 0.041 2.00e-02 2.50e+03 ... (remaining 16560 not shown) Histogram of nonbonded interaction distances: 1.43 - 2.13: 66 2.13 - 2.82: 39404 2.82 - 3.51: 195128 3.51 - 4.21: 426787 4.21 - 4.90: 622909 Nonbonded interactions: 1284294 Sorted by model distance: nonbonded pdb=" NH2 ARG R 98 " pdb=" OD1 ASN R 130 " model vdw 1.432 2.520 nonbonded pdb=" O ASP b 443 " pdb=" NH1 ARG u 75 " model vdw 1.461 2.520 nonbonded pdb=" OD1 ASN A 140 " pdb=" OE2 GLU A 143 " model vdw 1.492 3.040 nonbonded pdb=" OG SER P 8 " pdb=" OG1 THR c 85 " model vdw 1.648 2.440 nonbonded pdb=" O LYS T 69 " pdb=" OG SER T 70 " model vdw 1.742 2.440 ... (remaining 1284289 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.21 max=1.00 mean=0.99 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: 5.350 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: 0.170 Extract box with map and model: 19.280 Check model and map are aligned: 1.560 Set scattering table: 0.990 Process input model: 524.100 Find NCS groups from input model: 3.560 Set up NCS constraints: 0.370 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:10.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 565.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 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 : 0.004 0.112 156900 Z= 0.264 Angle : 0.871 22.557 227896 Z= 0.492 Chirality : 0.076 1.734 28257 Planarity : 0.007 0.085 16563 Dihedral : 22.492 179.597 80924 Min Nonbonded Distance : 1.432 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.43 % Allowed : 6.76 % Favored : 92.80 % Rotamer: Outliers : 0.17 % Allowed : 20.29 % Favored : 79.53 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 1.94 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.46 % 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: -2.93 (0.07), residues: 9491 helix: -1.26 (0.07), residues: 3735 sheet: -1.54 (0.13), residues: 1217 loop : -2.66 (0.08), residues: 4539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP r 147 HIS 0.011 0.001 HIS T 54 PHE 0.039 0.002 PHE F 229 TYR 0.027 0.002 TYR G 134 ARG 0.011 0.001 ARG L 100 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18982 Ramachandran restraints generated. 9491 Oldfield, 0 Emsley, 9491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18982 Ramachandran restraints generated. 9491 Oldfield, 0 Emsley, 9491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1556 residues out of total 8277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 1542 time to evaluate : 8.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 4 279 LEU cc_start: 0.6891 (tp) cc_final: 0.6637 (mm) REVERT: 4 401 PHE cc_start: 0.8224 (m-80) cc_final: 0.8007 (m-80) REVERT: 4 551 GLN cc_start: 0.4555 (mm-40) cc_final: 0.4272 (mm110) REVERT: 5 64 LEU cc_start: 0.8546 (tp) cc_final: 0.7755 (tp) REVERT: B 318 LYS cc_start: 0.8377 (mmmm) cc_final: 0.8002 (mmpt) REVERT: C 285 ASP cc_start: 0.7603 (t0) cc_final: 0.7182 (t70) REVERT: D 111 GLN cc_start: 0.7413 (tt0) cc_final: 0.7120 (mm-40) REVERT: D 173 VAL cc_start: 0.8149 (m) cc_final: 0.7936 (m) REVERT: D 203 HIS cc_start: 0.6643 (p-80) cc_final: 0.6303 (p-80) REVERT: E 102 ASN cc_start: 0.7576 (p0) cc_final: 0.6761 (p0) REVERT: F 64 GLN cc_start: 0.8059 (tp40) cc_final: 0.7761 (mm110) REVERT: I 88 GLU cc_start: 0.8123 (mp0) cc_final: 0.7918 (mp0) REVERT: J 131 MET cc_start: 0.8079 (mmm) cc_final: 0.7820 (mmm) REVERT: N 53 TYR cc_start: 0.8892 (t80) cc_final: 0.8507 (t80) REVERT: N 131 GLU cc_start: 0.8471 (mt-10) cc_final: 0.8271 (mt-10) REVERT: N 148 TYR cc_start: 0.8425 (m-80) cc_final: 0.8068 (m-80) REVERT: S 109 ASP cc_start: 0.7904 (t70) cc_final: 0.7608 (t0) REVERT: e 78 ASN cc_start: 0.8050 (p0) cc_final: 0.7568 (p0) REVERT: e 81 ASP cc_start: 0.8120 (m-30) cc_final: 0.7701 (m-30) REVERT: e 91 THR cc_start: 0.9291 (p) cc_final: 0.9030 (p) REVERT: m 57 ARG cc_start: 0.5567 (ttm170) cc_final: 0.5065 (ttm170) REVERT: s 24 SER cc_start: 0.8997 (t) cc_final: 0.8491 (p) REVERT: s 65 GLU cc_start: 0.5199 (tm-30) cc_final: 0.4721 (pm20) REVERT: x 293 TYR cc_start: 0.9179 (m-80) cc_final: 0.8841 (m-80) REVERT: x 490 TYR cc_start: 0.8592 (m-80) cc_final: 0.8264 (m-80) REVERT: y 219 GLU cc_start: 0.8003 (mt-10) cc_final: 0.7792 (mt-10) outliers start: 14 outliers final: 16 residues processed: 1552 average time/residue: 2.2909 time to fit residues: 5001.9234 Evaluate side-chains 1020 residues out of total 8277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 1004 time to evaluate : 8.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain G residue 67 ILE Chi-restraints excluded: chain K residue 36 PHE Chi-restraints excluded: chain M residue 64 VAL Chi-restraints excluded: chain S residue 123 ILE Chi-restraints excluded: chain T residue 128 LEU Chi-restraints excluded: chain V residue 36 ILE Chi-restraints excluded: chain V residue 85 TRP Chi-restraints excluded: chain W residue 220 TYR Chi-restraints excluded: chain b residue 317 ILE Chi-restraints excluded: chain b residue 420 TYR Chi-restraints excluded: chain b residue 440 ASN Chi-restraints excluded: chain e residue 99 ASN Chi-restraints excluded: chain m residue 82 ARG Chi-restraints excluded: chain m residue 83 VAL Chi-restraints excluded: chain r residue 168 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1269 random chunks: chunk 1071 optimal weight: 9.9990 chunk 961 optimal weight: 9.9990 chunk 533 optimal weight: 6.9990 chunk 328 optimal weight: 30.0000 chunk 648 optimal weight: 20.0000 chunk 513 optimal weight: 9.9990 chunk 994 optimal weight: 7.9990 chunk 384 optimal weight: 9.9990 chunk 604 optimal weight: 6.9990 chunk 740 optimal weight: 7.9990 chunk 1152 optimal weight: 7.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 36 GLN 4 85 ASN 4 118 ASN 4 273 HIS 4 274 GLN 4 544 ASN A 97 ASN ** B 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 68 HIS B 165 GLN B 279 ASN B 293 ASN B 319 ASN C 48 GLN C 196 ASN C 304 GLN C 311 HIS ** D 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 GLN D 175 HIS ** E 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 37 ASN F 186 HIS F 194 HIS G 77 GLN G 79 GLN H 49 ASN I 73 HIS I 97 ASN I 106 GLN ** J 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 43 GLN J 47 GLN J 62 ASN J 150 ASN K 110 GLN ** K 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 102 GLN ** M 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 56 GLN N 15 GLN N 37 HIS N 195 ASN Q 9 GLN Q 58 ASN Q 73 GLN R 66 HIS R 92 GLN S 46 GLN ** S 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 142 GLN T 146 ASN U 25 ASN U 49 ASN U 88 GLN U 101 ASN V 7 GLN W 22 ASN ** W 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 128 ASN X 19 ASN ** X 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 42 GLN Z 57 HIS Z 122 HIS a 65 GLN a 67 HIS b 362 HIS b 384 ASN b 413 ASN b 509 ASN b 534 HIS b 579 ASN b 616 HIS c 61 ASN c 64 ASN e 52 GLN g 11 ASN h 34 GLN j 20 ASN j 76 ASN k 40 GLN l 20 ASN l 38 ASN ** m 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 395 HIS m 452 GLN q 103 ASN r 14 HIS r 179 GLN t 19 ASN ** t 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 170 ASN ** t 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 340 GLN t 369 GLN ** t 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 45 ASN u 73 GLN u 130 ASN x 208 ASN x 219 GLN x 271 GLN x 424 ASN ** x 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 79 GLN y 140 GLN y 157 GLN y 228 GLN y 235 ASN Total number of N/Q/H flips: 96 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 156900 Z= 0.391 Angle : 0.699 10.082 227896 Z= 0.362 Chirality : 0.044 0.380 28257 Planarity : 0.006 0.089 16563 Dihedral : 22.744 179.768 61850 Min Nonbonded Distance : 1.777 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.86 % Favored : 92.90 % Rotamer: Outliers : 6.59 % Allowed : 21.65 % Favored : 71.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.94 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.37 % 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: -1.78 (0.08), residues: 9491 helix: -0.07 (0.08), residues: 3742 sheet: -1.03 (0.14), residues: 1255 loop : -2.23 (0.08), residues: 4494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP r 147 HIS 0.016 0.001 HIS D 81 PHE 0.029 0.002 PHE F 229 TYR 0.032 0.002 TYR G 134 ARG 0.012 0.001 ARG A 149 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18982 Ramachandran restraints generated. 9491 Oldfield, 0 Emsley, 9491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18982 Ramachandran restraints generated. 9491 Oldfield, 0 Emsley, 9491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1636 residues out of total 8277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 535 poor density : 1101 time to evaluate : 8.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 4 279 LEU cc_start: 0.6929 (tp) cc_final: 0.6636 (mm) REVERT: 4 401 PHE cc_start: 0.8048 (m-80) cc_final: 0.7841 (m-80) REVERT: 4 543 LEU cc_start: 0.7381 (tp) cc_final: 0.7122 (tp) REVERT: 5 52 LEU cc_start: 0.8540 (tp) cc_final: 0.7797 (mt) REVERT: B 137 TYR cc_start: 0.8530 (OUTLIER) cc_final: 0.7760 (t80) REVERT: B 338 LEU cc_start: 0.9225 (OUTLIER) cc_final: 0.8944 (mt) REVERT: C 285 ASP cc_start: 0.7803 (t0) cc_final: 0.7585 (t70) REVERT: D 101 THR cc_start: 0.8143 (OUTLIER) cc_final: 0.7892 (p) REVERT: D 111 GLN cc_start: 0.7407 (tt0) cc_final: 0.7132 (mm-40) REVERT: E 13 GLU cc_start: 0.8634 (OUTLIER) cc_final: 0.7305 (mm-30) REVERT: H 62 ARG cc_start: 0.7187 (OUTLIER) cc_final: 0.6870 (mtm180) REVERT: I 104 ARG cc_start: 0.7838 (tpt170) cc_final: 0.7601 (tpp80) REVERT: I 107 GLU cc_start: 0.7547 (pt0) cc_final: 0.7203 (pt0) REVERT: J 131 MET cc_start: 0.8309 (mmm) cc_final: 0.7797 (mmm) REVERT: K 170 ARG cc_start: 0.6401 (OUTLIER) cc_final: 0.5231 (mtp-110) REVERT: L 144 THR cc_start: 0.8807 (m) cc_final: 0.8605 (m) REVERT: L 161 ASP cc_start: 0.7352 (t70) cc_final: 0.6953 (t70) REVERT: L 188 ARG cc_start: 0.7483 (mtp-110) cc_final: 0.6953 (mtp180) REVERT: S 109 ASP cc_start: 0.8184 (t70) cc_final: 0.7877 (t0) REVERT: S 172 TYR cc_start: 0.7382 (OUTLIER) cc_final: 0.7087 (t80) REVERT: V 24 ASN cc_start: 0.8305 (m110) cc_final: 0.7999 (m-40) REVERT: V 61 THR cc_start: 0.9019 (p) cc_final: 0.8777 (p) REVERT: W 95 LEU cc_start: 0.8220 (OUTLIER) cc_final: 0.7926 (mp) REVERT: Y 74 TYR cc_start: 0.8998 (OUTLIER) cc_final: 0.7549 (m-80) REVERT: Z 92 PHE cc_start: 0.8791 (p90) cc_final: 0.8586 (p90) REVERT: a 139 ARG cc_start: 0.8314 (OUTLIER) cc_final: 0.7994 (mtm180) REVERT: b 254 MET cc_start: 0.8228 (mmm) cc_final: 0.7986 (mmm) REVERT: b 453 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8452 (mt) REVERT: b 506 GLU cc_start: 0.8044 (mt-10) cc_final: 0.7817 (mt-10) REVERT: b 608 MET cc_start: 0.8710 (ttm) cc_final: 0.8391 (ttm) REVERT: d 50 ARG cc_start: 0.8710 (OUTLIER) cc_final: 0.7479 (mmt90) REVERT: e 19 ARG cc_start: 0.8894 (OUTLIER) cc_final: 0.6668 (ttm170) REVERT: e 118 LYS cc_start: 0.8731 (OUTLIER) cc_final: 0.8012 (ttmm) REVERT: f 31 LYS cc_start: 0.8783 (OUTLIER) cc_final: 0.8127 (tttp) REVERT: h 76 GLN cc_start: 0.7789 (OUTLIER) cc_final: 0.7558 (pm20) REVERT: k 7 ASP cc_start: 0.7425 (t70) cc_final: 0.6728 (t70) REVERT: k 16 ARG cc_start: 0.8308 (OUTLIER) cc_final: 0.7987 (mpp80) REVERT: k 24 THR cc_start: 0.9261 (OUTLIER) cc_final: 0.8989 (m) REVERT: m 57 ARG cc_start: 0.5469 (ttm170) cc_final: 0.4911 (ttm170) REVERT: m 194 TRP cc_start: 0.4822 (p90) cc_final: 0.4524 (p-90) REVERT: n 59 TYR cc_start: 0.8888 (m-80) cc_final: 0.8610 (m-80) REVERT: r 143 ARG cc_start: 0.8154 (OUTLIER) cc_final: 0.6718 (mmp-170) REVERT: r 168 MET cc_start: 0.4931 (OUTLIER) cc_final: 0.3552 (mtp) REVERT: r 208 MET cc_start: 0.8471 (OUTLIER) cc_final: 0.8206 (ttm) REVERT: t 113 LYS cc_start: 0.8216 (OUTLIER) cc_final: 0.7833 (ttpm) REVERT: t 175 GLU cc_start: 0.7882 (OUTLIER) cc_final: 0.7628 (mt-10) REVERT: t 257 MET cc_start: 0.8246 (mmp) cc_final: 0.7996 (mpp) REVERT: t 476 LYS cc_start: 0.7843 (ttpp) cc_final: 0.7440 (tttt) REVERT: x 293 TYR cc_start: 0.9225 (m-80) cc_final: 0.8965 (m-80) REVERT: y 133 LEU cc_start: 0.2499 (OUTLIER) cc_final: 0.2036 (tt) REVERT: y 164 GLN cc_start: 0.8416 (OUTLIER) cc_final: 0.7828 (mp10) REVERT: y 236 LEU cc_start: 0.6926 (OUTLIER) cc_final: 0.6690 (pp) REVERT: y 241 ILE cc_start: 0.6978 (OUTLIER) cc_final: 0.6541 (mp) REVERT: z 46 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8160 (mt) outliers start: 535 outliers final: 216 residues processed: 1499 average time/residue: 1.9829 time to fit residues: 4407.8586 Evaluate side-chains 1230 residues out of total 8277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 244 poor density : 986 time to evaluate : 7.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 4 residue 42 VAL Chi-restraints excluded: chain 4 residue 43 THR Chi-restraints excluded: chain 4 residue 44 SER Chi-restraints excluded: chain 4 residue 98 ASP Chi-restraints excluded: chain 4 residue 142 THR Chi-restraints excluded: chain 4 residue 158 MET Chi-restraints excluded: chain 4 residue 159 VAL Chi-restraints excluded: chain 4 residue 177 LEU Chi-restraints excluded: chain 4 residue 316 VAL Chi-restraints excluded: chain 4 residue 335 VAL Chi-restraints excluded: chain 4 residue 344 THR Chi-restraints excluded: chain 4 residue 402 VAL Chi-restraints excluded: chain 4 residue 443 VAL Chi-restraints excluded: chain 4 residue 475 LEU Chi-restraints excluded: chain 4 residue 529 SER Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 137 TYR Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 340 LYS Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain C residue 12 THR Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 232 ASP Chi-restraints excluded: chain E residue 12 SER Chi-restraints excluded: chain E residue 13 GLU Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 102 ASN Chi-restraints excluded: chain E residue 164 SER Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain F residue 157 ASN Chi-restraints excluded: chain G residue 47 SER Chi-restraints excluded: chain G residue 67 ILE Chi-restraints excluded: chain G residue 121 SER Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 240 ASN Chi-restraints excluded: chain H residue 46 THR Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 62 ARG Chi-restraints excluded: chain H residue 64 HIS Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 150 SER Chi-restraints excluded: chain J residue 144 CYS Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 161 SER Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 86 LYS Chi-restraints excluded: chain K residue 89 LEU Chi-restraints excluded: chain K residue 145 ILE Chi-restraints excluded: chain K residue 168 VAL Chi-restraints excluded: chain K residue 170 ARG Chi-restraints excluded: chain K residue 223 CYS Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 100 ARG Chi-restraints excluded: chain L residue 124 ILE Chi-restraints excluded: chain M residue 53 VAL Chi-restraints excluded: chain M residue 64 VAL Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 90 VAL Chi-restraints excluded: chain M residue 91 CYS Chi-restraints excluded: chain M residue 130 THR Chi-restraints excluded: chain N residue 113 LEU Chi-restraints excluded: chain O residue 44 SER Chi-restraints excluded: chain O residue 52 LEU Chi-restraints excluded: chain O residue 84 LEU Chi-restraints excluded: chain O residue 150 GLU Chi-restraints excluded: chain P residue 120 ASN Chi-restraints excluded: chain P residue 141 SER Chi-restraints excluded: chain P residue 181 ARG Chi-restraints excluded: chain Q residue 7 SER Chi-restraints excluded: chain Q residue 22 ASP Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain Q residue 129 VAL Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain R residue 69 SER Chi-restraints excluded: chain S residue 9 VAL Chi-restraints excluded: chain S residue 32 SER Chi-restraints excluded: chain S residue 45 LEU Chi-restraints excluded: chain S residue 132 THR Chi-restraints excluded: chain S residue 172 TYR Chi-restraints excluded: chain T residue 29 THR Chi-restraints excluded: chain T residue 39 ILE Chi-restraints excluded: chain T residue 41 ASP Chi-restraints excluded: chain T residue 64 VAL Chi-restraints excluded: chain T residue 101 CYS Chi-restraints excluded: chain T residue 128 LEU Chi-restraints excluded: chain T residue 136 ARG Chi-restraints excluded: chain T residue 150 THR Chi-restraints excluded: chain U residue 57 THR Chi-restraints excluded: chain V residue 37 ILE Chi-restraints excluded: chain V residue 85 TRP Chi-restraints excluded: chain V residue 120 LYS Chi-restraints excluded: chain W residue 48 VAL Chi-restraints excluded: chain W residue 60 TRP Chi-restraints excluded: chain W residue 89 LEU Chi-restraints excluded: chain W residue 95 LEU Chi-restraints excluded: chain W residue 120 VAL Chi-restraints excluded: chain W residue 197 VAL Chi-restraints excluded: chain W residue 220 TYR Chi-restraints excluded: chain W residue 223 ASN Chi-restraints excluded: chain X residue 48 SER Chi-restraints excluded: chain X residue 112 THR Chi-restraints excluded: chain Y residue 70 ILE Chi-restraints excluded: chain Y residue 74 TYR Chi-restraints excluded: chain Y residue 105 VAL Chi-restraints excluded: chain Z residue 53 VAL Chi-restraints excluded: chain Z residue 86 THR Chi-restraints excluded: chain Z residue 96 VAL Chi-restraints excluded: chain Z residue 105 SER Chi-restraints excluded: chain Z residue 123 GLN Chi-restraints excluded: chain a residue 91 LEU Chi-restraints excluded: chain a residue 95 SER Chi-restraints excluded: chain a residue 130 VAL Chi-restraints excluded: chain a residue 131 SER Chi-restraints excluded: chain a residue 139 ARG Chi-restraints excluded: chain b residue 4 SER Chi-restraints excluded: chain b residue 73 ASP Chi-restraints excluded: chain b residue 162 SER Chi-restraints excluded: chain b residue 170 LEU Chi-restraints excluded: chain b residue 229 THR Chi-restraints excluded: chain b residue 250 VAL Chi-restraints excluded: chain b residue 382 VAL Chi-restraints excluded: chain b residue 420 TYR Chi-restraints excluded: chain b residue 440 ASN Chi-restraints excluded: chain b residue 453 LEU Chi-restraints excluded: chain b residue 477 ILE Chi-restraints excluded: chain b residue 522 SER Chi-restraints excluded: chain b residue 565 VAL Chi-restraints excluded: chain d residue 50 ARG Chi-restraints excluded: chain d residue 64 VAL Chi-restraints excluded: chain d residue 108 VAL Chi-restraints excluded: chain e residue 14 THR Chi-restraints excluded: chain e residue 19 ARG Chi-restraints excluded: chain e residue 75 LEU Chi-restraints excluded: chain e residue 84 THR Chi-restraints excluded: chain e residue 118 LYS Chi-restraints excluded: chain e residue 128 LEU Chi-restraints excluded: chain f residue 15 SER Chi-restraints excluded: chain f residue 22 VAL Chi-restraints excluded: chain f residue 31 LYS Chi-restraints excluded: chain f residue 49 ILE Chi-restraints excluded: chain f residue 56 SER Chi-restraints excluded: chain g residue 47 CYS Chi-restraints excluded: chain h residue 76 GLN Chi-restraints excluded: chain h residue 98 SER Chi-restraints excluded: chain i residue 9 ILE Chi-restraints excluded: chain i residue 60 LEU Chi-restraints excluded: chain j residue 33 THR Chi-restraints excluded: chain j residue 36 SER Chi-restraints excluded: chain j residue 46 SER Chi-restraints excluded: chain k residue 16 ARG Chi-restraints excluded: chain k residue 24 THR Chi-restraints excluded: chain k residue 66 ILE Chi-restraints excluded: chain l residue 6 SER Chi-restraints excluded: chain l residue 23 LEU Chi-restraints excluded: chain l residue 46 ARG Chi-restraints excluded: chain m residue 28 ASN Chi-restraints excluded: chain m residue 30 TYR Chi-restraints excluded: chain m residue 44 SER Chi-restraints excluded: chain m residue 60 SER Chi-restraints excluded: chain m residue 83 VAL Chi-restraints excluded: chain m residue 96 LEU Chi-restraints excluded: chain m residue 204 SER Chi-restraints excluded: chain m residue 221 SER Chi-restraints excluded: chain m residue 235 LEU Chi-restraints excluded: chain m residue 284 LEU Chi-restraints excluded: chain m residue 293 SER Chi-restraints excluded: chain m residue 315 GLN Chi-restraints excluded: chain m residue 379 GLU Chi-restraints excluded: chain m residue 418 ILE Chi-restraints excluded: chain p residue 16 VAL Chi-restraints excluded: chain p residue 42 CYS Chi-restraints excluded: chain p residue 56 THR Chi-restraints excluded: chain p residue 72 SER Chi-restraints excluded: chain p residue 81 SER Chi-restraints excluded: chain q residue 61 GLN Chi-restraints excluded: chain q residue 66 ASN Chi-restraints excluded: chain q residue 72 SER Chi-restraints excluded: chain q residue 110 ILE Chi-restraints excluded: chain r residue 7 ILE Chi-restraints excluded: chain r residue 129 SER Chi-restraints excluded: chain r residue 143 ARG Chi-restraints excluded: chain r residue 168 MET Chi-restraints excluded: chain r residue 175 SER Chi-restraints excluded: chain r residue 191 VAL Chi-restraints excluded: chain r residue 193 VAL Chi-restraints excluded: chain r residue 208 MET Chi-restraints excluded: chain r residue 250 ASP Chi-restraints excluded: chain r residue 252 ASP Chi-restraints excluded: chain t residue 27 SER Chi-restraints excluded: chain t residue 113 LYS Chi-restraints excluded: chain t residue 175 GLU Chi-restraints excluded: chain t residue 217 SER Chi-restraints excluded: chain t residue 400 VAL Chi-restraints excluded: chain t residue 413 ASP Chi-restraints excluded: chain t residue 459 ILE Chi-restraints excluded: chain t residue 462 ILE Chi-restraints excluded: chain t residue 485 LEU Chi-restraints excluded: chain u residue 20 MET Chi-restraints excluded: chain u residue 65 VAL Chi-restraints excluded: chain x residue 133 THR Chi-restraints excluded: chain x residue 136 SER Chi-restraints excluded: chain x residue 271 GLN Chi-restraints excluded: chain x residue 273 THR Chi-restraints excluded: chain x residue 275 SER Chi-restraints excluded: chain x residue 418 VAL Chi-restraints excluded: chain x residue 435 LYS Chi-restraints excluded: chain x residue 491 THR Chi-restraints excluded: chain y residue 76 THR Chi-restraints excluded: chain y residue 130 SER Chi-restraints excluded: chain y residue 132 VAL Chi-restraints excluded: chain y residue 133 LEU Chi-restraints excluded: chain y residue 164 GLN Chi-restraints excluded: chain y residue 165 THR Chi-restraints excluded: chain y residue 206 THR Chi-restraints excluded: chain y residue 236 LEU Chi-restraints excluded: chain y residue 241 ILE Chi-restraints excluded: chain z residue 4 SER Chi-restraints excluded: chain z residue 26 VAL Chi-restraints excluded: chain z residue 37 LEU Chi-restraints excluded: chain z residue 46 LEU Chi-restraints excluded: chain z residue 92 LYS Chi-restraints excluded: chain z residue 94 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1269 random chunks: chunk 640 optimal weight: 8.9990 chunk 357 optimal weight: 8.9990 chunk 959 optimal weight: 3.9990 chunk 784 optimal weight: 8.9990 chunk 317 optimal weight: 10.0000 chunk 1154 optimal weight: 5.9990 chunk 1247 optimal weight: 5.9990 chunk 1028 optimal weight: 10.0000 chunk 1144 optimal weight: 6.9990 chunk 393 optimal weight: 3.9990 chunk 926 optimal weight: 10.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 33 GLN 4 85 ASN 4 116 ASN ** 5 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 304 GLN ** D 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 GLN E 80 ASN ** E 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 ASN F 225 GLN G 79 GLN H 9 GLN H 58 HIS H 163 GLN I 37 GLN J 47 GLN J 150 ASN K 106 GLN K 107 GLN ** K 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 106 GLN ** M 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 9 GLN S 46 GLN T 45 ASN U 25 ASN U 49 ASN ** U 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 7 GLN W 44 HIS W 128 ASN X 111 ASN Z 106 GLN b 362 HIS b 570 GLN c 61 ASN e 52 GLN i 63 ASN i 92 ASN j 20 ASN m 395 HIS r 4 ASN r 211 GLN t 29 GLN t 214 GLN t 378 HIS ** t 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 130 ASN x 219 GLN ** x 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 289 GLN ** x 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.2252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 156900 Z= 0.284 Angle : 0.617 9.667 227896 Z= 0.321 Chirality : 0.040 0.330 28257 Planarity : 0.005 0.080 16563 Dihedral : 22.673 179.932 61836 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.40 % Favored : 93.44 % Rotamer: Outliers : 6.12 % Allowed : 23.02 % Favored : 70.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.94 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -1.19 (0.08), residues: 9491 helix: 0.50 (0.08), residues: 3752 sheet: -0.71 (0.14), residues: 1245 loop : -1.98 (0.08), residues: 4494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP r 147 HIS 0.007 0.001 HIS y 50 PHE 0.028 0.002 PHE J 127 TYR 0.027 0.002 TYR S 172 ARG 0.014 0.001 ARG J 61 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18982 Ramachandran restraints generated. 9491 Oldfield, 0 Emsley, 9491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18982 Ramachandran restraints generated. 9491 Oldfield, 0 Emsley, 9491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1577 residues out of total 8277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 497 poor density : 1080 time to evaluate : 8.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 4 395 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8402 (mt) REVERT: 4 543 LEU cc_start: 0.7288 (tp) cc_final: 0.7040 (tp) REVERT: 5 66 ASP cc_start: 0.7839 (OUTLIER) cc_final: 0.7504 (m-30) REVERT: B 137 TYR cc_start: 0.8418 (OUTLIER) cc_final: 0.7680 (t80) REVERT: B 146 ARG cc_start: 0.6714 (tpt170) cc_final: 0.6462 (tpt170) REVERT: C 285 ASP cc_start: 0.7928 (t0) cc_final: 0.7688 (t70) REVERT: D 111 GLN cc_start: 0.7329 (tt0) cc_final: 0.7076 (mm-40) REVERT: D 148 ILE cc_start: 0.7558 (OUTLIER) cc_final: 0.7315 (tp) REVERT: E 26 ARG cc_start: 0.8835 (OUTLIER) cc_final: 0.7959 (mtt90) REVERT: H 62 ARG cc_start: 0.7222 (OUTLIER) cc_final: 0.6892 (mtm180) REVERT: H 76 ASP cc_start: 0.8691 (m-30) cc_final: 0.8433 (m-30) REVERT: H 113 GLU cc_start: 0.7618 (OUTLIER) cc_final: 0.7393 (tt0) REVERT: J 131 MET cc_start: 0.8212 (mmm) cc_final: 0.7845 (mmm) REVERT: J 162 TRP cc_start: 0.7314 (OUTLIER) cc_final: 0.6041 (t60) REVERT: K 152 ASP cc_start: 0.8370 (m-30) cc_final: 0.8133 (t0) REVERT: K 170 ARG cc_start: 0.6392 (OUTLIER) cc_final: 0.5163 (mtp-110) REVERT: L 188 ARG cc_start: 0.7398 (mtp-110) cc_final: 0.7035 (mtp180) REVERT: N 73 ARG cc_start: 0.8599 (OUTLIER) cc_final: 0.7923 (ttm170) REVERT: R 100 ARG cc_start: 0.9306 (OUTLIER) cc_final: 0.9017 (mtt-85) REVERT: T 150 THR cc_start: 0.8728 (OUTLIER) cc_final: 0.8263 (m) REVERT: U 57 THR cc_start: 0.8141 (OUTLIER) cc_final: 0.7794 (m) REVERT: V 24 ASN cc_start: 0.8288 (m110) cc_final: 0.8015 (m-40) REVERT: W 5 LYS cc_start: 0.8826 (OUTLIER) cc_final: 0.8568 (mtmm) REVERT: W 95 LEU cc_start: 0.8246 (OUTLIER) cc_final: 0.8024 (mp) REVERT: Y 74 TYR cc_start: 0.8999 (OUTLIER) cc_final: 0.7513 (m-80) REVERT: a 139 ARG cc_start: 0.8311 (OUTLIER) cc_final: 0.7878 (mtm180) REVERT: b 254 MET cc_start: 0.8309 (mmm) cc_final: 0.8105 (mmm) REVERT: b 370 ASP cc_start: 0.7684 (OUTLIER) cc_final: 0.7455 (m-30) REVERT: b 398 LEU cc_start: 0.7711 (OUTLIER) cc_final: 0.7492 (tp) REVERT: b 453 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8498 (mt) REVERT: b 506 GLU cc_start: 0.8013 (mt-10) cc_final: 0.7769 (mt-10) REVERT: b 542 MET cc_start: 0.6832 (mpp) cc_final: 0.6552 (mpp) REVERT: b 608 MET cc_start: 0.8725 (ttm) cc_final: 0.8395 (ttm) REVERT: c 89 LEU cc_start: 0.8174 (OUTLIER) cc_final: 0.7916 (tm) REVERT: d 74 ARG cc_start: 0.8336 (OUTLIER) cc_final: 0.8031 (ttm170) REVERT: d 76 SER cc_start: 0.9284 (OUTLIER) cc_final: 0.9074 (p) REVERT: e 19 ARG cc_start: 0.8911 (OUTLIER) cc_final: 0.6772 (ttm170) REVERT: e 79 VAL cc_start: 0.9083 (m) cc_final: 0.8853 (t) REVERT: e 118 LYS cc_start: 0.8697 (OUTLIER) cc_final: 0.8079 (ttmm) REVERT: e 123 LYS cc_start: 0.7839 (OUTLIER) cc_final: 0.7387 (mtpp) REVERT: f 31 LYS cc_start: 0.8751 (OUTLIER) cc_final: 0.7974 (tttp) REVERT: h 76 GLN cc_start: 0.7777 (OUTLIER) cc_final: 0.7535 (pm20) REVERT: i 59 ASP cc_start: 0.7755 (t0) cc_final: 0.7047 (t0) REVERT: i 63 ASN cc_start: 0.8196 (m-40) cc_final: 0.7910 (m110) REVERT: j 84 SER cc_start: 0.7302 (OUTLIER) cc_final: 0.7013 (t) REVERT: k 7 ASP cc_start: 0.7133 (t70) cc_final: 0.6823 (t70) REVERT: k 16 ARG cc_start: 0.8320 (OUTLIER) cc_final: 0.7974 (mpp80) REVERT: k 32 ASN cc_start: 0.6688 (p0) cc_final: 0.6220 (p0) REVERT: m 57 ARG cc_start: 0.5553 (ttm170) cc_final: 0.5029 (ttm170) REVERT: m 337 LYS cc_start: 0.9018 (OUTLIER) cc_final: 0.8718 (tttm) REVERT: n 59 TYR cc_start: 0.8883 (m-80) cc_final: 0.8597 (m-80) REVERT: r 37 GLU cc_start: 0.7056 (mt-10) cc_final: 0.6842 (mt-10) REVERT: r 143 ARG cc_start: 0.8167 (OUTLIER) cc_final: 0.6756 (mmp-170) REVERT: t 236 ASP cc_start: 0.7465 (p0) cc_final: 0.7047 (m-30) REVERT: t 463 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8435 (tt) REVERT: t 476 LYS cc_start: 0.7811 (ttpp) cc_final: 0.7503 (tttt) REVERT: u 75 ARG cc_start: 0.8651 (OUTLIER) cc_final: 0.8204 (mtt-85) REVERT: x 293 TYR cc_start: 0.9217 (m-80) cc_final: 0.8947 (m-80) REVERT: y 12 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7317 (mt-10) REVERT: y 133 LEU cc_start: 0.2641 (OUTLIER) cc_final: 0.2314 (tt) REVERT: y 164 GLN cc_start: 0.8464 (OUTLIER) cc_final: 0.7915 (mp10) REVERT: y 241 ILE cc_start: 0.6969 (OUTLIER) cc_final: 0.6539 (mp) REVERT: z 46 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8184 (mt) REVERT: z 94 MET cc_start: 0.6207 (OUTLIER) cc_final: 0.5983 (tpt) REVERT: z 98 LYS cc_start: 0.6875 (mtpp) cc_final: 0.6576 (mmmm) outliers start: 497 outliers final: 216 residues processed: 1444 average time/residue: 2.0262 time to fit residues: 4328.9516 Evaluate side-chains 1245 residues out of total 8277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 256 poor density : 989 time to evaluate : 8.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 4 residue 85 ASN Chi-restraints excluded: chain 4 residue 101 SER Chi-restraints excluded: chain 4 residue 128 SER Chi-restraints excluded: chain 4 residue 142 THR Chi-restraints excluded: chain 4 residue 159 VAL Chi-restraints excluded: chain 4 residue 316 VAL Chi-restraints excluded: chain 4 residue 335 VAL Chi-restraints excluded: chain 4 residue 395 LEU Chi-restraints excluded: chain 4 residue 405 ASN Chi-restraints excluded: chain 4 residue 475 LEU Chi-restraints excluded: chain 4 residue 495 SER Chi-restraints excluded: chain 5 residue 66 ASP Chi-restraints excluded: chain 5 residue 67 GLU Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 137 TYR Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain B residue 212 ASN Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 243 HIS Chi-restraints excluded: chain B residue 340 LYS Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 371 GLN Chi-restraints excluded: chain C residue 12 THR Chi-restraints excluded: chain C residue 54 GLU Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 148 ILE Chi-restraints excluded: chain E residue 12 SER Chi-restraints excluded: chain E residue 26 ARG Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 82 LYS Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain G residue 47 SER Chi-restraints excluded: chain G residue 67 ILE Chi-restraints excluded: chain G residue 124 ASP Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain H residue 46 THR Chi-restraints excluded: chain H residue 62 ARG Chi-restraints excluded: chain H residue 113 GLU Chi-restraints excluded: chain H residue 137 SER Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 150 SER Chi-restraints excluded: chain I residue 62 ILE Chi-restraints excluded: chain J residue 112 LEU Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 155 THR Chi-restraints excluded: chain J residue 161 SER Chi-restraints excluded: chain J residue 162 TRP Chi-restraints excluded: chain K residue 13 ASP Chi-restraints excluded: chain K residue 21 VAL Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 89 LEU Chi-restraints excluded: chain K residue 168 VAL Chi-restraints excluded: chain K residue 170 ARG Chi-restraints excluded: chain K residue 223 CYS Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 100 ARG Chi-restraints excluded: chain L residue 124 ILE Chi-restraints excluded: chain M residue 53 VAL Chi-restraints excluded: chain M residue 64 VAL Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 90 VAL Chi-restraints excluded: chain M residue 91 CYS Chi-restraints excluded: chain M residue 130 THR Chi-restraints excluded: chain N residue 19 LEU Chi-restraints excluded: chain N residue 73 ARG Chi-restraints excluded: chain N residue 183 THR Chi-restraints excluded: chain O residue 52 LEU Chi-restraints excluded: chain O residue 84 LEU Chi-restraints excluded: chain O residue 150 GLU Chi-restraints excluded: chain P residue 49 GLU Chi-restraints excluded: chain P residue 114 VAL Chi-restraints excluded: chain P residue 120 ASN Chi-restraints excluded: chain P residue 136 ILE Chi-restraints excluded: chain P residue 181 ARG Chi-restraints excluded: chain Q residue 7 SER Chi-restraints excluded: chain Q residue 22 ASP Chi-restraints excluded: chain Q residue 47 VAL Chi-restraints excluded: chain Q residue 129 VAL Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain R residue 100 ARG Chi-restraints excluded: chain S residue 3 HIS Chi-restraints excluded: chain S residue 9 VAL Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain S residue 132 THR Chi-restraints excluded: chain T residue 29 THR Chi-restraints excluded: chain T residue 39 ILE Chi-restraints excluded: chain T residue 41 ASP Chi-restraints excluded: chain T residue 64 VAL Chi-restraints excluded: chain T residue 126 VAL Chi-restraints excluded: chain T residue 128 LEU Chi-restraints excluded: chain T residue 136 ARG Chi-restraints excluded: chain T residue 150 THR Chi-restraints excluded: chain U residue 57 THR Chi-restraints excluded: chain V residue 85 TRP Chi-restraints excluded: chain V residue 110 LYS Chi-restraints excluded: chain V residue 120 LYS Chi-restraints excluded: chain W residue 3 ARG Chi-restraints excluded: chain W residue 5 LYS Chi-restraints excluded: chain W residue 48 VAL Chi-restraints excluded: chain W residue 56 ILE Chi-restraints excluded: chain W residue 60 TRP Chi-restraints excluded: chain W residue 95 LEU Chi-restraints excluded: chain W residue 122 SER Chi-restraints excluded: chain W residue 135 PHE Chi-restraints excluded: chain W residue 220 TYR Chi-restraints excluded: chain W residue 223 ASN Chi-restraints excluded: chain W residue 231 THR Chi-restraints excluded: chain X residue 8 THR Chi-restraints excluded: chain X residue 48 SER Chi-restraints excluded: chain Y residue 70 ILE Chi-restraints excluded: chain Y residue 74 TYR Chi-restraints excluded: chain Y residue 105 VAL Chi-restraints excluded: chain Z residue 33 SER Chi-restraints excluded: chain Z residue 46 ILE Chi-restraints excluded: chain Z residue 53 VAL Chi-restraints excluded: chain Z residue 86 THR Chi-restraints excluded: chain Z residue 96 VAL Chi-restraints excluded: chain Z residue 105 SER Chi-restraints excluded: chain Z residue 123 GLN Chi-restraints excluded: chain a residue 91 LEU Chi-restraints excluded: chain a residue 95 SER Chi-restraints excluded: chain a residue 139 ARG Chi-restraints excluded: chain b residue 73 ASP Chi-restraints excluded: chain b residue 100 ARG Chi-restraints excluded: chain b residue 162 SER Chi-restraints excluded: chain b residue 170 LEU Chi-restraints excluded: chain b residue 177 ASN Chi-restraints excluded: chain b residue 229 THR Chi-restraints excluded: chain b residue 250 VAL Chi-restraints excluded: chain b residue 370 ASP Chi-restraints excluded: chain b residue 382 VAL Chi-restraints excluded: chain b residue 394 ASN Chi-restraints excluded: chain b residue 398 LEU Chi-restraints excluded: chain b residue 420 TYR Chi-restraints excluded: chain b residue 440 ASN Chi-restraints excluded: chain b residue 453 LEU Chi-restraints excluded: chain b residue 509 ASN Chi-restraints excluded: chain b residue 565 VAL Chi-restraints excluded: chain c residue 89 LEU Chi-restraints excluded: chain d residue 74 ARG Chi-restraints excluded: chain d residue 76 SER Chi-restraints excluded: chain d residue 106 THR Chi-restraints excluded: chain e residue 19 ARG Chi-restraints excluded: chain e residue 51 SER Chi-restraints excluded: chain e residue 75 LEU Chi-restraints excluded: chain e residue 84 THR Chi-restraints excluded: chain e residue 118 LYS Chi-restraints excluded: chain e residue 123 LYS Chi-restraints excluded: chain e residue 128 LEU Chi-restraints excluded: chain f residue 15 SER Chi-restraints excluded: chain f residue 22 VAL Chi-restraints excluded: chain f residue 31 LYS Chi-restraints excluded: chain f residue 49 ILE Chi-restraints excluded: chain g residue 47 CYS Chi-restraints excluded: chain g residue 57 LEU Chi-restraints excluded: chain g residue 79 SER Chi-restraints excluded: chain h residue 33 VAL Chi-restraints excluded: chain h residue 76 GLN Chi-restraints excluded: chain h residue 98 SER Chi-restraints excluded: chain i residue 9 ILE Chi-restraints excluded: chain i residue 58 ILE Chi-restraints excluded: chain i residue 79 SER Chi-restraints excluded: chain j residue 36 SER Chi-restraints excluded: chain j residue 46 SER Chi-restraints excluded: chain j residue 84 SER Chi-restraints excluded: chain k residue 12 LEU Chi-restraints excluded: chain k residue 16 ARG Chi-restraints excluded: chain k residue 66 ILE Chi-restraints excluded: chain l residue 6 SER Chi-restraints excluded: chain l residue 23 LEU Chi-restraints excluded: chain l residue 46 ARG Chi-restraints excluded: chain m residue 28 ASN Chi-restraints excluded: chain m residue 30 TYR Chi-restraints excluded: chain m residue 60 SER Chi-restraints excluded: chain m residue 96 LEU Chi-restraints excluded: chain m residue 204 SER Chi-restraints excluded: chain m residue 221 SER Chi-restraints excluded: chain m residue 284 LEU Chi-restraints excluded: chain m residue 293 SER Chi-restraints excluded: chain m residue 315 GLN Chi-restraints excluded: chain m residue 337 LYS Chi-restraints excluded: chain m residue 418 ILE Chi-restraints excluded: chain m residue 425 THR Chi-restraints excluded: chain n residue 29 SER Chi-restraints excluded: chain n residue 61 MET Chi-restraints excluded: chain n residue 63 SER Chi-restraints excluded: chain p residue 42 CYS Chi-restraints excluded: chain p residue 56 THR Chi-restraints excluded: chain p residue 60 CYS Chi-restraints excluded: chain p residue 72 SER Chi-restraints excluded: chain p residue 81 SER Chi-restraints excluded: chain q residue 66 ASN Chi-restraints excluded: chain q residue 72 SER Chi-restraints excluded: chain r residue 7 ILE Chi-restraints excluded: chain r residue 12 LYS Chi-restraints excluded: chain r residue 143 ARG Chi-restraints excluded: chain r residue 166 VAL Chi-restraints excluded: chain r residue 193 VAL Chi-restraints excluded: chain r residue 250 ASP Chi-restraints excluded: chain r residue 252 ASP Chi-restraints excluded: chain s residue 13 THR Chi-restraints excluded: chain t residue 27 SER Chi-restraints excluded: chain t residue 217 SER Chi-restraints excluded: chain t residue 413 ASP Chi-restraints excluded: chain t residue 463 LEU Chi-restraints excluded: chain u residue 65 VAL Chi-restraints excluded: chain u residue 75 ARG Chi-restraints excluded: chain x residue 201 ILE Chi-restraints excluded: chain x residue 253 SER Chi-restraints excluded: chain x residue 254 SER Chi-restraints excluded: chain x residue 273 THR Chi-restraints excluded: chain x residue 289 GLN Chi-restraints excluded: chain x residue 386 TRP Chi-restraints excluded: chain x residue 418 VAL Chi-restraints excluded: chain x residue 435 LYS Chi-restraints excluded: chain x residue 480 VAL Chi-restraints excluded: chain x residue 491 THR Chi-restraints excluded: chain y residue 12 GLU Chi-restraints excluded: chain y residue 76 THR Chi-restraints excluded: chain y residue 130 SER Chi-restraints excluded: chain y residue 133 LEU Chi-restraints excluded: chain y residue 164 GLN Chi-restraints excluded: chain y residue 165 THR Chi-restraints excluded: chain y residue 241 ILE Chi-restraints excluded: chain z residue 4 SER Chi-restraints excluded: chain z residue 15 SER Chi-restraints excluded: chain z residue 21 VAL Chi-restraints excluded: chain z residue 26 VAL Chi-restraints excluded: chain z residue 37 LEU Chi-restraints excluded: chain z residue 42 LEU Chi-restraints excluded: chain z residue 46 LEU Chi-restraints excluded: chain z residue 82 ASP Chi-restraints excluded: chain z residue 92 LYS Chi-restraints excluded: chain z residue 94 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1269 random chunks: chunk 1140 optimal weight: 6.9990 chunk 867 optimal weight: 9.9990 chunk 599 optimal weight: 7.9990 chunk 127 optimal weight: 10.0000 chunk 550 optimal weight: 5.9990 chunk 775 optimal weight: 8.9990 chunk 1158 optimal weight: 5.9990 chunk 1226 optimal weight: 0.5980 chunk 605 optimal weight: 0.0170 chunk 1098 optimal weight: 2.9990 chunk 330 optimal weight: 3.9990 overall best weight: 2.7224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 85 ASN ** B 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 173 GLN B 293 ASN C 304 GLN C 311 HIS ** D 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 GLN ** E 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 52 GLN G 59 GLN G 79 GLN H 5 GLN I 37 GLN J 47 GLN J 68 HIS J 150 ASN K 106 GLN ** K 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 19 GLN M 41 GLN N 34 ASN O 50 ASN O 90 HIS O 182 ASN Q 9 GLN R 39 ASN S 46 GLN S 142 GLN U 25 ASN U 49 ASN ** U 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 7 GLN ** V 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 61 ASN e 52 GLN h 62 GLN ** i 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 20 ASN ** m 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 395 HIS r 4 ASN r 211 GLN t 329 ASN ** t 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 130 ASN x 219 GLN x 271 GLN ** x 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.2465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 156900 Z= 0.176 Angle : 0.561 12.036 227896 Z= 0.293 Chirality : 0.036 0.321 28257 Planarity : 0.004 0.076 16563 Dihedral : 22.604 179.931 61832 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.53 % Favored : 93.31 % Rotamer: Outliers : 5.06 % Allowed : 24.77 % Favored : 70.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.94 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -0.75 (0.08), residues: 9491 helix: 0.92 (0.09), residues: 3745 sheet: -0.47 (0.14), residues: 1241 loop : -1.78 (0.09), residues: 4505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP r 147 HIS 0.007 0.001 HIS t 120 PHE 0.026 0.001 PHE K 300 TYR 0.023 0.001 TYR t 181 ARG 0.009 0.000 ARG A 149 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18982 Ramachandran restraints generated. 9491 Oldfield, 0 Emsley, 9491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18982 Ramachandran restraints generated. 9491 Oldfield, 0 Emsley, 9491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1502 residues out of total 8277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 411 poor density : 1091 time to evaluate : 8.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 4 76 LEU cc_start: 0.8986 (tp) cc_final: 0.8738 (mt) REVERT: 4 161 TYR cc_start: 0.4835 (p90) cc_final: 0.4617 (p90) REVERT: 4 338 GLU cc_start: 0.8447 (OUTLIER) cc_final: 0.8105 (pt0) REVERT: 4 395 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8460 (mt) REVERT: 4 454 PRO cc_start: 0.8617 (Cg_exo) cc_final: 0.8395 (Cg_endo) REVERT: 4 475 LEU cc_start: 0.7924 (OUTLIER) cc_final: 0.7527 (pt) REVERT: 4 530 LYS cc_start: 0.5975 (mptp) cc_final: 0.5762 (mttm) REVERT: 4 575 MET cc_start: 0.7180 (mtt) cc_final: 0.6950 (mtt) REVERT: 5 66 ASP cc_start: 0.7891 (OUTLIER) cc_final: 0.7467 (m-30) REVERT: B 102 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8093 (pt) REVERT: B 137 TYR cc_start: 0.8347 (OUTLIER) cc_final: 0.7650 (t80) REVERT: B 146 ARG cc_start: 0.6641 (tpt170) cc_final: 0.6372 (tpt170) REVERT: C 285 ASP cc_start: 0.7977 (t0) cc_final: 0.7602 (t0) REVERT: D 59 ASP cc_start: 0.7338 (OUTLIER) cc_final: 0.7079 (t70) REVERT: D 111 GLN cc_start: 0.7354 (tt0) cc_final: 0.6963 (mm-40) REVERT: E 26 ARG cc_start: 0.8824 (OUTLIER) cc_final: 0.7946 (mtt90) REVERT: H 46 THR cc_start: 0.8921 (OUTLIER) cc_final: 0.8639 (m) REVERT: H 62 ARG cc_start: 0.6965 (OUTLIER) cc_final: 0.6360 (mtm180) REVERT: H 76 ASP cc_start: 0.8578 (m-30) cc_final: 0.8236 (m-30) REVERT: H 113 GLU cc_start: 0.7537 (OUTLIER) cc_final: 0.7314 (tt0) REVERT: J 131 MET cc_start: 0.8221 (mmm) cc_final: 0.7890 (mmm) REVERT: K 152 ASP cc_start: 0.8347 (OUTLIER) cc_final: 0.8049 (t0) REVERT: K 170 ARG cc_start: 0.6382 (OUTLIER) cc_final: 0.5159 (mtp-110) REVERT: L 161 ASP cc_start: 0.7231 (t70) cc_final: 0.6797 (t70) REVERT: L 188 ARG cc_start: 0.7400 (mtp-110) cc_final: 0.7111 (mtp180) REVERT: N 73 ARG cc_start: 0.8556 (OUTLIER) cc_final: 0.7892 (ttm170) REVERT: O 106 GLU cc_start: 0.8533 (mp0) cc_final: 0.8155 (mm-30) REVERT: R 100 ARG cc_start: 0.9297 (OUTLIER) cc_final: 0.9025 (mtt-85) REVERT: S 46 GLN cc_start: 0.8366 (mt0) cc_final: 0.8163 (mt0) REVERT: S 78 TRP cc_start: 0.6607 (OUTLIER) cc_final: 0.6069 (m-10) REVERT: S 172 TYR cc_start: 0.7994 (OUTLIER) cc_final: 0.5534 (t80) REVERT: T 150 THR cc_start: 0.8765 (OUTLIER) cc_final: 0.8374 (m) REVERT: V 24 ASN cc_start: 0.8196 (m110) cc_final: 0.7871 (m-40) REVERT: Y 66 GLN cc_start: 0.8843 (OUTLIER) cc_final: 0.8571 (mt0) REVERT: Y 74 TYR cc_start: 0.8948 (OUTLIER) cc_final: 0.7441 (m-80) REVERT: b 370 ASP cc_start: 0.7674 (OUTLIER) cc_final: 0.7461 (m-30) REVERT: b 398 LEU cc_start: 0.7513 (OUTLIER) cc_final: 0.7248 (tp) REVERT: b 453 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8491 (mt) REVERT: b 506 GLU cc_start: 0.7982 (mt-10) cc_final: 0.7712 (mt-10) REVERT: b 542 MET cc_start: 0.6767 (mpp) cc_final: 0.6512 (OUTLIER) REVERT: b 608 MET cc_start: 0.8764 (ttm) cc_final: 0.8406 (ttm) REVERT: d 50 ARG cc_start: 0.8556 (OUTLIER) cc_final: 0.7134 (mmt90) REVERT: d 74 ARG cc_start: 0.8438 (OUTLIER) cc_final: 0.8081 (ttm170) REVERT: e 19 ARG cc_start: 0.8880 (OUTLIER) cc_final: 0.6769 (ttm170) REVERT: e 118 LYS cc_start: 0.8711 (OUTLIER) cc_final: 0.8123 (ttmm) REVERT: f 31 LYS cc_start: 0.8734 (OUTLIER) cc_final: 0.7902 (tttp) REVERT: g 16 ARG cc_start: 0.8847 (OUTLIER) cc_final: 0.8435 (ttm170) REVERT: j 84 SER cc_start: 0.7158 (OUTLIER) cc_final: 0.6873 (t) REVERT: k 7 ASP cc_start: 0.6908 (t70) cc_final: 0.6618 (t70) REVERT: k 16 ARG cc_start: 0.8293 (OUTLIER) cc_final: 0.7946 (mpp80) REVERT: k 32 ASN cc_start: 0.6480 (p0) cc_final: 0.5900 (p0) REVERT: m 57 ARG cc_start: 0.5793 (ttm170) cc_final: 0.5294 (ttm170) REVERT: m 337 LYS cc_start: 0.8925 (OUTLIER) cc_final: 0.8576 (tttm) REVERT: n 59 TYR cc_start: 0.8871 (m-80) cc_final: 0.8660 (m-80) REVERT: q 72 SER cc_start: 0.8388 (OUTLIER) cc_final: 0.8097 (p) REVERT: r 143 ARG cc_start: 0.8057 (OUTLIER) cc_final: 0.6703 (mmp-170) REVERT: r 168 MET cc_start: 0.4685 (OUTLIER) cc_final: 0.3469 (mtp) REVERT: r 254 CYS cc_start: 0.7729 (p) cc_final: 0.7504 (p) REVERT: t 236 ASP cc_start: 0.7423 (p0) cc_final: 0.7048 (m-30) REVERT: t 378 HIS cc_start: 0.8183 (m90) cc_final: 0.7776 (m90) REVERT: t 414 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.8220 (tt) REVERT: t 476 LYS cc_start: 0.7815 (ttpp) cc_final: 0.7426 (tttt) REVERT: u 75 ARG cc_start: 0.8635 (OUTLIER) cc_final: 0.8312 (mtt-85) REVERT: x 293 TYR cc_start: 0.9191 (m-80) cc_final: 0.8946 (m-80) REVERT: y 164 GLN cc_start: 0.8388 (OUTLIER) cc_final: 0.7909 (mp10) REVERT: y 236 LEU cc_start: 0.6869 (OUTLIER) cc_final: 0.6639 (pp) REVERT: y 241 ILE cc_start: 0.6943 (OUTLIER) cc_final: 0.6540 (mp) REVERT: z 46 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.8116 (mt) outliers start: 411 outliers final: 210 residues processed: 1384 average time/residue: 1.9818 time to fit residues: 4092.0612 Evaluate side-chains 1242 residues out of total 8277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 250 poor density : 992 time to evaluate : 8.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 4 residue 70 SER Chi-restraints excluded: chain 4 residue 128 SER Chi-restraints excluded: chain 4 residue 139 VAL Chi-restraints excluded: chain 4 residue 142 THR Chi-restraints excluded: chain 4 residue 177 LEU Chi-restraints excluded: chain 4 residue 203 THR Chi-restraints excluded: chain 4 residue 316 VAL Chi-restraints excluded: chain 4 residue 335 VAL Chi-restraints excluded: chain 4 residue 338 GLU Chi-restraints excluded: chain 4 residue 344 THR Chi-restraints excluded: chain 4 residue 395 LEU Chi-restraints excluded: chain 4 residue 405 ASN Chi-restraints excluded: chain 4 residue 475 LEU Chi-restraints excluded: chain 4 residue 493 LYS Chi-restraints excluded: chain 4 residue 495 SER Chi-restraints excluded: chain 4 residue 529 SER Chi-restraints excluded: chain 5 residue 66 ASP Chi-restraints excluded: chain 5 residue 67 GLU Chi-restraints excluded: chain 5 residue 93 GLU Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 137 TYR Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 243 HIS Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 327 CYS Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 340 LYS Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 371 GLN Chi-restraints excluded: chain C residue 54 GLU Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 327 LEU Chi-restraints excluded: chain C residue 349 THR Chi-restraints excluded: chain C residue 362 ASP Chi-restraints excluded: chain D residue 59 ASP Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 81 HIS Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain E residue 9 TRP Chi-restraints excluded: chain E residue 12 SER Chi-restraints excluded: chain E residue 26 ARG Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 164 SER Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 82 LYS Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain G residue 47 SER Chi-restraints excluded: chain G residue 124 ASP Chi-restraints excluded: chain H residue 46 THR Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 62 ARG Chi-restraints excluded: chain H residue 64 HIS Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 113 GLU Chi-restraints excluded: chain H residue 137 SER Chi-restraints excluded: chain H residue 150 SER Chi-restraints excluded: chain I residue 37 GLN Chi-restraints excluded: chain I residue 62 ILE Chi-restraints excluded: chain I residue 86 THR Chi-restraints excluded: chain I residue 99 ASN Chi-restraints excluded: chain J residue 112 LEU Chi-restraints excluded: chain J residue 155 THR Chi-restraints excluded: chain J residue 161 SER Chi-restraints excluded: chain K residue 21 VAL Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 145 ILE Chi-restraints excluded: chain K residue 152 ASP Chi-restraints excluded: chain K residue 168 VAL Chi-restraints excluded: chain K residue 170 ARG Chi-restraints excluded: chain K residue 223 CYS Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 100 ARG Chi-restraints excluded: chain L residue 124 ILE Chi-restraints excluded: chain M residue 53 VAL Chi-restraints excluded: chain M residue 64 VAL Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 90 VAL Chi-restraints excluded: chain N residue 19 LEU Chi-restraints excluded: chain N residue 73 ARG Chi-restraints excluded: chain N residue 117 ASN Chi-restraints excluded: chain O residue 16 VAL Chi-restraints excluded: chain O residue 27 LEU Chi-restraints excluded: chain O residue 46 GLU Chi-restraints excluded: chain O residue 52 LEU Chi-restraints excluded: chain O residue 84 LEU Chi-restraints excluded: chain O residue 150 GLU Chi-restraints excluded: chain P residue 114 VAL Chi-restraints excluded: chain P residue 120 ASN Chi-restraints excluded: chain P residue 136 ILE Chi-restraints excluded: chain Q residue 47 VAL Chi-restraints excluded: chain Q residue 145 ASN Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain R residue 91 SER Chi-restraints excluded: chain R residue 100 ARG Chi-restraints excluded: chain S residue 32 SER Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain S residue 78 TRP Chi-restraints excluded: chain S residue 132 THR Chi-restraints excluded: chain S residue 170 THR Chi-restraints excluded: chain S residue 172 TYR Chi-restraints excluded: chain T residue 29 THR Chi-restraints excluded: chain T residue 39 ILE Chi-restraints excluded: chain T residue 41 ASP Chi-restraints excluded: chain T residue 64 VAL Chi-restraints excluded: chain T residue 79 MET Chi-restraints excluded: chain T residue 101 CYS Chi-restraints excluded: chain T residue 126 VAL Chi-restraints excluded: chain T residue 128 LEU Chi-restraints excluded: chain T residue 136 ARG Chi-restraints excluded: chain T residue 150 THR Chi-restraints excluded: chain V residue 56 ASP Chi-restraints excluded: chain V residue 85 TRP Chi-restraints excluded: chain V residue 112 SER Chi-restraints excluded: chain V residue 115 THR Chi-restraints excluded: chain W residue 3 ARG Chi-restraints excluded: chain W residue 48 VAL Chi-restraints excluded: chain W residue 60 TRP Chi-restraints excluded: chain W residue 110 ASN Chi-restraints excluded: chain W residue 122 SER Chi-restraints excluded: chain W residue 220 TYR Chi-restraints excluded: chain W residue 223 ASN Chi-restraints excluded: chain X residue 48 SER Chi-restraints excluded: chain X residue 112 THR Chi-restraints excluded: chain Y residue 66 GLN Chi-restraints excluded: chain Y residue 74 TYR Chi-restraints excluded: chain Y residue 105 VAL Chi-restraints excluded: chain Z residue 53 VAL Chi-restraints excluded: chain Z residue 86 THR Chi-restraints excluded: chain Z residue 96 VAL Chi-restraints excluded: chain Z residue 102 GLU Chi-restraints excluded: chain a residue 85 ASP Chi-restraints excluded: chain a residue 91 LEU Chi-restraints excluded: chain a residue 95 SER Chi-restraints excluded: chain b residue 162 SER Chi-restraints excluded: chain b residue 170 LEU Chi-restraints excluded: chain b residue 177 ASN Chi-restraints excluded: chain b residue 229 THR Chi-restraints excluded: chain b residue 250 VAL Chi-restraints excluded: chain b residue 370 ASP Chi-restraints excluded: chain b residue 394 ASN Chi-restraints excluded: chain b residue 398 LEU Chi-restraints excluded: chain b residue 420 TYR Chi-restraints excluded: chain b residue 440 ASN Chi-restraints excluded: chain b residue 453 LEU Chi-restraints excluded: chain b residue 477 ILE Chi-restraints excluded: chain d residue 13 THR Chi-restraints excluded: chain d residue 50 ARG Chi-restraints excluded: chain d residue 64 VAL Chi-restraints excluded: chain d residue 74 ARG Chi-restraints excluded: chain d residue 106 THR Chi-restraints excluded: chain e residue 19 ARG Chi-restraints excluded: chain e residue 51 SER Chi-restraints excluded: chain e residue 75 LEU Chi-restraints excluded: chain e residue 84 THR Chi-restraints excluded: chain e residue 118 LYS Chi-restraints excluded: chain e residue 128 LEU Chi-restraints excluded: chain f residue 22 VAL Chi-restraints excluded: chain f residue 31 LYS Chi-restraints excluded: chain f residue 49 ILE Chi-restraints excluded: chain f residue 56 SER Chi-restraints excluded: chain g residue 16 ARG Chi-restraints excluded: chain g residue 17 SER Chi-restraints excluded: chain g residue 47 CYS Chi-restraints excluded: chain h residue 33 VAL Chi-restraints excluded: chain i residue 9 ILE Chi-restraints excluded: chain i residue 79 SER Chi-restraints excluded: chain i residue 94 ILE Chi-restraints excluded: chain j residue 17 THR Chi-restraints excluded: chain j residue 84 SER Chi-restraints excluded: chain k residue 12 LEU Chi-restraints excluded: chain k residue 16 ARG Chi-restraints excluded: chain k residue 66 ILE Chi-restraints excluded: chain l residue 5 LYS Chi-restraints excluded: chain l residue 23 LEU Chi-restraints excluded: chain m residue 28 ASN Chi-restraints excluded: chain m residue 30 TYR Chi-restraints excluded: chain m residue 60 SER Chi-restraints excluded: chain m residue 96 LEU Chi-restraints excluded: chain m residue 204 SER Chi-restraints excluded: chain m residue 221 SER Chi-restraints excluded: chain m residue 337 LYS Chi-restraints excluded: chain m residue 418 ILE Chi-restraints excluded: chain n residue 63 SER Chi-restraints excluded: chain p residue 42 CYS Chi-restraints excluded: chain p residue 72 SER Chi-restraints excluded: chain p residue 81 SER Chi-restraints excluded: chain q residue 54 LYS Chi-restraints excluded: chain q residue 66 ASN Chi-restraints excluded: chain q residue 72 SER Chi-restraints excluded: chain r residue 7 ILE Chi-restraints excluded: chain r residue 12 LYS Chi-restraints excluded: chain r residue 129 SER Chi-restraints excluded: chain r residue 143 ARG Chi-restraints excluded: chain r residue 166 VAL Chi-restraints excluded: chain r residue 168 MET Chi-restraints excluded: chain r residue 175 SER Chi-restraints excluded: chain r residue 250 ASP Chi-restraints excluded: chain r residue 252 ASP Chi-restraints excluded: chain t residue 27 SER Chi-restraints excluded: chain t residue 118 GLU Chi-restraints excluded: chain t residue 413 ASP Chi-restraints excluded: chain t residue 414 LEU Chi-restraints excluded: chain t residue 485 LEU Chi-restraints excluded: chain u residue 30 ARG Chi-restraints excluded: chain u residue 65 VAL Chi-restraints excluded: chain u residue 75 ARG Chi-restraints excluded: chain u residue 132 GLU Chi-restraints excluded: chain x residue 133 THR Chi-restraints excluded: chain x residue 201 ILE Chi-restraints excluded: chain x residue 254 SER Chi-restraints excluded: chain x residue 269 VAL Chi-restraints excluded: chain x residue 272 TYR Chi-restraints excluded: chain x residue 273 THR Chi-restraints excluded: chain x residue 275 SER Chi-restraints excluded: chain x residue 418 VAL Chi-restraints excluded: chain x residue 435 LYS Chi-restraints excluded: chain x residue 480 VAL Chi-restraints excluded: chain x residue 491 THR Chi-restraints excluded: chain y residue 34 PHE Chi-restraints excluded: chain y residue 76 THR Chi-restraints excluded: chain y residue 130 SER Chi-restraints excluded: chain y residue 164 GLN Chi-restraints excluded: chain y residue 165 THR Chi-restraints excluded: chain y residue 236 LEU Chi-restraints excluded: chain y residue 241 ILE Chi-restraints excluded: chain z residue 15 SER Chi-restraints excluded: chain z residue 26 VAL Chi-restraints excluded: chain z residue 46 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1269 random chunks: chunk 1021 optimal weight: 5.9990 chunk 696 optimal weight: 7.9990 chunk 17 optimal weight: 30.0000 chunk 913 optimal weight: 7.9990 chunk 506 optimal weight: 0.0050 chunk 1046 optimal weight: 3.9990 chunk 847 optimal weight: 9.9990 chunk 1 optimal weight: 10.0000 chunk 626 optimal weight: 10.0000 chunk 1100 optimal weight: 10.0000 chunk 309 optimal weight: 10.0000 overall best weight: 5.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 85 ASN ** B 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 173 GLN C 304 GLN C 311 HIS ** D 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 GLN ** E 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 59 GLN H 163 GLN I 37 GLN I 87 GLN I 103 ASN J 47 GLN J 101 ASN J 150 ASN K 106 GLN ** K 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 41 GLN Q 9 GLN R 39 ASN S 142 GLN T 131 GLN U 25 ASN ** U 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 7 GLN V 81 GLN a 89 GLN c 61 ASN e 52 GLN f 42 GLN h 62 GLN ** i 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 92 ASN j 20 ASN m 395 HIS t 163 HIS ** t 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 130 ASN x 208 ASN x 219 GLN x 271 GLN x 289 GLN ** x 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 157 GLN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.2627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 156900 Z= 0.280 Angle : 0.600 11.862 227896 Z= 0.311 Chirality : 0.039 0.316 28257 Planarity : 0.004 0.078 16563 Dihedral : 22.566 179.510 61830 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.75 % Favored : 93.10 % Rotamer: Outliers : 6.36 % Allowed : 23.89 % Favored : 69.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.94 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -0.65 (0.08), residues: 9491 helix: 0.97 (0.09), residues: 3746 sheet: -0.32 (0.14), residues: 1224 loop : -1.72 (0.09), residues: 4521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP r 147 HIS 0.008 0.001 HIS y 50 PHE 0.028 0.002 PHE K 300 TYR 0.026 0.002 TYR G 134 ARG 0.010 0.000 ARG F 30 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18982 Ramachandran restraints generated. 9491 Oldfield, 0 Emsley, 9491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18982 Ramachandran restraints generated. 9491 Oldfield, 0 Emsley, 9491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1556 residues out of total 8277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 516 poor density : 1040 time to evaluate : 8.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 4 269 TRP cc_start: 0.8305 (m-90) cc_final: 0.7961 (m-90) REVERT: 4 395 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8500 (mt) REVERT: 4 454 PRO cc_start: 0.8658 (Cg_exo) cc_final: 0.8422 (Cg_endo) REVERT: 4 475 LEU cc_start: 0.7995 (OUTLIER) cc_final: 0.7644 (pt) REVERT: 4 530 LYS cc_start: 0.6102 (mptp) cc_final: 0.5878 (mttm) REVERT: 4 575 MET cc_start: 0.7337 (mtt) cc_final: 0.7030 (mtt) REVERT: 5 48 LYS cc_start: 0.8052 (OUTLIER) cc_final: 0.7725 (ttmt) REVERT: 5 67 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.7261 (pm20) REVERT: B 102 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8259 (pt) REVERT: B 137 TYR cc_start: 0.8373 (OUTLIER) cc_final: 0.7655 (t80) REVERT: D 111 GLN cc_start: 0.7357 (tt0) cc_final: 0.6973 (mm-40) REVERT: D 183 TRP cc_start: 0.7940 (t-100) cc_final: 0.7301 (t-100) REVERT: D 203 HIS cc_start: 0.7028 (p-80) cc_final: 0.6390 (p-80) REVERT: E 8 LYS cc_start: 0.5406 (OUTLIER) cc_final: 0.3999 (pttt) REVERT: E 26 ARG cc_start: 0.8835 (OUTLIER) cc_final: 0.7948 (mtt90) REVERT: H 62 ARG cc_start: 0.7173 (OUTLIER) cc_final: 0.6843 (mtm180) REVERT: H 76 ASP cc_start: 0.8632 (m-30) cc_final: 0.8287 (m-30) REVERT: H 113 GLU cc_start: 0.7569 (OUTLIER) cc_final: 0.7349 (tt0) REVERT: I 104 ARG cc_start: 0.7853 (tpt170) cc_final: 0.7625 (tpp-160) REVERT: J 131 MET cc_start: 0.8087 (mmm) cc_final: 0.7863 (mmm) REVERT: K 152 ASP cc_start: 0.8414 (OUTLIER) cc_final: 0.8160 (t0) REVERT: K 170 ARG cc_start: 0.6430 (OUTLIER) cc_final: 0.5197 (mtp-110) REVERT: L 131 LYS cc_start: 0.5685 (mppt) cc_final: 0.5337 (mmmt) REVERT: L 188 ARG cc_start: 0.7542 (mtp-110) cc_final: 0.7210 (mtp180) REVERT: N 73 ARG cc_start: 0.8576 (OUTLIER) cc_final: 0.7932 (ttm170) REVERT: N 92 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8504 (mp) REVERT: N 142 ILE cc_start: 0.8955 (OUTLIER) cc_final: 0.8727 (mt) REVERT: O 106 GLU cc_start: 0.8606 (mp0) cc_final: 0.8204 (mm-30) REVERT: Q 22 ASP cc_start: 0.7617 (t0) cc_final: 0.7388 (t0) REVERT: S 46 GLN cc_start: 0.8438 (mt0) cc_final: 0.8218 (mt0) REVERT: S 78 TRP cc_start: 0.6648 (OUTLIER) cc_final: 0.6057 (m-10) REVERT: S 172 TYR cc_start: 0.8337 (OUTLIER) cc_final: 0.5590 (t80) REVERT: T 150 THR cc_start: 0.8737 (OUTLIER) cc_final: 0.8487 (m) REVERT: V 24 ASN cc_start: 0.8193 (m110) cc_final: 0.7850 (m-40) REVERT: V 109 MET cc_start: 0.8294 (OUTLIER) cc_final: 0.7938 (mtm) REVERT: Y 66 GLN cc_start: 0.8877 (OUTLIER) cc_final: 0.8635 (mt0) REVERT: b 254 MET cc_start: 0.8286 (mmm) cc_final: 0.8063 (mmm) REVERT: b 398 LEU cc_start: 0.7592 (OUTLIER) cc_final: 0.7349 (tp) REVERT: b 453 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8509 (mt) REVERT: b 506 GLU cc_start: 0.8032 (mt-10) cc_final: 0.7773 (mt-10) REVERT: b 542 MET cc_start: 0.6720 (mpp) cc_final: 0.6517 (OUTLIER) REVERT: b 608 MET cc_start: 0.8760 (ttm) cc_final: 0.8408 (ttm) REVERT: d 50 ARG cc_start: 0.8531 (OUTLIER) cc_final: 0.7076 (mmt90) REVERT: e 19 ARG cc_start: 0.8937 (OUTLIER) cc_final: 0.6809 (ttm170) REVERT: e 47 ARG cc_start: 0.9017 (OUTLIER) cc_final: 0.7752 (ttm-80) REVERT: e 118 LYS cc_start: 0.8697 (OUTLIER) cc_final: 0.8082 (ttmm) REVERT: f 31 LYS cc_start: 0.8752 (OUTLIER) cc_final: 0.7993 (tttp) REVERT: g 16 ARG cc_start: 0.8842 (OUTLIER) cc_final: 0.8417 (ttm170) REVERT: j 84 SER cc_start: 0.7325 (OUTLIER) cc_final: 0.7023 (t) REVERT: k 7 ASP cc_start: 0.6960 (t70) cc_final: 0.6721 (t0) REVERT: k 16 ARG cc_start: 0.8299 (OUTLIER) cc_final: 0.7923 (mpp80) REVERT: m 57 ARG cc_start: 0.5880 (ttm170) cc_final: 0.5370 (ttm170) REVERT: m 315 GLN cc_start: 0.7565 (OUTLIER) cc_final: 0.7202 (pt0) REVERT: m 337 LYS cc_start: 0.8973 (OUTLIER) cc_final: 0.8629 (tttm) REVERT: n 59 TYR cc_start: 0.8883 (m-80) cc_final: 0.8633 (m-80) REVERT: q 72 SER cc_start: 0.8473 (OUTLIER) cc_final: 0.8169 (p) REVERT: r 143 ARG cc_start: 0.8113 (OUTLIER) cc_final: 0.6791 (mmp-170) REVERT: r 168 MET cc_start: 0.4657 (OUTLIER) cc_final: 0.3471 (mtp) REVERT: r 254 CYS cc_start: 0.7820 (p) cc_final: 0.7589 (p) REVERT: t 214 GLN cc_start: 0.7095 (OUTLIER) cc_final: 0.6572 (mp10) REVERT: t 236 ASP cc_start: 0.7529 (p0) cc_final: 0.7097 (m-30) REVERT: t 378 HIS cc_start: 0.8180 (m90) cc_final: 0.7852 (m90) REVERT: t 476 LYS cc_start: 0.7880 (ttpp) cc_final: 0.7519 (tttt) REVERT: u 75 ARG cc_start: 0.8657 (OUTLIER) cc_final: 0.8139 (mtt-85) REVERT: x 293 TYR cc_start: 0.9216 (m-80) cc_final: 0.8907 (m-80) REVERT: y 12 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.7467 (mt-10) REVERT: y 164 GLN cc_start: 0.8396 (OUTLIER) cc_final: 0.7845 (mp10) REVERT: y 236 LEU cc_start: 0.6864 (OUTLIER) cc_final: 0.6619 (pp) REVERT: y 241 ILE cc_start: 0.7180 (OUTLIER) cc_final: 0.6753 (mp) REVERT: z 46 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.8110 (mt) REVERT: z 94 MET cc_start: 0.7121 (tpp) cc_final: 0.6086 (tpt) outliers start: 516 outliers final: 290 residues processed: 1426 average time/residue: 1.9432 time to fit residues: 4137.9761 Evaluate side-chains 1330 residues out of total 8277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 331 poor density : 999 time to evaluate : 8.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 4 residue 43 THR Chi-restraints excluded: chain 4 residue 44 SER Chi-restraints excluded: chain 4 residue 70 SER Chi-restraints excluded: chain 4 residue 101 SER Chi-restraints excluded: chain 4 residue 128 SER Chi-restraints excluded: chain 4 residue 137 ASP Chi-restraints excluded: chain 4 residue 139 VAL Chi-restraints excluded: chain 4 residue 142 THR Chi-restraints excluded: chain 4 residue 159 VAL Chi-restraints excluded: chain 4 residue 177 LEU Chi-restraints excluded: chain 4 residue 203 THR Chi-restraints excluded: chain 4 residue 247 ILE Chi-restraints excluded: chain 4 residue 279 LEU Chi-restraints excluded: chain 4 residue 316 VAL Chi-restraints excluded: chain 4 residue 335 VAL Chi-restraints excluded: chain 4 residue 344 THR Chi-restraints excluded: chain 4 residue 367 THR Chi-restraints excluded: chain 4 residue 395 LEU Chi-restraints excluded: chain 4 residue 405 ASN Chi-restraints excluded: chain 4 residue 411 SER Chi-restraints excluded: chain 4 residue 443 VAL Chi-restraints excluded: chain 4 residue 475 LEU Chi-restraints excluded: chain 4 residue 493 LYS Chi-restraints excluded: chain 4 residue 495 SER Chi-restraints excluded: chain 4 residue 529 SER Chi-restraints excluded: chain 5 residue 48 LYS Chi-restraints excluded: chain 5 residue 67 GLU Chi-restraints excluded: chain 5 residue 93 GLU Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 137 TYR Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 243 HIS Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 340 LYS Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 371 GLN Chi-restraints excluded: chain C residue 12 THR Chi-restraints excluded: chain C residue 54 GLU Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 327 LEU Chi-restraints excluded: chain C residue 349 THR Chi-restraints excluded: chain C residue 362 ASP Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 81 HIS Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain E residue 8 LYS Chi-restraints excluded: chain E residue 9 TRP Chi-restraints excluded: chain E residue 12 SER Chi-restraints excluded: chain E residue 26 ARG Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 164 SER Chi-restraints excluded: chain F residue 82 LYS Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain G residue 36 ILE Chi-restraints excluded: chain G residue 47 SER Chi-restraints excluded: chain G residue 124 ASP Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 197 VAL Chi-restraints excluded: chain H residue 7 GLU Chi-restraints excluded: chain H residue 46 THR Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 62 ARG Chi-restraints excluded: chain H residue 64 HIS Chi-restraints excluded: chain H residue 113 GLU Chi-restraints excluded: chain H residue 137 SER Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 150 SER Chi-restraints excluded: chain I residue 62 ILE Chi-restraints excluded: chain J residue 112 LEU Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 155 THR Chi-restraints excluded: chain J residue 161 SER Chi-restraints excluded: chain K residue 21 VAL Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 145 ILE Chi-restraints excluded: chain K residue 152 ASP Chi-restraints excluded: chain K residue 168 VAL Chi-restraints excluded: chain K residue 170 ARG Chi-restraints excluded: chain K residue 223 CYS Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 100 ARG Chi-restraints excluded: chain L residue 124 ILE Chi-restraints excluded: chain M residue 53 VAL Chi-restraints excluded: chain M residue 64 VAL Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 90 VAL Chi-restraints excluded: chain M residue 91 CYS Chi-restraints excluded: chain M residue 130 THR Chi-restraints excluded: chain N residue 19 LEU Chi-restraints excluded: chain N residue 73 ARG Chi-restraints excluded: chain N residue 92 LEU Chi-restraints excluded: chain N residue 117 ASN Chi-restraints excluded: chain N residue 142 ILE Chi-restraints excluded: chain N residue 183 THR Chi-restraints excluded: chain O residue 16 VAL Chi-restraints excluded: chain O residue 52 LEU Chi-restraints excluded: chain O residue 84 LEU Chi-restraints excluded: chain O residue 150 GLU Chi-restraints excluded: chain O residue 151 ASP Chi-restraints excluded: chain P residue 49 GLU Chi-restraints excluded: chain P residue 114 VAL Chi-restraints excluded: chain P residue 120 ASN Chi-restraints excluded: chain P residue 136 ILE Chi-restraints excluded: chain P residue 141 SER Chi-restraints excluded: chain P residue 181 ARG Chi-restraints excluded: chain Q residue 7 SER Chi-restraints excluded: chain Q residue 47 VAL Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain S residue 3 HIS Chi-restraints excluded: chain S residue 9 VAL Chi-restraints excluded: chain S residue 32 SER Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain S residue 78 TRP Chi-restraints excluded: chain S residue 132 THR Chi-restraints excluded: chain S residue 170 THR Chi-restraints excluded: chain S residue 172 TYR Chi-restraints excluded: chain T residue 29 THR Chi-restraints excluded: chain T residue 39 ILE Chi-restraints excluded: chain T residue 41 ASP Chi-restraints excluded: chain T residue 52 MET Chi-restraints excluded: chain T residue 64 VAL Chi-restraints excluded: chain T residue 79 MET Chi-restraints excluded: chain T residue 101 CYS Chi-restraints excluded: chain T residue 126 VAL Chi-restraints excluded: chain T residue 128 LEU Chi-restraints excluded: chain T residue 136 ARG Chi-restraints excluded: chain T residue 150 THR Chi-restraints excluded: chain U residue 111 THR Chi-restraints excluded: chain V residue 56 ASP Chi-restraints excluded: chain V residue 85 TRP Chi-restraints excluded: chain V residue 91 VAL Chi-restraints excluded: chain V residue 98 ASN Chi-restraints excluded: chain V residue 109 MET Chi-restraints excluded: chain V residue 112 SER Chi-restraints excluded: chain V residue 115 THR Chi-restraints excluded: chain V residue 120 LYS Chi-restraints excluded: chain W residue 3 ARG Chi-restraints excluded: chain W residue 48 VAL Chi-restraints excluded: chain W residue 56 ILE Chi-restraints excluded: chain W residue 60 TRP Chi-restraints excluded: chain W residue 110 ASN Chi-restraints excluded: chain W residue 120 VAL Chi-restraints excluded: chain W residue 122 SER Chi-restraints excluded: chain W residue 142 VAL Chi-restraints excluded: chain W residue 197 VAL Chi-restraints excluded: chain W residue 223 ASN Chi-restraints excluded: chain W residue 231 THR Chi-restraints excluded: chain X residue 8 THR Chi-restraints excluded: chain X residue 48 SER Chi-restraints excluded: chain X residue 51 VAL Chi-restraints excluded: chain X residue 112 THR Chi-restraints excluded: chain Y residue 66 GLN Chi-restraints excluded: chain Y residue 70 ILE Chi-restraints excluded: chain Y residue 74 TYR Chi-restraints excluded: chain Y residue 105 VAL Chi-restraints excluded: chain Z residue 33 SER Chi-restraints excluded: chain Z residue 53 VAL Chi-restraints excluded: chain Z residue 86 THR Chi-restraints excluded: chain Z residue 96 VAL Chi-restraints excluded: chain a residue 91 LEU Chi-restraints excluded: chain a residue 95 SER Chi-restraints excluded: chain a residue 101 VAL Chi-restraints excluded: chain b residue 73 ASP Chi-restraints excluded: chain b residue 162 SER Chi-restraints excluded: chain b residue 170 LEU Chi-restraints excluded: chain b residue 172 ILE Chi-restraints excluded: chain b residue 229 THR Chi-restraints excluded: chain b residue 250 VAL Chi-restraints excluded: chain b residue 260 CYS Chi-restraints excluded: chain b residue 273 SER Chi-restraints excluded: chain b residue 382 VAL Chi-restraints excluded: chain b residue 394 ASN Chi-restraints excluded: chain b residue 398 LEU Chi-restraints excluded: chain b residue 411 VAL Chi-restraints excluded: chain b residue 420 TYR Chi-restraints excluded: chain b residue 440 ASN Chi-restraints excluded: chain b residue 453 LEU Chi-restraints excluded: chain b residue 477 ILE Chi-restraints excluded: chain b residue 509 ASN Chi-restraints excluded: chain c residue 43 VAL Chi-restraints excluded: chain c residue 106 GLN Chi-restraints excluded: chain d residue 6 ASP Chi-restraints excluded: chain d residue 13 THR Chi-restraints excluded: chain d residue 50 ARG Chi-restraints excluded: chain d residue 106 THR Chi-restraints excluded: chain d residue 108 VAL Chi-restraints excluded: chain e residue 10 VAL Chi-restraints excluded: chain e residue 19 ARG Chi-restraints excluded: chain e residue 47 ARG Chi-restraints excluded: chain e residue 51 SER Chi-restraints excluded: chain e residue 75 LEU Chi-restraints excluded: chain e residue 84 THR Chi-restraints excluded: chain e residue 118 LYS Chi-restraints excluded: chain e residue 128 LEU Chi-restraints excluded: chain f residue 22 VAL Chi-restraints excluded: chain f residue 31 LYS Chi-restraints excluded: chain f residue 49 ILE Chi-restraints excluded: chain f residue 56 SER Chi-restraints excluded: chain f residue 97 SER Chi-restraints excluded: chain g residue 16 ARG Chi-restraints excluded: chain g residue 17 SER Chi-restraints excluded: chain g residue 47 CYS Chi-restraints excluded: chain g residue 57 LEU Chi-restraints excluded: chain g residue 68 THR Chi-restraints excluded: chain g residue 71 THR Chi-restraints excluded: chain g residue 79 SER Chi-restraints excluded: chain h residue 33 VAL Chi-restraints excluded: chain h residue 84 LYS Chi-restraints excluded: chain i residue 9 ILE Chi-restraints excluded: chain i residue 58 ILE Chi-restraints excluded: chain i residue 60 LEU Chi-restraints excluded: chain i residue 79 SER Chi-restraints excluded: chain i residue 94 ILE Chi-restraints excluded: chain j residue 17 THR Chi-restraints excluded: chain j residue 33 THR Chi-restraints excluded: chain j residue 36 SER Chi-restraints excluded: chain j residue 46 SER Chi-restraints excluded: chain j residue 84 SER Chi-restraints excluded: chain k residue 12 LEU Chi-restraints excluded: chain k residue 16 ARG Chi-restraints excluded: chain k residue 66 ILE Chi-restraints excluded: chain k residue 68 SER Chi-restraints excluded: chain l residue 5 LYS Chi-restraints excluded: chain l residue 6 SER Chi-restraints excluded: chain l residue 23 LEU Chi-restraints excluded: chain m residue 28 ASN Chi-restraints excluded: chain m residue 30 TYR Chi-restraints excluded: chain m residue 44 SER Chi-restraints excluded: chain m residue 60 SER Chi-restraints excluded: chain m residue 96 LEU Chi-restraints excluded: chain m residue 204 SER Chi-restraints excluded: chain m residue 221 SER Chi-restraints excluded: chain m residue 235 LEU Chi-restraints excluded: chain m residue 293 SER Chi-restraints excluded: chain m residue 315 GLN Chi-restraints excluded: chain m residue 337 LYS Chi-restraints excluded: chain m residue 418 ILE Chi-restraints excluded: chain m residue 425 THR Chi-restraints excluded: chain n residue 17 VAL Chi-restraints excluded: chain n residue 29 SER Chi-restraints excluded: chain n residue 63 SER Chi-restraints excluded: chain p residue 42 CYS Chi-restraints excluded: chain p residue 56 THR Chi-restraints excluded: chain p residue 60 CYS Chi-restraints excluded: chain p residue 72 SER Chi-restraints excluded: chain p residue 81 SER Chi-restraints excluded: chain p residue 89 MET Chi-restraints excluded: chain q residue 59 THR Chi-restraints excluded: chain q residue 66 ASN Chi-restraints excluded: chain q residue 72 SER Chi-restraints excluded: chain q residue 110 ILE Chi-restraints excluded: chain r residue 7 ILE Chi-restraints excluded: chain r residue 12 LYS Chi-restraints excluded: chain r residue 129 SER Chi-restraints excluded: chain r residue 143 ARG Chi-restraints excluded: chain r residue 166 VAL Chi-restraints excluded: chain r residue 168 MET Chi-restraints excluded: chain r residue 175 SER Chi-restraints excluded: chain r residue 193 VAL Chi-restraints excluded: chain r residue 252 ASP Chi-restraints excluded: chain s residue 13 THR Chi-restraints excluded: chain t residue 27 SER Chi-restraints excluded: chain t residue 118 GLU Chi-restraints excluded: chain t residue 212 LEU Chi-restraints excluded: chain t residue 214 GLN Chi-restraints excluded: chain t residue 382 VAL Chi-restraints excluded: chain t residue 412 HIS Chi-restraints excluded: chain t residue 413 ASP Chi-restraints excluded: chain t residue 485 LEU Chi-restraints excluded: chain t residue 500 LYS Chi-restraints excluded: chain u residue 30 ARG Chi-restraints excluded: chain u residue 65 VAL Chi-restraints excluded: chain u residue 75 ARG Chi-restraints excluded: chain u residue 132 GLU Chi-restraints excluded: chain x residue 133 THR Chi-restraints excluded: chain x residue 136 SER Chi-restraints excluded: chain x residue 201 ILE Chi-restraints excluded: chain x residue 254 SER Chi-restraints excluded: chain x residue 269 VAL Chi-restraints excluded: chain x residue 272 TYR Chi-restraints excluded: chain x residue 273 THR Chi-restraints excluded: chain x residue 275 SER Chi-restraints excluded: chain x residue 386 TRP Chi-restraints excluded: chain x residue 418 VAL Chi-restraints excluded: chain x residue 435 LYS Chi-restraints excluded: chain x residue 480 VAL Chi-restraints excluded: chain x residue 491 THR Chi-restraints excluded: chain y residue 12 GLU Chi-restraints excluded: chain y residue 34 PHE Chi-restraints excluded: chain y residue 76 THR Chi-restraints excluded: chain y residue 130 SER Chi-restraints excluded: chain y residue 155 SER Chi-restraints excluded: chain y residue 164 GLN Chi-restraints excluded: chain y residue 165 THR Chi-restraints excluded: chain y residue 236 LEU Chi-restraints excluded: chain y residue 241 ILE Chi-restraints excluded: chain z residue 15 SER Chi-restraints excluded: chain z residue 21 VAL Chi-restraints excluded: chain z residue 26 VAL Chi-restraints excluded: chain z residue 42 LEU Chi-restraints excluded: chain z residue 46 LEU Chi-restraints excluded: chain z residue 82 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1269 random chunks: chunk 412 optimal weight: 0.5980 chunk 1104 optimal weight: 9.9990 chunk 242 optimal weight: 20.0000 chunk 720 optimal weight: 9.9990 chunk 302 optimal weight: 10.0000 chunk 1227 optimal weight: 6.9990 chunk 1019 optimal weight: 9.9990 chunk 568 optimal weight: 10.0000 chunk 102 optimal weight: 20.0000 chunk 406 optimal weight: 0.6980 chunk 644 optimal weight: 10.0000 overall best weight: 5.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 4 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 455 ASN ** B 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 311 HIS ** D 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 GLN E 57 HIS ** E 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 232 HIS H 163 GLN J 47 GLN J 150 ASN K 106 GLN K 107 GLN ** K 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 41 GLN O 182 ASN Q 9 GLN R 39 ASN S 142 GLN ** U 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 89 GLN c 61 ASN e 52 GLN ** i 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 92 ASN m 395 HIS n 71 GLN p 25 GLN ** t 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 130 ASN x 208 ASN x 219 GLN x 289 GLN ** x 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.2805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 156900 Z= 0.297 Angle : 0.612 12.982 227896 Z= 0.318 Chirality : 0.039 0.311 28257 Planarity : 0.005 0.076 16563 Dihedral : 22.580 179.932 61828 Min Nonbonded Distance : 1.782 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.03 % Favored : 92.85 % Rotamer: Outliers : 6.35 % Allowed : 24.54 % Favored : 69.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.94 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -0.64 (0.08), residues: 9491 helix: 0.96 (0.09), residues: 3767 sheet: -0.30 (0.14), residues: 1221 loop : -1.71 (0.09), residues: 4503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP r 147 HIS 0.006 0.001 HIS t 120 PHE 0.030 0.002 PHE K 300 TYR 0.026 0.002 TYR G 134 ARG 0.019 0.000 ARG K 292 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18982 Ramachandran restraints generated. 9491 Oldfield, 0 Emsley, 9491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18982 Ramachandran restraints generated. 9491 Oldfield, 0 Emsley, 9491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1563 residues out of total 8277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 515 poor density : 1048 time to evaluate : 8.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 4 269 TRP cc_start: 0.8408 (m-90) cc_final: 0.8067 (m-90) REVERT: 4 395 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8529 (mt) REVERT: 4 454 PRO cc_start: 0.8689 (Cg_exo) cc_final: 0.8458 (Cg_endo) REVERT: 4 475 LEU cc_start: 0.8081 (OUTLIER) cc_final: 0.7752 (pt) REVERT: 4 530 LYS cc_start: 0.6265 (mptp) cc_final: 0.6051 (mttm) REVERT: 5 48 LYS cc_start: 0.8109 (OUTLIER) cc_final: 0.7731 (ttmm) REVERT: 5 67 GLU cc_start: 0.7590 (OUTLIER) cc_final: 0.7212 (pm20) REVERT: B 102 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8330 (pt) REVERT: B 137 TYR cc_start: 0.8327 (OUTLIER) cc_final: 0.7765 (t80) REVERT: B 196 ARG cc_start: 0.8135 (OUTLIER) cc_final: 0.7584 (mmm-85) REVERT: C 222 VAL cc_start: 0.9508 (OUTLIER) cc_final: 0.9243 (t) REVERT: D 32 GLN cc_start: 0.8660 (tt0) cc_final: 0.8363 (tt0) REVERT: D 111 GLN cc_start: 0.7481 (tt0) cc_final: 0.7019 (mm-40) REVERT: D 203 HIS cc_start: 0.7154 (p-80) cc_final: 0.6499 (p-80) REVERT: E 8 LYS cc_start: 0.5414 (OUTLIER) cc_final: 0.4044 (pttt) REVERT: E 15 VAL cc_start: 0.8755 (m) cc_final: 0.8437 (t) REVERT: E 26 ARG cc_start: 0.8841 (OUTLIER) cc_final: 0.7949 (mtt90) REVERT: H 62 ARG cc_start: 0.7276 (OUTLIER) cc_final: 0.6914 (mtm180) REVERT: H 76 ASP cc_start: 0.8686 (m-30) cc_final: 0.8334 (m-30) REVERT: I 104 ARG cc_start: 0.7903 (tpt170) cc_final: 0.7556 (tpp-160) REVERT: J 162 TRP cc_start: 0.7383 (OUTLIER) cc_final: 0.5835 (t60) REVERT: K 137 TYR cc_start: 0.8820 (m-80) cc_final: 0.8479 (m-80) REVERT: K 152 ASP cc_start: 0.8466 (OUTLIER) cc_final: 0.8179 (t0) REVERT: K 170 ARG cc_start: 0.6450 (OUTLIER) cc_final: 0.5204 (mtp-110) REVERT: L 131 LYS cc_start: 0.5771 (mppt) cc_final: 0.5306 (mmmt) REVERT: L 188 ARG cc_start: 0.7584 (mtp-110) cc_final: 0.7200 (mtp180) REVERT: N 73 ARG cc_start: 0.8584 (OUTLIER) cc_final: 0.7918 (ttm170) REVERT: N 92 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8526 (mp) REVERT: O 106 GLU cc_start: 0.8649 (mp0) cc_final: 0.8206 (mm-30) REVERT: Q 22 ASP cc_start: 0.7584 (t0) cc_final: 0.7199 (t0) REVERT: R 28 GLU cc_start: 0.8532 (OUTLIER) cc_final: 0.8123 (mm-30) REVERT: R 81 ARG cc_start: 0.9099 (OUTLIER) cc_final: 0.8185 (mtp180) REVERT: S 46 GLN cc_start: 0.8506 (mt0) cc_final: 0.8272 (mt0) REVERT: S 78 TRP cc_start: 0.6632 (OUTLIER) cc_final: 0.6196 (m-10) REVERT: S 172 TYR cc_start: 0.8551 (OUTLIER) cc_final: 0.5586 (t80) REVERT: V 24 ASN cc_start: 0.8183 (m110) cc_final: 0.7893 (m-40) REVERT: V 109 MET cc_start: 0.8389 (OUTLIER) cc_final: 0.7808 (mtm) REVERT: Y 66 GLN cc_start: 0.8911 (OUTLIER) cc_final: 0.8645 (mt0) REVERT: b 254 MET cc_start: 0.8240 (mmm) cc_final: 0.8005 (mmm) REVERT: b 398 LEU cc_start: 0.7694 (OUTLIER) cc_final: 0.7457 (tp) REVERT: b 453 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8573 (mt) REVERT: b 506 GLU cc_start: 0.8028 (mt-10) cc_final: 0.7767 (mt-10) REVERT: b 608 MET cc_start: 0.8780 (ttm) cc_final: 0.8440 (ttm) REVERT: c 98 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.7373 (mt-10) REVERT: d 50 ARG cc_start: 0.8540 (OUTLIER) cc_final: 0.7062 (mmt90) REVERT: d 74 ARG cc_start: 0.8502 (OUTLIER) cc_final: 0.8172 (ttm170) REVERT: d 105 GLN cc_start: 0.9295 (OUTLIER) cc_final: 0.9072 (pt0) REVERT: e 19 ARG cc_start: 0.8955 (OUTLIER) cc_final: 0.6872 (ttm170) REVERT: e 47 ARG cc_start: 0.9034 (OUTLIER) cc_final: 0.7752 (ttm-80) REVERT: e 118 LYS cc_start: 0.8704 (OUTLIER) cc_final: 0.8070 (ttmm) REVERT: e 123 LYS cc_start: 0.7750 (OUTLIER) cc_final: 0.7303 (mtpp) REVERT: f 31 LYS cc_start: 0.8754 (OUTLIER) cc_final: 0.7995 (tttp) REVERT: g 16 ARG cc_start: 0.8849 (OUTLIER) cc_final: 0.8370 (ttm170) REVERT: j 84 SER cc_start: 0.7560 (OUTLIER) cc_final: 0.7262 (t) REVERT: k 16 ARG cc_start: 0.8282 (OUTLIER) cc_final: 0.7868 (mpp80) REVERT: m 57 ARG cc_start: 0.5781 (ttm170) cc_final: 0.5266 (ttm170) REVERT: n 59 TYR cc_start: 0.8884 (m-80) cc_final: 0.8624 (m-80) REVERT: p 83 ILE cc_start: 0.9053 (mm) cc_final: 0.8806 (mp) REVERT: q 72 SER cc_start: 0.8457 (OUTLIER) cc_final: 0.8144 (p) REVERT: r 143 ARG cc_start: 0.8137 (OUTLIER) cc_final: 0.6800 (mmp-170) REVERT: r 168 MET cc_start: 0.4696 (OUTLIER) cc_final: 0.3486 (mtp) REVERT: r 254 CYS cc_start: 0.8018 (p) cc_final: 0.7775 (p) REVERT: t 214 GLN cc_start: 0.7032 (OUTLIER) cc_final: 0.6482 (mp10) REVERT: t 236 ASP cc_start: 0.7566 (p0) cc_final: 0.7182 (m-30) REVERT: t 378 HIS cc_start: 0.8214 (m90) cc_final: 0.7922 (m90) REVERT: t 476 LYS cc_start: 0.7904 (ttpp) cc_final: 0.7570 (tttt) REVERT: u 75 ARG cc_start: 0.8604 (OUTLIER) cc_final: 0.7976 (mtt-85) REVERT: x 293 TYR cc_start: 0.9224 (m-80) cc_final: 0.8929 (m-80) REVERT: y 12 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.8136 (mp0) REVERT: y 164 GLN cc_start: 0.8404 (OUTLIER) cc_final: 0.7861 (mp10) REVERT: y 197 MET cc_start: 0.8374 (OUTLIER) cc_final: 0.8155 (ptp) REVERT: y 236 LEU cc_start: 0.6895 (OUTLIER) cc_final: 0.6621 (pp) REVERT: y 241 ILE cc_start: 0.7252 (OUTLIER) cc_final: 0.6821 (mp) REVERT: z 46 LEU cc_start: 0.8236 (OUTLIER) cc_final: 0.7990 (mt) REVERT: z 94 MET cc_start: 0.7082 (tpp) cc_final: 0.6363 (tpt) outliers start: 515 outliers final: 309 residues processed: 1436 average time/residue: 1.9598 time to fit residues: 4199.1569 Evaluate side-chains 1342 residues out of total 8277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 356 poor density : 986 time to evaluate : 8.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 4 residue 39 LEU Chi-restraints excluded: chain 4 residue 43 THR Chi-restraints excluded: chain 4 residue 44 SER Chi-restraints excluded: chain 4 residue 70 SER Chi-restraints excluded: chain 4 residue 101 SER Chi-restraints excluded: chain 4 residue 128 SER Chi-restraints excluded: chain 4 residue 137 ASP Chi-restraints excluded: chain 4 residue 139 VAL Chi-restraints excluded: chain 4 residue 142 THR Chi-restraints excluded: chain 4 residue 161 TYR Chi-restraints excluded: chain 4 residue 177 LEU Chi-restraints excluded: chain 4 residue 203 THR Chi-restraints excluded: chain 4 residue 247 ILE Chi-restraints excluded: chain 4 residue 316 VAL Chi-restraints excluded: chain 4 residue 326 LEU Chi-restraints excluded: chain 4 residue 335 VAL Chi-restraints excluded: chain 4 residue 344 THR Chi-restraints excluded: chain 4 residue 367 THR Chi-restraints excluded: chain 4 residue 395 LEU Chi-restraints excluded: chain 4 residue 405 ASN Chi-restraints excluded: chain 4 residue 411 SER Chi-restraints excluded: chain 4 residue 443 VAL Chi-restraints excluded: chain 4 residue 455 ASN Chi-restraints excluded: chain 4 residue 475 LEU Chi-restraints excluded: chain 4 residue 493 LYS Chi-restraints excluded: chain 4 residue 495 SER Chi-restraints excluded: chain 4 residue 504 CYS Chi-restraints excluded: chain 4 residue 529 SER Chi-restraints excluded: chain 5 residue 48 LYS Chi-restraints excluded: chain 5 residue 67 GLU Chi-restraints excluded: chain 5 residue 93 GLU Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 137 TYR Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 196 ARG Chi-restraints excluded: chain B residue 212 ASN Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 243 HIS Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 327 CYS Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 340 LYS Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 371 GLN Chi-restraints excluded: chain C residue 12 THR Chi-restraints excluded: chain C residue 54 GLU Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 321 LYS Chi-restraints excluded: chain C residue 327 LEU Chi-restraints excluded: chain C residue 349 THR Chi-restraints excluded: chain C residue 362 ASP Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 81 HIS Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 186 GLU Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain E residue 8 LYS Chi-restraints excluded: chain E residue 12 SER Chi-restraints excluded: chain E residue 26 ARG Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 164 SER Chi-restraints excluded: chain F residue 82 LYS Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain G residue 47 SER Chi-restraints excluded: chain G residue 124 ASP Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain G residue 197 VAL Chi-restraints excluded: chain H residue 7 GLU Chi-restraints excluded: chain H residue 46 THR Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 62 ARG Chi-restraints excluded: chain H residue 64 HIS Chi-restraints excluded: chain H residue 137 SER Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 150 SER Chi-restraints excluded: chain I residue 37 GLN Chi-restraints excluded: chain J residue 112 LEU Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 155 THR Chi-restraints excluded: chain J residue 161 SER Chi-restraints excluded: chain J residue 162 TRP Chi-restraints excluded: chain K residue 13 ASP Chi-restraints excluded: chain K residue 21 VAL Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 152 ASP Chi-restraints excluded: chain K residue 154 THR Chi-restraints excluded: chain K residue 164 CYS Chi-restraints excluded: chain K residue 168 VAL Chi-restraints excluded: chain K residue 170 ARG Chi-restraints excluded: chain K residue 223 CYS Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 100 ARG Chi-restraints excluded: chain L residue 124 ILE Chi-restraints excluded: chain M residue 53 VAL Chi-restraints excluded: chain M residue 64 VAL Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 90 VAL Chi-restraints excluded: chain M residue 91 CYS Chi-restraints excluded: chain M residue 130 THR Chi-restraints excluded: chain N residue 19 LEU Chi-restraints excluded: chain N residue 73 ARG Chi-restraints excluded: chain N residue 92 LEU Chi-restraints excluded: chain N residue 155 VAL Chi-restraints excluded: chain N residue 183 THR Chi-restraints excluded: chain O residue 16 VAL Chi-restraints excluded: chain O residue 52 LEU Chi-restraints excluded: chain O residue 84 LEU Chi-restraints excluded: chain O residue 150 GLU Chi-restraints excluded: chain O residue 151 ASP Chi-restraints excluded: chain O residue 189 ASP Chi-restraints excluded: chain P residue 87 SER Chi-restraints excluded: chain P residue 114 VAL Chi-restraints excluded: chain P residue 120 ASN Chi-restraints excluded: chain P residue 136 ILE Chi-restraints excluded: chain P residue 141 SER Chi-restraints excluded: chain P residue 146 ILE Chi-restraints excluded: chain Q residue 7 SER Chi-restraints excluded: chain Q residue 47 VAL Chi-restraints excluded: chain Q residue 50 LYS Chi-restraints excluded: chain Q residue 145 ASN Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain R residue 28 GLU Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 81 ARG Chi-restraints excluded: chain R residue 91 SER Chi-restraints excluded: chain S residue 3 HIS Chi-restraints excluded: chain S residue 9 VAL Chi-restraints excluded: chain S residue 32 SER Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain S residue 78 TRP Chi-restraints excluded: chain S residue 132 THR Chi-restraints excluded: chain S residue 172 TYR Chi-restraints excluded: chain T residue 29 THR Chi-restraints excluded: chain T residue 39 ILE Chi-restraints excluded: chain T residue 52 MET Chi-restraints excluded: chain T residue 64 VAL Chi-restraints excluded: chain T residue 79 MET Chi-restraints excluded: chain T residue 101 CYS Chi-restraints excluded: chain T residue 126 VAL Chi-restraints excluded: chain T residue 128 LEU Chi-restraints excluded: chain T residue 136 ARG Chi-restraints excluded: chain T residue 141 VAL Chi-restraints excluded: chain U residue 111 THR Chi-restraints excluded: chain V residue 56 ASP Chi-restraints excluded: chain V residue 85 TRP Chi-restraints excluded: chain V residue 91 VAL Chi-restraints excluded: chain V residue 98 ASN Chi-restraints excluded: chain V residue 109 MET Chi-restraints excluded: chain V residue 112 SER Chi-restraints excluded: chain V residue 115 THR Chi-restraints excluded: chain V residue 120 LYS Chi-restraints excluded: chain W residue 3 ARG Chi-restraints excluded: chain W residue 48 VAL Chi-restraints excluded: chain W residue 60 TRP Chi-restraints excluded: chain W residue 89 LEU Chi-restraints excluded: chain W residue 110 ASN Chi-restraints excluded: chain W residue 120 VAL Chi-restraints excluded: chain W residue 122 SER Chi-restraints excluded: chain W residue 142 VAL Chi-restraints excluded: chain W residue 197 VAL Chi-restraints excluded: chain W residue 223 ASN Chi-restraints excluded: chain W residue 231 THR Chi-restraints excluded: chain X residue 8 THR Chi-restraints excluded: chain X residue 48 SER Chi-restraints excluded: chain X residue 51 VAL Chi-restraints excluded: chain X residue 112 THR Chi-restraints excluded: chain Y residue 66 GLN Chi-restraints excluded: chain Y residue 70 ILE Chi-restraints excluded: chain Y residue 74 TYR Chi-restraints excluded: chain Y residue 105 VAL Chi-restraints excluded: chain Z residue 33 SER Chi-restraints excluded: chain Z residue 53 VAL Chi-restraints excluded: chain Z residue 86 THR Chi-restraints excluded: chain Z residue 96 VAL Chi-restraints excluded: chain a residue 91 LEU Chi-restraints excluded: chain a residue 95 SER Chi-restraints excluded: chain b residue 40 THR Chi-restraints excluded: chain b residue 73 ASP Chi-restraints excluded: chain b residue 116 LEU Chi-restraints excluded: chain b residue 162 SER Chi-restraints excluded: chain b residue 170 LEU Chi-restraints excluded: chain b residue 172 ILE Chi-restraints excluded: chain b residue 250 VAL Chi-restraints excluded: chain b residue 260 CYS Chi-restraints excluded: chain b residue 273 SER Chi-restraints excluded: chain b residue 375 THR Chi-restraints excluded: chain b residue 382 VAL Chi-restraints excluded: chain b residue 394 ASN Chi-restraints excluded: chain b residue 398 LEU Chi-restraints excluded: chain b residue 405 GLU Chi-restraints excluded: chain b residue 411 VAL Chi-restraints excluded: chain b residue 420 TYR Chi-restraints excluded: chain b residue 440 ASN Chi-restraints excluded: chain b residue 453 LEU Chi-restraints excluded: chain b residue 477 ILE Chi-restraints excluded: chain b residue 509 ASN Chi-restraints excluded: chain b residue 542 MET Chi-restraints excluded: chain c residue 43 VAL Chi-restraints excluded: chain c residue 98 GLU Chi-restraints excluded: chain c residue 106 GLN Chi-restraints excluded: chain d residue 13 THR Chi-restraints excluded: chain d residue 50 ARG Chi-restraints excluded: chain d residue 74 ARG Chi-restraints excluded: chain d residue 105 GLN Chi-restraints excluded: chain d residue 106 THR Chi-restraints excluded: chain d residue 108 VAL Chi-restraints excluded: chain e residue 10 VAL Chi-restraints excluded: chain e residue 19 ARG Chi-restraints excluded: chain e residue 47 ARG Chi-restraints excluded: chain e residue 51 SER Chi-restraints excluded: chain e residue 84 THR Chi-restraints excluded: chain e residue 118 LYS Chi-restraints excluded: chain e residue 123 LYS Chi-restraints excluded: chain e residue 128 LEU Chi-restraints excluded: chain f residue 15 SER Chi-restraints excluded: chain f residue 22 VAL Chi-restraints excluded: chain f residue 31 LYS Chi-restraints excluded: chain f residue 49 ILE Chi-restraints excluded: chain f residue 97 SER Chi-restraints excluded: chain g residue 16 ARG Chi-restraints excluded: chain g residue 17 SER Chi-restraints excluded: chain g residue 47 CYS Chi-restraints excluded: chain g residue 57 LEU Chi-restraints excluded: chain g residue 68 THR Chi-restraints excluded: chain g residue 79 SER Chi-restraints excluded: chain h residue 33 VAL Chi-restraints excluded: chain h residue 84 LYS Chi-restraints excluded: chain i residue 9 ILE Chi-restraints excluded: chain i residue 58 ILE Chi-restraints excluded: chain i residue 60 LEU Chi-restraints excluded: chain i residue 79 SER Chi-restraints excluded: chain i residue 94 ILE Chi-restraints excluded: chain j residue 17 THR Chi-restraints excluded: chain j residue 33 THR Chi-restraints excluded: chain j residue 36 SER Chi-restraints excluded: chain j residue 46 SER Chi-restraints excluded: chain j residue 84 SER Chi-restraints excluded: chain k residue 12 LEU Chi-restraints excluded: chain k residue 16 ARG Chi-restraints excluded: chain k residue 66 ILE Chi-restraints excluded: chain k residue 68 SER Chi-restraints excluded: chain l residue 5 LYS Chi-restraints excluded: chain l residue 6 SER Chi-restraints excluded: chain l residue 23 LEU Chi-restraints excluded: chain m residue 28 ASN Chi-restraints excluded: chain m residue 30 TYR Chi-restraints excluded: chain m residue 60 SER Chi-restraints excluded: chain m residue 65 THR Chi-restraints excluded: chain m residue 96 LEU Chi-restraints excluded: chain m residue 204 SER Chi-restraints excluded: chain m residue 221 SER Chi-restraints excluded: chain m residue 235 LEU Chi-restraints excluded: chain m residue 293 SER Chi-restraints excluded: chain m residue 315 GLN Chi-restraints excluded: chain m residue 418 ILE Chi-restraints excluded: chain m residue 425 THR Chi-restraints excluded: chain n residue 17 VAL Chi-restraints excluded: chain n residue 29 SER Chi-restraints excluded: chain n residue 63 SER Chi-restraints excluded: chain n residue 74 ASN Chi-restraints excluded: chain p residue 42 CYS Chi-restraints excluded: chain p residue 56 THR Chi-restraints excluded: chain p residue 60 CYS Chi-restraints excluded: chain p residue 72 SER Chi-restraints excluded: chain p residue 81 SER Chi-restraints excluded: chain q residue 54 LYS Chi-restraints excluded: chain q residue 59 THR Chi-restraints excluded: chain q residue 66 ASN Chi-restraints excluded: chain q residue 72 SER Chi-restraints excluded: chain r residue 7 ILE Chi-restraints excluded: chain r residue 12 LYS Chi-restraints excluded: chain r residue 53 LYS Chi-restraints excluded: chain r residue 61 MET Chi-restraints excluded: chain r residue 129 SER Chi-restraints excluded: chain r residue 143 ARG Chi-restraints excluded: chain r residue 166 VAL Chi-restraints excluded: chain r residue 168 MET Chi-restraints excluded: chain r residue 175 SER Chi-restraints excluded: chain r residue 191 VAL Chi-restraints excluded: chain r residue 193 VAL Chi-restraints excluded: chain r residue 245 VAL Chi-restraints excluded: chain r residue 252 ASP Chi-restraints excluded: chain s residue 13 THR Chi-restraints excluded: chain t residue 27 SER Chi-restraints excluded: chain t residue 118 GLU Chi-restraints excluded: chain t residue 212 LEU Chi-restraints excluded: chain t residue 214 GLN Chi-restraints excluded: chain t residue 382 VAL Chi-restraints excluded: chain t residue 412 HIS Chi-restraints excluded: chain t residue 413 ASP Chi-restraints excluded: chain t residue 485 LEU Chi-restraints excluded: chain t residue 500 LYS Chi-restraints excluded: chain t residue 501 ASP Chi-restraints excluded: chain u residue 30 ARG Chi-restraints excluded: chain u residue 65 VAL Chi-restraints excluded: chain u residue 75 ARG Chi-restraints excluded: chain u residue 132 GLU Chi-restraints excluded: chain x residue 133 THR Chi-restraints excluded: chain x residue 136 SER Chi-restraints excluded: chain x residue 192 VAL Chi-restraints excluded: chain x residue 201 ILE Chi-restraints excluded: chain x residue 254 SER Chi-restraints excluded: chain x residue 269 VAL Chi-restraints excluded: chain x residue 272 TYR Chi-restraints excluded: chain x residue 273 THR Chi-restraints excluded: chain x residue 275 SER Chi-restraints excluded: chain x residue 386 TRP Chi-restraints excluded: chain x residue 418 VAL Chi-restraints excluded: chain x residue 480 VAL Chi-restraints excluded: chain x residue 491 THR Chi-restraints excluded: chain y residue 12 GLU Chi-restraints excluded: chain y residue 34 PHE Chi-restraints excluded: chain y residue 76 THR Chi-restraints excluded: chain y residue 130 SER Chi-restraints excluded: chain y residue 155 SER Chi-restraints excluded: chain y residue 164 GLN Chi-restraints excluded: chain y residue 165 THR Chi-restraints excluded: chain y residue 197 MET Chi-restraints excluded: chain y residue 236 LEU Chi-restraints excluded: chain y residue 241 ILE Chi-restraints excluded: chain z residue 4 SER Chi-restraints excluded: chain z residue 15 SER Chi-restraints excluded: chain z residue 21 VAL Chi-restraints excluded: chain z residue 26 VAL Chi-restraints excluded: chain z residue 42 LEU Chi-restraints excluded: chain z residue 46 LEU Chi-restraints excluded: chain z residue 82 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1269 random chunks: chunk 1183 optimal weight: 7.9990 chunk 138 optimal weight: 10.0000 chunk 699 optimal weight: 0.3980 chunk 896 optimal weight: 9.9990 chunk 694 optimal weight: 3.9990 chunk 1033 optimal weight: 7.9990 chunk 685 optimal weight: 10.0000 chunk 1223 optimal weight: 20.0000 chunk 765 optimal weight: 5.9990 chunk 745 optimal weight: 4.9990 chunk 564 optimal weight: 3.9990 overall best weight: 3.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 173 GLN D 32 GLN ** D 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 GLN ** E 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 172 HIS ** G 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 41 GLN G 232 HIS H 163 GLN I 53 HIS J 47 GLN J 150 ASN K 106 GLN ** K 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 19 GLN M 41 GLN Q 9 GLN R 39 ASN T 131 GLN U 25 ASN ** U 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 74 GLN a 89 GLN b 323 GLN ** b 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 61 ASN e 52 GLN i 63 ASN i 92 ASN m 146 GLN r 4 ASN ** t 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 130 ASN x 219 GLN x 289 GLN ** x 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.2873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 156900 Z= 0.221 Angle : 0.580 13.672 227896 Z= 0.302 Chirality : 0.037 0.303 28257 Planarity : 0.004 0.074 16563 Dihedral : 22.569 179.506 61828 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.65 % Favored : 93.25 % Rotamer: Outliers : 5.53 % Allowed : 25.91 % Favored : 68.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.94 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -0.51 (0.08), residues: 9491 helix: 1.08 (0.09), residues: 3763 sheet: -0.26 (0.14), residues: 1232 loop : -1.65 (0.09), residues: 4496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP r 147 HIS 0.008 0.001 HIS G 232 PHE 0.027 0.001 PHE K 300 TYR 0.026 0.001 TYR K 163 ARG 0.011 0.000 ARG K 29 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18982 Ramachandran restraints generated. 9491 Oldfield, 0 Emsley, 9491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18982 Ramachandran restraints generated. 9491 Oldfield, 0 Emsley, 9491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1485 residues out of total 8277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 449 poor density : 1036 time to evaluate : 8.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 4 76 LEU cc_start: 0.9035 (OUTLIER) cc_final: 0.8832 (mt) REVERT: 4 269 TRP cc_start: 0.8407 (m-90) cc_final: 0.8053 (m-90) REVERT: 4 349 LYS cc_start: 0.8362 (OUTLIER) cc_final: 0.8050 (ptpp) REVERT: 4 395 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8570 (mt) REVERT: 4 454 PRO cc_start: 0.8709 (Cg_exo) cc_final: 0.8482 (Cg_endo) REVERT: 4 475 LEU cc_start: 0.7991 (OUTLIER) cc_final: 0.7658 (pt) REVERT: 4 530 LYS cc_start: 0.6421 (mptp) cc_final: 0.6207 (mttm) REVERT: 5 48 LYS cc_start: 0.8061 (OUTLIER) cc_final: 0.7707 (ttmm) REVERT: 5 66 ASP cc_start: 0.7796 (OUTLIER) cc_final: 0.7551 (m-30) REVERT: 5 67 GLU cc_start: 0.7668 (OUTLIER) cc_final: 0.7247 (pm20) REVERT: B 102 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8428 (tp) REVERT: B 137 TYR cc_start: 0.8314 (OUTLIER) cc_final: 0.7723 (t80) REVERT: B 196 ARG cc_start: 0.8131 (OUTLIER) cc_final: 0.7611 (mmm-85) REVERT: D 32 GLN cc_start: 0.8716 (tt0) cc_final: 0.8429 (tt0) REVERT: D 111 GLN cc_start: 0.7460 (tt0) cc_final: 0.6982 (mm-40) REVERT: D 198 TYR cc_start: 0.7839 (OUTLIER) cc_final: 0.7214 (t80) REVERT: E 8 LYS cc_start: 0.5397 (OUTLIER) cc_final: 0.4030 (pttt) REVERT: E 15 VAL cc_start: 0.8701 (m) cc_final: 0.8409 (t) REVERT: E 26 ARG cc_start: 0.8857 (OUTLIER) cc_final: 0.7962 (mtt90) REVERT: H 62 ARG cc_start: 0.7154 (OUTLIER) cc_final: 0.6775 (mtm180) REVERT: H 76 ASP cc_start: 0.8660 (m-30) cc_final: 0.8311 (m-30) REVERT: J 162 TRP cc_start: 0.7386 (OUTLIER) cc_final: 0.5803 (t60) REVERT: K 137 TYR cc_start: 0.8797 (m-80) cc_final: 0.8402 (m-80) REVERT: K 152 ASP cc_start: 0.8458 (OUTLIER) cc_final: 0.8183 (t0) REVERT: K 170 ARG cc_start: 0.6438 (OUTLIER) cc_final: 0.5193 (mtp-110) REVERT: L 131 LYS cc_start: 0.5709 (mppt) cc_final: 0.5333 (mmmt) REVERT: L 188 ARG cc_start: 0.7639 (mtp-110) cc_final: 0.7282 (mtp180) REVERT: N 73 ARG cc_start: 0.8572 (OUTLIER) cc_final: 0.7907 (ttm170) REVERT: N 92 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8505 (mp) REVERT: O 106 GLU cc_start: 0.8615 (mp0) cc_final: 0.8159 (mm-30) REVERT: Q 22 ASP cc_start: 0.7599 (t0) cc_final: 0.7174 (t0) REVERT: S 34 GLU cc_start: 0.7539 (OUTLIER) cc_final: 0.7017 (mm-30) REVERT: S 46 GLN cc_start: 0.8480 (mt0) cc_final: 0.8218 (mt0) REVERT: S 78 TRP cc_start: 0.6599 (OUTLIER) cc_final: 0.6214 (m-10) REVERT: S 172 TYR cc_start: 0.8515 (OUTLIER) cc_final: 0.5695 (t80) REVERT: V 15 LEU cc_start: 0.9190 (OUTLIER) cc_final: 0.8861 (mt) REVERT: V 24 ASN cc_start: 0.8173 (m110) cc_final: 0.7873 (m-40) REVERT: V 93 LEU cc_start: 0.9098 (OUTLIER) cc_final: 0.8805 (pt) REVERT: V 109 MET cc_start: 0.8350 (OUTLIER) cc_final: 0.7792 (mtm) REVERT: Y 66 GLN cc_start: 0.8876 (OUTLIER) cc_final: 0.8608 (mt0) REVERT: a 63 LYS cc_start: 0.8922 (OUTLIER) cc_final: 0.8703 (tttt) REVERT: a 70 LYS cc_start: 0.9180 (OUTLIER) cc_final: 0.8678 (ttmm) REVERT: b 254 MET cc_start: 0.8234 (mmm) cc_final: 0.7978 (mmm) REVERT: b 398 LEU cc_start: 0.7617 (OUTLIER) cc_final: 0.7334 (tp) REVERT: b 506 GLU cc_start: 0.7965 (mt-10) cc_final: 0.7691 (mt-10) REVERT: b 608 MET cc_start: 0.8778 (ttm) cc_final: 0.8423 (ttm) REVERT: c 98 GLU cc_start: 0.7527 (OUTLIER) cc_final: 0.7319 (mt-10) REVERT: d 50 ARG cc_start: 0.8522 (OUTLIER) cc_final: 0.7068 (mmt90) REVERT: d 74 ARG cc_start: 0.8491 (OUTLIER) cc_final: 0.8164 (ttm170) REVERT: d 105 GLN cc_start: 0.9245 (OUTLIER) cc_final: 0.9030 (pt0) REVERT: e 19 ARG cc_start: 0.8938 (OUTLIER) cc_final: 0.6865 (ttm170) REVERT: e 47 ARG cc_start: 0.9018 (OUTLIER) cc_final: 0.7731 (ttm-80) REVERT: e 118 LYS cc_start: 0.8687 (OUTLIER) cc_final: 0.8066 (ttmm) REVERT: f 31 LYS cc_start: 0.8747 (OUTLIER) cc_final: 0.7916 (tttp) REVERT: g 16 ARG cc_start: 0.8840 (OUTLIER) cc_final: 0.8341 (ttm170) REVERT: j 84 SER cc_start: 0.7551 (OUTLIER) cc_final: 0.7258 (t) REVERT: k 16 ARG cc_start: 0.8239 (OUTLIER) cc_final: 0.7832 (mpp80) REVERT: m 57 ARG cc_start: 0.5736 (ttm170) cc_final: 0.5225 (ttm170) REVERT: m 315 GLN cc_start: 0.7546 (OUTLIER) cc_final: 0.7218 (pt0) REVERT: m 337 LYS cc_start: 0.8956 (OUTLIER) cc_final: 0.8564 (tttm) REVERT: n 59 TYR cc_start: 0.8871 (m-80) cc_final: 0.8657 (m-80) REVERT: p 83 ILE cc_start: 0.9029 (mm) cc_final: 0.8767 (mp) REVERT: r 143 ARG cc_start: 0.8092 (OUTLIER) cc_final: 0.6777 (mmp-170) REVERT: r 168 MET cc_start: 0.4675 (OUTLIER) cc_final: 0.3530 (mtp) REVERT: r 254 CYS cc_start: 0.8048 (p) cc_final: 0.7816 (p) REVERT: t 214 GLN cc_start: 0.6956 (OUTLIER) cc_final: 0.6447 (mp10) REVERT: t 236 ASP cc_start: 0.7657 (p0) cc_final: 0.7254 (m-30) REVERT: t 378 HIS cc_start: 0.8217 (m90) cc_final: 0.7967 (m90) REVERT: t 476 LYS cc_start: 0.7868 (ttpp) cc_final: 0.7538 (tttt) REVERT: u 75 ARG cc_start: 0.8604 (OUTLIER) cc_final: 0.7981 (mtt-85) REVERT: x 293 TYR cc_start: 0.9192 (m-80) cc_final: 0.8894 (m-80) REVERT: x 432 ARG cc_start: 0.8057 (OUTLIER) cc_final: 0.7837 (mtt-85) REVERT: y 12 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.7512 (mt-10) REVERT: y 164 GLN cc_start: 0.8366 (OUTLIER) cc_final: 0.7831 (mp10) REVERT: y 236 LEU cc_start: 0.6875 (OUTLIER) cc_final: 0.6627 (pp) REVERT: y 241 ILE cc_start: 0.7241 (OUTLIER) cc_final: 0.6823 (mp) REVERT: z 46 LEU cc_start: 0.8252 (OUTLIER) cc_final: 0.8023 (mt) REVERT: z 94 MET cc_start: 0.7128 (tpp) cc_final: 0.6381 (tpt) outliers start: 449 outliers final: 286 residues processed: 1362 average time/residue: 1.9812 time to fit residues: 4029.8981 Evaluate side-chains 1341 residues out of total 8277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 338 poor density : 1003 time to evaluate : 8.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 4 residue 43 THR Chi-restraints excluded: chain 4 residue 44 SER Chi-restraints excluded: chain 4 residue 70 SER Chi-restraints excluded: chain 4 residue 76 LEU Chi-restraints excluded: chain 4 residue 101 SER Chi-restraints excluded: chain 4 residue 128 SER Chi-restraints excluded: chain 4 residue 137 ASP Chi-restraints excluded: chain 4 residue 139 VAL Chi-restraints excluded: chain 4 residue 142 THR Chi-restraints excluded: chain 4 residue 159 VAL Chi-restraints excluded: chain 4 residue 161 TYR Chi-restraints excluded: chain 4 residue 177 LEU Chi-restraints excluded: chain 4 residue 193 THR Chi-restraints excluded: chain 4 residue 203 THR Chi-restraints excluded: chain 4 residue 247 ILE Chi-restraints excluded: chain 4 residue 279 LEU Chi-restraints excluded: chain 4 residue 316 VAL Chi-restraints excluded: chain 4 residue 326 LEU Chi-restraints excluded: chain 4 residue 335 VAL Chi-restraints excluded: chain 4 residue 344 THR Chi-restraints excluded: chain 4 residue 349 LYS Chi-restraints excluded: chain 4 residue 367 THR Chi-restraints excluded: chain 4 residue 395 LEU Chi-restraints excluded: chain 4 residue 405 ASN Chi-restraints excluded: chain 4 residue 411 SER Chi-restraints excluded: chain 4 residue 443 VAL Chi-restraints excluded: chain 4 residue 475 LEU Chi-restraints excluded: chain 4 residue 495 SER Chi-restraints excluded: chain 4 residue 504 CYS Chi-restraints excluded: chain 4 residue 529 SER Chi-restraints excluded: chain 5 residue 48 LYS Chi-restraints excluded: chain 5 residue 66 ASP Chi-restraints excluded: chain 5 residue 67 GLU Chi-restraints excluded: chain 5 residue 93 GLU Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 137 TYR Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 196 ARG Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 243 HIS Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 327 CYS Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 340 LYS Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 371 GLN Chi-restraints excluded: chain C residue 12 THR Chi-restraints excluded: chain C residue 54 GLU Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 321 LYS Chi-restraints excluded: chain C residue 327 LEU Chi-restraints excluded: chain C residue 349 THR Chi-restraints excluded: chain C residue 362 ASP Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 81 HIS Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 186 GLU Chi-restraints excluded: chain D residue 198 TYR Chi-restraints excluded: chain E residue 8 LYS Chi-restraints excluded: chain E residue 26 ARG Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 164 SER Chi-restraints excluded: chain F residue 82 LYS Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain G residue 47 SER Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 124 ASP Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain G residue 183 LYS Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 197 VAL Chi-restraints excluded: chain H residue 46 THR Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 62 ARG Chi-restraints excluded: chain H residue 64 HIS Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 134 ILE Chi-restraints excluded: chain H residue 137 SER Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 150 SER Chi-restraints excluded: chain I residue 37 GLN Chi-restraints excluded: chain I residue 86 THR Chi-restraints excluded: chain J residue 112 LEU Chi-restraints excluded: chain J residue 161 SER Chi-restraints excluded: chain J residue 162 TRP Chi-restraints excluded: chain K residue 13 ASP Chi-restraints excluded: chain K residue 21 VAL Chi-restraints excluded: chain K residue 152 ASP Chi-restraints excluded: chain K residue 154 THR Chi-restraints excluded: chain K residue 164 CYS Chi-restraints excluded: chain K residue 168 VAL Chi-restraints excluded: chain K residue 170 ARG Chi-restraints excluded: chain K residue 223 CYS Chi-restraints excluded: chain K residue 303 ILE Chi-restraints excluded: chain L residue 46 ILE Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 100 ARG Chi-restraints excluded: chain L residue 124 ILE Chi-restraints excluded: chain M residue 53 VAL Chi-restraints excluded: chain M residue 64 VAL Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 90 VAL Chi-restraints excluded: chain M residue 91 CYS Chi-restraints excluded: chain M residue 130 THR Chi-restraints excluded: chain N residue 19 LEU Chi-restraints excluded: chain N residue 73 ARG Chi-restraints excluded: chain N residue 92 LEU Chi-restraints excluded: chain N residue 117 ASN Chi-restraints excluded: chain N residue 155 VAL Chi-restraints excluded: chain N residue 183 THR Chi-restraints excluded: chain O residue 16 VAL Chi-restraints excluded: chain O residue 84 LEU Chi-restraints excluded: chain O residue 113 ASP Chi-restraints excluded: chain O residue 148 LYS Chi-restraints excluded: chain O residue 150 GLU Chi-restraints excluded: chain O residue 189 ASP Chi-restraints excluded: chain P residue 49 GLU Chi-restraints excluded: chain P residue 87 SER Chi-restraints excluded: chain P residue 114 VAL Chi-restraints excluded: chain P residue 120 ASN Chi-restraints excluded: chain P residue 136 ILE Chi-restraints excluded: chain P residue 146 ILE Chi-restraints excluded: chain Q residue 7 SER Chi-restraints excluded: chain Q residue 47 VAL Chi-restraints excluded: chain Q residue 50 LYS Chi-restraints excluded: chain Q residue 122 ILE Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain R residue 91 SER Chi-restraints excluded: chain S residue 32 SER Chi-restraints excluded: chain S residue 34 GLU Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain S residue 78 TRP Chi-restraints excluded: chain S residue 132 THR Chi-restraints excluded: chain S residue 172 TYR Chi-restraints excluded: chain T residue 29 THR Chi-restraints excluded: chain T residue 39 ILE Chi-restraints excluded: chain T residue 52 MET Chi-restraints excluded: chain T residue 64 VAL Chi-restraints excluded: chain T residue 79 MET Chi-restraints excluded: chain T residue 101 CYS Chi-restraints excluded: chain T residue 126 VAL Chi-restraints excluded: chain T residue 128 LEU Chi-restraints excluded: chain T residue 136 ARG Chi-restraints excluded: chain T residue 141 VAL Chi-restraints excluded: chain U residue 111 THR Chi-restraints excluded: chain V residue 15 LEU Chi-restraints excluded: chain V residue 91 VAL Chi-restraints excluded: chain V residue 93 LEU Chi-restraints excluded: chain V residue 98 ASN Chi-restraints excluded: chain V residue 109 MET Chi-restraints excluded: chain V residue 112 SER Chi-restraints excluded: chain V residue 115 THR Chi-restraints excluded: chain W residue 3 ARG Chi-restraints excluded: chain W residue 48 VAL Chi-restraints excluded: chain W residue 60 TRP Chi-restraints excluded: chain W residue 110 ASN Chi-restraints excluded: chain W residue 120 VAL Chi-restraints excluded: chain W residue 122 SER Chi-restraints excluded: chain W residue 197 VAL Chi-restraints excluded: chain W residue 231 THR Chi-restraints excluded: chain X residue 48 SER Chi-restraints excluded: chain X residue 112 THR Chi-restraints excluded: chain Y residue 50 ILE Chi-restraints excluded: chain Y residue 66 GLN Chi-restraints excluded: chain Y residue 70 ILE Chi-restraints excluded: chain Y residue 74 TYR Chi-restraints excluded: chain Y residue 105 VAL Chi-restraints excluded: chain Z residue 53 VAL Chi-restraints excluded: chain Z residue 86 THR Chi-restraints excluded: chain Z residue 96 VAL Chi-restraints excluded: chain a residue 63 LYS Chi-restraints excluded: chain a residue 70 LYS Chi-restraints excluded: chain a residue 95 SER Chi-restraints excluded: chain b residue 73 ASP Chi-restraints excluded: chain b residue 116 LEU Chi-restraints excluded: chain b residue 162 SER Chi-restraints excluded: chain b residue 170 LEU Chi-restraints excluded: chain b residue 172 ILE Chi-restraints excluded: chain b residue 193 ASP Chi-restraints excluded: chain b residue 229 THR Chi-restraints excluded: chain b residue 250 VAL Chi-restraints excluded: chain b residue 260 CYS Chi-restraints excluded: chain b residue 273 SER Chi-restraints excluded: chain b residue 375 THR Chi-restraints excluded: chain b residue 382 VAL Chi-restraints excluded: chain b residue 394 ASN Chi-restraints excluded: chain b residue 398 LEU Chi-restraints excluded: chain b residue 405 GLU Chi-restraints excluded: chain b residue 411 VAL Chi-restraints excluded: chain b residue 420 TYR Chi-restraints excluded: chain b residue 421 LEU Chi-restraints excluded: chain b residue 440 ASN Chi-restraints excluded: chain b residue 453 LEU Chi-restraints excluded: chain b residue 477 ILE Chi-restraints excluded: chain b residue 509 ASN Chi-restraints excluded: chain b residue 522 SER Chi-restraints excluded: chain c residue 43 VAL Chi-restraints excluded: chain c residue 98 GLU Chi-restraints excluded: chain c residue 106 GLN Chi-restraints excluded: chain d residue 13 THR Chi-restraints excluded: chain d residue 50 ARG Chi-restraints excluded: chain d residue 74 ARG Chi-restraints excluded: chain d residue 105 GLN Chi-restraints excluded: chain d residue 106 THR Chi-restraints excluded: chain e residue 10 VAL Chi-restraints excluded: chain e residue 19 ARG Chi-restraints excluded: chain e residue 47 ARG Chi-restraints excluded: chain e residue 51 SER Chi-restraints excluded: chain e residue 75 LEU Chi-restraints excluded: chain e residue 84 THR Chi-restraints excluded: chain e residue 118 LYS Chi-restraints excluded: chain e residue 128 LEU Chi-restraints excluded: chain f residue 15 SER Chi-restraints excluded: chain f residue 22 VAL Chi-restraints excluded: chain f residue 31 LYS Chi-restraints excluded: chain f residue 49 ILE Chi-restraints excluded: chain g residue 16 ARG Chi-restraints excluded: chain g residue 17 SER Chi-restraints excluded: chain g residue 47 CYS Chi-restraints excluded: chain g residue 57 LEU Chi-restraints excluded: chain g residue 68 THR Chi-restraints excluded: chain h residue 33 VAL Chi-restraints excluded: chain h residue 84 LYS Chi-restraints excluded: chain i residue 9 ILE Chi-restraints excluded: chain i residue 58 ILE Chi-restraints excluded: chain i residue 60 LEU Chi-restraints excluded: chain i residue 64 SER Chi-restraints excluded: chain i residue 79 SER Chi-restraints excluded: chain i residue 94 ILE Chi-restraints excluded: chain j residue 17 THR Chi-restraints excluded: chain j residue 33 THR Chi-restraints excluded: chain j residue 36 SER Chi-restraints excluded: chain j residue 84 SER Chi-restraints excluded: chain k residue 16 ARG Chi-restraints excluded: chain k residue 66 ILE Chi-restraints excluded: chain k residue 68 SER Chi-restraints excluded: chain l residue 5 LYS Chi-restraints excluded: chain l residue 6 SER Chi-restraints excluded: chain l residue 23 LEU Chi-restraints excluded: chain m residue 28 ASN Chi-restraints excluded: chain m residue 30 TYR Chi-restraints excluded: chain m residue 60 SER Chi-restraints excluded: chain m residue 96 LEU Chi-restraints excluded: chain m residue 204 SER Chi-restraints excluded: chain m residue 221 SER Chi-restraints excluded: chain m residue 293 SER Chi-restraints excluded: chain m residue 315 GLN Chi-restraints excluded: chain m residue 337 LYS Chi-restraints excluded: chain m residue 418 ILE Chi-restraints excluded: chain m residue 425 THR Chi-restraints excluded: chain n residue 17 VAL Chi-restraints excluded: chain n residue 63 SER Chi-restraints excluded: chain p residue 42 CYS Chi-restraints excluded: chain p residue 56 THR Chi-restraints excluded: chain p residue 60 CYS Chi-restraints excluded: chain p residue 72 SER Chi-restraints excluded: chain p residue 81 SER Chi-restraints excluded: chain q residue 66 ASN Chi-restraints excluded: chain q residue 156 ASN Chi-restraints excluded: chain r residue 7 ILE Chi-restraints excluded: chain r residue 12 LYS Chi-restraints excluded: chain r residue 61 MET Chi-restraints excluded: chain r residue 129 SER Chi-restraints excluded: chain r residue 143 ARG Chi-restraints excluded: chain r residue 166 VAL Chi-restraints excluded: chain r residue 168 MET Chi-restraints excluded: chain r residue 175 SER Chi-restraints excluded: chain r residue 193 VAL Chi-restraints excluded: chain r residue 252 ASP Chi-restraints excluded: chain s residue 13 THR Chi-restraints excluded: chain t residue 27 SER Chi-restraints excluded: chain t residue 118 GLU Chi-restraints excluded: chain t residue 212 LEU Chi-restraints excluded: chain t residue 214 GLN Chi-restraints excluded: chain t residue 382 VAL Chi-restraints excluded: chain t residue 412 HIS Chi-restraints excluded: chain t residue 413 ASP Chi-restraints excluded: chain t residue 485 LEU Chi-restraints excluded: chain t residue 500 LYS Chi-restraints excluded: chain t residue 501 ASP Chi-restraints excluded: chain u residue 30 ARG Chi-restraints excluded: chain u residue 65 VAL Chi-restraints excluded: chain u residue 75 ARG Chi-restraints excluded: chain u residue 132 GLU Chi-restraints excluded: chain x residue 133 THR Chi-restraints excluded: chain x residue 136 SER Chi-restraints excluded: chain x residue 201 ILE Chi-restraints excluded: chain x residue 254 SER Chi-restraints excluded: chain x residue 269 VAL Chi-restraints excluded: chain x residue 272 TYR Chi-restraints excluded: chain x residue 273 THR Chi-restraints excluded: chain x residue 275 SER Chi-restraints excluded: chain x residue 289 GLN Chi-restraints excluded: chain x residue 418 VAL Chi-restraints excluded: chain x residue 432 ARG Chi-restraints excluded: chain x residue 480 VAL Chi-restraints excluded: chain x residue 491 THR Chi-restraints excluded: chain y residue 12 GLU Chi-restraints excluded: chain y residue 34 PHE Chi-restraints excluded: chain y residue 76 THR Chi-restraints excluded: chain y residue 164 GLN Chi-restraints excluded: chain y residue 165 THR Chi-restraints excluded: chain y residue 236 LEU Chi-restraints excluded: chain y residue 241 ILE Chi-restraints excluded: chain z residue 15 SER Chi-restraints excluded: chain z residue 21 VAL Chi-restraints excluded: chain z residue 26 VAL Chi-restraints excluded: chain z residue 42 LEU Chi-restraints excluded: chain z residue 46 LEU Chi-restraints excluded: chain z residue 82 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1269 random chunks: chunk 756 optimal weight: 7.9990 chunk 488 optimal weight: 5.9990 chunk 730 optimal weight: 5.9990 chunk 368 optimal weight: 2.9990 chunk 240 optimal weight: 40.0000 chunk 236 optimal weight: 20.0000 chunk 777 optimal weight: 20.0000 chunk 833 optimal weight: 1.9990 chunk 604 optimal weight: 6.9990 chunk 113 optimal weight: 10.0000 chunk 961 optimal weight: 1.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 398 ASN ** B 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 GLN E 138 GLN ** G 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 59 GLN ** G 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 163 GLN J 47 GLN J 150 ASN K 106 GLN ** K 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 41 GLN Q 9 GLN R 39 ASN S 142 GLN ** U 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 7 GLN W 74 GLN W 223 ASN Y 120 GLN a 89 GLN b 323 GLN b 550 ASN c 61 ASN e 52 GLN i 63 ASN i 92 ASN r 4 ASN ** t 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 130 ASN x 219 GLN ** x 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 44 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.2952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 156900 Z= 0.218 Angle : 0.576 13.630 227896 Z= 0.299 Chirality : 0.037 0.297 28257 Planarity : 0.004 0.073 16563 Dihedral : 22.534 179.918 61826 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.86 % Favored : 93.06 % Rotamer: Outliers : 5.61 % Allowed : 25.95 % Favored : 68.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.94 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -0.44 (0.09), residues: 9491 helix: 1.14 (0.09), residues: 3759 sheet: -0.26 (0.14), residues: 1247 loop : -1.59 (0.09), residues: 4485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP V 85 HIS 0.008 0.001 HIS G 232 PHE 0.029 0.001 PHE K 300 TYR 0.025 0.001 TYR S 43 ARG 0.016 0.000 ARG i 98 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18982 Ramachandran restraints generated. 9491 Oldfield, 0 Emsley, 9491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18982 Ramachandran restraints generated. 9491 Oldfield, 0 Emsley, 9491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1485 residues out of total 8277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 455 poor density : 1030 time to evaluate : 8.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 4 76 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8807 (mt) REVERT: 4 269 TRP cc_start: 0.8491 (m-90) cc_final: 0.8140 (m-90) REVERT: 4 338 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.8108 (pt0) REVERT: 4 349 LYS cc_start: 0.8366 (OUTLIER) cc_final: 0.8021 (ptpp) REVERT: 4 395 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8512 (mt) REVERT: 4 454 PRO cc_start: 0.8635 (Cg_exo) cc_final: 0.8408 (Cg_endo) REVERT: 4 475 LEU cc_start: 0.7964 (OUTLIER) cc_final: 0.7610 (pt) REVERT: 5 48 LYS cc_start: 0.8064 (OUTLIER) cc_final: 0.7711 (ttmm) REVERT: 5 66 ASP cc_start: 0.7709 (OUTLIER) cc_final: 0.7470 (m-30) REVERT: 5 67 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.7242 (pm20) REVERT: B 102 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8418 (tp) REVERT: B 137 TYR cc_start: 0.8340 (OUTLIER) cc_final: 0.7765 (t80) REVERT: B 196 ARG cc_start: 0.8110 (OUTLIER) cc_final: 0.7599 (mmm-85) REVERT: B 340 LYS cc_start: 0.8522 (OUTLIER) cc_final: 0.8113 (mtmm) REVERT: C 222 VAL cc_start: 0.9485 (OUTLIER) cc_final: 0.9276 (t) REVERT: D 32 GLN cc_start: 0.8726 (tt0) cc_final: 0.8410 (tt0) REVERT: D 111 GLN cc_start: 0.7474 (tt0) cc_final: 0.7003 (mm-40) REVERT: D 198 TYR cc_start: 0.7788 (OUTLIER) cc_final: 0.7268 (t80) REVERT: E 8 LYS cc_start: 0.5402 (OUTLIER) cc_final: 0.4049 (pttt) REVERT: E 26 ARG cc_start: 0.8855 (OUTLIER) cc_final: 0.7947 (mtt90) REVERT: H 62 ARG cc_start: 0.7123 (OUTLIER) cc_final: 0.6771 (mtm180) REVERT: H 76 ASP cc_start: 0.8635 (m-30) cc_final: 0.8275 (m-30) REVERT: H 113 GLU cc_start: 0.7563 (OUTLIER) cc_final: 0.7331 (tt0) REVERT: I 104 ARG cc_start: 0.7886 (tpt170) cc_final: 0.7492 (tpp-160) REVERT: J 131 MET cc_start: 0.7632 (mmm) cc_final: 0.7230 (mmm) REVERT: J 162 TRP cc_start: 0.7411 (OUTLIER) cc_final: 0.5906 (t60) REVERT: K 137 TYR cc_start: 0.8771 (m-80) cc_final: 0.8431 (m-80) REVERT: K 152 ASP cc_start: 0.8469 (OUTLIER) cc_final: 0.8200 (t0) REVERT: K 170 ARG cc_start: 0.6441 (OUTLIER) cc_final: 0.5219 (mtp-110) REVERT: L 131 LYS cc_start: 0.5604 (mppt) cc_final: 0.5260 (mmmt) REVERT: L 188 ARG cc_start: 0.7624 (mtp-110) cc_final: 0.7286 (mtp180) REVERT: N 73 ARG cc_start: 0.8573 (OUTLIER) cc_final: 0.7908 (ttm170) REVERT: O 106 GLU cc_start: 0.8601 (mp0) cc_final: 0.8130 (mm-30) REVERT: Q 22 ASP cc_start: 0.7567 (t0) cc_final: 0.7174 (t0) REVERT: R 81 ARG cc_start: 0.9043 (OUTLIER) cc_final: 0.7976 (mtp180) REVERT: S 34 GLU cc_start: 0.7538 (OUTLIER) cc_final: 0.7014 (mm-30) REVERT: S 46 GLN cc_start: 0.8472 (mt0) cc_final: 0.8232 (mt0) REVERT: S 78 TRP cc_start: 0.6574 (OUTLIER) cc_final: 0.6198 (m-10) REVERT: S 172 TYR cc_start: 0.8505 (OUTLIER) cc_final: 0.5741 (t80) REVERT: V 15 LEU cc_start: 0.9183 (OUTLIER) cc_final: 0.8851 (mt) REVERT: V 24 ASN cc_start: 0.8150 (m110) cc_final: 0.7851 (m-40) REVERT: V 109 MET cc_start: 0.8360 (OUTLIER) cc_final: 0.7793 (mtm) REVERT: W 125 SER cc_start: 0.8111 (m) cc_final: 0.7838 (p) REVERT: W 135 PHE cc_start: 0.5332 (OUTLIER) cc_final: 0.5100 (t80) REVERT: Y 66 GLN cc_start: 0.8881 (OUTLIER) cc_final: 0.8601 (mt0) REVERT: Z 119 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7728 (tt0) REVERT: a 63 LYS cc_start: 0.8883 (OUTLIER) cc_final: 0.8666 (tttt) REVERT: b 254 MET cc_start: 0.8256 (mmm) cc_final: 0.7996 (mmm) REVERT: b 398 LEU cc_start: 0.7631 (OUTLIER) cc_final: 0.7347 (tp) REVERT: b 453 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8567 (mt) REVERT: b 506 GLU cc_start: 0.7964 (mt-10) cc_final: 0.7685 (mt-10) REVERT: b 608 MET cc_start: 0.8782 (ttm) cc_final: 0.8430 (ttm) REVERT: d 50 ARG cc_start: 0.8524 (OUTLIER) cc_final: 0.7061 (mmt90) REVERT: d 74 ARG cc_start: 0.8481 (OUTLIER) cc_final: 0.8165 (ttm170) REVERT: d 105 GLN cc_start: 0.9287 (OUTLIER) cc_final: 0.9057 (pt0) REVERT: e 19 ARG cc_start: 0.8928 (OUTLIER) cc_final: 0.6848 (ttm170) REVERT: e 47 ARG cc_start: 0.8983 (OUTLIER) cc_final: 0.7722 (ttm-80) REVERT: e 118 LYS cc_start: 0.8713 (OUTLIER) cc_final: 0.8112 (ttmm) REVERT: f 31 LYS cc_start: 0.8752 (OUTLIER) cc_final: 0.7914 (tttp) REVERT: g 16 ARG cc_start: 0.8844 (OUTLIER) cc_final: 0.8388 (ttm170) REVERT: h 76 GLN cc_start: 0.7977 (OUTLIER) cc_final: 0.7751 (mt0) REVERT: i 59 ASP cc_start: 0.7831 (t0) cc_final: 0.7163 (t0) REVERT: i 63 ASN cc_start: 0.8124 (m-40) cc_final: 0.7920 (m110) REVERT: j 84 SER cc_start: 0.7469 (OUTLIER) cc_final: 0.7171 (t) REVERT: k 10 GLN cc_start: 0.8161 (mp10) cc_final: 0.7925 (mp10) REVERT: k 16 ARG cc_start: 0.8224 (OUTLIER) cc_final: 0.7820 (mpp80) REVERT: k 32 ASN cc_start: 0.6720 (p0) cc_final: 0.6306 (p0) REVERT: m 57 ARG cc_start: 0.5847 (ttm170) cc_final: 0.5412 (ttm170) REVERT: m 315 GLN cc_start: 0.7566 (OUTLIER) cc_final: 0.7223 (pt0) REVERT: n 59 TYR cc_start: 0.8866 (m-80) cc_final: 0.8647 (m-80) REVERT: p 83 ILE cc_start: 0.9033 (mm) cc_final: 0.8776 (mp) REVERT: r 143 ARG cc_start: 0.8089 (OUTLIER) cc_final: 0.6738 (mmp-170) REVERT: r 168 MET cc_start: 0.4658 (OUTLIER) cc_final: 0.3524 (mtp) REVERT: s 65 GLU cc_start: 0.5709 (tm-30) cc_final: 0.5138 (pm20) REVERT: t 214 GLN cc_start: 0.6852 (OUTLIER) cc_final: 0.6363 (mp10) REVERT: t 236 ASP cc_start: 0.7670 (p0) cc_final: 0.7259 (m-30) REVERT: t 378 HIS cc_start: 0.8239 (m90) cc_final: 0.8012 (m90) REVERT: t 476 LYS cc_start: 0.7844 (ttpp) cc_final: 0.7478 (tttt) REVERT: u 75 ARG cc_start: 0.8648 (OUTLIER) cc_final: 0.8133 (mtt-85) REVERT: x 293 TYR cc_start: 0.9197 (m-80) cc_final: 0.8940 (m-80) REVERT: x 432 ARG cc_start: 0.8071 (OUTLIER) cc_final: 0.7833 (mtt-85) REVERT: y 12 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.7515 (mt-10) REVERT: y 164 GLN cc_start: 0.8344 (OUTLIER) cc_final: 0.7848 (mp10) REVERT: y 197 MET cc_start: 0.8350 (OUTLIER) cc_final: 0.8092 (ptp) REVERT: y 236 LEU cc_start: 0.6869 (OUTLIER) cc_final: 0.6625 (pp) REVERT: y 241 ILE cc_start: 0.7270 (OUTLIER) cc_final: 0.6844 (mp) REVERT: z 46 LEU cc_start: 0.8246 (OUTLIER) cc_final: 0.8024 (mt) REVERT: z 94 MET cc_start: 0.7111 (tpp) cc_final: 0.6383 (tpt) outliers start: 455 outliers final: 298 residues processed: 1371 average time/residue: 1.9682 time to fit residues: 4038.3606 Evaluate side-chains 1341 residues out of total 8277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 355 poor density : 986 time to evaluate : 8.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 4 residue 43 THR Chi-restraints excluded: chain 4 residue 44 SER Chi-restraints excluded: chain 4 residue 70 SER Chi-restraints excluded: chain 4 residue 76 LEU Chi-restraints excluded: chain 4 residue 101 SER Chi-restraints excluded: chain 4 residue 128 SER Chi-restraints excluded: chain 4 residue 137 ASP Chi-restraints excluded: chain 4 residue 139 VAL Chi-restraints excluded: chain 4 residue 142 THR Chi-restraints excluded: chain 4 residue 152 SER Chi-restraints excluded: chain 4 residue 159 VAL Chi-restraints excluded: chain 4 residue 161 TYR Chi-restraints excluded: chain 4 residue 177 LEU Chi-restraints excluded: chain 4 residue 193 THR Chi-restraints excluded: chain 4 residue 203 THR Chi-restraints excluded: chain 4 residue 247 ILE Chi-restraints excluded: chain 4 residue 279 LEU Chi-restraints excluded: chain 4 residue 316 VAL Chi-restraints excluded: chain 4 residue 326 LEU Chi-restraints excluded: chain 4 residue 335 VAL Chi-restraints excluded: chain 4 residue 338 GLU Chi-restraints excluded: chain 4 residue 344 THR Chi-restraints excluded: chain 4 residue 349 LYS Chi-restraints excluded: chain 4 residue 367 THR Chi-restraints excluded: chain 4 residue 395 LEU Chi-restraints excluded: chain 4 residue 405 ASN Chi-restraints excluded: chain 4 residue 443 VAL Chi-restraints excluded: chain 4 residue 475 LEU Chi-restraints excluded: chain 4 residue 493 LYS Chi-restraints excluded: chain 4 residue 495 SER Chi-restraints excluded: chain 4 residue 504 CYS Chi-restraints excluded: chain 4 residue 529 SER Chi-restraints excluded: chain 5 residue 48 LYS Chi-restraints excluded: chain 5 residue 66 ASP Chi-restraints excluded: chain 5 residue 67 GLU Chi-restraints excluded: chain 5 residue 93 GLU Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 137 TYR Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 196 ARG Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 243 HIS Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 327 CYS Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 340 LYS Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 371 GLN Chi-restraints excluded: chain C residue 12 THR Chi-restraints excluded: chain C residue 54 GLU Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 327 LEU Chi-restraints excluded: chain C residue 349 THR Chi-restraints excluded: chain C residue 362 ASP Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 81 HIS Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 186 GLU Chi-restraints excluded: chain D residue 198 TYR Chi-restraints excluded: chain E residue 8 LYS Chi-restraints excluded: chain E residue 26 ARG Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 164 SER Chi-restraints excluded: chain F residue 82 LYS Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain G residue 47 SER Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 124 ASP Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain G residue 183 LYS Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 197 VAL Chi-restraints excluded: chain H residue 46 THR Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 62 ARG Chi-restraints excluded: chain H residue 64 HIS Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 113 GLU Chi-restraints excluded: chain H residue 134 ILE Chi-restraints excluded: chain H residue 137 SER Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 150 SER Chi-restraints excluded: chain I residue 37 GLN Chi-restraints excluded: chain I residue 86 THR Chi-restraints excluded: chain J residue 112 LEU Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 162 TRP Chi-restraints excluded: chain K residue 13 ASP Chi-restraints excluded: chain K residue 21 VAL Chi-restraints excluded: chain K residue 152 ASP Chi-restraints excluded: chain K residue 154 THR Chi-restraints excluded: chain K residue 164 CYS Chi-restraints excluded: chain K residue 168 VAL Chi-restraints excluded: chain K residue 170 ARG Chi-restraints excluded: chain K residue 183 VAL Chi-restraints excluded: chain K residue 223 CYS Chi-restraints excluded: chain K residue 291 THR Chi-restraints excluded: chain K residue 303 ILE Chi-restraints excluded: chain L residue 46 ILE Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 100 ARG Chi-restraints excluded: chain L residue 124 ILE Chi-restraints excluded: chain M residue 53 VAL Chi-restraints excluded: chain M residue 64 VAL Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 90 VAL Chi-restraints excluded: chain M residue 91 CYS Chi-restraints excluded: chain M residue 130 THR Chi-restraints excluded: chain N residue 19 LEU Chi-restraints excluded: chain N residue 73 ARG Chi-restraints excluded: chain N residue 117 ASN Chi-restraints excluded: chain N residue 155 VAL Chi-restraints excluded: chain N residue 183 THR Chi-restraints excluded: chain O residue 16 VAL Chi-restraints excluded: chain O residue 27 LEU Chi-restraints excluded: chain O residue 52 LEU Chi-restraints excluded: chain O residue 84 LEU Chi-restraints excluded: chain O residue 148 LYS Chi-restraints excluded: chain O residue 150 GLU Chi-restraints excluded: chain O residue 189 ASP Chi-restraints excluded: chain P residue 49 GLU Chi-restraints excluded: chain P residue 87 SER Chi-restraints excluded: chain P residue 114 VAL Chi-restraints excluded: chain P residue 120 ASN Chi-restraints excluded: chain P residue 136 ILE Chi-restraints excluded: chain P residue 146 ILE Chi-restraints excluded: chain Q residue 7 SER Chi-restraints excluded: chain Q residue 47 VAL Chi-restraints excluded: chain Q residue 50 LYS Chi-restraints excluded: chain Q residue 145 ASN Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 81 ARG Chi-restraints excluded: chain R residue 91 SER Chi-restraints excluded: chain S residue 32 SER Chi-restraints excluded: chain S residue 34 GLU Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain S residue 78 TRP Chi-restraints excluded: chain S residue 132 THR Chi-restraints excluded: chain S residue 172 TYR Chi-restraints excluded: chain T residue 29 THR Chi-restraints excluded: chain T residue 39 ILE Chi-restraints excluded: chain T residue 52 MET Chi-restraints excluded: chain T residue 64 VAL Chi-restraints excluded: chain T residue 101 CYS Chi-restraints excluded: chain T residue 126 VAL Chi-restraints excluded: chain T residue 128 LEU Chi-restraints excluded: chain T residue 136 ARG Chi-restraints excluded: chain T residue 141 VAL Chi-restraints excluded: chain V residue 15 LEU Chi-restraints excluded: chain V residue 56 ASP Chi-restraints excluded: chain V residue 91 VAL Chi-restraints excluded: chain V residue 98 ASN Chi-restraints excluded: chain V residue 109 MET Chi-restraints excluded: chain V residue 115 THR Chi-restraints excluded: chain W residue 3 ARG Chi-restraints excluded: chain W residue 48 VAL Chi-restraints excluded: chain W residue 60 TRP Chi-restraints excluded: chain W residue 89 LEU Chi-restraints excluded: chain W residue 110 ASN Chi-restraints excluded: chain W residue 120 VAL Chi-restraints excluded: chain W residue 122 SER Chi-restraints excluded: chain W residue 135 PHE Chi-restraints excluded: chain W residue 197 VAL Chi-restraints excluded: chain W residue 231 THR Chi-restraints excluded: chain X residue 8 THR Chi-restraints excluded: chain X residue 48 SER Chi-restraints excluded: chain X residue 51 VAL Chi-restraints excluded: chain X residue 112 THR Chi-restraints excluded: chain Y residue 66 GLN Chi-restraints excluded: chain Y residue 70 ILE Chi-restraints excluded: chain Y residue 74 TYR Chi-restraints excluded: chain Y residue 105 VAL Chi-restraints excluded: chain Z residue 33 SER Chi-restraints excluded: chain Z residue 53 VAL Chi-restraints excluded: chain Z residue 86 THR Chi-restraints excluded: chain Z residue 96 VAL Chi-restraints excluded: chain Z residue 119 GLU Chi-restraints excluded: chain a residue 63 LYS Chi-restraints excluded: chain a residue 91 LEU Chi-restraints excluded: chain a residue 95 SER Chi-restraints excluded: chain b residue 5 TRP Chi-restraints excluded: chain b residue 40 THR Chi-restraints excluded: chain b residue 73 ASP Chi-restraints excluded: chain b residue 74 VAL Chi-restraints excluded: chain b residue 116 LEU Chi-restraints excluded: chain b residue 162 SER Chi-restraints excluded: chain b residue 170 LEU Chi-restraints excluded: chain b residue 172 ILE Chi-restraints excluded: chain b residue 250 VAL Chi-restraints excluded: chain b residue 260 CYS Chi-restraints excluded: chain b residue 286 VAL Chi-restraints excluded: chain b residue 375 THR Chi-restraints excluded: chain b residue 382 VAL Chi-restraints excluded: chain b residue 394 ASN Chi-restraints excluded: chain b residue 398 LEU Chi-restraints excluded: chain b residue 405 GLU Chi-restraints excluded: chain b residue 411 VAL Chi-restraints excluded: chain b residue 420 TYR Chi-restraints excluded: chain b residue 421 LEU Chi-restraints excluded: chain b residue 440 ASN Chi-restraints excluded: chain b residue 453 LEU Chi-restraints excluded: chain b residue 477 ILE Chi-restraints excluded: chain b residue 509 ASN Chi-restraints excluded: chain c residue 43 VAL Chi-restraints excluded: chain c residue 106 GLN Chi-restraints excluded: chain d residue 6 ASP Chi-restraints excluded: chain d residue 13 THR Chi-restraints excluded: chain d residue 50 ARG Chi-restraints excluded: chain d residue 74 ARG Chi-restraints excluded: chain d residue 105 GLN Chi-restraints excluded: chain d residue 106 THR Chi-restraints excluded: chain d residue 108 VAL Chi-restraints excluded: chain e residue 10 VAL Chi-restraints excluded: chain e residue 19 ARG Chi-restraints excluded: chain e residue 47 ARG Chi-restraints excluded: chain e residue 51 SER Chi-restraints excluded: chain e residue 75 LEU Chi-restraints excluded: chain e residue 84 THR Chi-restraints excluded: chain e residue 118 LYS Chi-restraints excluded: chain e residue 128 LEU Chi-restraints excluded: chain f residue 15 SER Chi-restraints excluded: chain f residue 22 VAL Chi-restraints excluded: chain f residue 31 LYS Chi-restraints excluded: chain f residue 49 ILE Chi-restraints excluded: chain g residue 16 ARG Chi-restraints excluded: chain g residue 17 SER Chi-restraints excluded: chain g residue 47 CYS Chi-restraints excluded: chain g residue 57 LEU Chi-restraints excluded: chain g residue 68 THR Chi-restraints excluded: chain g residue 79 SER Chi-restraints excluded: chain h residue 33 VAL Chi-restraints excluded: chain h residue 76 GLN Chi-restraints excluded: chain h residue 84 LYS Chi-restraints excluded: chain i residue 58 ILE Chi-restraints excluded: chain i residue 60 LEU Chi-restraints excluded: chain i residue 79 SER Chi-restraints excluded: chain i residue 94 ILE Chi-restraints excluded: chain j residue 17 THR Chi-restraints excluded: chain j residue 33 THR Chi-restraints excluded: chain j residue 36 SER Chi-restraints excluded: chain j residue 46 SER Chi-restraints excluded: chain j residue 84 SER Chi-restraints excluded: chain k residue 16 ARG Chi-restraints excluded: chain k residue 66 ILE Chi-restraints excluded: chain k residue 68 SER Chi-restraints excluded: chain l residue 5 LYS Chi-restraints excluded: chain l residue 6 SER Chi-restraints excluded: chain m residue 28 ASN Chi-restraints excluded: chain m residue 30 TYR Chi-restraints excluded: chain m residue 60 SER Chi-restraints excluded: chain m residue 96 LEU Chi-restraints excluded: chain m residue 176 VAL Chi-restraints excluded: chain m residue 204 SER Chi-restraints excluded: chain m residue 221 SER Chi-restraints excluded: chain m residue 293 SER Chi-restraints excluded: chain m residue 315 GLN Chi-restraints excluded: chain m residue 418 ILE Chi-restraints excluded: chain m residue 425 THR Chi-restraints excluded: chain n residue 17 VAL Chi-restraints excluded: chain n residue 63 SER Chi-restraints excluded: chain n residue 74 ASN Chi-restraints excluded: chain p residue 42 CYS Chi-restraints excluded: chain p residue 56 THR Chi-restraints excluded: chain p residue 60 CYS Chi-restraints excluded: chain p residue 72 SER Chi-restraints excluded: chain p residue 81 SER Chi-restraints excluded: chain q residue 59 THR Chi-restraints excluded: chain q residue 66 ASN Chi-restraints excluded: chain q residue 156 ASN Chi-restraints excluded: chain r residue 7 ILE Chi-restraints excluded: chain r residue 12 LYS Chi-restraints excluded: chain r residue 61 MET Chi-restraints excluded: chain r residue 129 SER Chi-restraints excluded: chain r residue 143 ARG Chi-restraints excluded: chain r residue 166 VAL Chi-restraints excluded: chain r residue 168 MET Chi-restraints excluded: chain r residue 175 SER Chi-restraints excluded: chain r residue 191 VAL Chi-restraints excluded: chain r residue 193 VAL Chi-restraints excluded: chain r residue 250 ASP Chi-restraints excluded: chain r residue 252 ASP Chi-restraints excluded: chain s residue 13 THR Chi-restraints excluded: chain t residue 27 SER Chi-restraints excluded: chain t residue 118 GLU Chi-restraints excluded: chain t residue 212 LEU Chi-restraints excluded: chain t residue 214 GLN Chi-restraints excluded: chain t residue 253 VAL Chi-restraints excluded: chain t residue 382 VAL Chi-restraints excluded: chain t residue 412 HIS Chi-restraints excluded: chain t residue 413 ASP Chi-restraints excluded: chain t residue 485 LEU Chi-restraints excluded: chain t residue 500 LYS Chi-restraints excluded: chain t residue 501 ASP Chi-restraints excluded: chain u residue 30 ARG Chi-restraints excluded: chain u residue 65 VAL Chi-restraints excluded: chain u residue 75 ARG Chi-restraints excluded: chain u residue 79 VAL Chi-restraints excluded: chain u residue 132 GLU Chi-restraints excluded: chain x residue 133 THR Chi-restraints excluded: chain x residue 201 ILE Chi-restraints excluded: chain x residue 254 SER Chi-restraints excluded: chain x residue 269 VAL Chi-restraints excluded: chain x residue 272 TYR Chi-restraints excluded: chain x residue 273 THR Chi-restraints excluded: chain x residue 275 SER Chi-restraints excluded: chain x residue 418 VAL Chi-restraints excluded: chain x residue 432 ARG Chi-restraints excluded: chain x residue 480 VAL Chi-restraints excluded: chain x residue 491 THR Chi-restraints excluded: chain y residue 12 GLU Chi-restraints excluded: chain y residue 34 PHE Chi-restraints excluded: chain y residue 52 THR Chi-restraints excluded: chain y residue 76 THR Chi-restraints excluded: chain y residue 155 SER Chi-restraints excluded: chain y residue 164 GLN Chi-restraints excluded: chain y residue 165 THR Chi-restraints excluded: chain y residue 197 MET Chi-restraints excluded: chain y residue 236 LEU Chi-restraints excluded: chain y residue 241 ILE Chi-restraints excluded: chain z residue 15 SER Chi-restraints excluded: chain z residue 21 VAL Chi-restraints excluded: chain z residue 26 VAL Chi-restraints excluded: chain z residue 42 LEU Chi-restraints excluded: chain z residue 46 LEU Chi-restraints excluded: chain z residue 82 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1269 random chunks: chunk 1112 optimal weight: 0.8980 chunk 1171 optimal weight: 4.9990 chunk 1069 optimal weight: 7.9990 chunk 1139 optimal weight: 20.0000 chunk 686 optimal weight: 7.9990 chunk 496 optimal weight: 0.8980 chunk 895 optimal weight: 9.9990 chunk 349 optimal weight: 2.9990 chunk 1029 optimal weight: 4.9990 chunk 1077 optimal weight: 3.9990 chunk 1135 optimal weight: 3.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 33 GLN 4 551 GLN ** B 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 GLN ** G 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 59 GLN ** G 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 139 ASN H 163 GLN J 47 GLN J 150 ASN K 106 GLN ** K 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 41 GLN Q 9 GLN R 39 ASN S 142 GLN ** U 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 74 GLN W 223 ASN a 89 GLN b 323 GLN c 61 ASN e 52 GLN i 92 ASN l 50 ASN ** t 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 130 ASN x 219 GLN x 289 GLN ** x 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 44 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.2975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 156900 Z= 0.173 Angle : 0.568 17.552 227896 Z= 0.295 Chirality : 0.036 0.360 28257 Planarity : 0.004 0.081 16563 Dihedral : 22.541 179.890 61826 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.62 % Favored : 93.31 % Rotamer: Outliers : 4.85 % Allowed : 26.75 % Favored : 68.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.94 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -0.37 (0.09), residues: 9491 helix: 1.20 (0.09), residues: 3757 sheet: -0.22 (0.14), residues: 1252 loop : -1.57 (0.09), residues: 4482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP r 147 HIS 0.014 0.001 HIS D 203 PHE 0.036 0.001 PHE W 135 TYR 0.033 0.001 TYR D 198 ARG 0.019 0.000 ARG i 98 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18982 Ramachandran restraints generated. 9491 Oldfield, 0 Emsley, 9491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18982 Ramachandran restraints generated. 9491 Oldfield, 0 Emsley, 9491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1406 residues out of total 8277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 394 poor density : 1012 time to evaluate : 8.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 4 76 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8809 (mt) REVERT: 4 269 TRP cc_start: 0.8471 (m-90) cc_final: 0.8162 (m-90) REVERT: 4 338 GLU cc_start: 0.8489 (OUTLIER) cc_final: 0.8096 (pt0) REVERT: 4 349 LYS cc_start: 0.8359 (OUTLIER) cc_final: 0.7991 (ptpp) REVERT: 4 395 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8492 (mt) REVERT: 4 454 PRO cc_start: 0.8655 (Cg_exo) cc_final: 0.8428 (Cg_endo) REVERT: 4 475 LEU cc_start: 0.7943 (OUTLIER) cc_final: 0.7595 (pt) REVERT: 5 48 LYS cc_start: 0.8062 (OUTLIER) cc_final: 0.7711 (ttmm) REVERT: 5 66 ASP cc_start: 0.7690 (OUTLIER) cc_final: 0.7463 (m-30) REVERT: 5 67 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.7236 (pm20) REVERT: A 142 ASP cc_start: 0.7858 (OUTLIER) cc_final: 0.7641 (m-30) REVERT: B 102 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8387 (tp) REVERT: B 137 TYR cc_start: 0.8266 (OUTLIER) cc_final: 0.7577 (t80) REVERT: B 340 LYS cc_start: 0.8487 (OUTLIER) cc_final: 0.8086 (mtmm) REVERT: D 32 GLN cc_start: 0.8722 (tt0) cc_final: 0.8381 (tt0) REVERT: D 111 GLN cc_start: 0.7465 (tt0) cc_final: 0.7002 (mm-40) REVERT: D 198 TYR cc_start: 0.7675 (OUTLIER) cc_final: 0.7208 (t80) REVERT: E 8 LYS cc_start: 0.5543 (OUTLIER) cc_final: 0.4186 (pttt) REVERT: E 26 ARG cc_start: 0.8846 (OUTLIER) cc_final: 0.7972 (mtt90) REVERT: H 62 ARG cc_start: 0.7081 (OUTLIER) cc_final: 0.6456 (mtm180) REVERT: H 76 ASP cc_start: 0.8620 (m-30) cc_final: 0.8247 (m-30) REVERT: H 113 GLU cc_start: 0.7556 (OUTLIER) cc_final: 0.7311 (tt0) REVERT: J 131 MET cc_start: 0.7828 (mmm) cc_final: 0.7508 (mmm) REVERT: J 162 TRP cc_start: 0.7505 (OUTLIER) cc_final: 0.6009 (t60) REVERT: K 137 TYR cc_start: 0.8791 (m-80) cc_final: 0.8435 (m-80) REVERT: K 152 ASP cc_start: 0.8455 (OUTLIER) cc_final: 0.8174 (t0) REVERT: K 170 ARG cc_start: 0.6476 (OUTLIER) cc_final: 0.5269 (mtp-110) REVERT: L 131 LYS cc_start: 0.5604 (mppt) cc_final: 0.5294 (mmmt) REVERT: L 188 ARG cc_start: 0.7618 (mtp-110) cc_final: 0.7272 (mtp180) REVERT: N 73 ARG cc_start: 0.8568 (OUTLIER) cc_final: 0.7902 (ttm170) REVERT: O 106 GLU cc_start: 0.8591 (mp0) cc_final: 0.8134 (mm-30) REVERT: Q 22 ASP cc_start: 0.7557 (t0) cc_final: 0.7138 (t0) REVERT: S 46 GLN cc_start: 0.8468 (mt0) cc_final: 0.8216 (mt0) REVERT: S 78 TRP cc_start: 0.6579 (OUTLIER) cc_final: 0.6303 (m-10) REVERT: S 172 TYR cc_start: 0.8492 (OUTLIER) cc_final: 0.5861 (t80) REVERT: V 15 LEU cc_start: 0.9158 (OUTLIER) cc_final: 0.8832 (mt) REVERT: V 24 ASN cc_start: 0.8140 (m110) cc_final: 0.7850 (m-40) REVERT: V 54 LEU cc_start: 0.5057 (OUTLIER) cc_final: 0.4755 (pt) REVERT: V 109 MET cc_start: 0.8322 (OUTLIER) cc_final: 0.7909 (mtm) REVERT: W 125 SER cc_start: 0.8114 (m) cc_final: 0.7905 (p) REVERT: Y 66 GLN cc_start: 0.8872 (OUTLIER) cc_final: 0.8590 (mt0) REVERT: Z 119 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7711 (tt0) REVERT: a 63 LYS cc_start: 0.8840 (OUTLIER) cc_final: 0.8612 (tttt) REVERT: b 254 MET cc_start: 0.8248 (mmm) cc_final: 0.7985 (mmm) REVERT: b 398 LEU cc_start: 0.7503 (OUTLIER) cc_final: 0.7207 (tp) REVERT: b 453 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8565 (mt) REVERT: b 506 GLU cc_start: 0.7947 (mt-10) cc_final: 0.7669 (mt-10) REVERT: b 608 MET cc_start: 0.8777 (ttm) cc_final: 0.8421 (ttm) REVERT: d 50 ARG cc_start: 0.8519 (OUTLIER) cc_final: 0.7057 (mmt90) REVERT: d 74 ARG cc_start: 0.8479 (OUTLIER) cc_final: 0.8158 (ttm170) REVERT: d 105 GLN cc_start: 0.9286 (OUTLIER) cc_final: 0.9078 (pt0) REVERT: e 19 ARG cc_start: 0.8915 (OUTLIER) cc_final: 0.6839 (ttm170) REVERT: e 47 ARG cc_start: 0.8974 (OUTLIER) cc_final: 0.7716 (ttm-80) REVERT: e 118 LYS cc_start: 0.8705 (OUTLIER) cc_final: 0.8109 (ttmm) REVERT: f 31 LYS cc_start: 0.8743 (OUTLIER) cc_final: 0.7904 (tttp) REVERT: g 16 ARG cc_start: 0.8835 (OUTLIER) cc_final: 0.8365 (ttm170) REVERT: h 76 GLN cc_start: 0.7938 (OUTLIER) cc_final: 0.7704 (mt0) REVERT: i 59 ASP cc_start: 0.7744 (t0) cc_final: 0.7050 (t0) REVERT: i 63 ASN cc_start: 0.8087 (m-40) cc_final: 0.7786 (m110) REVERT: j 84 SER cc_start: 0.7505 (OUTLIER) cc_final: 0.7216 (t) REVERT: k 16 ARG cc_start: 0.8215 (OUTLIER) cc_final: 0.7811 (mpp80) REVERT: k 32 ASN cc_start: 0.6600 (p0) cc_final: 0.6137 (p0) REVERT: m 57 ARG cc_start: 0.5833 (ttm170) cc_final: 0.5399 (ttm170) REVERT: n 59 TYR cc_start: 0.8858 (m-80) cc_final: 0.8633 (m-80) REVERT: p 83 ILE cc_start: 0.9023 (mm) cc_final: 0.8755 (mp) REVERT: r 143 ARG cc_start: 0.8077 (OUTLIER) cc_final: 0.6736 (mmp-170) REVERT: r 168 MET cc_start: 0.4694 (OUTLIER) cc_final: 0.3559 (mtp) REVERT: t 214 GLN cc_start: 0.6857 (OUTLIER) cc_final: 0.6373 (mp10) REVERT: t 236 ASP cc_start: 0.7610 (p0) cc_final: 0.7247 (m-30) REVERT: t 378 HIS cc_start: 0.8235 (m90) cc_final: 0.7966 (m90) REVERT: t 423 MET cc_start: 0.8060 (ttp) cc_final: 0.7752 (mtm) REVERT: t 476 LYS cc_start: 0.7805 (ttpp) cc_final: 0.7495 (tttt) REVERT: u 75 ARG cc_start: 0.8637 (OUTLIER) cc_final: 0.8181 (mtt-85) REVERT: x 293 TYR cc_start: 0.9176 (m-80) cc_final: 0.8927 (m-80) REVERT: x 353 GLN cc_start: 0.8224 (OUTLIER) cc_final: 0.6818 (tp40) REVERT: x 432 ARG cc_start: 0.8086 (OUTLIER) cc_final: 0.7842 (mtt-85) REVERT: y 113 TYR cc_start: 0.8255 (m-80) cc_final: 0.8008 (m-10) REVERT: y 164 GLN cc_start: 0.8315 (OUTLIER) cc_final: 0.7830 (mp10) REVERT: y 236 LEU cc_start: 0.6856 (OUTLIER) cc_final: 0.6627 (pp) REVERT: y 241 ILE cc_start: 0.7260 (OUTLIER) cc_final: 0.6841 (mp) REVERT: z 46 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.8016 (mt) REVERT: z 94 MET cc_start: 0.7104 (tpp) cc_final: 0.6361 (tpt) outliers start: 394 outliers final: 274 residues processed: 1299 average time/residue: 1.9463 time to fit residues: 3775.4406 Evaluate side-chains 1312 residues out of total 8277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 326 poor density : 986 time to evaluate : 8.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 4 residue 43 THR Chi-restraints excluded: chain 4 residue 44 SER Chi-restraints excluded: chain 4 residue 70 SER Chi-restraints excluded: chain 4 residue 76 LEU Chi-restraints excluded: chain 4 residue 128 SER Chi-restraints excluded: chain 4 residue 137 ASP Chi-restraints excluded: chain 4 residue 139 VAL Chi-restraints excluded: chain 4 residue 142 THR Chi-restraints excluded: chain 4 residue 159 VAL Chi-restraints excluded: chain 4 residue 161 TYR Chi-restraints excluded: chain 4 residue 193 THR Chi-restraints excluded: chain 4 residue 203 THR Chi-restraints excluded: chain 4 residue 247 ILE Chi-restraints excluded: chain 4 residue 279 LEU Chi-restraints excluded: chain 4 residue 316 VAL Chi-restraints excluded: chain 4 residue 326 LEU Chi-restraints excluded: chain 4 residue 335 VAL Chi-restraints excluded: chain 4 residue 338 GLU Chi-restraints excluded: chain 4 residue 344 THR Chi-restraints excluded: chain 4 residue 349 LYS Chi-restraints excluded: chain 4 residue 367 THR Chi-restraints excluded: chain 4 residue 395 LEU Chi-restraints excluded: chain 4 residue 405 ASN Chi-restraints excluded: chain 4 residue 411 SER Chi-restraints excluded: chain 4 residue 443 VAL Chi-restraints excluded: chain 4 residue 475 LEU Chi-restraints excluded: chain 4 residue 495 SER Chi-restraints excluded: chain 4 residue 504 CYS Chi-restraints excluded: chain 4 residue 529 SER Chi-restraints excluded: chain 5 residue 48 LYS Chi-restraints excluded: chain 5 residue 66 ASP Chi-restraints excluded: chain 5 residue 67 GLU Chi-restraints excluded: chain 5 residue 93 GLU Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 142 ASP Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 137 TYR Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 243 HIS Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 327 CYS Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 340 LYS Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 371 GLN Chi-restraints excluded: chain C residue 12 THR Chi-restraints excluded: chain C residue 54 GLU Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 327 LEU Chi-restraints excluded: chain C residue 349 THR Chi-restraints excluded: chain C residue 362 ASP Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 81 HIS Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 186 GLU Chi-restraints excluded: chain D residue 198 TYR Chi-restraints excluded: chain E residue 8 LYS Chi-restraints excluded: chain E residue 26 ARG Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 164 SER Chi-restraints excluded: chain F residue 82 LYS Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain G residue 47 SER Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 124 ASP Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain G residue 183 LYS Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 197 VAL Chi-restraints excluded: chain H residue 46 THR Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 62 ARG Chi-restraints excluded: chain H residue 64 HIS Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 113 GLU Chi-restraints excluded: chain H residue 134 ILE Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 150 SER Chi-restraints excluded: chain I residue 15 THR Chi-restraints excluded: chain I residue 37 GLN Chi-restraints excluded: chain I residue 86 THR Chi-restraints excluded: chain J residue 112 LEU Chi-restraints excluded: chain J residue 162 TRP Chi-restraints excluded: chain K residue 13 ASP Chi-restraints excluded: chain K residue 21 VAL Chi-restraints excluded: chain K residue 152 ASP Chi-restraints excluded: chain K residue 154 THR Chi-restraints excluded: chain K residue 164 CYS Chi-restraints excluded: chain K residue 168 VAL Chi-restraints excluded: chain K residue 170 ARG Chi-restraints excluded: chain K residue 223 CYS Chi-restraints excluded: chain K residue 303 ILE Chi-restraints excluded: chain L residue 46 ILE Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 100 ARG Chi-restraints excluded: chain L residue 124 ILE Chi-restraints excluded: chain M residue 53 VAL Chi-restraints excluded: chain M residue 64 VAL Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 90 VAL Chi-restraints excluded: chain M residue 91 CYS Chi-restraints excluded: chain N residue 19 LEU Chi-restraints excluded: chain N residue 73 ARG Chi-restraints excluded: chain N residue 117 ASN Chi-restraints excluded: chain N residue 155 VAL Chi-restraints excluded: chain N residue 183 THR Chi-restraints excluded: chain O residue 16 VAL Chi-restraints excluded: chain O residue 27 LEU Chi-restraints excluded: chain O residue 52 LEU Chi-restraints excluded: chain O residue 84 LEU Chi-restraints excluded: chain O residue 150 GLU Chi-restraints excluded: chain O residue 189 ASP Chi-restraints excluded: chain P residue 49 GLU Chi-restraints excluded: chain P residue 114 VAL Chi-restraints excluded: chain P residue 120 ASN Chi-restraints excluded: chain P residue 141 SER Chi-restraints excluded: chain P residue 146 ILE Chi-restraints excluded: chain Q residue 7 SER Chi-restraints excluded: chain Q residue 47 VAL Chi-restraints excluded: chain Q residue 50 LYS Chi-restraints excluded: chain Q residue 145 ASN Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain R residue 91 SER Chi-restraints excluded: chain S residue 32 SER Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain S residue 78 TRP Chi-restraints excluded: chain S residue 132 THR Chi-restraints excluded: chain S residue 172 TYR Chi-restraints excluded: chain T residue 29 THR Chi-restraints excluded: chain T residue 39 ILE Chi-restraints excluded: chain T residue 64 VAL Chi-restraints excluded: chain T residue 101 CYS Chi-restraints excluded: chain T residue 126 VAL Chi-restraints excluded: chain T residue 128 LEU Chi-restraints excluded: chain T residue 136 ARG Chi-restraints excluded: chain T residue 141 VAL Chi-restraints excluded: chain V residue 15 LEU Chi-restraints excluded: chain V residue 54 LEU Chi-restraints excluded: chain V residue 56 ASP Chi-restraints excluded: chain V residue 91 VAL Chi-restraints excluded: chain V residue 98 ASN Chi-restraints excluded: chain V residue 109 MET Chi-restraints excluded: chain V residue 115 THR Chi-restraints excluded: chain W residue 48 VAL Chi-restraints excluded: chain W residue 60 TRP Chi-restraints excluded: chain W residue 89 LEU Chi-restraints excluded: chain W residue 110 ASN Chi-restraints excluded: chain W residue 120 VAL Chi-restraints excluded: chain W residue 122 SER Chi-restraints excluded: chain W residue 197 VAL Chi-restraints excluded: chain W residue 231 THR Chi-restraints excluded: chain X residue 8 THR Chi-restraints excluded: chain X residue 48 SER Chi-restraints excluded: chain X residue 112 THR Chi-restraints excluded: chain Y residue 55 GLU Chi-restraints excluded: chain Y residue 66 GLN Chi-restraints excluded: chain Y residue 70 ILE Chi-restraints excluded: chain Y residue 74 TYR Chi-restraints excluded: chain Y residue 105 VAL Chi-restraints excluded: chain Z residue 33 SER Chi-restraints excluded: chain Z residue 53 VAL Chi-restraints excluded: chain Z residue 86 THR Chi-restraints excluded: chain Z residue 96 VAL Chi-restraints excluded: chain Z residue 119 GLU Chi-restraints excluded: chain a residue 63 LYS Chi-restraints excluded: chain a residue 78 LEU Chi-restraints excluded: chain a residue 91 LEU Chi-restraints excluded: chain a residue 95 SER Chi-restraints excluded: chain b residue 5 TRP Chi-restraints excluded: chain b residue 73 ASP Chi-restraints excluded: chain b residue 74 VAL Chi-restraints excluded: chain b residue 116 LEU Chi-restraints excluded: chain b residue 162 SER Chi-restraints excluded: chain b residue 170 LEU Chi-restraints excluded: chain b residue 172 ILE Chi-restraints excluded: chain b residue 193 ASP Chi-restraints excluded: chain b residue 250 VAL Chi-restraints excluded: chain b residue 260 CYS Chi-restraints excluded: chain b residue 273 SER Chi-restraints excluded: chain b residue 375 THR Chi-restraints excluded: chain b residue 394 ASN Chi-restraints excluded: chain b residue 398 LEU Chi-restraints excluded: chain b residue 405 GLU Chi-restraints excluded: chain b residue 411 VAL Chi-restraints excluded: chain b residue 420 TYR Chi-restraints excluded: chain b residue 440 ASN Chi-restraints excluded: chain b residue 453 LEU Chi-restraints excluded: chain b residue 477 ILE Chi-restraints excluded: chain c residue 43 VAL Chi-restraints excluded: chain c residue 106 GLN Chi-restraints excluded: chain d residue 6 ASP Chi-restraints excluded: chain d residue 13 THR Chi-restraints excluded: chain d residue 50 ARG Chi-restraints excluded: chain d residue 74 ARG Chi-restraints excluded: chain d residue 105 GLN Chi-restraints excluded: chain d residue 106 THR Chi-restraints excluded: chain e residue 10 VAL Chi-restraints excluded: chain e residue 19 ARG Chi-restraints excluded: chain e residue 47 ARG Chi-restraints excluded: chain e residue 51 SER Chi-restraints excluded: chain e residue 75 LEU Chi-restraints excluded: chain e residue 84 THR Chi-restraints excluded: chain e residue 118 LYS Chi-restraints excluded: chain e residue 128 LEU Chi-restraints excluded: chain f residue 22 VAL Chi-restraints excluded: chain f residue 31 LYS Chi-restraints excluded: chain f residue 49 ILE Chi-restraints excluded: chain g residue 16 ARG Chi-restraints excluded: chain g residue 17 SER Chi-restraints excluded: chain g residue 47 CYS Chi-restraints excluded: chain g residue 57 LEU Chi-restraints excluded: chain g residue 79 SER Chi-restraints excluded: chain h residue 33 VAL Chi-restraints excluded: chain h residue 76 GLN Chi-restraints excluded: chain h residue 84 LYS Chi-restraints excluded: chain i residue 9 ILE Chi-restraints excluded: chain i residue 58 ILE Chi-restraints excluded: chain i residue 79 SER Chi-restraints excluded: chain i residue 94 ILE Chi-restraints excluded: chain j residue 17 THR Chi-restraints excluded: chain j residue 46 SER Chi-restraints excluded: chain j residue 84 SER Chi-restraints excluded: chain k residue 16 ARG Chi-restraints excluded: chain k residue 66 ILE Chi-restraints excluded: chain k residue 68 SER Chi-restraints excluded: chain l residue 5 LYS Chi-restraints excluded: chain l residue 6 SER Chi-restraints excluded: chain m residue 28 ASN Chi-restraints excluded: chain m residue 30 TYR Chi-restraints excluded: chain m residue 60 SER Chi-restraints excluded: chain m residue 65 THR Chi-restraints excluded: chain m residue 96 LEU Chi-restraints excluded: chain m residue 176 VAL Chi-restraints excluded: chain m residue 204 SER Chi-restraints excluded: chain m residue 221 SER Chi-restraints excluded: chain m residue 418 ILE Chi-restraints excluded: chain n residue 17 VAL Chi-restraints excluded: chain n residue 63 SER Chi-restraints excluded: chain n residue 74 ASN Chi-restraints excluded: chain p residue 42 CYS Chi-restraints excluded: chain p residue 56 THR Chi-restraints excluded: chain p residue 72 SER Chi-restraints excluded: chain p residue 81 SER Chi-restraints excluded: chain q residue 59 THR Chi-restraints excluded: chain q residue 66 ASN Chi-restraints excluded: chain q residue 85 LEU Chi-restraints excluded: chain r residue 7 ILE Chi-restraints excluded: chain r residue 12 LYS Chi-restraints excluded: chain r residue 61 MET Chi-restraints excluded: chain r residue 129 SER Chi-restraints excluded: chain r residue 143 ARG Chi-restraints excluded: chain r residue 166 VAL Chi-restraints excluded: chain r residue 168 MET Chi-restraints excluded: chain r residue 175 SER Chi-restraints excluded: chain r residue 191 VAL Chi-restraints excluded: chain r residue 193 VAL Chi-restraints excluded: chain r residue 245 VAL Chi-restraints excluded: chain r residue 250 ASP Chi-restraints excluded: chain r residue 252 ASP Chi-restraints excluded: chain s residue 13 THR Chi-restraints excluded: chain t residue 27 SER Chi-restraints excluded: chain t residue 118 GLU Chi-restraints excluded: chain t residue 212 LEU Chi-restraints excluded: chain t residue 214 GLN Chi-restraints excluded: chain t residue 253 VAL Chi-restraints excluded: chain t residue 382 VAL Chi-restraints excluded: chain t residue 412 HIS Chi-restraints excluded: chain t residue 413 ASP Chi-restraints excluded: chain t residue 485 LEU Chi-restraints excluded: chain t residue 500 LYS Chi-restraints excluded: chain t residue 501 ASP Chi-restraints excluded: chain u residue 30 ARG Chi-restraints excluded: chain u residue 65 VAL Chi-restraints excluded: chain u residue 75 ARG Chi-restraints excluded: chain u residue 79 VAL Chi-restraints excluded: chain u residue 132 GLU Chi-restraints excluded: chain x residue 133 THR Chi-restraints excluded: chain x residue 201 ILE Chi-restraints excluded: chain x residue 254 SER Chi-restraints excluded: chain x residue 269 VAL Chi-restraints excluded: chain x residue 272 TYR Chi-restraints excluded: chain x residue 273 THR Chi-restraints excluded: chain x residue 275 SER Chi-restraints excluded: chain x residue 353 GLN Chi-restraints excluded: chain x residue 418 VAL Chi-restraints excluded: chain x residue 432 ARG Chi-restraints excluded: chain x residue 480 VAL Chi-restraints excluded: chain x residue 491 THR Chi-restraints excluded: chain y residue 34 PHE Chi-restraints excluded: chain y residue 52 THR Chi-restraints excluded: chain y residue 76 THR Chi-restraints excluded: chain y residue 155 SER Chi-restraints excluded: chain y residue 164 GLN Chi-restraints excluded: chain y residue 165 THR Chi-restraints excluded: chain y residue 236 LEU Chi-restraints excluded: chain y residue 241 ILE Chi-restraints excluded: chain z residue 15 SER Chi-restraints excluded: chain z residue 21 VAL Chi-restraints excluded: chain z residue 26 VAL Chi-restraints excluded: chain z residue 42 LEU Chi-restraints excluded: chain z residue 46 LEU Chi-restraints excluded: chain z residue 82 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1269 random chunks: chunk 748 optimal weight: 9.9990 chunk 1205 optimal weight: 2.9990 chunk 735 optimal weight: 7.9990 chunk 571 optimal weight: 10.0000 chunk 837 optimal weight: 4.9990 chunk 1264 optimal weight: 9.9990 chunk 1163 optimal weight: 6.9990 chunk 1006 optimal weight: 10.0000 chunk 104 optimal weight: 20.0000 chunk 777 optimal weight: 10.0000 chunk 617 optimal weight: 0.5980 overall best weight: 4.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 33 GLN 4 551 GLN ** B 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 GLN ** G 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 59 GLN G 145 ASN ** G 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 163 GLN J 47 GLN J 101 ASN J 150 ASN K 106 GLN ** K 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 41 GLN Q 9 GLN R 39 ASN S 142 GLN T 131 GLN ** U 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 74 GLN W 223 ASN a 89 GLN b 323 GLN ** b 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 61 ASN e 52 GLN ** i 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 92 ASN ** t 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 130 ASN x 219 GLN ** x 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 44 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.3023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 156900 Z= 0.255 Angle : 0.593 18.015 227896 Z= 0.307 Chirality : 0.038 0.332 28257 Planarity : 0.004 0.085 16563 Dihedral : 22.514 179.528 61826 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.98 % Favored : 92.93 % Rotamer: Outliers : 4.66 % Allowed : 27.18 % Favored : 68.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.94 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -0.42 (0.09), residues: 9491 helix: 1.15 (0.09), residues: 3757 sheet: -0.24 (0.14), residues: 1254 loop : -1.58 (0.09), residues: 4480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP r 147 HIS 0.013 0.001 HIS G 232 PHE 0.029 0.001 PHE K 300 TYR 0.026 0.002 TYR K 163 ARG 0.019 0.000 ARG i 98 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18982 Ramachandran restraints generated. 9491 Oldfield, 0 Emsley, 9491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18982 Ramachandran restraints generated. 9491 Oldfield, 0 Emsley, 9491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1383 residues out of total 8277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 378 poor density : 1005 time to evaluate : 8.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 4 76 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8774 (mt) REVERT: 4 242 SER cc_start: 0.8061 (OUTLIER) cc_final: 0.7438 (m) REVERT: 4 269 TRP cc_start: 0.8534 (m-90) cc_final: 0.8124 (m-90) REVERT: 4 338 GLU cc_start: 0.8498 (OUTLIER) cc_final: 0.8107 (pt0) REVERT: 4 395 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8516 (mt) REVERT: 4 454 PRO cc_start: 0.8681 (Cg_exo) cc_final: 0.8457 (Cg_endo) REVERT: 4 475 LEU cc_start: 0.7988 (OUTLIER) cc_final: 0.7650 (pt) REVERT: 5 48 LYS cc_start: 0.8016 (OUTLIER) cc_final: 0.7710 (ttmm) REVERT: 5 66 ASP cc_start: 0.7700 (OUTLIER) cc_final: 0.7474 (m-30) REVERT: 5 67 GLU cc_start: 0.7715 (OUTLIER) cc_final: 0.7289 (pm20) REVERT: A 142 ASP cc_start: 0.7918 (OUTLIER) cc_final: 0.7712 (m-30) REVERT: B 102 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8474 (tp) REVERT: B 137 TYR cc_start: 0.8323 (OUTLIER) cc_final: 0.7724 (t80) REVERT: D 32 GLN cc_start: 0.8725 (tt0) cc_final: 0.8388 (tt0) REVERT: D 111 GLN cc_start: 0.7434 (tt0) cc_final: 0.6956 (mm-40) REVERT: E 8 LYS cc_start: 0.5619 (OUTLIER) cc_final: 0.4146 (pttt) REVERT: E 15 VAL cc_start: 0.8678 (m) cc_final: 0.8410 (t) REVERT: E 26 ARG cc_start: 0.8856 (OUTLIER) cc_final: 0.7946 (mtt90) REVERT: H 62 ARG cc_start: 0.7188 (OUTLIER) cc_final: 0.6810 (mtm180) REVERT: H 76 ASP cc_start: 0.8640 (m-30) cc_final: 0.8278 (m-30) REVERT: H 113 GLU cc_start: 0.7572 (OUTLIER) cc_final: 0.7330 (tt0) REVERT: J 131 MET cc_start: 0.7734 (mmm) cc_final: 0.7380 (mmm) REVERT: J 162 TRP cc_start: 0.7530 (OUTLIER) cc_final: 0.5960 (t60) REVERT: K 137 TYR cc_start: 0.8815 (m-80) cc_final: 0.8455 (m-80) REVERT: K 152 ASP cc_start: 0.8476 (OUTLIER) cc_final: 0.8235 (t0) REVERT: K 170 ARG cc_start: 0.6452 (OUTLIER) cc_final: 0.5221 (mtp-110) REVERT: L 131 LYS cc_start: 0.5723 (mppt) cc_final: 0.5368 (mmmt) REVERT: L 188 ARG cc_start: 0.7561 (mtp-110) cc_final: 0.7230 (mtp180) REVERT: N 73 ARG cc_start: 0.8596 (OUTLIER) cc_final: 0.7929 (ttm170) REVERT: O 106 GLU cc_start: 0.8608 (mp0) cc_final: 0.8152 (mm-30) REVERT: Q 22 ASP cc_start: 0.7626 (t0) cc_final: 0.7179 (t0) REVERT: S 46 GLN cc_start: 0.8476 (mt0) cc_final: 0.8227 (mt0) REVERT: S 78 TRP cc_start: 0.6615 (OUTLIER) cc_final: 0.6259 (m-10) REVERT: S 172 TYR cc_start: 0.8573 (OUTLIER) cc_final: 0.5824 (t80) REVERT: V 15 LEU cc_start: 0.9166 (OUTLIER) cc_final: 0.8837 (mt) REVERT: V 24 ASN cc_start: 0.8192 (m110) cc_final: 0.7884 (m-40) REVERT: V 109 MET cc_start: 0.8378 (OUTLIER) cc_final: 0.7784 (mtm) REVERT: W 125 SER cc_start: 0.8227 (m) cc_final: 0.7972 (p) REVERT: Y 66 GLN cc_start: 0.8887 (OUTLIER) cc_final: 0.8595 (mt0) REVERT: Z 119 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.7733 (tt0) REVERT: a 63 LYS cc_start: 0.8884 (OUTLIER) cc_final: 0.8681 (tttt) REVERT: b 254 MET cc_start: 0.8280 (mmm) cc_final: 0.7977 (mmm) REVERT: b 398 LEU cc_start: 0.7646 (OUTLIER) cc_final: 0.7357 (tp) REVERT: b 440 ASN cc_start: 0.8299 (OUTLIER) cc_final: 0.7657 (m-40) REVERT: b 453 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8595 (mt) REVERT: b 506 GLU cc_start: 0.7969 (mt-10) cc_final: 0.7688 (mt-10) REVERT: b 608 MET cc_start: 0.8785 (ttm) cc_final: 0.8419 (ttm) REVERT: d 50 ARG cc_start: 0.8535 (OUTLIER) cc_final: 0.7056 (mmt90) REVERT: d 74 ARG cc_start: 0.8484 (OUTLIER) cc_final: 0.8174 (ttm170) REVERT: d 105 GLN cc_start: 0.9291 (OUTLIER) cc_final: 0.9070 (pt0) REVERT: e 19 ARG cc_start: 0.8939 (OUTLIER) cc_final: 0.6830 (ttm170) REVERT: e 47 ARG cc_start: 0.8994 (OUTLIER) cc_final: 0.7731 (ttm-80) REVERT: e 118 LYS cc_start: 0.8721 (OUTLIER) cc_final: 0.8114 (ttmm) REVERT: f 31 LYS cc_start: 0.8755 (OUTLIER) cc_final: 0.7943 (tttp) REVERT: g 16 ARG cc_start: 0.8843 (OUTLIER) cc_final: 0.8399 (ttm170) REVERT: j 84 SER cc_start: 0.7473 (OUTLIER) cc_final: 0.7205 (t) REVERT: k 16 ARG cc_start: 0.8220 (OUTLIER) cc_final: 0.7832 (mpp80) REVERT: k 32 ASN cc_start: 0.6557 (p0) cc_final: 0.6220 (p0) REVERT: m 57 ARG cc_start: 0.5918 (ttm170) cc_final: 0.5482 (ttm170) REVERT: n 19 LYS cc_start: 0.8603 (mtmt) cc_final: 0.8289 (ptpp) REVERT: n 59 TYR cc_start: 0.8868 (m-80) cc_final: 0.8645 (m-80) REVERT: p 83 ILE cc_start: 0.9043 (mm) cc_final: 0.8779 (mp) REVERT: r 143 ARG cc_start: 0.8116 (OUTLIER) cc_final: 0.6756 (mmp-170) REVERT: r 168 MET cc_start: 0.4568 (OUTLIER) cc_final: 0.3414 (mtp) REVERT: s 65 GLU cc_start: 0.5719 (tm-30) cc_final: 0.5052 (pm20) REVERT: t 214 GLN cc_start: 0.6854 (OUTLIER) cc_final: 0.6368 (mp10) REVERT: t 236 ASP cc_start: 0.7716 (p0) cc_final: 0.7335 (m-30) REVERT: t 378 HIS cc_start: 0.8213 (m90) cc_final: 0.7968 (m90) REVERT: t 476 LYS cc_start: 0.7845 (ttpp) cc_final: 0.7533 (tttt) REVERT: u 75 ARG cc_start: 0.8621 (OUTLIER) cc_final: 0.8083 (mtt-85) REVERT: x 293 TYR cc_start: 0.9184 (m-80) cc_final: 0.8903 (m-80) REVERT: x 432 ARG cc_start: 0.8128 (OUTLIER) cc_final: 0.7882 (mtt-85) REVERT: y 12 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.7521 (mt-10) REVERT: y 113 TYR cc_start: 0.8363 (m-80) cc_final: 0.8126 (m-10) REVERT: y 164 GLN cc_start: 0.8353 (OUTLIER) cc_final: 0.7860 (mp10) REVERT: y 236 LEU cc_start: 0.6871 (OUTLIER) cc_final: 0.6631 (pp) REVERT: y 241 ILE cc_start: 0.7292 (OUTLIER) cc_final: 0.6862 (mp) REVERT: z 46 LEU cc_start: 0.8175 (OUTLIER) cc_final: 0.7957 (mt) REVERT: z 94 MET cc_start: 0.7092 (tpp) cc_final: 0.6405 (tpt) outliers start: 378 outliers final: 286 residues processed: 1292 average time/residue: 1.9719 time to fit residues: 3804.3764 Evaluate side-chains 1322 residues out of total 8277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 335 poor density : 987 time to evaluate : 8.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 4 residue 43 THR Chi-restraints excluded: chain 4 residue 44 SER Chi-restraints excluded: chain 4 residue 70 SER Chi-restraints excluded: chain 4 residue 76 LEU Chi-restraints excluded: chain 4 residue 128 SER Chi-restraints excluded: chain 4 residue 137 ASP Chi-restraints excluded: chain 4 residue 139 VAL Chi-restraints excluded: chain 4 residue 142 THR Chi-restraints excluded: chain 4 residue 152 SER Chi-restraints excluded: chain 4 residue 159 VAL Chi-restraints excluded: chain 4 residue 161 TYR Chi-restraints excluded: chain 4 residue 177 LEU Chi-restraints excluded: chain 4 residue 193 THR Chi-restraints excluded: chain 4 residue 203 THR Chi-restraints excluded: chain 4 residue 242 SER Chi-restraints excluded: chain 4 residue 247 ILE Chi-restraints excluded: chain 4 residue 279 LEU Chi-restraints excluded: chain 4 residue 316 VAL Chi-restraints excluded: chain 4 residue 326 LEU Chi-restraints excluded: chain 4 residue 335 VAL Chi-restraints excluded: chain 4 residue 338 GLU Chi-restraints excluded: chain 4 residue 344 THR Chi-restraints excluded: chain 4 residue 367 THR Chi-restraints excluded: chain 4 residue 395 LEU Chi-restraints excluded: chain 4 residue 405 ASN Chi-restraints excluded: chain 4 residue 411 SER Chi-restraints excluded: chain 4 residue 443 VAL Chi-restraints excluded: chain 4 residue 475 LEU Chi-restraints excluded: chain 4 residue 495 SER Chi-restraints excluded: chain 4 residue 504 CYS Chi-restraints excluded: chain 4 residue 529 SER Chi-restraints excluded: chain 5 residue 48 LYS Chi-restraints excluded: chain 5 residue 66 ASP Chi-restraints excluded: chain 5 residue 67 GLU Chi-restraints excluded: chain 5 residue 93 GLU Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 142 ASP Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 137 TYR Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 243 HIS Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 327 CYS Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 340 LYS Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 371 GLN Chi-restraints excluded: chain C residue 12 THR Chi-restraints excluded: chain C residue 54 GLU Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 327 LEU Chi-restraints excluded: chain C residue 349 THR Chi-restraints excluded: chain C residue 362 ASP Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 81 HIS Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain E residue 8 LYS Chi-restraints excluded: chain E residue 26 ARG Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 164 SER Chi-restraints excluded: chain F residue 82 LYS Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain G residue 36 ILE Chi-restraints excluded: chain G residue 47 SER Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 124 ASP Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain G residue 183 LYS Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 197 VAL Chi-restraints excluded: chain H residue 46 THR Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 62 ARG Chi-restraints excluded: chain H residue 64 HIS Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 113 GLU Chi-restraints excluded: chain H residue 134 ILE Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 150 SER Chi-restraints excluded: chain I residue 15 THR Chi-restraints excluded: chain I residue 37 GLN Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 162 TRP Chi-restraints excluded: chain K residue 13 ASP Chi-restraints excluded: chain K residue 21 VAL Chi-restraints excluded: chain K residue 152 ASP Chi-restraints excluded: chain K residue 154 THR Chi-restraints excluded: chain K residue 164 CYS Chi-restraints excluded: chain K residue 168 VAL Chi-restraints excluded: chain K residue 170 ARG Chi-restraints excluded: chain K residue 183 VAL Chi-restraints excluded: chain K residue 223 CYS Chi-restraints excluded: chain K residue 303 ILE Chi-restraints excluded: chain L residue 46 ILE Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 100 ARG Chi-restraints excluded: chain L residue 124 ILE Chi-restraints excluded: chain M residue 53 VAL Chi-restraints excluded: chain M residue 64 VAL Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 90 VAL Chi-restraints excluded: chain M residue 91 CYS Chi-restraints excluded: chain N residue 19 LEU Chi-restraints excluded: chain N residue 73 ARG Chi-restraints excluded: chain N residue 117 ASN Chi-restraints excluded: chain N residue 155 VAL Chi-restraints excluded: chain N residue 183 THR Chi-restraints excluded: chain O residue 16 VAL Chi-restraints excluded: chain O residue 27 LEU Chi-restraints excluded: chain O residue 52 LEU Chi-restraints excluded: chain O residue 84 LEU Chi-restraints excluded: chain O residue 150 GLU Chi-restraints excluded: chain O residue 189 ASP Chi-restraints excluded: chain P residue 49 GLU Chi-restraints excluded: chain P residue 87 SER Chi-restraints excluded: chain P residue 114 VAL Chi-restraints excluded: chain P residue 120 ASN Chi-restraints excluded: chain P residue 136 ILE Chi-restraints excluded: chain P residue 141 SER Chi-restraints excluded: chain Q residue 7 SER Chi-restraints excluded: chain Q residue 47 VAL Chi-restraints excluded: chain Q residue 50 LYS Chi-restraints excluded: chain Q residue 145 ASN Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain R residue 91 SER Chi-restraints excluded: chain S residue 32 SER Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain S residue 78 TRP Chi-restraints excluded: chain S residue 172 TYR Chi-restraints excluded: chain T residue 29 THR Chi-restraints excluded: chain T residue 39 ILE Chi-restraints excluded: chain T residue 64 VAL Chi-restraints excluded: chain T residue 101 CYS Chi-restraints excluded: chain T residue 126 VAL Chi-restraints excluded: chain T residue 128 LEU Chi-restraints excluded: chain T residue 136 ARG Chi-restraints excluded: chain T residue 141 VAL Chi-restraints excluded: chain U residue 111 THR Chi-restraints excluded: chain V residue 15 LEU Chi-restraints excluded: chain V residue 56 ASP Chi-restraints excluded: chain V residue 91 VAL Chi-restraints excluded: chain V residue 98 ASN Chi-restraints excluded: chain V residue 109 MET Chi-restraints excluded: chain W residue 48 VAL Chi-restraints excluded: chain W residue 60 TRP Chi-restraints excluded: chain W residue 89 LEU Chi-restraints excluded: chain W residue 110 ASN Chi-restraints excluded: chain W residue 120 VAL Chi-restraints excluded: chain W residue 122 SER Chi-restraints excluded: chain W residue 197 VAL Chi-restraints excluded: chain W residue 231 THR Chi-restraints excluded: chain X residue 8 THR Chi-restraints excluded: chain X residue 48 SER Chi-restraints excluded: chain X residue 112 THR Chi-restraints excluded: chain Y residue 66 GLN Chi-restraints excluded: chain Y residue 70 ILE Chi-restraints excluded: chain Y residue 74 TYR Chi-restraints excluded: chain Y residue 105 VAL Chi-restraints excluded: chain Z residue 33 SER Chi-restraints excluded: chain Z residue 53 VAL Chi-restraints excluded: chain Z residue 86 THR Chi-restraints excluded: chain Z residue 96 VAL Chi-restraints excluded: chain Z residue 119 GLU Chi-restraints excluded: chain a residue 63 LYS Chi-restraints excluded: chain a residue 78 LEU Chi-restraints excluded: chain a residue 91 LEU Chi-restraints excluded: chain a residue 95 SER Chi-restraints excluded: chain b residue 5 TRP Chi-restraints excluded: chain b residue 73 ASP Chi-restraints excluded: chain b residue 116 LEU Chi-restraints excluded: chain b residue 162 SER Chi-restraints excluded: chain b residue 170 LEU Chi-restraints excluded: chain b residue 172 ILE Chi-restraints excluded: chain b residue 193 ASP Chi-restraints excluded: chain b residue 250 VAL Chi-restraints excluded: chain b residue 260 CYS Chi-restraints excluded: chain b residue 273 SER Chi-restraints excluded: chain b residue 286 VAL Chi-restraints excluded: chain b residue 375 THR Chi-restraints excluded: chain b residue 394 ASN Chi-restraints excluded: chain b residue 398 LEU Chi-restraints excluded: chain b residue 405 GLU Chi-restraints excluded: chain b residue 411 VAL Chi-restraints excluded: chain b residue 420 TYR Chi-restraints excluded: chain b residue 440 ASN Chi-restraints excluded: chain b residue 453 LEU Chi-restraints excluded: chain b residue 477 ILE Chi-restraints excluded: chain b residue 509 ASN Chi-restraints excluded: chain c residue 43 VAL Chi-restraints excluded: chain c residue 106 GLN Chi-restraints excluded: chain d residue 6 ASP Chi-restraints excluded: chain d residue 13 THR Chi-restraints excluded: chain d residue 50 ARG Chi-restraints excluded: chain d residue 74 ARG Chi-restraints excluded: chain d residue 105 GLN Chi-restraints excluded: chain d residue 106 THR Chi-restraints excluded: chain d residue 108 VAL Chi-restraints excluded: chain e residue 10 VAL Chi-restraints excluded: chain e residue 19 ARG Chi-restraints excluded: chain e residue 47 ARG Chi-restraints excluded: chain e residue 51 SER Chi-restraints excluded: chain e residue 75 LEU Chi-restraints excluded: chain e residue 84 THR Chi-restraints excluded: chain e residue 118 LYS Chi-restraints excluded: chain e residue 128 LEU Chi-restraints excluded: chain f residue 15 SER Chi-restraints excluded: chain f residue 22 VAL Chi-restraints excluded: chain f residue 31 LYS Chi-restraints excluded: chain f residue 49 ILE Chi-restraints excluded: chain f residue 97 SER Chi-restraints excluded: chain g residue 16 ARG Chi-restraints excluded: chain g residue 17 SER Chi-restraints excluded: chain g residue 47 CYS Chi-restraints excluded: chain g residue 57 LEU Chi-restraints excluded: chain g residue 79 SER Chi-restraints excluded: chain h residue 33 VAL Chi-restraints excluded: chain h residue 48 ARG Chi-restraints excluded: chain h residue 84 LYS Chi-restraints excluded: chain i residue 58 ILE Chi-restraints excluded: chain i residue 60 LEU Chi-restraints excluded: chain i residue 79 SER Chi-restraints excluded: chain i residue 94 ILE Chi-restraints excluded: chain j residue 17 THR Chi-restraints excluded: chain j residue 46 SER Chi-restraints excluded: chain j residue 84 SER Chi-restraints excluded: chain k residue 16 ARG Chi-restraints excluded: chain k residue 33 LYS Chi-restraints excluded: chain k residue 66 ILE Chi-restraints excluded: chain k residue 68 SER Chi-restraints excluded: chain l residue 5 LYS Chi-restraints excluded: chain l residue 6 SER Chi-restraints excluded: chain m residue 28 ASN Chi-restraints excluded: chain m residue 30 TYR Chi-restraints excluded: chain m residue 60 SER Chi-restraints excluded: chain m residue 65 THR Chi-restraints excluded: chain m residue 96 LEU Chi-restraints excluded: chain m residue 176 VAL Chi-restraints excluded: chain m residue 204 SER Chi-restraints excluded: chain m residue 221 SER Chi-restraints excluded: chain m residue 418 ILE Chi-restraints excluded: chain n residue 17 VAL Chi-restraints excluded: chain n residue 29 SER Chi-restraints excluded: chain n residue 63 SER Chi-restraints excluded: chain n residue 74 ASN Chi-restraints excluded: chain p residue 42 CYS Chi-restraints excluded: chain p residue 56 THR Chi-restraints excluded: chain p residue 60 CYS Chi-restraints excluded: chain p residue 72 SER Chi-restraints excluded: chain p residue 81 SER Chi-restraints excluded: chain q residue 59 THR Chi-restraints excluded: chain q residue 66 ASN Chi-restraints excluded: chain q residue 74 VAL Chi-restraints excluded: chain q residue 85 LEU Chi-restraints excluded: chain r residue 7 ILE Chi-restraints excluded: chain r residue 12 LYS Chi-restraints excluded: chain r residue 61 MET Chi-restraints excluded: chain r residue 129 SER Chi-restraints excluded: chain r residue 143 ARG Chi-restraints excluded: chain r residue 166 VAL Chi-restraints excluded: chain r residue 168 MET Chi-restraints excluded: chain r residue 175 SER Chi-restraints excluded: chain r residue 191 VAL Chi-restraints excluded: chain r residue 193 VAL Chi-restraints excluded: chain r residue 245 VAL Chi-restraints excluded: chain r residue 250 ASP Chi-restraints excluded: chain r residue 252 ASP Chi-restraints excluded: chain s residue 13 THR Chi-restraints excluded: chain t residue 27 SER Chi-restraints excluded: chain t residue 118 GLU Chi-restraints excluded: chain t residue 212 LEU Chi-restraints excluded: chain t residue 214 GLN Chi-restraints excluded: chain t residue 253 VAL Chi-restraints excluded: chain t residue 382 VAL Chi-restraints excluded: chain t residue 412 HIS Chi-restraints excluded: chain t residue 413 ASP Chi-restraints excluded: chain t residue 485 LEU Chi-restraints excluded: chain t residue 500 LYS Chi-restraints excluded: chain t residue 501 ASP Chi-restraints excluded: chain u residue 30 ARG Chi-restraints excluded: chain u residue 65 VAL Chi-restraints excluded: chain u residue 75 ARG Chi-restraints excluded: chain u residue 79 VAL Chi-restraints excluded: chain u residue 132 GLU Chi-restraints excluded: chain x residue 133 THR Chi-restraints excluded: chain x residue 201 ILE Chi-restraints excluded: chain x residue 254 SER Chi-restraints excluded: chain x residue 269 VAL Chi-restraints excluded: chain x residue 272 TYR Chi-restraints excluded: chain x residue 273 THR Chi-restraints excluded: chain x residue 275 SER Chi-restraints excluded: chain x residue 418 VAL Chi-restraints excluded: chain x residue 432 ARG Chi-restraints excluded: chain x residue 480 VAL Chi-restraints excluded: chain x residue 491 THR Chi-restraints excluded: chain y residue 12 GLU Chi-restraints excluded: chain y residue 34 PHE Chi-restraints excluded: chain y residue 52 THR Chi-restraints excluded: chain y residue 76 THR Chi-restraints excluded: chain y residue 155 SER Chi-restraints excluded: chain y residue 164 GLN Chi-restraints excluded: chain y residue 165 THR Chi-restraints excluded: chain y residue 236 LEU Chi-restraints excluded: chain y residue 241 ILE Chi-restraints excluded: chain z residue 15 SER Chi-restraints excluded: chain z residue 21 VAL Chi-restraints excluded: chain z residue 26 VAL Chi-restraints excluded: chain z residue 42 LEU Chi-restraints excluded: chain z residue 46 LEU Chi-restraints excluded: chain z residue 82 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1269 random chunks: chunk 799 optimal weight: 9.9990 chunk 1072 optimal weight: 3.9990 chunk 308 optimal weight: 10.0000 chunk 928 optimal weight: 5.9990 chunk 148 optimal weight: 10.0000 chunk 279 optimal weight: 10.0000 chunk 1008 optimal weight: 0.9980 chunk 421 optimal weight: 7.9990 chunk 1035 optimal weight: 10.0000 chunk 127 optimal weight: 10.0000 chunk 185 optimal weight: 20.0000 overall best weight: 5.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 33 GLN 4 455 ASN 4 551 GLN ** B 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 GLN ** G 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 59 GLN ** G 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 163 GLN J 47 GLN J 150 ASN K 106 GLN ** K 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 41 GLN P 28 ASN Q 9 GLN R 39 ASN S 138 GLN ** U 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 74 GLN W 223 ASN b 323 GLN ** b 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 61 ASN e 52 GLN i 63 ASN i 92 ASN t 329 ASN ** t 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 130 ASN x 142 HIS x 219 GLN ** x 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 44 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.101489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.075404 restraints weight = 279089.281| |-----------------------------------------------------------------------------| r_work (start): 0.2895 rms_B_bonded: 1.19 r_work: 0.2721 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2622 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2622 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2620 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2620 r_free = 0.2620 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2608 r_free = 0.2608 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2608 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8871 moved from start: 0.3086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 156900 Z= 0.307 Angle : 0.625 20.446 227896 Z= 0.323 Chirality : 0.040 0.325 28257 Planarity : 0.005 0.087 16563 Dihedral : 22.534 179.514 61826 Min Nonbonded Distance : 1.781 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.07 % Favored : 92.81 % Rotamer: Outliers : 4.84 % Allowed : 27.05 % Favored : 68.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.94 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -0.51 (0.08), residues: 9491 helix: 1.05 (0.09), residues: 3768 sheet: -0.30 (0.14), residues: 1253 loop : -1.59 (0.09), residues: 4470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP r 147 HIS 0.014 0.001 HIS G 232 PHE 0.028 0.002 PHE K 300 TYR 0.026 0.002 TYR S 43 ARG 0.019 0.000 ARG i 98 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 54497.34 seconds wall clock time: 944 minutes 8.77 seconds (56648.77 seconds total)