Starting phenix.real_space_refine on Sun Mar 10 20:25:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rdr_4828/03_2024/6rdr_4828_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rdr_4828/03_2024/6rdr_4828.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rdr_4828/03_2024/6rdr_4828.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rdr_4828/03_2024/6rdr_4828.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rdr_4828/03_2024/6rdr_4828_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rdr_4828/03_2024/6rdr_4828_updated.pdb" } resolution = 4.1 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= 0.004 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 1 6.06 5 P 13 5.49 5 Mg 5 5.21 5 S 149 5.16 5 C 34297 2.51 5 N 9112 2.21 5 O 10171 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "0 TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ARG 28": "NH1" <-> "NH2" Residue "1 PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 GLU 33": "OE1" <-> "OE2" Residue "1 ASP 106": "OD1" <-> "OD2" Residue "1 GLU 136": "OE1" <-> "OE2" Residue "1 GLU 138": "OE1" <-> "OE2" Residue "1 ARG 150": "NH1" <-> "NH2" Residue "1 GLU 165": "OE1" <-> "OE2" Residue "1 ASP 172": "OD1" <-> "OD2" Residue "1 ARG 182": "NH1" <-> "NH2" Residue "1 ASP 199": "OD1" <-> "OD2" Residue "1 GLU 255": "OE1" <-> "OE2" Residue "1 ARG 259": "NH1" <-> "NH2" Residue "1 GLU 273": "OE1" <-> "OE2" Residue "1 GLU 281": "OE1" <-> "OE2" Residue "1 GLU 299": "OE1" <-> "OE2" Residue "1 PHE 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 GLU 329": "OE1" <-> "OE2" Residue "1 GLU 332": "OE1" <-> "OE2" Residue "1 GLU 334": "OE1" <-> "OE2" Residue "1 GLU 350": "OE1" <-> "OE2" Residue "1 GLU 355": "OE1" <-> "OE2" Residue "1 ARG 359": "NH1" <-> "NH2" Residue "1 GLU 385": "OE1" <-> "OE2" Residue "1 ARG 387": "NH1" <-> "NH2" Residue "1 GLU 409": "OE1" <-> "OE2" Residue "1 TYR 420": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ARG 434": "NH1" <-> "NH2" Residue "1 GLU 457": "OE1" <-> "OE2" Residue "1 GLU 475": "OE1" <-> "OE2" Residue "1 GLU 496": "OE1" <-> "OE2" Residue "1 GLU 499": "OE1" <-> "OE2" Residue "1 GLU 501": "OE1" <-> "OE2" Residue "1 GLU 513": "OE1" <-> "OE2" Residue "1 ASP 549": "OD1" <-> "OD2" Residue "1 ASP 573": "OD1" <-> "OD2" Residue "1 GLU 577": "OE1" <-> "OE2" Residue "1 ARG 609": "NH1" <-> "NH2" Residue "2 TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ARG 45": "NH1" <-> "NH2" Residue "2 TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 GLU 86": "OE1" <-> "OE2" Residue "2 GLU 139": "OE1" <-> "OE2" Residue "2 TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ARG 173": "NH1" <-> "NH2" Residue "2 ASP 189": "OD1" <-> "OD2" Residue "2 PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ASP 209": "OD1" <-> "OD2" Residue "2 PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ASP 230": "OD1" <-> "OD2" Residue "2 PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ASP 316": "OD1" <-> "OD2" Residue "2 ASP 332": "OD1" <-> "OD2" Residue "2 PHE 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ARG 346": "NH1" <-> "NH2" Residue "2 ASP 374": "OD1" <-> "OD2" Residue "2 TYR 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 TYR 411": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 TYR 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ASP 102": "OD1" <-> "OD2" Residue "3 ASP 119": "OD1" <-> "OD2" Residue "3 PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 GLU 126": "OE1" <-> "OE2" Residue "3 ASP 139": "OD1" <-> "OD2" Residue "3 ARG 149": "NH1" <-> "NH2" Residue "3 ASP 154": "OD1" <-> "OD2" Residue "3 PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 GLU 175": "OE1" <-> "OE2" Residue "3 PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 213": "NH1" <-> "NH2" Residue "3 GLU 218": "OE1" <-> "OE2" Residue "3 TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 233": "NH1" <-> "NH2" Residue "3 ARG 242": "NH1" <-> "NH2" Residue "3 ARG 257": "NH1" <-> "NH2" Residue "3 PHE 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ARG 84": "NH1" <-> "NH2" Residue "4 TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ARG 176": "NH1" <-> "NH2" Residue "4 TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 202": "OE1" <-> "OE2" Residue "4 PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ASP 231": "OD1" <-> "OD2" Residue "4 ARG 232": "NH1" <-> "NH2" Residue "4 GLU 244": "OE1" <-> "OE2" Residue "4 ARG 255": "NH1" <-> "NH2" Residue "4 ASP 271": "OD1" <-> "OD2" Residue "4 PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 GLU 11": "OE1" <-> "OE2" Residue "5 ARG 36": "NH1" <-> "NH2" Residue "5 ARG 50": "NH1" <-> "NH2" Residue "5 ASP 63": "OD1" <-> "OD2" Residue "5 ARG 112": "NH1" <-> "NH2" Residue "5 PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ASP 102": "OD1" <-> "OD2" Residue "7 PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 GLU 78": "OE1" <-> "OE2" Residue "7 ARG 81": "NH1" <-> "NH2" Residue "7 TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ASP 109": "OD1" <-> "OD2" Residue "7 PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ASP 117": "OD1" <-> "OD2" Residue "7 PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ARG 164": "NH1" <-> "NH2" Residue "7 ARG 165": "NH1" <-> "NH2" Residue "7 ARG 166": "NH1" <-> "NH2" Residue "7 PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 ARG 13": "NH1" <-> "NH2" Residue "8 ASP 62": "OD1" <-> "OD2" Residue "8 ARG 65": "NH1" <-> "NH2" Residue "8 TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 TYR 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 ARG 28": "NH1" <-> "NH2" Residue "9 ARG 40": "NH1" <-> "NH2" Residue "9 PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 115": "NH1" <-> "NH2" Residue "M ASP 132": "OD1" <-> "OD2" Residue "M ARG 145": "NH1" <-> "NH2" Residue "M PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 232": "NH1" <-> "NH2" Residue "M ARG 239": "NH1" <-> "NH2" Residue "M PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 288": "OE1" <-> "OE2" Residue "M TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 93": "OD1" <-> "OD2" Residue "P TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 151": "OE1" <-> "OE2" Residue "P TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 163": "OD1" <-> "OD2" Residue "P GLU 166": "OE1" <-> "OE2" Residue "P ASP 179": "OD1" <-> "OD2" Residue "P PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 191": "OD1" <-> "OD2" Residue "P ASP 204": "OD1" <-> "OD2" Residue "P ARG 206": "NH1" <-> "NH2" Residue "P ASP 208": "OD1" <-> "OD2" Residue "P PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 42": "NH1" <-> "NH2" Residue "Q ARG 48": "NH1" <-> "NH2" Residue "Q TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 54": "OD1" <-> "OD2" Residue "Q TYR 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 66": "OE1" <-> "OE2" Residue "R GLU 23": "OE1" <-> "OE2" Residue "R GLU 32": "OE1" <-> "OE2" Residue "R PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 35": "OE1" <-> "OE2" Residue "R PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 177": "OE1" <-> "OE2" Residue "R GLU 186": "OE1" <-> "OE2" Residue "R GLU 196": "OE1" <-> "OE2" Residue "S ARG 46": "NH1" <-> "NH2" Residue "S PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 91": "OD1" <-> "OD2" Residue "S PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 147": "NH1" <-> "NH2" Residue "S ARG 152": "NH1" <-> "NH2" Residue "S ARG 157": "NH1" <-> "NH2" Residue "S TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 222": "OD1" <-> "OD2" Residue "S ARG 244": "NH1" <-> "NH2" Residue "S TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 49": "NH1" <-> "NH2" Residue "T GLU 74": "OE1" <-> "OE2" Residue "T ARG 86": "NH1" <-> "NH2" Residue "T ASP 142": "OD1" <-> "OD2" Residue "T ARG 162": "NH1" <-> "NH2" Residue "T ASP 172": "OD1" <-> "OD2" Residue "T ARG 195": "NH1" <-> "NH2" Residue "T ARG 199": "NH1" <-> "NH2" Residue "T PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 283": "NH1" <-> "NH2" Residue "T TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 294": "OD1" <-> "OD2" Residue "T TYR 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 325": "OD1" <-> "OD2" Residue "T ASP 326": "OD1" <-> "OD2" Residue "T PHE 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 389": "OD1" <-> "OD2" Residue "T PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 429": "NH1" <-> "NH2" Residue "T ARG 454": "NH1" <-> "NH2" Residue "T PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 467": "OD1" <-> "OD2" Residue "T PHE 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 555": "NH1" <-> "NH2" Residue "U ASP 41": "OD1" <-> "OD2" Residue "U GLU 47": "OE1" <-> "OE2" Residue "U ARG 49": "NH1" <-> "NH2" Residue "U TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 96": "NH1" <-> "NH2" Residue "U TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 107": "OE1" <-> "OE2" Residue "U ASP 112": "OD1" <-> "OD2" Residue "U TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 146": "NH1" <-> "NH2" Residue "U ARG 162": "NH1" <-> "NH2" Residue "U ARG 181": "NH1" <-> "NH2" Residue "U ARG 199": "NH1" <-> "NH2" Residue "U GLU 221": "OE1" <-> "OE2" Residue "U ARG 227": "NH1" <-> "NH2" Residue "U ASP 237": "OD1" <-> "OD2" Residue "U ARG 254": "NH1" <-> "NH2" Residue "U TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 283": "NH1" <-> "NH2" Residue "U TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 311": "OE1" <-> "OE2" Residue "U PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 314": "NH1" <-> "NH2" Residue "U ARG 342": "NH1" <-> "NH2" Residue "U ARG 343": "NH1" <-> "NH2" Residue "U ARG 364": "NH1" <-> "NH2" Residue "U PHE 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 407": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 409": "OE1" <-> "OE2" Residue "U GLU 411": "OE1" <-> "OE2" Residue "U PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 454": "NH1" <-> "NH2" Residue "U GLU 455": "OE1" <-> "OE2" Residue "U GLU 475": "OE1" <-> "OE2" Residue "U ARG 479": "NH1" <-> "NH2" Residue "U GLU 482": "OE1" <-> "OE2" Residue "U ARG 496": "NH1" <-> "NH2" Residue "U ARG 513": "NH1" <-> "NH2" Residue "U PHE 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 46": "OD1" <-> "OD2" Residue "V GLU 47": "OE1" <-> "OE2" Residue "V ARG 49": "NH1" <-> "NH2" Residue "V PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 142": "OD1" <-> "OD2" Residue "V ARG 181": "NH1" <-> "NH2" Residue "V ASP 210": "OD1" <-> "OD2" Residue "V ARG 217": "NH1" <-> "NH2" Residue "V ARG 220": "NH1" <-> "NH2" Residue "V ASP 226": "OD1" <-> "OD2" Residue "V ASP 237": "OD1" <-> "OD2" Residue "V ARG 266": "NH1" <-> "NH2" Residue "V PHE 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 314": "NH1" <-> "NH2" Residue "V ARG 335": "NH1" <-> "NH2" Residue "V ARG 342": "NH1" <-> "NH2" Residue "V ARG 343": "NH1" <-> "NH2" Residue "V ARG 347": "NH1" <-> "NH2" Residue "V ARG 360": "NH1" <-> "NH2" Residue "V PHE 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 403": "OD1" <-> "OD2" Residue "V PHE 407": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 429": "NH1" <-> "NH2" Residue "V ARG 454": "NH1" <-> "NH2" Residue "V GLU 455": "OE1" <-> "OE2" Residue "V PHE 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 465": "OD1" <-> "OD2" Residue "V ARG 476": "NH1" <-> "NH2" Residue "V PHE 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 496": "NH1" <-> "NH2" Residue "V ARG 513": "NH1" <-> "NH2" Residue "V ARG 555": "NH1" <-> "NH2" Residue "X ASP 36": "OD1" <-> "OD2" Residue "X ARG 51": "NH1" <-> "NH2" Residue "X PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 91": "OD1" <-> "OD2" Residue "X PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 152": "OE1" <-> "OE2" Residue "X GLU 156": "OE1" <-> "OE2" Residue "X PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 218": "NH1" <-> "NH2" Residue "X GLU 219": "OE1" <-> "OE2" Residue "X ARG 225": "NH1" <-> "NH2" Residue "X GLU 238": "OE1" <-> "OE2" Residue "X ARG 239": "NH1" <-> "NH2" Residue "X GLU 296": "OE1" <-> "OE2" Residue "X TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 385": "NH1" <-> "NH2" Residue "X TYR 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 401": "NH1" <-> "NH2" Residue "X ASP 409": "OD1" <-> "OD2" Residue "X ASP 462": "OD1" <-> "OD2" Residue "X ASP 480": "OD1" <-> "OD2" Residue "X GLU 494": "OE1" <-> "OE2" Residue "X ASP 500": "OD1" <-> "OD2" Residue "X ARG 509": "NH1" <-> "NH2" Residue "X GLU 511": "OE1" <-> "OE2" Residue "X ASP 513": "OD1" <-> "OD2" Residue "X GLU 519": "OE1" <-> "OE2" Residue "X GLU 520": "OE1" <-> "OE2" Residue "X GLU 536": "OE1" <-> "OE2" Residue "X GLU 563": "OE1" <-> "OE2" Residue "Y PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 64": "OE1" <-> "OE2" Residue "Y ARG 71": "NH1" <-> "NH2" Residue "Y ASP 82": "OD1" <-> "OD2" Residue "Y ARG 86": "NH1" <-> "NH2" Residue "Y ASP 104": "OD1" <-> "OD2" Residue "Y ARG 115": "NH1" <-> "NH2" Residue "Y ARG 120": "NH1" <-> "NH2" Residue "Y ARG 145": "NH1" <-> "NH2" Residue "Y GLU 149": "OE1" <-> "OE2" Residue "Y PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 215": "OE1" <-> "OE2" Residue "Y GLU 238": "OE1" <-> "OE2" Residue "Y ARG 258": "NH1" <-> "NH2" Residue "Y GLU 270": "OE1" <-> "OE2" Residue "Y GLU 296": "OE1" <-> "OE2" Residue "Y TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 345": "OD1" <-> "OD2" Residue "Y ARG 366": "NH1" <-> "NH2" Residue "Y ASP 378": "OD1" <-> "OD2" Residue "Y ARG 385": "NH1" <-> "NH2" Residue "Y ASP 423": "OD1" <-> "OD2" Residue "Y PHE 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 460": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 511": "OE1" <-> "OE2" Residue "Y ASP 513": "OD1" <-> "OD2" Residue "Y GLU 519": "OE1" <-> "OE2" Residue "Y ASP 523": "OD1" <-> "OD2" Residue "Y ASP 528": "OD1" <-> "OD2" Residue "Y GLU 533": "OE1" <-> "OE2" Residue "Y GLU 541": "OE1" <-> "OE2" Residue "Y GLU 547": "OE1" <-> "OE2" Residue "Y PHE 549": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 49": "OD1" <-> "OD2" Residue "Z ARG 51": "NH1" <-> "NH2" Residue "Z ARG 71": "NH1" <-> "NH2" Residue "Z ARG 86": "NH1" <-> "NH2" Residue "Z ARG 98": "NH1" <-> "NH2" Residue "Z ARG 120": "NH1" <-> "NH2" Residue "Z ASP 136": "OD1" <-> "OD2" Residue "Z GLU 156": "OE1" <-> "OE2" Residue "Z PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 216": "NH1" <-> "NH2" Residue "Z ARG 258": "NH1" <-> "NH2" Residue "Z GLU 270": "OE1" <-> "OE2" Residue "Z PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 289": "NH1" <-> "NH2" Residue "Z GLU 323": "OE1" <-> "OE2" Residue "Z ASP 348": "OD1" <-> "OD2" Residue "Z PHE 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 385": "NH1" <-> "NH2" Residue "Z ARG 401": "NH1" <-> "NH2" Residue "Z TYR 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 415": "OD1" <-> "OD2" Residue "Z ASP 423": "OD1" <-> "OD2" Residue "Z GLU 424": "OE1" <-> "OE2" Residue "Z GLU 428": "OE1" <-> "OE2" Residue "Z ARG 435": "NH1" <-> "NH2" Residue "Z ARG 437": "NH1" <-> "NH2" Residue "Z PHE 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 465": "OD1" <-> "OD2" Residue "Z ASP 505": "OD1" <-> "OD2" Residue "Z ARG 509": "NH1" <-> "NH2" Residue "Z GLU 520": "OE1" <-> "OE2" Residue "Z GLU 536": "OE1" <-> "OE2" Residue "Z GLU 541": "OE1" <-> "OE2" Residue "Z PHE 549": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 552": "OE1" <-> "OE2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 53748 Number of models: 1 Model: "" Number of chains: 37 Chain: "0" Number of atoms: 607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 607 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 8, 'TRANS': 72} Chain: "1" Number of atoms: 4661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4661 Classifications: {'peptide': 595} Link IDs: {'PTRANS': 31, 'TRANS': 563} Chain: "2" Number of atoms: 3163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3163 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 17, 'TRANS': 423} Chain: "3" Number of atoms: 1874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1874 Classifications: {'peptide': 245} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 239} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 7 Chain: "4" Number of atoms: 2177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2177 Classifications: {'peptide': 290} Link IDs: {'PTRANS': 9, 'TRANS': 280} Chain: "5" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 986 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 7, 'TRANS': 115} Chain: "6" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 926 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "7" Number of atoms: 1347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1347 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 5, 'TRANS': 170} Chain: "8" Number of atoms: 692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 692 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 7, 'TRANS': 80} Chain: "9" Number of atoms: 776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 776 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 5, 'TRANS': 91} Chain: "A" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "B" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "C" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain breaks: 1 Chain: "D" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "E" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "F" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "G" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "H" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "I" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "J" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "M" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1640 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 12, 'TRANS': 204} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "P" Number of atoms: 1532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1532 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 5, 'TRANS': 187} Chain: "Q" Number of atoms: 561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 561 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 5, 'TRANS': 66} Chain: "R" Number of atoms: 1303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1303 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 13, 'TRANS': 163} Chain: "S" Number of atoms: 2130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2130 Classifications: {'peptide': 277} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 271} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "T" Number of atoms: 3979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 3979 Classifications: {'peptide': 523} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 497} Chain: "U" Number of atoms: 3980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 3980 Classifications: {'peptide': 523} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 497} Chain: "V" Number of atoms: 3962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 3962 Classifications: {'peptide': 520} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 494} Chain: "X" Number of atoms: 4115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 542, 4115 Classifications: {'peptide': 542} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 517} Chain: "Y" Number of atoms: 3957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 521, 3957 Classifications: {'peptide': 521} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 498} Chain: "Z" Number of atoms: 4087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 538, 4087 Classifications: {'peptide': 538} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 513} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "U" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "V" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 21.62, per 1000 atoms: 0.40 Number of scatterers: 53748 At special positions: 0 Unit cell: (208.494, 133.731, 263.25, 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 1 29.99 S 149 16.00 P 13 15.00 Mg 5 11.99 O 10171 8.00 N 9112 7.00 C 34297 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=0, symmetry=0 Time building additional restraints: 17.48 Conformation dependent library (CDL) restraints added in 7.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN M 600 " pdb="ZN ZN M 600 " - pdb=" NE2 HIS M 248 " pdb="ZN ZN M 600 " - pdb=" NE2 HIS M 252 " 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13086 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 284 helices and 31 sheets defined 51.3% alpha, 6.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.38 Creating SS restraints... Processing helix chain '0' and resid 4 through 9 removed outlier: 3.877A pdb=" N ALA 0 8 " --> pdb=" O SER 0 4 " (cutoff:3.500A) Processing helix chain '0' and resid 18 through 30 Processing helix chain '0' and resid 44 through 48 Processing helix chain '0' and resid 52 through 55 No H-bonds generated for 'chain '0' and resid 52 through 55' Processing helix chain '1' and resid 46 through 72 Processing helix chain '1' and resid 97 through 99 No H-bonds generated for 'chain '1' and resid 97 through 99' Processing helix chain '1' and resid 104 through 141 removed outlier: 4.317A pdb=" N VAL 1 107 " --> pdb=" O ALA 1 104 " (cutoff:3.500A) Proline residue: 1 108 - end of helix removed outlier: 3.588A pdb=" N ARG 1 118 " --> pdb=" O ILE 1 115 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N THR 1 135 " --> pdb=" O GLY 1 132 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N SER 1 141 " --> pdb=" O GLU 1 138 " (cutoff:3.500A) Processing helix chain '1' and resid 164 through 175 removed outlier: 4.024A pdb=" N THR 1 169 " --> pdb=" O GLU 1 165 " (cutoff:3.500A) Processing helix chain '1' and resid 191 through 204 removed outlier: 3.909A pdb=" N ALA 1 196 " --> pdb=" O GLY 1 192 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL 1 204 " --> pdb=" O PHE 1 200 " (cutoff:3.500A) Processing helix chain '1' and resid 207 through 223 removed outlier: 3.509A pdb=" N ALA 1 210 " --> pdb=" O ALA 1 207 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N SER 1 211 " --> pdb=" O LYS 1 208 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N VAL 1 213 " --> pdb=" O ALA 1 210 " (cutoff:3.500A) Processing helix chain '1' and resid 242 through 270 removed outlier: 3.544A pdb=" N ARG 1 267 " --> pdb=" O LEU 1 263 " (cutoff:3.500A) Processing helix chain '1' and resid 272 through 276 removed outlier: 3.996A pdb=" N ALA 1 275 " --> pdb=" O PRO 1 272 " (cutoff:3.500A) Processing helix chain '1' and resid 298 through 306 removed outlier: 3.500A pdb=" N GLN 1 306 " --> pdb=" O SER 1 302 " (cutoff:3.500A) Processing helix chain '1' and resid 311 through 316 Processing helix chain '1' and resid 324 through 326 No H-bonds generated for 'chain '1' and resid 324 through 326' Processing helix chain '1' and resid 331 through 334 No H-bonds generated for 'chain '1' and resid 331 through 334' Processing helix chain '1' and resid 339 through 352 Processing helix chain '1' and resid 354 through 361 Processing helix chain '1' and resid 363 through 366 Processing helix chain '1' and resid 376 through 387 Processing helix chain '1' and resid 393 through 420 removed outlier: 3.776A pdb=" N GLU 1 415 " --> pdb=" O ALA 1 411 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N VAL 1 418 " --> pdb=" O GLU 1 414 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N ILE 1 419 " --> pdb=" O GLU 1 415 " (cutoff:3.500A) Processing helix chain '1' and resid 426 through 430 Processing helix chain '1' and resid 436 through 443 Processing helix chain '1' and resid 447 through 459 Processing helix chain '1' and resid 464 through 477 Processing helix chain '1' and resid 480 through 482 No H-bonds generated for 'chain '1' and resid 480 through 482' Processing helix chain '1' and resid 486 through 489 No H-bonds generated for 'chain '1' and resid 486 through 489' Processing helix chain '1' and resid 491 through 515 removed outlier: 3.959A pdb=" N GLU 1 501 " --> pdb=" O LEU 1 497 " (cutoff:3.500A) Processing helix chain '1' and resid 519 through 535 Processing helix chain '1' and resid 542 through 548 Processing helix chain '1' and resid 550 through 561 Processing helix chain '1' and resid 567 through 573 Processing helix chain '1' and resid 577 through 587 Processing helix chain '1' and resid 589 through 591 No H-bonds generated for 'chain '1' and resid 589 through 591' Processing helix chain '1' and resid 593 through 605 Processing helix chain '2' and resid 8 through 18 Processing helix chain '2' and resid 26 through 37 Processing helix chain '2' and resid 45 through 57 Processing helix chain '2' and resid 63 through 75 Processing helix chain '2' and resid 81 through 93 removed outlier: 3.746A pdb=" N LEU 2 87 " --> pdb=" O THR 2 83 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ALA 2 88 " --> pdb=" O VAL 2 84 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N GLY 2 89 " --> pdb=" O ALA 2 85 " (cutoff:3.500A) Proline residue: 2 90 - end of helix Processing helix chain '2' and resid 100 through 112 Processing helix chain '2' and resid 118 through 130 Processing helix chain '2' and resid 132 through 134 No H-bonds generated for 'chain '2' and resid 132 through 134' Processing helix chain '2' and resid 137 through 148 Processing helix chain '2' and resid 155 through 165 removed outlier: 3.691A pdb=" N VAL 2 164 " --> pdb=" O ALA 2 160 " (cutoff:3.500A) Processing helix chain '2' and resid 172 through 185 Processing helix chain '2' and resid 190 through 199 removed outlier: 3.531A pdb=" N ALA 2 195 " --> pdb=" O ALA 2 191 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N LYS 2 198 " --> pdb=" O ASP 2 194 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N SER 2 199 " --> pdb=" O ALA 2 195 " (cutoff:3.500A) Processing helix chain '2' and resid 207 through 219 Processing helix chain '2' and resid 228 through 234 Processing helix chain '2' and resid 241 through 254 Processing helix chain '2' and resid 259 through 275 removed outlier: 3.988A pdb=" N VAL 2 268 " --> pdb=" O ALA 2 264 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL 2 269 " --> pdb=" O LEU 2 265 " (cutoff:3.500A) Proline residue: 2 271 - end of helix Processing helix chain '2' and resid 282 through 294 Processing helix chain '2' and resid 301 through 320 removed outlier: 4.340A pdb=" N SER 2 305 " --> pdb=" O ALA 2 301 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N PHE 2 306 " --> pdb=" O ALA 2 302 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLY 2 312 " --> pdb=" O ALA 2 308 " (cutoff:3.500A) Processing helix chain '2' and resid 326 through 340 Processing helix chain '2' and resid 346 through 354 Processing helix chain '2' and resid 397 through 407 Processing helix chain '2' and resid 427 through 441 removed outlier: 3.871A pdb=" N VAL 2 441 " --> pdb=" O ALA 2 437 " (cutoff:3.500A) Processing helix chain '3' and resid 78 through 88 removed outlier: 3.593A pdb=" N LYS 3 88 " --> pdb=" O THR 3 84 " (cutoff:3.500A) Processing helix chain '3' and resid 98 through 100 No H-bonds generated for 'chain '3' and resid 98 through 100' Processing helix chain '3' and resid 103 through 112 Processing helix chain '3' and resid 118 through 124 removed outlier: 4.804A pdb=" N LYS 3 123 " --> pdb=" O ASP 3 119 " (cutoff:3.500A) Processing helix chain '3' and resid 132 through 134 No H-bonds generated for 'chain '3' and resid 132 through 134' Processing helix chain '3' and resid 137 through 149 Processing helix chain '3' and resid 155 through 167 Processing helix chain '3' and resid 174 through 186 removed outlier: 3.597A pdb=" N GLN 3 179 " --> pdb=" O GLU 3 175 " (cutoff:3.500A) Processing helix chain '3' and resid 192 through 204 Processing helix chain '3' and resid 216 through 228 removed outlier: 4.052A pdb=" N THR 3 221 " --> pdb=" O ASP 3 217 " (cutoff:3.500A) Processing helix chain '3' and resid 234 through 243 removed outlier: 3.745A pdb=" N ARG 3 242 " --> pdb=" O ALA 3 238 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLY 3 243 " --> pdb=" O THR 3 239 " (cutoff:3.500A) Processing helix chain '3' and resid 246 through 249 No H-bonds generated for 'chain '3' and resid 246 through 249' Processing helix chain '3' and resid 254 through 271 removed outlier: 3.669A pdb=" N PHE 3 271 " --> pdb=" O ALA 3 267 " (cutoff:3.500A) Processing helix chain '3' and resid 276 through 286 removed outlier: 3.592A pdb=" N GLU 3 279 " --> pdb=" O GLU 3 276 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ALA 3 280 " --> pdb=" O SER 3 277 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE 3 282 " --> pdb=" O GLU 3 279 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ALA 3 284 " --> pdb=" O VAL 3 281 " (cutoff:3.500A) Processing helix chain '3' and resid 289 through 291 No H-bonds generated for 'chain '3' and resid 289 through 291' Processing helix chain '3' and resid 294 through 311 removed outlier: 3.739A pdb=" N VAL 3 303 " --> pdb=" O GLU 3 299 " (cutoff:3.500A) Processing helix chain '4' and resid 10 through 13 No H-bonds generated for 'chain '4' and resid 10 through 13' Processing helix chain '4' and resid 23 through 34 Processing helix chain '4' and resid 48 through 68 removed outlier: 4.062A pdb=" N GLN 4 61 " --> pdb=" O TYR 4 57 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL 4 62 " --> pdb=" O LEU 4 58 " (cutoff:3.500A) Proline residue: 4 65 - end of helix removed outlier: 3.591A pdb=" N HIS 4 68 " --> pdb=" O GLU 4 64 " (cutoff:3.500A) Processing helix chain '4' and resid 79 through 95 removed outlier: 3.804A pdb=" N LYS 4 83 " --> pdb=" O SER 4 79 " (cutoff:3.500A) Processing helix chain '4' and resid 101 through 112 Processing helix chain '4' and resid 119 through 125 Processing helix chain '4' and resid 132 through 149 removed outlier: 3.806A pdb=" N VAL 4 141 " --> pdb=" O ALA 4 137 " (cutoff:3.500A) Processing helix chain '4' and resid 160 through 176 removed outlier: 4.072A pdb=" N LYS 4 168 " --> pdb=" O LYS 4 164 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ALA 4 171 " --> pdb=" O ALA 4 167 " (cutoff:3.500A) Processing helix chain '4' and resid 180 through 188 Processing helix chain '4' and resid 194 through 233 removed outlier: 3.922A pdb=" N LYS 4 198 " --> pdb=" O ASP 4 194 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N VAL 4 199 " --> pdb=" O ALA 4 195 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLU 4 202 " --> pdb=" O LYS 4 198 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N THR 4 205 " --> pdb=" O LYS 4 201 " (cutoff:3.500A) Processing helix chain '4' and resid 238 through 258 removed outlier: 3.873A pdb=" N ALA 4 256 " --> pdb=" O LEU 4 252 " (cutoff:3.500A) Processing helix chain '4' and resid 263 through 283 Processing helix chain '5' and resid 8 through 29 Processing helix chain '5' and resid 31 through 58 removed outlier: 3.916A pdb=" N GLU 5 37 " --> pdb=" O THR 5 33 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N HIS 5 41 " --> pdb=" O GLU 5 37 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N LYS 5 49 " --> pdb=" O ALA 5 45 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N ARG 5 50 " --> pdb=" O ALA 5 46 " (cutoff:3.500A) Processing helix chain '5' and resid 63 through 67 Processing helix chain '5' and resid 73 through 80 Processing helix chain '5' and resid 88 through 105 removed outlier: 3.709A pdb=" N LEU 5 92 " --> pdb=" O PRO 5 88 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N LYS 5 101 " --> pdb=" O SER 5 97 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA 5 105 " --> pdb=" O LYS 5 101 " (cutoff:3.500A) Processing helix chain '5' and resid 114 through 117 Processing helix chain '6' and resid 31 through 40 Processing helix chain '6' and resid 51 through 58 Processing helix chain '6' and resid 73 through 93 Processing helix chain '6' and resid 99 through 118 removed outlier: 4.033A pdb=" N VAL 6 107 " --> pdb=" O LEU 6 103 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N TRP 6 112 " --> pdb=" O LEU 6 108 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU 6 113 " --> pdb=" O GLN 6 109 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N SER 6 118 " --> pdb=" O ILE 6 114 " (cutoff:3.500A) Processing helix chain '6' and resid 122 through 130 Processing helix chain '7' and resid 63 through 69 removed outlier: 3.804A pdb=" N ARG 7 67 " --> pdb=" O ALA 7 63 " (cutoff:3.500A) Processing helix chain '7' and resid 84 through 101 Processing helix chain '7' and resid 111 through 113 No H-bonds generated for 'chain '7' and resid 111 through 113' Processing helix chain '7' and resid 116 through 119 No H-bonds generated for 'chain '7' and resid 116 through 119' Processing helix chain '7' and resid 124 through 144 Processing helix chain '7' and resid 147 through 156 removed outlier: 3.889A pdb=" N SER 7 151 " --> pdb=" O ASP 7 148 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ALA 7 154 " --> pdb=" O SER 7 151 " (cutoff:3.500A) Processing helix chain '7' and resid 158 through 164 Processing helix chain '7' and resid 175 through 186 Processing helix chain '8' and resid 27 through 30 No H-bonds generated for 'chain '8' and resid 27 through 30' Processing helix chain '8' and resid 32 through 38 Processing helix chain '8' and resid 41 through 79 removed outlier: 7.020A pdb=" N TYR 8 46 " --> pdb=" O PRO 8 42 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N LEU 8 47 " --> pdb=" O ARG 8 43 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA 8 79 " --> pdb=" O GLU 8 75 " (cutoff:3.500A) Processing helix chain '9' and resid 6 through 16 Processing helix chain '9' and resid 37 through 54 removed outlier: 4.169A pdb=" N VAL 9 42 " --> pdb=" O ALA 9 38 " (cutoff:3.500A) Processing helix chain '9' and resid 83 through 94 Processing helix chain 'A' and resid 55 through 71 removed outlier: 3.863A pdb=" N MET A 61 " --> pdb=" O ALA A 57 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N CYS A 66 " --> pdb=" O VAL A 62 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ILE A 69 " --> pdb=" O GLY A 65 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N ALA A 70 " --> pdb=" O CYS A 66 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N LEU A 71 " --> pdb=" O ALA A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 91 removed outlier: 3.735A pdb=" N GLY A 79 " --> pdb=" O GLY A 75 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ILE A 86 " --> pdb=" O PHE A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 95 No H-bonds generated for 'chain 'A' and resid 93 through 95' Processing helix chain 'A' and resid 98 through 125 removed outlier: 3.708A pdb=" N LEU A 105 " --> pdb=" O GLY A 101 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N ILE A 113 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ALA A 114 " --> pdb=" O THR A 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 91 removed outlier: 3.778A pdb=" N MET B 61 " --> pdb=" O ALA B 57 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N CYS B 66 " --> pdb=" O VAL B 62 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N THR B 68 " --> pdb=" O ALA B 64 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ILE B 69 " --> pdb=" O GLY B 65 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N ALA B 70 " --> pdb=" O CYS B 66 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N LEU B 71 " --> pdb=" O ALA B 67 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N ALA B 72 " --> pdb=" O THR B 68 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N GLY B 73 " --> pdb=" O ILE B 69 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL B 74 " --> pdb=" O ALA B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 126 removed outlier: 3.619A pdb=" N ALA B 96 " --> pdb=" O PRO B 93 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N LYS B 97 " --> pdb=" O ASN B 94 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU B 99 " --> pdb=" O ALA B 96 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N VAL B 100 " --> pdb=" O LYS B 97 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N LEU B 104 " --> pdb=" O GLY B 101 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ALA B 108 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N SER B 112 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU B 115 " --> pdb=" O SER B 112 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N LEU B 125 " --> pdb=" O PHE B 122 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N PHE B 126 " --> pdb=" O LEU B 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 89 removed outlier: 4.198A pdb=" N MET C 61 " --> pdb=" O ALA C 57 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL C 62 " --> pdb=" O ALA C 58 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ILE C 69 " --> pdb=" O GLY C 65 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N ALA C 70 " --> pdb=" O CYS C 66 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N LEU C 71 " --> pdb=" O ALA C 67 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N ALA C 72 " --> pdb=" O THR C 68 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N GLY C 73 " --> pdb=" O ILE C 69 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N VAL C 74 " --> pdb=" O ALA C 70 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE C 86 " --> pdb=" O PHE C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 95 No H-bonds generated for 'chain 'C' and resid 93 through 95' Processing helix chain 'C' and resid 98 through 126 removed outlier: 3.893A pdb=" N LEU C 109 " --> pdb=" O LEU C 105 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ILE C 113 " --> pdb=" O LEU C 109 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ALA C 114 " --> pdb=" O THR C 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 91 removed outlier: 3.972A pdb=" N LYS D 60 " --> pdb=" O LEU D 56 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N MET D 61 " --> pdb=" O ALA D 57 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL D 62 " --> pdb=" O ALA D 58 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N THR D 68 " --> pdb=" O ALA D 64 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N ILE D 69 " --> pdb=" O GLY D 65 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N ALA D 70 " --> pdb=" O CYS D 66 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N LEU D 71 " --> pdb=" O ALA D 67 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N ALA D 72 " --> pdb=" O THR D 68 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N GLY D 73 " --> pdb=" O ILE D 69 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL D 74 " --> pdb=" O ALA D 70 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLY D 79 " --> pdb=" O GLY D 75 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ILE D 86 " --> pdb=" O PHE D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 126 removed outlier: 3.902A pdb=" N VAL D 100 " --> pdb=" O LYS D 97 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N SER D 112 " --> pdb=" O LEU D 109 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU D 115 " --> pdb=" O SER D 112 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N LEU D 119 " --> pdb=" O PHE D 116 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ILE D 124 " --> pdb=" O VAL D 121 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N PHE D 126 " --> pdb=" O LEU D 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 89 removed outlier: 3.634A pdb=" N LYS E 60 " --> pdb=" O LEU E 56 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N THR E 68 " --> pdb=" O ALA E 64 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ILE E 69 " --> pdb=" O GLY E 65 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N ALA E 70 " --> pdb=" O CYS E 66 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N LEU E 71 " --> pdb=" O ALA E 67 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N ALA E 72 " --> pdb=" O THR E 68 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N GLY E 73 " --> pdb=" O ILE E 69 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N VAL E 74 " --> pdb=" O ALA E 70 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 95 No H-bonds generated for 'chain 'E' and resid 93 through 95' Processing helix chain 'E' and resid 99 through 126 removed outlier: 3.809A pdb=" N LEU E 105 " --> pdb=" O GLY E 101 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N SER E 112 " --> pdb=" O ALA E 108 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N ILE E 113 " --> pdb=" O LEU E 109 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ALA E 114 " --> pdb=" O THR E 110 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LEU E 125 " --> pdb=" O VAL E 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 91 removed outlier: 3.991A pdb=" N MET F 61 " --> pdb=" O ALA F 57 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ILE F 69 " --> pdb=" O GLY F 65 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N ALA F 70 " --> pdb=" O CYS F 66 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N LEU F 71 " --> pdb=" O ALA F 67 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N ALA F 72 " --> pdb=" O THR F 68 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLY F 73 " --> pdb=" O ILE F 69 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ILE F 86 " --> pdb=" O PHE F 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 98 through 126 removed outlier: 4.847A pdb=" N ILE F 113 " --> pdb=" O LEU F 109 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N VAL F 120 " --> pdb=" O PHE F 116 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N PHE F 122 " --> pdb=" O LEU F 118 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LEU F 125 " --> pdb=" O VAL F 121 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 91 removed outlier: 3.900A pdb=" N LYS G 60 " --> pdb=" O LEU G 56 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N MET G 61 " --> pdb=" O ALA G 57 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ILE G 69 " --> pdb=" O GLY G 65 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N ALA G 70 " --> pdb=" O CYS G 66 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N LEU G 71 " --> pdb=" O ALA G 67 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N ALA G 72 " --> pdb=" O THR G 68 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N GLY G 73 " --> pdb=" O ILE G 69 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL G 74 " --> pdb=" O ALA G 70 " (cutoff:3.500A) Processing helix chain 'G' and resid 93 through 121 removed outlier: 5.128A pdb=" N LYS G 97 " --> pdb=" O ASN G 94 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LEU G 99 " --> pdb=" O ALA G 96 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N SER G 112 " --> pdb=" O LEU G 109 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU G 118 " --> pdb=" O LEU G 115 " (cutoff:3.500A) Processing helix chain 'H' and resid 56 through 91 removed outlier: 4.081A pdb=" N THR H 68 " --> pdb=" O ALA H 64 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ILE H 69 " --> pdb=" O GLY H 65 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N ALA H 70 " --> pdb=" O CYS H 66 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N LEU H 71 " --> pdb=" O ALA H 67 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N ALA H 72 " --> pdb=" O THR H 68 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N GLY H 73 " --> pdb=" O ILE H 69 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N VAL H 74 " --> pdb=" O ALA H 70 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE H 86 " --> pdb=" O PHE H 82 " (cutoff:3.500A) Processing helix chain 'H' and resid 93 through 125 removed outlier: 3.642A pdb=" N ALA H 96 " --> pdb=" O PRO H 93 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N LYS H 97 " --> pdb=" O ASN H 94 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLU H 111 " --> pdb=" O ALA H 108 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N SER H 112 " --> pdb=" O LEU H 109 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU H 119 " --> pdb=" O PHE H 116 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL H 120 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N VAL H 121 " --> pdb=" O LEU H 118 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ILE H 124 " --> pdb=" O VAL H 121 " (cutoff:3.500A) Processing helix chain 'I' and resid 55 through 91 removed outlier: 3.583A pdb=" N MET I 61 " --> pdb=" O ALA I 57 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N THR I 68 " --> pdb=" O ALA I 64 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N ILE I 69 " --> pdb=" O GLY I 65 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ALA I 70 " --> pdb=" O CYS I 66 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N LEU I 71 " --> pdb=" O ALA I 67 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ALA I 72 " --> pdb=" O THR I 68 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLY I 73 " --> pdb=" O ILE I 69 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE I 86 " --> pdb=" O PHE I 82 " (cutoff:3.500A) Processing helix chain 'I' and resid 93 through 126 removed outlier: 3.584A pdb=" N ALA I 96 " --> pdb=" O PRO I 93 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N LYS I 97 " --> pdb=" O ASN I 94 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N LEU I 99 " --> pdb=" O ALA I 96 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL I 100 " --> pdb=" O LYS I 97 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ALA I 108 " --> pdb=" O LEU I 105 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N GLU I 111 " --> pdb=" O ALA I 108 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N SER I 112 " --> pdb=" O LEU I 109 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ILE I 113 " --> pdb=" O THR I 110 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N VAL I 121 " --> pdb=" O LEU I 118 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ILE I 124 " --> pdb=" O VAL I 121 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N PHE I 126 " --> pdb=" O LEU I 123 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 65 removed outlier: 3.865A pdb=" N LYS J 60 " --> pdb=" O LEU J 56 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N MET J 61 " --> pdb=" O ALA J 57 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N VAL J 62 " --> pdb=" O ALA J 58 " (cutoff:3.500A) Processing helix chain 'J' and resid 68 through 89 removed outlier: 3.866A pdb=" N GLY J 73 " --> pdb=" O ALA J 70 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N VAL J 74 " --> pdb=" O LEU J 71 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU J 78 " --> pdb=" O GLY J 75 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N MET J 81 " --> pdb=" O LEU J 78 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE J 82 " --> pdb=" O GLY J 79 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU J 85 " --> pdb=" O PHE J 82 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLY J 88 " --> pdb=" O LEU J 85 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA J 89 " --> pdb=" O ILE J 86 " (cutoff:3.500A) Processing helix chain 'J' and resid 96 through 125 removed outlier: 3.595A pdb=" N LEU J 105 " --> pdb=" O GLY J 101 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N THR J 110 " --> pdb=" O GLY J 106 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N ILE J 113 " --> pdb=" O LEU J 109 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA J 114 " --> pdb=" O THR J 110 " (cutoff:3.500A) Processing helix chain 'M' and resid 105 through 119 Processing helix chain 'M' and resid 134 through 144 removed outlier: 3.549A pdb=" N ASP M 140 " --> pdb=" O ALA M 137 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ASP M 143 " --> pdb=" O ASP M 140 " (cutoff:3.500A) Processing helix chain 'M' and resid 148 through 165 Processing helix chain 'M' and resid 178 through 200 removed outlier: 3.547A pdb=" N LYS M 199 " --> pdb=" O LEU M 195 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N THR M 200 " --> pdb=" O GLY M 196 " (cutoff:3.500A) Processing helix chain 'M' and resid 221 through 264 removed outlier: 3.899A pdb=" N ARG M 232 " --> pdb=" O SER M 228 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ALA M 233 " --> pdb=" O TYR M 229 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N VAL M 234 " --> pdb=" O THR M 230 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLY M 237 " --> pdb=" O ALA M 233 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N LEU M 240 " --> pdb=" O LEU M 236 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N GLY M 247 " --> pdb=" O ASN M 243 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N HIS M 248 " --> pdb=" O MET M 244 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ALA M 260 " --> pdb=" O GLY M 256 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N LEU M 261 " --> pdb=" O MET M 257 " (cutoff:3.500A) Proline residue: M 262 - end of helix Processing helix chain 'M' and resid 271 through 308 removed outlier: 3.768A pdb=" N VAL M 277 " --> pdb=" O ALA M 273 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N LEU M 280 " --> pdb=" O GLY M 276 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N SER M 296 " --> pdb=" O ALA M 292 " (cutoff:3.500A) Processing helix chain 'P' and resid 51 through 64 removed outlier: 3.680A pdb=" N LYS P 63 " --> pdb=" O GLN P 59 " (cutoff:3.500A) Processing helix chain 'P' and resid 69 through 83 removed outlier: 3.812A pdb=" N PHE P 77 " --> pdb=" O GLU P 73 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU P 79 " --> pdb=" O TYR P 75 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE P 81 " --> pdb=" O PHE P 77 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LYS P 82 " --> pdb=" O ILE P 78 " (cutoff:3.500A) Processing helix chain 'P' and resid 85 through 92 removed outlier: 4.103A pdb=" N LEU P 90 " --> pdb=" O GLU P 86 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ALA P 91 " --> pdb=" O LEU P 87 " (cutoff:3.500A) Processing helix chain 'P' and resid 98 through 108 removed outlier: 3.879A pdb=" N ILE P 105 " --> pdb=" O ARG P 101 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N SER P 106 " --> pdb=" O THR P 102 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N SER P 107 " --> pdb=" O LYS P 103 " (cutoff:3.500A) Processing helix chain 'P' and resid 118 through 121 No H-bonds generated for 'chain 'P' and resid 118 through 121' Processing helix chain 'P' and resid 124 through 127 No H-bonds generated for 'chain 'P' and resid 124 through 127' Processing helix chain 'P' and resid 130 through 149 removed outlier: 4.105A pdb=" N LEU P 135 " --> pdb=" O SER P 132 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N THR P 138 " --> pdb=" O LEU P 135 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N VAL P 139 " --> pdb=" O GLU P 136 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASN P 140 " --> pdb=" O VAL P 137 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLU P 142 " --> pdb=" O VAL P 139 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N GLU P 143 " --> pdb=" O ASN P 140 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N MET P 145 " --> pdb=" O GLU P 142 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS P 149 " --> pdb=" O LEU P 146 " (cutoff:3.500A) Processing helix chain 'P' and resid 164 through 174 removed outlier: 3.723A pdb=" N VAL P 168 " --> pdb=" O LYS P 164 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS P 172 " --> pdb=" O VAL P 168 " (cutoff:3.500A) Processing helix chain 'P' and resid 211 through 228 removed outlier: 3.681A pdb=" N LEU P 227 " --> pdb=" O ASN P 223 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER P 228 " --> pdb=" O LYS P 224 " (cutoff:3.500A) Processing helix chain 'Q' and resid 8 through 11 No H-bonds generated for 'chain 'Q' and resid 8 through 11' Processing helix chain 'Q' and resid 16 through 30 removed outlier: 3.993A pdb=" N VAL Q 30 " --> pdb=" O LEU Q 26 " (cutoff:3.500A) Processing helix chain 'Q' and resid 33 through 36 No H-bonds generated for 'chain 'Q' and resid 33 through 36' Processing helix chain 'Q' and resid 38 through 41 No H-bonds generated for 'chain 'Q' and resid 38 through 41' Processing helix chain 'R' and resid 30 through 40 removed outlier: 3.649A pdb=" N THR R 34 " --> pdb=" O PRO R 30 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N GLU R 35 " --> pdb=" O LYS R 31 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LYS R 39 " --> pdb=" O GLU R 35 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N LYS R 40 " --> pdb=" O VAL R 36 " (cutoff:3.500A) Processing helix chain 'R' and resid 159 through 167 Processing helix chain 'R' and resid 175 through 196 Processing helix chain 'S' and resid 41 through 70 removed outlier: 3.960A pdb=" N MET S 62 " --> pdb=" O LYS S 58 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LYS S 69 " --> pdb=" O ALA S 65 " (cutoff:3.500A) Processing helix chain 'S' and resid 72 through 78 removed outlier: 4.479A pdb=" N GLU S 76 " --> pdb=" O GLN S 72 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N GLN S 77 " --> pdb=" O ILE S 73 " (cutoff:3.500A) Processing helix chain 'S' and resid 83 through 89 Processing helix chain 'S' and resid 116 through 128 removed outlier: 3.663A pdb=" N ARG S 124 " --> pdb=" O THR S 120 " (cutoff:3.500A) Processing helix chain 'S' and resid 144 through 147 No H-bonds generated for 'chain 'S' and resid 144 through 147' Processing helix chain 'S' and resid 150 through 153 No H-bonds generated for 'chain 'S' and resid 150 through 153' Processing helix chain 'S' and resid 172 through 183 Processing helix chain 'S' and resid 217 through 220 No H-bonds generated for 'chain 'S' and resid 217 through 220' Processing helix chain 'S' and resid 239 through 312 removed outlier: 4.043A pdb=" N ARG S 244 " --> pdb=" O SER S 240 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ASP S 245 " --> pdb=" O ASP S 241 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ASN S 263 " --> pdb=" O MET S 259 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ASN S 276 " --> pdb=" O SER S 272 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS S 279 " --> pdb=" O GLU S 275 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU S 285 " --> pdb=" O ALA S 281 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE S 307 " --> pdb=" O GLU S 303 " (cutoff:3.500A) Processing helix chain 'T' and resid 58 through 75 Proline residue: T 68 - end of helix removed outlier: 3.680A pdb=" N GLU T 72 " --> pdb=" O PRO T 68 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N TRP T 73 " --> pdb=" O ALA T 69 " (cutoff:3.500A) Processing helix chain 'T' and resid 135 through 137 No H-bonds generated for 'chain 'T' and resid 135 through 137' Processing helix chain 'T' and resid 157 through 159 No H-bonds generated for 'chain 'T' and resid 157 through 159' Processing helix chain 'T' and resid 207 through 210 No H-bonds generated for 'chain 'T' and resid 207 through 210' Processing helix chain 'T' and resid 231 through 246 removed outlier: 3.853A pdb=" N ALA T 238 " --> pdb=" O VAL T 234 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLN T 242 " --> pdb=" O ALA T 238 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LYS T 243 " --> pdb=" O ILE T 239 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ASN T 244 " --> pdb=" O ILE T 240 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASN T 246 " --> pdb=" O GLN T 242 " (cutoff:3.500A) Processing helix chain 'T' and resid 266 through 279 Processing helix chain 'T' and resid 281 through 283 No H-bonds generated for 'chain 'T' and resid 281 through 283' Processing helix chain 'T' and resid 296 through 299 No H-bonds generated for 'chain 'T' and resid 296 through 299' Processing helix chain 'T' and resid 302 through 315 removed outlier: 3.616A pdb=" N TYR T 312 " --> pdb=" O ALA T 308 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N PHE T 313 " --> pdb=" O MET T 309 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG T 314 " --> pdb=" O ALA T 310 " (cutoff:3.500A) Processing helix chain 'T' and resid 327 through 338 removed outlier: 4.011A pdb=" N VAL T 332 " --> pdb=" O SER T 328 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N MET T 337 " --> pdb=" O ALA T 333 " (cutoff:3.500A) Processing helix chain 'T' and resid 352 through 364 removed outlier: 3.942A pdb=" N PHE T 355 " --> pdb=" O GLY T 352 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N SER T 359 " --> pdb=" O TYR T 356 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ARG T 360 " --> pdb=" O LEU T 357 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N LEU T 362 " --> pdb=" O SER T 359 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N GLU T 363 " --> pdb=" O ARG T 360 " (cutoff:3.500A) Processing helix chain 'T' and resid 393 through 401 removed outlier: 3.551A pdb=" N ASN T 397 " --> pdb=" O TYR T 393 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL T 398 " --> pdb=" O ILE T 394 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N SER T 400 " --> pdb=" O THR T 396 " (cutoff:3.500A) Processing helix chain 'T' and resid 410 through 413 No H-bonds generated for 'chain 'T' and resid 410 through 413' Processing helix chain 'T' and resid 431 through 434 Processing helix chain 'T' and resid 437 through 442 removed outlier: 4.032A pdb=" N GLN T 441 " --> pdb=" O PRO T 437 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N VAL T 442 " --> pdb=" O GLY T 438 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 437 through 442' Processing helix chain 'T' and resid 446 through 457 removed outlier: 3.525A pdb=" N ARG T 454 " --> pdb=" O LEU T 450 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N GLU T 455 " --> pdb=" O ALA T 451 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N VAL T 456 " --> pdb=" O GLN T 452 " (cutoff:3.500A) Processing helix chain 'T' and resid 460 through 462 No H-bonds generated for 'chain 'T' and resid 460 through 462' Processing helix chain 'T' and resid 470 through 481 Processing helix chain 'T' and resid 495 through 505 removed outlier: 3.777A pdb=" N VAL T 499 " --> pdb=" O GLU T 495 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ALA T 500 " --> pdb=" O ARG T 496 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ALA T 504 " --> pdb=" O ALA T 500 " (cutoff:3.500A) Processing helix chain 'T' and resid 517 through 526 removed outlier: 4.965A pdb=" N GLU T 522 " --> pdb=" O VAL T 518 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ALA T 523 " --> pdb=" O ALA T 519 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL T 524 " --> pdb=" O ALA T 520 " (cutoff:3.500A) Processing helix chain 'T' and resid 531 through 538 removed outlier: 3.825A pdb=" N ILE T 535 " --> pdb=" O ALA T 531 " (cutoff:3.500A) Processing helix chain 'T' and resid 544 through 553 removed outlier: 4.537A pdb=" N HIS T 549 " --> pdb=" O ALA T 545 " (cutoff:3.500A) Processing helix chain 'U' and resid 42 through 48 removed outlier: 4.892A pdb=" N GLU U 47 " --> pdb=" O LYS U 43 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N LEU U 48 " --> pdb=" O ALA U 44 " (cutoff:3.500A) Processing helix chain 'U' and resid 59 through 63 Processing helix chain 'U' and resid 66 through 72 Processing helix chain 'U' and resid 135 through 137 No H-bonds generated for 'chain 'U' and resid 135 through 137' Processing helix chain 'U' and resid 207 through 212 Processing helix chain 'U' and resid 231 through 248 removed outlier: 3.912A pdb=" N ALA U 235 " --> pdb=" O LYS U 231 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N GLU U 247 " --> pdb=" O LYS U 243 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N GLN U 248 " --> pdb=" O ASN U 244 " (cutoff:3.500A) Processing helix chain 'U' and resid 266 through 279 Processing helix chain 'U' and resid 281 through 283 No H-bonds generated for 'chain 'U' and resid 281 through 283' Processing helix chain 'U' and resid 296 through 315 Proline residue: U 303 - end of helix removed outlier: 3.655A pdb=" N TYR U 312 " --> pdb=" O ALA U 308 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N PHE U 313 " --> pdb=" O MET U 309 " (cutoff:3.500A) Processing helix chain 'U' and resid 327 through 341 removed outlier: 3.694A pdb=" N LEU U 341 " --> pdb=" O MET U 337 " (cutoff:3.500A) Processing helix chain 'U' and resid 354 through 364 removed outlier: 4.857A pdb=" N ARG U 364 " --> pdb=" O ARG U 360 " (cutoff:3.500A) Processing helix chain 'U' and resid 394 through 399 Processing helix chain 'U' and resid 410 through 414 Processing helix chain 'U' and resid 437 through 459 removed outlier: 4.417A pdb=" N VAL U 442 " --> pdb=" O GLY U 438 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLY U 444 " --> pdb=" O LYS U 440 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N THR U 445 " --> pdb=" O GLN U 441 " (cutoff:3.500A) Processing helix chain 'U' and resid 470 through 484 removed outlier: 3.757A pdb=" N ALA U 478 " --> pdb=" O LEU U 474 " (cutoff:3.500A) Processing helix chain 'U' and resid 495 through 505 removed outlier: 3.815A pdb=" N VAL U 499 " --> pdb=" O GLU U 495 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ALA U 500 " --> pdb=" O ARG U 496 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ALA U 504 " --> pdb=" O ALA U 500 " (cutoff:3.500A) Processing helix chain 'U' and resid 515 through 527 removed outlier: 3.773A pdb=" N VAL U 518 " --> pdb=" O GLN U 515 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N GLU U 521 " --> pdb=" O VAL U 518 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU U 522 " --> pdb=" O ALA U 519 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLN U 527 " --> pdb=" O VAL U 524 " (cutoff:3.500A) Processing helix chain 'U' and resid 531 through 539 Processing helix chain 'U' and resid 544 through 555 removed outlier: 4.282A pdb=" N HIS U 549 " --> pdb=" O ALA U 545 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU U 554 " --> pdb=" O LEU U 550 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ARG U 555 " --> pdb=" O LYS U 551 " (cutoff:3.500A) Processing helix chain 'V' and resid 46 through 48 No H-bonds generated for 'chain 'V' and resid 46 through 48' Processing helix chain 'V' and resid 56 through 69 removed outlier: 4.696A pdb=" N ILE V 59 " --> pdb=" O LYS V 56 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N GLN V 60 " --> pdb=" O TYR V 57 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N SER V 63 " --> pdb=" O GLN V 60 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N ILE V 67 " --> pdb=" O GLN V 64 " (cutoff:3.500A) Proline residue: V 68 - end of helix Processing helix chain 'V' and resid 135 through 137 No H-bonds generated for 'chain 'V' and resid 135 through 137' Processing helix chain 'V' and resid 157 through 159 No H-bonds generated for 'chain 'V' and resid 157 through 159' Processing helix chain 'V' and resid 207 through 212 Processing helix chain 'V' and resid 231 through 248 removed outlier: 4.305A pdb=" N GLU V 247 " --> pdb=" O LYS V 243 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N GLN V 248 " --> pdb=" O ASN V 244 " (cutoff:3.500A) Processing helix chain 'V' and resid 251 through 253 No H-bonds generated for 'chain 'V' and resid 251 through 253' Processing helix chain 'V' and resid 266 through 279 Processing helix chain 'V' and resid 281 through 283 No H-bonds generated for 'chain 'V' and resid 281 through 283' Processing helix chain 'V' and resid 296 through 314 Proline residue: V 303 - end of helix removed outlier: 3.826A pdb=" N TYR V 312 " --> pdb=" O ALA V 308 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N PHE V 313 " --> pdb=" O MET V 309 " (cutoff:3.500A) Processing helix chain 'V' and resid 327 through 341 Processing helix chain 'V' and resid 352 through 364 removed outlier: 4.124A pdb=" N PHE V 355 " --> pdb=" O GLY V 352 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU V 357 " --> pdb=" O VAL V 354 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N GLU V 363 " --> pdb=" O ARG V 360 " (cutoff:3.500A) Processing helix chain 'V' and resid 393 through 401 Processing helix chain 'V' and resid 431 through 434 removed outlier: 3.981A pdb=" N ALA V 434 " --> pdb=" O GLY V 431 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 431 through 434' Processing helix chain 'V' and resid 440 through 456 removed outlier: 3.979A pdb=" N GLY V 444 " --> pdb=" O LYS V 440 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N THR V 445 " --> pdb=" O GLN V 441 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU V 455 " --> pdb=" O ALA V 451 " (cutoff:3.500A) Processing helix chain 'V' and resid 470 through 481 Processing helix chain 'V' and resid 494 through 506 Processing helix chain 'V' and resid 514 through 520 removed outlier: 4.179A pdb=" N ILE V 517 " --> pdb=" O VAL V 514 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N VAL V 518 " --> pdb=" O GLN V 515 " (cutoff:3.500A) Processing helix chain 'V' and resid 522 through 525 No H-bonds generated for 'chain 'V' and resid 522 through 525' Processing helix chain 'V' and resid 530 through 539 removed outlier: 3.510A pdb=" N LYS V 534 " --> pdb=" O PRO V 530 " (cutoff:3.500A) Processing helix chain 'V' and resid 544 through 555 removed outlier: 4.487A pdb=" N ARG V 555 " --> pdb=" O LYS V 551 " (cutoff:3.500A) Processing helix chain 'X' and resid 115 through 117 No H-bonds generated for 'chain 'X' and resid 115 through 117' Processing helix chain 'X' and resid 165 through 170 Processing helix chain 'X' and resid 189 through 203 removed outlier: 5.141A pdb=" N LYS X 202 " --> pdb=" O ASN X 198 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ALA X 203 " --> pdb=" O ASN X 199 " (cutoff:3.500A) Processing helix chain 'X' and resid 217 through 229 removed outlier: 3.731A pdb=" N GLU X 229 " --> pdb=" O ARG X 225 " (cutoff:3.500A) Processing helix chain 'X' and resid 239 through 241 No H-bonds generated for 'chain 'X' and resid 239 through 241' Processing helix chain 'X' and resid 261 through 274 removed outlier: 3.571A pdb=" N PHE X 272 " --> pdb=" O VAL X 268 " (cutoff:3.500A) Processing helix chain 'X' and resid 288 through 298 Processing helix chain 'X' and resid 314 through 322 Processing helix chain 'X' and resid 349 through 357 removed outlier: 4.287A pdb=" N ALA X 356 " --> pdb=" O ALA X 352 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N HIS X 357 " --> pdb=" O THR X 353 " (cutoff:3.500A) Processing helix chain 'X' and resid 367 through 370 No H-bonds generated for 'chain 'X' and resid 367 through 370' Processing helix chain 'X' and resid 394 through 419 removed outlier: 4.998A pdb=" N ASP X 415 " --> pdb=" O LYS X 411 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N ILE X 416 " --> pdb=" O ASN X 412 " (cutoff:3.500A) Processing helix chain 'X' and resid 427 through 442 Processing helix chain 'X' and resid 450 through 452 No H-bonds generated for 'chain 'X' and resid 450 through 452' Processing helix chain 'X' and resid 463 through 475 Processing helix chain 'X' and resid 484 through 486 No H-bonds generated for 'chain 'X' and resid 484 through 486' Processing helix chain 'X' and resid 492 through 506 removed outlier: 3.595A pdb=" N LYS X 496 " --> pdb=" O ILE X 492 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ILE X 506 " --> pdb=" O MET X 502 " (cutoff:3.500A) Processing helix chain 'X' and resid 527 through 531 Processing helix chain 'Y' and resid 115 through 117 No H-bonds generated for 'chain 'Y' and resid 115 through 117' Processing helix chain 'Y' and resid 165 through 170 Processing helix chain 'Y' and resid 189 through 200 Processing helix chain 'Y' and resid 217 through 229 Processing helix chain 'Y' and resid 236 through 241 removed outlier: 4.561A pdb=" N GLY Y 240 " --> pdb=" O ALA Y 237 " (cutoff:3.500A) Processing helix chain 'Y' and resid 255 through 258 No H-bonds generated for 'chain 'Y' and resid 255 through 258' Processing helix chain 'Y' and resid 261 through 274 Processing helix chain 'Y' and resid 287 through 297 removed outlier: 3.581A pdb=" N GLU Y 296 " --> pdb=" O ALA Y 293 " (cutoff:3.500A) Processing helix chain 'Y' and resid 314 through 324 removed outlier: 4.677A pdb=" N ARG Y 324 " --> pdb=" O GLY Y 320 " (cutoff:3.500A) Processing helix chain 'Y' and resid 349 through 357 removed outlier: 3.892A pdb=" N THR Y 354 " --> pdb=" O ALA Y 350 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ALA Y 356 " --> pdb=" O ALA Y 352 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N HIS Y 357 " --> pdb=" O THR Y 353 " (cutoff:3.500A) Processing helix chain 'Y' and resid 366 through 370 Processing helix chain 'Y' and resid 389 through 392 No H-bonds generated for 'chain 'Y' and resid 389 through 392' Processing helix chain 'Y' and resid 394 through 415 removed outlier: 3.611A pdb=" N VAL Y 399 " --> pdb=" O GLU Y 395 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ASP Y 415 " --> pdb=" O LYS Y 411 " (cutoff:3.500A) Processing helix chain 'Y' and resid 429 through 442 Processing helix chain 'Y' and resid 450 through 452 No H-bonds generated for 'chain 'Y' and resid 450 through 452' Processing helix chain 'Y' and resid 463 through 474 Processing helix chain 'Y' and resid 483 through 486 removed outlier: 3.862A pdb=" N PHE Y 486 " --> pdb=" O GLU Y 483 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 483 through 486' Processing helix chain 'Y' and resid 492 through 508 removed outlier: 3.892A pdb=" N ASP Y 500 " --> pdb=" O LYS Y 496 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LYS Y 501 " --> pdb=" O GLU Y 497 " (cutoff:3.500A) Processing helix chain 'Y' and resid 527 through 531 Processing helix chain 'Y' and resid 545 through 554 removed outlier: 3.901A pdb=" N LYS Y 550 " --> pdb=" O GLU Y 546 " (cutoff:3.500A) Processing helix chain 'Z' and resid 115 through 117 No H-bonds generated for 'chain 'Z' and resid 115 through 117' Processing helix chain 'Z' and resid 165 through 169 Processing helix chain 'Z' and resid 189 through 203 Processing helix chain 'Z' and resid 217 through 229 Processing helix chain 'Z' and resid 236 through 241 removed outlier: 4.318A pdb=" N GLY Z 240 " --> pdb=" O ALA Z 237 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ASN Z 241 " --> pdb=" O GLU Z 238 " (cutoff:3.500A) Processing helix chain 'Z' and resid 255 through 258 No H-bonds generated for 'chain 'Z' and resid 255 through 258' Processing helix chain 'Z' and resid 261 through 274 Processing helix chain 'Z' and resid 287 through 300 Processing helix chain 'Z' and resid 314 through 322 removed outlier: 4.227A pdb=" N LEU Z 321 " --> pdb=" O ASP Z 317 " (cutoff:3.500A) Processing helix chain 'Z' and resid 349 through 354 Processing helix chain 'Z' and resid 367 through 370 No H-bonds generated for 'chain 'Z' and resid 367 through 370' Processing helix chain 'Z' and resid 394 through 412 removed outlier: 3.612A pdb=" N ASN Z 412 " --> pdb=" O GLN Z 408 " (cutoff:3.500A) Processing helix chain 'Z' and resid 416 through 419 No H-bonds generated for 'chain 'Z' and resid 416 through 419' Processing helix chain 'Z' and resid 422 through 424 No H-bonds generated for 'chain 'Z' and resid 422 through 424' Processing helix chain 'Z' and resid 427 through 439 removed outlier: 3.789A pdb=" N LEU Z 431 " --> pdb=" O GLU Z 427 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N THR Z 432 " --> pdb=" O GLU Z 428 " (cutoff:3.500A) Processing helix chain 'Z' and resid 448 through 454 removed outlier: 3.605A pdb=" N GLU Z 451 " --> pdb=" O GLN Z 448 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N VAL Z 452 " --> pdb=" O VAL Z 449 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N THR Z 454 " --> pdb=" O GLU Z 451 " (cutoff:3.500A) Processing helix chain 'Z' and resid 463 through 475 removed outlier: 3.875A pdb=" N VAL Z 473 " --> pdb=" O GLY Z 469 " (cutoff:3.500A) Processing helix chain 'Z' and resid 492 through 509 removed outlier: 3.735A pdb=" N LYS Z 496 " --> pdb=" O ILE Z 492 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLU Z 497 " --> pdb=" O LYS Z 493 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA Z 503 " --> pdb=" O ALA Z 499 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N ILE Z 506 " --> pdb=" O MET Z 502 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N ALA Z 507 " --> pdb=" O ALA Z 503 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N SER Z 508 " --> pdb=" O LYS Z 504 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ARG Z 509 " --> pdb=" O ASP Z 505 " (cutoff:3.500A) Processing helix chain 'Z' and resid 527 through 531 Processing sheet with id= A, first strand: chain '2' and resid 369 through 372 removed outlier: 3.544A pdb=" N GLN 2 380 " --> pdb=" O ALA 2 414 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain '7' and resid 35 through 38 Processing sheet with id= C, first strand: chain '7' and resid 45 through 47 Processing sheet with id= D, first strand: chain 'P' and resid 155 through 158 Processing sheet with id= E, first strand: chain 'Q' and resid 45 through 49 removed outlier: 3.571A pdb=" N PHE Q 47 " --> pdb=" O TYR Q 63 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'R' and resid 72 through 75 removed outlier: 6.515A pdb=" N THR R 142 " --> pdb=" O ASN R 73 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N TYR R 75 " --> pdb=" O THR R 142 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ILE R 144 " --> pdb=" O TYR R 75 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'R' and resid 96 through 100 removed outlier: 6.831A pdb=" N VAL R 115 " --> pdb=" O PRO R 92 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'S' and resid 158 through 162 removed outlier: 7.992A pdb=" N VAL S 139 " --> pdb=" O GLN S 159 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ALA S 161 " --> pdb=" O VAL S 139 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N SER S 141 " --> pdb=" O ALA S 161 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N SER S 189 " --> pdb=" O VAL S 101 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N VAL S 103 " --> pdb=" O SER S 189 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N GLN S 191 " --> pdb=" O VAL S 103 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N VAL S 105 " --> pdb=" O GLN S 191 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N LEU S 193 " --> pdb=" O VAL S 105 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LYS S 204 " --> pdb=" O LYS S 196 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'T' and resid 144 through 146 removed outlier: 3.765A pdb=" N GLU T 107 " --> pdb=" O ALA T 119 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N GLY T 128 " --> pdb=" O LEU T 120 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'T' and resid 152 through 155 Processing sheet with id= K, first strand: chain 'T' and resid 223 through 225 Processing sheet with id= L, first strand: chain 'T' and resid 376 through 379 removed outlier: 6.360A pdb=" N ILE T 286 " --> pdb=" O TYR T 259 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N ALA T 261 " --> pdb=" O ILE T 286 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N VAL T 288 " --> pdb=" O ALA T 261 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N GLY T 263 " --> pdb=" O VAL T 288 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N ALA T 290 " --> pdb=" O GLY T 263 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'T' and resid 85 through 91 removed outlier: 6.557A pdb=" N ARG T 96 " --> pdb=" O LEU T 88 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N VAL T 90 " --> pdb=" O ILE T 94 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ILE T 94 " --> pdb=" O VAL T 90 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'U' and resid 85 through 91 removed outlier: 6.728A pdb=" N ARG U 96 " --> pdb=" O LEU U 88 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N VAL U 90 " --> pdb=" O ILE U 94 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ILE U 94 " --> pdb=" O VAL U 90 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASN U 121 " --> pdb=" O GLY U 128 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N VAL U 130 " --> pdb=" O ALA U 119 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N ALA U 119 " --> pdb=" O VAL U 130 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLU U 107 " --> pdb=" O ALA U 119 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'U' and resid 152 through 155 Processing sheet with id= P, first strand: chain 'U' and resid 405 through 408 removed outlier: 6.717A pdb=" N LEU U 222 " --> pdb=" O ILE U 406 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N LEU U 408 " --> pdb=" O LEU U 222 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N ILE U 224 " --> pdb=" O LEU U 408 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'U' and resid 319 through 325 removed outlier: 3.538A pdb=" N LEU U 321 " --> pdb=" O TYR U 256 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'V' and resid 84 through 86 removed outlier: 7.127A pdb=" N LEU V 108 " --> pdb=" O THR V 147 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLU V 107 " --> pdb=" O ALA V 119 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N GLY V 128 " --> pdb=" O LEU V 120 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N LEU V 122 " --> pdb=" O HIS V 126 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N HIS V 126 " --> pdb=" O LEU V 122 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'V' and resid 152 through 155 Processing sheet with id= T, first strand: chain 'V' and resid 223 through 226 Processing sheet with id= U, first strand: chain 'V' and resid 286 through 290 removed outlier: 6.702A pdb=" N HIS V 319 " --> pdb=" O TYR V 256 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N VAL V 258 " --> pdb=" O HIS V 319 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N LEU V 321 " --> pdb=" O VAL V 258 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N VAL V 260 " --> pdb=" O LEU V 321 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ILE V 323 " --> pdb=" O VAL V 260 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N VAL V 262 " --> pdb=" O ILE V 323 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N ASP V 325 " --> pdb=" O VAL V 262 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N SER V 376 " --> pdb=" O GLY V 320 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N ILE V 322 " --> pdb=" O SER V 376 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N THR V 378 " --> pdb=" O ILE V 322 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N TYR V 324 " --> pdb=" O THR V 378 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'X' and resid 39 through 44 removed outlier: 6.653A pdb=" N ASP X 49 " --> pdb=" O SER X 41 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N VAL X 43 " --> pdb=" O VAL X 47 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N VAL X 47 " --> pdb=" O VAL X 43 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ILE X 88 " --> pdb=" O VAL X 76 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N VAL X 76 " --> pdb=" O ILE X 88 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'X' and resid 110 through 113 Processing sheet with id= X, first strand: chain 'X' and resid 360 through 363 removed outlier: 7.258A pdb=" N ILE X 179 " --> pdb=" O ILE X 333 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N SER X 335 " --> pdb=" O ILE X 179 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N LEU X 181 " --> pdb=" O SER X 335 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N GLN X 337 " --> pdb=" O LEU X 181 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N GLY X 183 " --> pdb=" O GLN X 337 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N VAL X 339 " --> pdb=" O GLY X 183 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'X' and resid 559 through 561 Processing sheet with id= Z, first strand: chain 'Y' and resid 38 through 44 removed outlier: 6.292A pdb=" N ASP Y 49 " --> pdb=" O SER Y 41 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N VAL Y 43 " --> pdb=" O VAL Y 47 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N VAL Y 47 " --> pdb=" O VAL Y 43 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ILE Y 88 " --> pdb=" O VAL Y 76 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N VAL Y 76 " --> pdb=" O ILE Y 88 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N LEU Y 72 " --> pdb=" O VAL Y 65 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'Y' and resid 361 through 363 removed outlier: 7.931A pdb=" N THR Y 362 " --> pdb=" O LYS Y 178 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N GLY Y 180 " --> pdb=" O THR Y 362 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N ILE Y 179 " --> pdb=" O ILE Y 333 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N SER Y 335 " --> pdb=" O ILE Y 179 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N LEU Y 181 " --> pdb=" O SER Y 335 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N GLN Y 337 " --> pdb=" O LEU Y 181 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N PHE Y 207 " --> pdb=" O LEU Y 281 " (cutoff:3.500A) removed outlier: 8.510A pdb=" N PHE Y 283 " --> pdb=" O PHE Y 207 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N VAL Y 209 " --> pdb=" O PHE Y 283 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N ASP Y 285 " --> pdb=" O VAL Y 209 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N ALA Y 211 " --> pdb=" O ASP Y 285 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'Z' and resid 39 through 44 removed outlier: 6.573A pdb=" N ASP Z 49 " --> pdb=" O SER Z 41 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N VAL Z 43 " --> pdb=" O VAL Z 47 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N VAL Z 47 " --> pdb=" O VAL Z 43 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLN Z 78 " --> pdb=" O ARG Z 86 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N ILE Z 88 " --> pdb=" O VAL Z 76 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N VAL Z 76 " --> pdb=" O ILE Z 88 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU Z 64 " --> pdb=" O VAL Z 103 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'Z' and resid 110 through 113 removed outlier: 3.594A pdb=" N ASP Z 139 " --> pdb=" O VAL Z 113 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'Z' and resid 360 through 363 removed outlier: 8.192A pdb=" N ILE Z 179 " --> pdb=" O ILE Z 333 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N SER Z 335 " --> pdb=" O ILE Z 179 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N LEU Z 181 " --> pdb=" O SER Z 335 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N GLN Z 337 " --> pdb=" O LEU Z 181 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL Z 284 " --> pdb=" O VAL Z 336 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA Z 338 " --> pdb=" O VAL Z 284 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'Z' and resid 559 through 561 2395 hydrogen bonds defined for protein. 6453 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 17.79 Time building geometry restraints manager: 19.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 17172 1.34 - 1.46: 10554 1.46 - 1.58: 26685 1.58 - 1.70: 21 1.70 - 1.82: 254 Bond restraints: 54686 Sorted by residual: bond pdb=" C4 ATP V1001 " pdb=" C5 ATP V1001 " ideal model delta sigma weight residual 1.388 1.464 -0.076 1.00e-02 1.00e+04 5.79e+01 bond pdb=" C4 ATP T1001 " pdb=" C5 ATP T1001 " ideal model delta sigma weight residual 1.388 1.464 -0.076 1.00e-02 1.00e+04 5.75e+01 bond pdb=" C4 ATP U1001 " pdb=" C5 ATP U1001 " ideal model delta sigma weight residual 1.388 1.463 -0.075 1.00e-02 1.00e+04 5.61e+01 bond pdb=" C5 ATP U1001 " pdb=" C6 ATP U1001 " ideal model delta sigma weight residual 1.409 1.479 -0.070 1.00e-02 1.00e+04 4.88e+01 bond pdb=" C5 ATP V1001 " pdb=" C6 ATP V1001 " ideal model delta sigma weight residual 1.409 1.474 -0.065 1.00e-02 1.00e+04 4.24e+01 ... (remaining 54681 not shown) Histogram of bond angle deviations from ideal: 97.99 - 105.60: 1118 105.60 - 113.21: 30499 113.21 - 120.81: 26702 120.81 - 128.42: 15561 128.42 - 136.03: 281 Bond angle restraints: 74161 Sorted by residual: angle pdb=" PB ATP T1001 " pdb=" O3B ATP T1001 " pdb=" PG ATP T1001 " ideal model delta sigma weight residual 139.87 116.69 23.18 1.00e+00 1.00e+00 5.38e+02 angle pdb=" PB ATP U1001 " pdb=" O3B ATP U1001 " pdb=" PG ATP U1001 " ideal model delta sigma weight residual 139.87 117.28 22.59 1.00e+00 1.00e+00 5.10e+02 angle pdb=" PB ATP V1001 " pdb=" O3B ATP V1001 " pdb=" PG ATP V1001 " ideal model delta sigma weight residual 139.87 119.00 20.87 1.00e+00 1.00e+00 4.36e+02 angle pdb=" PA ATP V1001 " pdb=" O3A ATP V1001 " pdb=" PB ATP V1001 " ideal model delta sigma weight residual 136.83 117.89 18.94 1.00e+00 1.00e+00 3.59e+02 angle pdb=" PA ATP T1001 " pdb=" O3A ATP T1001 " pdb=" PB ATP T1001 " ideal model delta sigma weight residual 136.83 119.79 17.04 1.00e+00 1.00e+00 2.90e+02 ... (remaining 74156 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.60: 31447 26.60 - 53.19: 1408 53.19 - 79.79: 134 79.79 - 106.39: 33 106.39 - 132.99: 3 Dihedral angle restraints: 33025 sinusoidal: 12667 harmonic: 20358 Sorted by residual: dihedral pdb=" CA ALA X 307 " pdb=" C ALA X 307 " pdb=" N VAL X 308 " pdb=" CA VAL X 308 " ideal model delta harmonic sigma weight residual -180.00 -120.84 -59.16 0 5.00e+00 4.00e-02 1.40e+02 dihedral pdb=" CA ALA Y 307 " pdb=" C ALA Y 307 " pdb=" N VAL Y 308 " pdb=" CA VAL Y 308 " ideal model delta harmonic sigma weight residual -180.00 -123.55 -56.45 0 5.00e+00 4.00e-02 1.27e+02 dihedral pdb=" CA ALA Z 307 " pdb=" C ALA Z 307 " pdb=" N VAL Z 308 " pdb=" CA VAL Z 308 " ideal model delta harmonic sigma weight residual -180.00 -123.79 -56.21 0 5.00e+00 4.00e-02 1.26e+02 ... (remaining 33022 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 6944 0.066 - 0.132: 1532 0.132 - 0.198: 193 0.198 - 0.264: 15 0.264 - 0.329: 5 Chirality restraints: 8689 Sorted by residual: chirality pdb=" CB VAL 2 41 " pdb=" CA VAL 2 41 " pdb=" CG1 VAL 2 41 " pdb=" CG2 VAL 2 41 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.33 2.00e-01 2.50e+01 2.71e+00 chirality pdb=" CB VAL 2 357 " pdb=" CA VAL 2 357 " pdb=" CG1 VAL 2 357 " pdb=" CG2 VAL 2 357 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.11e+00 chirality pdb=" CB VAL U 137 " pdb=" CA VAL U 137 " pdb=" CG1 VAL U 137 " pdb=" CG2 VAL U 137 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.88e+00 ... (remaining 8686 not shown) Planarity restraints: 9510 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA Z 503 " 0.030 2.00e-02 2.50e+03 5.88e-02 3.46e+01 pdb=" C ALA Z 503 " -0.102 2.00e-02 2.50e+03 pdb=" O ALA Z 503 " 0.038 2.00e-02 2.50e+03 pdb=" N LYS Z 504 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA 3 210 " 0.056 5.00e-02 4.00e+02 8.34e-02 1.11e+01 pdb=" N PRO 3 211 " -0.144 5.00e-02 4.00e+02 pdb=" CA PRO 3 211 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO 3 211 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY 1 611 " -0.051 5.00e-02 4.00e+02 7.77e-02 9.67e+00 pdb=" N PRO 1 612 " 0.134 5.00e-02 4.00e+02 pdb=" CA PRO 1 612 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO 1 612 " -0.042 5.00e-02 4.00e+02 ... (remaining 9507 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 392 2.51 - 3.10: 37606 3.10 - 3.70: 86498 3.70 - 4.30: 121136 4.30 - 4.90: 198097 Nonbonded interactions: 443729 Sorted by model distance: nonbonded pdb=" CZ PHE I 107 " pdb=" OE2 GLU I 111 " model vdw 1.908 3.340 nonbonded pdb=" OG1 THR X 190 " pdb="MG MG X 602 " model vdw 2.068 2.170 nonbonded pdb=" O2B ADP X 601 " pdb="MG MG X 602 " model vdw 2.117 2.170 nonbonded pdb=" O GLN P 187 " pdb=" O GLU P 188 " model vdw 2.143 3.040 nonbonded pdb=" OG1 THR U 232 " pdb="MG MG U1002 " model vdw 2.174 2.170 ... (remaining 443724 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = (chain 'T' and (resid 43 through 562 or resid 1001 through 1002)) selection = (chain 'U' and (resid 43 through 561 or (resid 562 and (name N or name CA or nam \ e C or name O or name CB )) or resid 1001 through 1002)) selection = (chain 'V' and (resid 43 through 561 or (resid 562 and (name N or name CA or nam \ e C or name O or name CB )) or resid 1001 through 1002)) } ncs_group { reference = (chain 'X' and resid 37 through 556) selection = (chain 'Y' and resid 37 through 556) selection = (chain 'Z' and resid 37 through 556) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 5.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 24.480 Check model and map are aligned: 0.650 Set scattering table: 0.390 Process input model: 121.480 Find NCS groups from input model: 2.760 Set up NCS constraints: 0.350 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:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 158.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.109 54686 Z= 0.426 Angle : 0.937 23.184 74161 Z= 0.542 Chirality : 0.055 0.329 8689 Planarity : 0.007 0.083 9510 Dihedral : 15.030 132.986 19939 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.19 % Favored : 94.63 % Rotamer: Outliers : 0.44 % Allowed : 9.70 % Favored : 89.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.09 % 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: -4.22 (0.08), residues: 7038 helix: -2.96 (0.06), residues: 3782 sheet: -2.07 (0.19), residues: 621 loop : -2.41 (0.10), residues: 2635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP Z 141 HIS 0.010 0.002 HIS U 549 PHE 0.039 0.002 PHE X 355 TYR 0.031 0.002 TYR 4 211 ARG 0.007 0.001 ARG U 217 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1277 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 1252 time to evaluate : 4.924 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: 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: 0 71 MET cc_start: 0.8890 (mtp) cc_final: 0.8352 (mtp) REVERT: 1 269 LEU cc_start: 0.9393 (mt) cc_final: 0.9190 (mt) REVERT: 1 273 GLU cc_start: 0.8270 (mp0) cc_final: 0.7903 (mp0) REVERT: 1 566 ASP cc_start: 0.7930 (p0) cc_final: 0.7417 (p0) REVERT: 1 586 GLU cc_start: 0.8744 (mm-30) cc_final: 0.8401 (mm-30) REVERT: 2 378 LEU cc_start: 0.8239 (mt) cc_final: 0.7872 (tt) REVERT: 2 394 LYS cc_start: 0.8080 (mmmm) cc_final: 0.7672 (mttt) REVERT: 3 108 TYR cc_start: 0.7822 (t80) cc_final: 0.6976 (t80) REVERT: 3 159 THR cc_start: 0.8257 (m) cc_final: 0.8054 (t) REVERT: 5 79 ASN cc_start: 0.9073 (m-40) cc_final: 0.8863 (t0) REVERT: 5 90 GLU cc_start: 0.8000 (tm-30) cc_final: 0.7702 (tm-30) REVERT: 5 107 ASN cc_start: 0.7958 (t0) cc_final: 0.7694 (t0) REVERT: 6 54 ILE cc_start: 0.9385 (mt) cc_final: 0.9133 (mt) REVERT: 7 20 PHE cc_start: 0.8939 (m-80) cc_final: 0.8616 (m-10) REVERT: 8 8 LEU cc_start: 0.9529 (mt) cc_final: 0.9291 (mt) REVERT: 8 66 ASP cc_start: 0.7107 (t70) cc_final: 0.6881 (t70) REVERT: 9 1 MET cc_start: 0.2282 (ptt) cc_final: 0.1286 (mmt) REVERT: 9 73 TRP cc_start: 0.7476 (m100) cc_final: 0.7228 (m100) REVERT: M 230 THR cc_start: 0.8980 (t) cc_final: 0.8759 (m) REVERT: M 232 ARG cc_start: 0.8351 (ptp-170) cc_final: 0.7954 (ptp-170) REVERT: M 301 ILE cc_start: 0.9541 (mm) cc_final: 0.9125 (mt) REVERT: M 306 TYR cc_start: 0.9181 (m-10) cc_final: 0.8786 (m-80) REVERT: P 58 TRP cc_start: 0.8731 (t60) cc_final: 0.8176 (t60) REVERT: P 122 PHE cc_start: 0.8843 (m-10) cc_final: 0.8533 (m-80) REVERT: P 142 GLU cc_start: 0.8569 (pp20) cc_final: 0.8368 (pp20) REVERT: R 133 PHE cc_start: 0.7282 (m-80) cc_final: 0.6908 (m-10) REVERT: R 144 ILE cc_start: 0.6900 (mm) cc_final: 0.6593 (mt) REVERT: S 315 MET cc_start: 0.6888 (ppp) cc_final: 0.6432 (ptt) REVERT: T 98 TYR cc_start: 0.7473 (t80) cc_final: 0.7083 (t80) REVERT: T 171 ILE cc_start: 0.7944 (pt) cc_final: 0.7641 (tt) REVERT: U 456 VAL cc_start: 0.8633 (m) cc_final: 0.8407 (p) REVERT: V 48 LEU cc_start: 0.8483 (mp) cc_final: 0.8014 (mp) REVERT: V 64 GLN cc_start: 0.7911 (mt0) cc_final: 0.7708 (tp40) REVERT: V 120 LEU cc_start: 0.9218 (mt) cc_final: 0.9016 (tp) REVERT: V 326 ASP cc_start: 0.6983 (t0) cc_final: 0.5480 (t0) REVERT: V 418 ARG cc_start: 0.6444 (mtt180) cc_final: 0.5775 (mtt180) REVERT: V 481 THR cc_start: 0.8156 (p) cc_final: 0.7870 (m) REVERT: X 187 VAL cc_start: 0.8564 (m) cc_final: 0.8313 (t) REVERT: X 264 THR cc_start: 0.8639 (m) cc_final: 0.8332 (m) REVERT: X 325 ILE cc_start: 0.8167 (OUTLIER) cc_final: 0.7839 (mt) REVERT: Y 102 VAL cc_start: 0.9024 (t) cc_final: 0.8787 (p) REVERT: Y 181 LEU cc_start: 0.8775 (mt) cc_final: 0.8211 (pp) REVERT: Y 233 ILE cc_start: 0.7404 (mt) cc_final: 0.7012 (mt) REVERT: Y 286 ASN cc_start: 0.5968 (m-40) cc_final: 0.5361 (m-40) REVERT: Y 386 MET cc_start: 0.7643 (mmm) cc_final: 0.6910 (tpp) REVERT: Z 422 MET cc_start: 0.4370 (tmm) cc_final: 0.3542 (ttm) REVERT: Z 484 MET cc_start: 0.7252 (mmm) cc_final: 0.6966 (tmm) outliers start: 25 outliers final: 12 residues processed: 1273 average time/residue: 0.5372 time to fit residues: 1131.5179 Evaluate side-chains 671 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 658 time to evaluate : 4.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 589 optimal weight: 20.0000 chunk 529 optimal weight: 8.9990 chunk 293 optimal weight: 4.9990 chunk 180 optimal weight: 6.9990 chunk 356 optimal weight: 4.9990 chunk 282 optimal weight: 1.9990 chunk 547 optimal weight: 4.9990 chunk 211 optimal weight: 0.9980 chunk 332 optimal weight: 0.5980 chunk 407 optimal weight: 0.9990 chunk 633 optimal weight: 10.0000 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 48 ASN 1 65 GLN 1 100 GLN ** 1 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 285 GLN 1 298 GLN 1 316 ASN ** 1 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 587 ASN 1 606 ASN 2 122 ASN 2 243 GLN 2 289 HIS 2 380 GLN 3 179 GLN 3 188 ASN ** 3 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 229 ASN 4 38 GLN 4 240 GLN 5 38 HIS ** 5 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 117 GLN 6 74 GLN ** 6 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 90 GLN 7 123 HIS ** 7 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 26 HIS 9 60 ASN A 94 ASN ** C 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 GLN F 94 ASN I 94 ASN M 108 ASN M 163 ASN P 65 ASN P 140 ASN P 220 ASN P 223 ASN Q 21 ASN Q 40 GLN Q 46 HIS R 38 ASN R 53 ASN R 83 GLN ** R 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 96 ASN S 174 GLN ** S 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 262 ASN T 64 GLN ** T 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 386 GLN T 435 GLN T 441 GLN ** T 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 61 HIS U 123 GLN U 140 GLN U 179 ASN U 242 GLN U 246 ASN U 248 GLN U 319 HIS U 358 HIS U 397 ASN U 497 GLN ** U 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 64 GLN V 104 GLN V 139 HIS ** V 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 486 GLN ** V 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 497 GLN V 515 GLN ** V 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 68 HIS X 174 GLN X 221 ASN X 278 GLN ** X 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 388 ASN X 390 ASN ** X 445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 68 HIS Y 79 HIS Y 83 ASN Y 144 HIS ** Y 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 278 GLN Z 199 ASN Z 250 GLN Z 278 GLN Z 294 ASN Total number of N/Q/H flips: 79 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 54686 Z= 0.213 Angle : 0.618 12.511 74161 Z= 0.320 Chirality : 0.042 0.222 8689 Planarity : 0.005 0.057 9510 Dihedral : 6.529 106.992 7670 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.36 % Favored : 95.48 % Rotamer: Outliers : 0.05 % Allowed : 4.56 % Favored : 95.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.34 % Twisted General : 0.10 % 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: -2.47 (0.09), residues: 7038 helix: -1.32 (0.08), residues: 3798 sheet: -1.56 (0.21), residues: 583 loop : -1.94 (0.11), residues: 2657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP X 141 HIS 0.009 0.001 HIS S 185 PHE 0.027 0.002 PHE H 82 TYR 0.025 0.002 TYR 4 211 ARG 0.007 0.000 ARG V 513 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 895 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 892 time to evaluate : 4.969 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: 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: 0 19 SER cc_start: 0.8837 (p) cc_final: 0.8536 (p) REVERT: 0 68 VAL cc_start: 0.8916 (t) cc_final: 0.8576 (t) REVERT: 0 71 MET cc_start: 0.8850 (mtp) cc_final: 0.8280 (mtp) REVERT: 1 586 GLU cc_start: 0.8796 (mm-30) cc_final: 0.8560 (mm-30) REVERT: 1 609 ARG cc_start: 0.7780 (mtp85) cc_final: 0.7543 (mtm-85) REVERT: 2 394 LYS cc_start: 0.8131 (mmmm) cc_final: 0.7680 (mttt) REVERT: 3 108 TYR cc_start: 0.7742 (t80) cc_final: 0.6968 (t80) REVERT: 5 107 ASN cc_start: 0.7706 (t0) cc_final: 0.7398 (t0) REVERT: 7 113 MET cc_start: 0.7680 (mtt) cc_final: 0.7391 (mtp) REVERT: 8 46 TYR cc_start: 0.8282 (m-80) cc_final: 0.7928 (m-80) REVERT: 8 66 ASP cc_start: 0.7059 (t70) cc_final: 0.6827 (t70) REVERT: 9 1 MET cc_start: 0.2187 (ptt) cc_final: 0.1717 (mmt) REVERT: 9 82 ASP cc_start: 0.5685 (p0) cc_final: 0.5397 (p0) REVERT: 9 89 MET cc_start: 0.8082 (mtp) cc_final: 0.7826 (mtp) REVERT: 9 93 TRP cc_start: 0.8216 (t60) cc_final: 0.7870 (t60) REVERT: B 110 THR cc_start: 0.8832 (m) cc_final: 0.8536 (t) REVERT: D 91 ARG cc_start: 0.7531 (ttm170) cc_final: 0.7074 (ttm170) REVERT: G 71 LEU cc_start: 0.7285 (tp) cc_final: 0.7081 (tt) REVERT: M 301 ILE cc_start: 0.9499 (mm) cc_final: 0.9180 (mt) REVERT: M 306 TYR cc_start: 0.9150 (m-10) cc_final: 0.8809 (m-80) REVERT: P 53 ILE cc_start: 0.9119 (mp) cc_final: 0.8741 (tt) REVERT: P 58 TRP cc_start: 0.8873 (t60) cc_final: 0.8253 (t60) REVERT: P 89 ARG cc_start: 0.7937 (ttt180) cc_final: 0.7561 (ttt-90) REVERT: P 122 PHE cc_start: 0.8831 (m-10) cc_final: 0.8571 (m-10) REVERT: R 75 TYR cc_start: 0.6230 (m-80) cc_final: 0.5773 (m-80) REVERT: R 133 PHE cc_start: 0.7298 (m-80) cc_final: 0.7079 (m-10) REVERT: R 144 ILE cc_start: 0.6855 (mm) cc_final: 0.6568 (mt) REVERT: S 315 MET cc_start: 0.7108 (ppp) cc_final: 0.6568 (ptt) REVERT: T 98 TYR cc_start: 0.7464 (t80) cc_final: 0.7170 (t80) REVERT: U 215 ILE cc_start: 0.8480 (mm) cc_final: 0.8260 (mm) REVERT: U 401 ILE cc_start: 0.8684 (mt) cc_final: 0.8450 (mt) REVERT: U 403 ASP cc_start: 0.7324 (m-30) cc_final: 0.7110 (m-30) REVERT: V 418 ARG cc_start: 0.6367 (mtt180) cc_final: 0.5727 (mtt180) REVERT: V 481 THR cc_start: 0.8303 (p) cc_final: 0.7921 (m) REVERT: X 187 VAL cc_start: 0.8514 (m) cc_final: 0.8295 (t) REVERT: X 368 ILE cc_start: 0.7927 (tt) cc_final: 0.7408 (tt) REVERT: Y 181 LEU cc_start: 0.8807 (mt) cc_final: 0.8206 (pp) REVERT: Y 386 MET cc_start: 0.7740 (mmm) cc_final: 0.6958 (tpp) REVERT: Z 80 MET cc_start: 0.7484 (mmm) cc_final: 0.6847 (mmm) REVERT: Z 125 ILE cc_start: 0.8422 (pt) cc_final: 0.8169 (pt) REVERT: Z 251 MET cc_start: 0.7709 (mtp) cc_final: 0.7358 (mtp) REVERT: Z 422 MET cc_start: 0.5072 (tmm) cc_final: 0.4104 (ttm) REVERT: Z 484 MET cc_start: 0.7408 (mmm) cc_final: 0.6972 (tmm) outliers start: 3 outliers final: 1 residues processed: 895 average time/residue: 0.5314 time to fit residues: 814.4793 Evaluate side-chains 579 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 578 time to evaluate : 4.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 352 optimal weight: 9.9990 chunk 196 optimal weight: 3.9990 chunk 527 optimal weight: 10.0000 chunk 431 optimal weight: 0.8980 chunk 174 optimal weight: 7.9990 chunk 635 optimal weight: 7.9990 chunk 685 optimal weight: 10.0000 chunk 565 optimal weight: 5.9990 chunk 629 optimal weight: 5.9990 chunk 216 optimal weight: 0.9990 chunk 509 optimal weight: 4.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 40 ASN 6 104 ASN ** 6 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 178 GLN ** S 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 263 ASN S 297 GLN T 126 HIS T 228 GLN T 253 GLN T 264 GLN U 61 HIS U 139 HIS U 169 GLN U 397 ASN ** U 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 539 ASN X 153 GLN ** X 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 471 GLN Z 132 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.2875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 54686 Z= 0.286 Angle : 0.658 13.350 74161 Z= 0.336 Chirality : 0.044 0.183 8689 Planarity : 0.005 0.067 9510 Dihedral : 6.352 104.425 7670 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 14.31 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.07 % Favored : 94.76 % Rotamer: Outliers : 0.05 % Allowed : 5.52 % Favored : 94.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.72 (0.10), residues: 7038 helix: -0.67 (0.08), residues: 3797 sheet: -1.13 (0.21), residues: 585 loop : -1.68 (0.12), residues: 2656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP Y 141 HIS 0.007 0.001 HIS Y 79 PHE 0.031 0.002 PHE R 98 TYR 0.027 0.002 TYR P 141 ARG 0.007 0.001 ARG X 441 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 797 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 794 time to evaluate : 4.942 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 19 SER cc_start: 0.8795 (p) cc_final: 0.8548 (p) REVERT: 0 36 THR cc_start: 0.7605 (t) cc_final: 0.7393 (t) REVERT: 0 68 VAL cc_start: 0.8959 (t) cc_final: 0.8611 (t) REVERT: 0 71 MET cc_start: 0.8904 (mtp) cc_final: 0.8312 (mtp) REVERT: 1 586 GLU cc_start: 0.8869 (mm-30) cc_final: 0.8644 (mm-30) REVERT: 1 609 ARG cc_start: 0.7797 (mtp85) cc_final: 0.7585 (mtm-85) REVERT: 2 394 LYS cc_start: 0.8145 (mmmm) cc_final: 0.7673 (mttt) REVERT: 3 108 TYR cc_start: 0.7804 (t80) cc_final: 0.6911 (t80) REVERT: 3 177 LEU cc_start: 0.9478 (mt) cc_final: 0.9174 (mt) REVERT: 4 279 ASP cc_start: 0.8527 (m-30) cc_final: 0.8131 (t0) REVERT: 5 1 MET cc_start: 0.6808 (ptt) cc_final: 0.6434 (ptt) REVERT: 5 43 CYS cc_start: 0.8593 (m) cc_final: 0.8182 (t) REVERT: 5 107 ASN cc_start: 0.7752 (t0) cc_final: 0.7357 (t0) REVERT: 6 41 GLU cc_start: 0.8324 (pp20) cc_final: 0.8109 (pp20) REVERT: 8 10 ASP cc_start: 0.8092 (m-30) cc_final: 0.7303 (t0) REVERT: 9 1 MET cc_start: 0.2295 (ptt) cc_final: 0.1339 (mmt) REVERT: 9 80 GLN cc_start: 0.7851 (mm-40) cc_final: 0.7461 (mp10) REVERT: 9 89 MET cc_start: 0.8096 (mtp) cc_final: 0.7750 (mtm) REVERT: P 55 THR cc_start: 0.9389 (m) cc_final: 0.8991 (t) REVERT: P 89 ARG cc_start: 0.8080 (ttt180) cc_final: 0.7627 (ttt-90) REVERT: P 141 TYR cc_start: 0.8576 (t80) cc_final: 0.8291 (t80) REVERT: P 145 MET cc_start: 0.8611 (mmp) cc_final: 0.8144 (mmm) REVERT: R 75 TYR cc_start: 0.6429 (m-80) cc_final: 0.6021 (m-80) REVERT: R 133 PHE cc_start: 0.7500 (m-80) cc_final: 0.7120 (m-80) REVERT: S 315 MET cc_start: 0.6555 (ppp) cc_final: 0.6350 (ptt) REVERT: T 98 TYR cc_start: 0.7563 (t80) cc_final: 0.7187 (t80) REVERT: T 312 TYR cc_start: 0.6899 (t80) cc_final: 0.6595 (t80) REVERT: U 455 GLU cc_start: 0.7690 (pt0) cc_final: 0.6363 (tp30) REVERT: X 187 VAL cc_start: 0.8584 (m) cc_final: 0.8310 (t) REVERT: X 437 ARG cc_start: 0.7097 (mtt-85) cc_final: 0.6581 (tpt170) REVERT: Y 196 LEU cc_start: 0.8670 (mt) cc_final: 0.8425 (mm) REVERT: Y 286 ASN cc_start: 0.6500 (m-40) cc_final: 0.6161 (m-40) REVERT: Y 386 MET cc_start: 0.7854 (mmm) cc_final: 0.6910 (tpp) REVERT: Z 80 MET cc_start: 0.7650 (mmm) cc_final: 0.6962 (ttp) REVERT: Z 422 MET cc_start: 0.5106 (tmm) cc_final: 0.4074 (ttm) REVERT: Z 484 MET cc_start: 0.7128 (mmm) cc_final: 0.6696 (tmm) outliers start: 3 outliers final: 2 residues processed: 797 average time/residue: 0.4954 time to fit residues: 678.6030 Evaluate side-chains 529 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 527 time to evaluate : 4.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 627 optimal weight: 8.9990 chunk 477 optimal weight: 7.9990 chunk 329 optimal weight: 0.6980 chunk 70 optimal weight: 9.9990 chunk 303 optimal weight: 0.0270 chunk 426 optimal weight: 4.9990 chunk 637 optimal weight: 10.0000 chunk 674 optimal weight: 6.9990 chunk 332 optimal weight: 0.0010 chunk 603 optimal weight: 0.3980 chunk 181 optimal weight: 0.9990 overall best weight: 0.4246 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 68 HIS 5 9 GLN ** 5 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 98 GLN ** M 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 181 ASN ** S 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 186 ASN S 297 GLN ** T 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 196 GLN U 397 ASN ** U 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 539 ASN ** X 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 157 GLN ** Z 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.3156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 54686 Z= 0.151 Angle : 0.559 10.748 74161 Z= 0.283 Chirality : 0.041 0.228 8689 Planarity : 0.004 0.047 9510 Dihedral : 5.816 91.338 7670 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.01 % Favored : 95.87 % Rotamer: Outliers : 0.02 % Allowed : 3.05 % Favored : 96.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.20 (0.10), residues: 7038 helix: -0.21 (0.09), residues: 3777 sheet: -0.98 (0.22), residues: 572 loop : -1.47 (0.12), residues: 2689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP 9 93 HIS 0.006 0.001 HIS Y 204 PHE 0.036 0.001 PHE Y 355 TYR 0.023 0.001 TYR 4 211 ARG 0.009 0.000 ARG T 364 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 853 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 852 time to evaluate : 4.798 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 19 SER cc_start: 0.8724 (p) cc_final: 0.8476 (p) REVERT: 0 36 THR cc_start: 0.7549 (t) cc_final: 0.7335 (t) REVERT: 0 71 MET cc_start: 0.8836 (mtp) cc_final: 0.8305 (mtp) REVERT: 1 586 GLU cc_start: 0.8638 (mm-30) cc_final: 0.8237 (mm-30) REVERT: 2 118 TYR cc_start: 0.7253 (m-80) cc_final: 0.6983 (m-80) REVERT: 2 394 LYS cc_start: 0.8118 (mmmm) cc_final: 0.7605 (mttt) REVERT: 3 108 TYR cc_start: 0.7676 (t80) cc_final: 0.6866 (t80) REVERT: 3 279 GLU cc_start: 0.7320 (pt0) cc_final: 0.7051 (pt0) REVERT: 3 299 GLU cc_start: 0.7112 (pt0) cc_final: 0.6875 (pt0) REVERT: 4 279 ASP cc_start: 0.8606 (m-30) cc_final: 0.8365 (t70) REVERT: 5 1 MET cc_start: 0.6570 (ptt) cc_final: 0.6119 (ptt) REVERT: 5 107 ASN cc_start: 0.7670 (t0) cc_final: 0.7393 (t0) REVERT: 7 20 PHE cc_start: 0.9039 (m-80) cc_final: 0.8595 (m-10) REVERT: 7 113 MET cc_start: 0.7324 (mtp) cc_final: 0.7013 (mtt) REVERT: 8 46 TYR cc_start: 0.8204 (m-80) cc_final: 0.7828 (m-80) REVERT: 9 1 MET cc_start: 0.1545 (ptt) cc_final: 0.1298 (mmt) REVERT: 9 89 MET cc_start: 0.8122 (mtp) cc_final: 0.7897 (mtp) REVERT: A 61 MET cc_start: 0.6865 (mmm) cc_final: 0.6385 (tmm) REVERT: J 82 PHE cc_start: 0.7185 (m-80) cc_final: 0.6828 (m-10) REVERT: M 281 LEU cc_start: 0.8804 (mt) cc_final: 0.8345 (mt) REVERT: P 89 ARG cc_start: 0.8012 (ttt180) cc_final: 0.7542 (ttt-90) REVERT: P 141 TYR cc_start: 0.8458 (t80) cc_final: 0.8109 (t80) REVERT: P 145 MET cc_start: 0.8584 (mmp) cc_final: 0.8141 (mmt) REVERT: R 75 TYR cc_start: 0.6286 (m-80) cc_final: 0.5928 (m-80) REVERT: R 133 PHE cc_start: 0.7694 (m-80) cc_final: 0.7224 (m-10) REVERT: S 92 PHE cc_start: 0.6287 (m-10) cc_final: 0.5950 (m-10) REVERT: S 315 MET cc_start: 0.6432 (ppp) cc_final: 0.6188 (ptt) REVERT: T 98 TYR cc_start: 0.7490 (t80) cc_final: 0.7171 (t80) REVERT: T 452 GLN cc_start: 0.8179 (mm-40) cc_final: 0.7701 (mm-40) REVERT: U 112 ASP cc_start: 0.8430 (p0) cc_final: 0.8072 (p0) REVERT: V 73 TRP cc_start: 0.8018 (m-10) cc_final: 0.7628 (m-10) REVERT: X 187 VAL cc_start: 0.8416 (m) cc_final: 0.8096 (t) REVERT: X 374 TYR cc_start: 0.8593 (m-80) cc_final: 0.7092 (m-80) REVERT: Y 181 LEU cc_start: 0.8738 (mt) cc_final: 0.8531 (mt) REVERT: Y 286 ASN cc_start: 0.5923 (m-40) cc_final: 0.5565 (m-40) REVERT: Y 386 MET cc_start: 0.7886 (mmm) cc_final: 0.6816 (tpp) REVERT: Y 405 LYS cc_start: 0.8082 (mtmm) cc_final: 0.7576 (tptt) REVERT: Y 502 MET cc_start: 0.7824 (tpt) cc_final: 0.7155 (ptt) REVERT: Z 80 MET cc_start: 0.7410 (mmm) cc_final: 0.6803 (ttp) REVERT: Z 157 GLN cc_start: 0.8113 (OUTLIER) cc_final: 0.7787 (pp30) REVERT: Z 422 MET cc_start: 0.5080 (tmm) cc_final: 0.3988 (ttm) REVERT: Z 484 MET cc_start: 0.7094 (mmm) cc_final: 0.6626 (tpp) outliers start: 1 outliers final: 0 residues processed: 853 average time/residue: 0.4893 time to fit residues: 720.5020 Evaluate side-chains 573 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 572 time to evaluate : 4.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 561 optimal weight: 5.9990 chunk 382 optimal weight: 0.7980 chunk 9 optimal weight: 6.9990 chunk 502 optimal weight: 4.9990 chunk 278 optimal weight: 10.0000 chunk 575 optimal weight: 9.9990 chunk 466 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 344 optimal weight: 4.9990 chunk 605 optimal weight: 3.9990 chunk 170 optimal weight: 4.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 74 GLN ** 6 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 90 GLN ** 7 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 121 ASN ** M 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 140 ASN R 181 ASN ** S 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 297 GLN ** T 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 196 GLN ** U 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 549 HIS ** V 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 539 ASN ** X 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 412 ASN ** Z 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.3459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 54686 Z= 0.278 Angle : 0.632 12.755 74161 Z= 0.318 Chirality : 0.043 0.172 8689 Planarity : 0.004 0.094 9510 Dihedral : 5.871 89.113 7670 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 14.60 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.13 % Favored : 94.69 % Rotamer: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.06 (0.10), residues: 7038 helix: -0.11 (0.09), residues: 3800 sheet: -0.93 (0.22), residues: 578 loop : -1.39 (0.12), residues: 2660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP Z 141 HIS 0.007 0.001 HIS 1 590 PHE 0.042 0.002 PHE X 355 TYR 0.023 0.002 TYR 7 101 ARG 0.008 0.001 ARG X 86 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 756 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 756 time to evaluate : 4.859 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: 0 19 SER cc_start: 0.8769 (p) cc_final: 0.8530 (p) REVERT: 1 566 ASP cc_start: 0.7699 (p0) cc_final: 0.7496 (p0) REVERT: 2 118 TYR cc_start: 0.7407 (m-80) cc_final: 0.7099 (m-80) REVERT: 2 394 LYS cc_start: 0.8254 (mmmm) cc_final: 0.7771 (mttt) REVERT: 2 396 LEU cc_start: 0.8261 (mt) cc_final: 0.7943 (mp) REVERT: 3 108 TYR cc_start: 0.7740 (t80) cc_final: 0.6868 (t80) REVERT: 3 143 LEU cc_start: 0.8775 (mt) cc_final: 0.8319 (tt) REVERT: 3 177 LEU cc_start: 0.9473 (mt) cc_final: 0.9147 (mt) REVERT: 3 205 CYS cc_start: 0.8822 (m) cc_final: 0.8538 (m) REVERT: 5 1 MET cc_start: 0.6634 (ptt) cc_final: 0.6220 (ptt) REVERT: 5 107 ASN cc_start: 0.7724 (t0) cc_final: 0.7345 (t0) REVERT: 6 41 GLU cc_start: 0.8542 (pp20) cc_final: 0.8071 (pp20) REVERT: 7 140 LEU cc_start: 0.9014 (mt) cc_final: 0.8811 (mt) REVERT: 8 10 ASP cc_start: 0.8083 (m-30) cc_final: 0.7334 (t0) REVERT: 8 46 TYR cc_start: 0.8319 (m-80) cc_final: 0.7934 (m-80) REVERT: 9 1 MET cc_start: 0.2179 (ptt) cc_final: 0.1281 (mmt) REVERT: 9 80 GLN cc_start: 0.8071 (mm-40) cc_final: 0.7532 (mp10) REVERT: D 69 ILE cc_start: 0.7740 (mm) cc_final: 0.7222 (mt) REVERT: M 281 LEU cc_start: 0.8831 (mt) cc_final: 0.8374 (mt) REVERT: P 77 PHE cc_start: 0.7982 (m-80) cc_final: 0.7242 (m-80) REVERT: P 141 TYR cc_start: 0.8517 (t80) cc_final: 0.8157 (t80) REVERT: P 145 MET cc_start: 0.8604 (mmp) cc_final: 0.8146 (mmt) REVERT: R 75 TYR cc_start: 0.6620 (m-80) cc_final: 0.6179 (m-80) REVERT: R 133 PHE cc_start: 0.7757 (m-80) cc_final: 0.7349 (m-10) REVERT: T 98 TYR cc_start: 0.7622 (t80) cc_final: 0.7269 (t80) REVERT: T 312 TYR cc_start: 0.6753 (t80) cc_final: 0.6421 (t80) REVERT: U 57 TYR cc_start: 0.6498 (p90) cc_final: 0.6222 (p90) REVERT: U 112 ASP cc_start: 0.8588 (p0) cc_final: 0.8152 (p0) REVERT: V 73 TRP cc_start: 0.8104 (m-10) cc_final: 0.7728 (m-10) REVERT: V 401 ILE cc_start: 0.8280 (tp) cc_final: 0.8075 (tp) REVERT: V 439 MET cc_start: 0.6868 (mmt) cc_final: 0.6625 (mmm) REVERT: X 187 VAL cc_start: 0.8512 (m) cc_final: 0.8174 (t) REVERT: X 335 SER cc_start: 0.8790 (t) cc_final: 0.8140 (p) REVERT: Y 286 ASN cc_start: 0.5966 (m-40) cc_final: 0.5728 (m-40) REVERT: Y 386 MET cc_start: 0.7962 (mmm) cc_final: 0.7341 (tpp) REVERT: Y 502 MET cc_start: 0.7870 (tpt) cc_final: 0.7196 (ptt) REVERT: Z 80 MET cc_start: 0.7607 (mmm) cc_final: 0.6953 (ttp) REVERT: Z 386 MET cc_start: 0.6338 (mtt) cc_final: 0.6018 (mtt) REVERT: Z 422 MET cc_start: 0.5106 (tmm) cc_final: 0.4056 (ttm) REVERT: Z 484 MET cc_start: 0.7136 (mmm) cc_final: 0.6645 (tpp) outliers start: 0 outliers final: 0 residues processed: 756 average time/residue: 0.4802 time to fit residues: 634.2115 Evaluate side-chains 520 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 520 time to evaluate : 4.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 226 optimal weight: 7.9990 chunk 607 optimal weight: 6.9990 chunk 133 optimal weight: 8.9990 chunk 396 optimal weight: 3.9990 chunk 166 optimal weight: 0.9980 chunk 675 optimal weight: 0.0570 chunk 560 optimal weight: 5.9990 chunk 312 optimal weight: 2.9990 chunk 56 optimal weight: 0.6980 chunk 223 optimal weight: 6.9990 chunk 354 optimal weight: 5.9990 overall best weight: 1.7502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 233 HIS 5 9 GLN ** 5 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 97 HIS ** 6 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 90 GLN 7 91 ASN ** 7 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 ASN E 94 ASN J 98 GLN ** M 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 140 ASN ** R 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 181 ASN ** S 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 139 HIS U 196 GLN U 397 ASN ** U 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 539 ASN ** X 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 414 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.3632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 54686 Z= 0.190 Angle : 0.578 11.888 74161 Z= 0.291 Chirality : 0.042 0.223 8689 Planarity : 0.004 0.048 9510 Dihedral : 5.631 85.581 7670 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.53 % Favored : 95.34 % Rotamer: Outliers : 0.02 % Allowed : 1.99 % Favored : 97.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.86 (0.10), residues: 7038 helix: 0.04 (0.09), residues: 3801 sheet: -0.81 (0.22), residues: 587 loop : -1.28 (0.12), residues: 2650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP Y 141 HIS 0.007 0.001 HIS Y 204 PHE 0.045 0.001 PHE E 116 TYR 0.019 0.001 TYR S 122 ARG 0.007 0.000 ARG X 441 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 768 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 767 time to evaluate : 4.883 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: symmetry clash revert: symmetry clash REVERT: 0 19 SER cc_start: 0.8732 (p) cc_final: 0.8488 (p) REVERT: 0 36 THR cc_start: 0.7387 (t) cc_final: 0.7152 (t) REVERT: 1 298 GLN cc_start: 0.8095 (tp40) cc_final: 0.7737 (tp-100) REVERT: 1 566 ASP cc_start: 0.7611 (p0) cc_final: 0.7341 (p0) REVERT: 2 47 LEU cc_start: 0.8506 (tp) cc_final: 0.8296 (tp) REVERT: 2 118 TYR cc_start: 0.7270 (m-80) cc_final: 0.6981 (m-80) REVERT: 2 394 LYS cc_start: 0.8226 (mmmm) cc_final: 0.7774 (mttt) REVERT: 2 396 LEU cc_start: 0.8192 (mt) cc_final: 0.7848 (mp) REVERT: 3 108 TYR cc_start: 0.7735 (t80) cc_final: 0.6798 (t80) REVERT: 3 177 LEU cc_start: 0.9403 (mt) cc_final: 0.9095 (mt) REVERT: 4 231 ASP cc_start: 0.7919 (m-30) cc_final: 0.7601 (m-30) REVERT: 5 1 MET cc_start: 0.6623 (ptt) cc_final: 0.6239 (ptt) REVERT: 5 107 ASN cc_start: 0.7777 (t0) cc_final: 0.7458 (t0) REVERT: 6 41 GLU cc_start: 0.8523 (pp20) cc_final: 0.7929 (pp20) REVERT: 7 113 MET cc_start: 0.7371 (mtp) cc_final: 0.7065 (mtt) REVERT: 7 140 LEU cc_start: 0.8940 (mt) cc_final: 0.8723 (mt) REVERT: 8 10 ASP cc_start: 0.8048 (m-30) cc_final: 0.7257 (t0) REVERT: 8 46 TYR cc_start: 0.8257 (m-80) cc_final: 0.7926 (m-80) REVERT: 9 1 MET cc_start: 0.2116 (ptt) cc_final: 0.1497 (mmt) REVERT: 9 83 LYS cc_start: 0.8225 (tttt) cc_final: 0.7900 (tmtt) REVERT: 9 85 LYS cc_start: 0.7840 (ptmm) cc_final: 0.7576 (ptmm) REVERT: D 69 ILE cc_start: 0.7553 (mm) cc_final: 0.7021 (mt) REVERT: M 244 MET cc_start: 0.7982 (mmm) cc_final: 0.7673 (mmm) REVERT: M 281 LEU cc_start: 0.8818 (mt) cc_final: 0.8439 (mt) REVERT: P 141 TYR cc_start: 0.8484 (t80) cc_final: 0.8092 (t80) REVERT: P 145 MET cc_start: 0.8520 (mmp) cc_final: 0.8040 (mmt) REVERT: R 75 TYR cc_start: 0.6668 (m-80) cc_final: 0.6267 (m-80) REVERT: R 133 PHE cc_start: 0.7729 (m-80) cc_final: 0.7396 (m-10) REVERT: S 92 PHE cc_start: 0.6359 (m-10) cc_final: 0.6037 (m-10) REVERT: T 98 TYR cc_start: 0.7588 (t80) cc_final: 0.7241 (t80) REVERT: U 57 TYR cc_start: 0.6343 (p90) cc_final: 0.6112 (p90) REVERT: U 112 ASP cc_start: 0.8512 (p0) cc_final: 0.8088 (p0) REVERT: U 454 ARG cc_start: 0.8236 (ptp90) cc_final: 0.7903 (ptm160) REVERT: V 73 TRP cc_start: 0.8156 (m-10) cc_final: 0.7830 (m-10) REVERT: V 326 ASP cc_start: 0.7747 (t0) cc_final: 0.7434 (t0) REVERT: X 187 VAL cc_start: 0.8298 (m) cc_final: 0.8019 (t) REVERT: X 543 ASP cc_start: 0.3686 (m-30) cc_final: 0.3486 (m-30) REVERT: Y 286 ASN cc_start: 0.5838 (m-40) cc_final: 0.5597 (m-40) REVERT: Y 386 MET cc_start: 0.7979 (mmm) cc_final: 0.7360 (tpp) REVERT: Y 405 LYS cc_start: 0.8040 (mtmm) cc_final: 0.7568 (tptt) REVERT: Y 502 MET cc_start: 0.7925 (tpt) cc_final: 0.7224 (ptt) REVERT: Z 80 MET cc_start: 0.7543 (mmm) cc_final: 0.6892 (ttp) REVERT: Z 422 MET cc_start: 0.5152 (tmm) cc_final: 0.4019 (ttm) REVERT: Z 484 MET cc_start: 0.7106 (mmm) cc_final: 0.6624 (tpp) outliers start: 1 outliers final: 0 residues processed: 768 average time/residue: 0.4840 time to fit residues: 651.2642 Evaluate side-chains 531 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 531 time to evaluate : 4.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 651 optimal weight: 6.9990 chunk 76 optimal weight: 8.9990 chunk 384 optimal weight: 3.9990 chunk 493 optimal weight: 1.9990 chunk 382 optimal weight: 0.7980 chunk 568 optimal weight: 4.9990 chunk 377 optimal weight: 0.7980 chunk 672 optimal weight: 6.9990 chunk 421 optimal weight: 7.9990 chunk 410 optimal weight: 5.9990 chunk 310 optimal weight: 1.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 ASN J 98 GLN ** M 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 140 ASN ** R 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 181 ASN ** S 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 196 GLN ** U 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 539 ASN ** X 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 337 GLN Y 440 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.3782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 54686 Z= 0.203 Angle : 0.578 11.430 74161 Z= 0.290 Chirality : 0.042 0.221 8689 Planarity : 0.004 0.049 9510 Dihedral : 5.535 80.881 7670 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.10 % Favored : 94.79 % Rotamer: Outliers : 0.02 % Allowed : 1.70 % Favored : 98.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.72 (0.10), residues: 7038 helix: 0.13 (0.09), residues: 3816 sheet: -0.69 (0.22), residues: 574 loop : -1.18 (0.12), residues: 2648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP Z 141 HIS 0.008 0.001 HIS R 104 PHE 0.027 0.001 PHE D 82 TYR 0.021 0.001 TYR 2 180 ARG 0.008 0.000 ARG X 441 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 760 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 759 time to evaluate : 4.878 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: symmetry clash revert: symmetry clash REVERT: 0 19 SER cc_start: 0.8749 (p) cc_final: 0.8487 (p) REVERT: 0 81 HIS cc_start: 0.7279 (m90) cc_final: 0.5218 (p90) REVERT: 1 298 GLN cc_start: 0.8074 (tp40) cc_final: 0.7778 (tp-100) REVERT: 1 566 ASP cc_start: 0.7682 (p0) cc_final: 0.7354 (p0) REVERT: 1 574 MET cc_start: 0.7763 (mtp) cc_final: 0.7531 (mtm) REVERT: 2 394 LYS cc_start: 0.8205 (mmmm) cc_final: 0.7758 (mttt) REVERT: 2 396 LEU cc_start: 0.8168 (mt) cc_final: 0.7827 (mp) REVERT: 3 108 TYR cc_start: 0.7695 (t80) cc_final: 0.6788 (t80) REVERT: 3 177 LEU cc_start: 0.9430 (mt) cc_final: 0.9149 (mt) REVERT: 3 296 GLU cc_start: 0.7087 (mm-30) cc_final: 0.6817 (mm-30) REVERT: 4 231 ASP cc_start: 0.7927 (m-30) cc_final: 0.7515 (m-30) REVERT: 5 107 ASN cc_start: 0.7783 (t0) cc_final: 0.7512 (t0) REVERT: 6 41 GLU cc_start: 0.8510 (pp20) cc_final: 0.8289 (pp20) REVERT: 7 140 LEU cc_start: 0.8965 (mt) cc_final: 0.8762 (mt) REVERT: 8 10 ASP cc_start: 0.8050 (m-30) cc_final: 0.7247 (t0) REVERT: 8 46 TYR cc_start: 0.8304 (m-80) cc_final: 0.7966 (m-80) REVERT: 9 1 MET cc_start: 0.2125 (ptt) cc_final: 0.1512 (mmt) REVERT: 9 80 GLN cc_start: 0.8070 (mm-40) cc_final: 0.7518 (mp10) REVERT: 9 83 LYS cc_start: 0.8169 (tttt) cc_final: 0.7942 (tmtt) REVERT: B 99 LEU cc_start: 0.7360 (tp) cc_final: 0.7084 (tp) REVERT: F 85 LEU cc_start: 0.5805 (tt) cc_final: 0.5595 (tt) REVERT: P 141 TYR cc_start: 0.8470 (t80) cc_final: 0.8054 (t80) REVERT: P 145 MET cc_start: 0.8552 (mmp) cc_final: 0.8084 (mmt) REVERT: R 75 TYR cc_start: 0.6665 (m-80) cc_final: 0.6237 (m-80) REVERT: R 133 PHE cc_start: 0.7807 (m-80) cc_final: 0.7394 (m-10) REVERT: S 92 PHE cc_start: 0.6420 (m-10) cc_final: 0.6143 (m-10) REVERT: T 98 TYR cc_start: 0.7564 (t80) cc_final: 0.7212 (t80) REVERT: U 57 TYR cc_start: 0.6507 (p90) cc_final: 0.6269 (p90) REVERT: U 112 ASP cc_start: 0.8584 (p0) cc_final: 0.8149 (p0) REVERT: U 494 ILE cc_start: 0.5555 (tp) cc_final: 0.5138 (tp) REVERT: V 73 TRP cc_start: 0.8141 (m-10) cc_final: 0.7806 (m-10) REVERT: V 326 ASP cc_start: 0.7549 (t0) cc_final: 0.7163 (t0) REVERT: X 187 VAL cc_start: 0.8333 (m) cc_final: 0.8033 (t) REVERT: Y 311 GLN cc_start: 0.8273 (pm20) cc_final: 0.8036 (pm20) REVERT: Y 386 MET cc_start: 0.8009 (mmm) cc_final: 0.7342 (tpp) REVERT: Y 405 LYS cc_start: 0.8021 (mtmm) cc_final: 0.7586 (tptt) REVERT: Y 468 SER cc_start: 0.7272 (m) cc_final: 0.6562 (p) REVERT: Y 502 MET cc_start: 0.7889 (tpt) cc_final: 0.7214 (ptt) REVERT: Z 80 MET cc_start: 0.7521 (mmm) cc_final: 0.6871 (ttp) REVERT: Z 422 MET cc_start: 0.5176 (tmm) cc_final: 0.4081 (ttm) REVERT: Z 484 MET cc_start: 0.7074 (mmm) cc_final: 0.6636 (tpp) outliers start: 1 outliers final: 0 residues processed: 759 average time/residue: 0.4856 time to fit residues: 641.5623 Evaluate side-chains 532 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 532 time to evaluate : 4.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 416 optimal weight: 10.0000 chunk 268 optimal weight: 0.6980 chunk 401 optimal weight: 7.9990 chunk 202 optimal weight: 2.9990 chunk 132 optimal weight: 10.0000 chunk 130 optimal weight: 0.9990 chunk 427 optimal weight: 0.7980 chunk 458 optimal weight: 0.9980 chunk 332 optimal weight: 6.9990 chunk 62 optimal weight: 6.9990 chunk 528 optimal weight: 8.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 209 ASN 3 164 ASN ** 3 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 25 HIS 5 29 GLN ** 5 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 ASN J 98 GLN ** M 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 181 ASN ** S 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 196 GLN U 397 ASN ** U 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 539 ASN X 157 GLN X 337 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.3923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 54686 Z= 0.174 Angle : 0.570 10.642 74161 Z= 0.285 Chirality : 0.042 0.200 8689 Planarity : 0.004 0.053 9510 Dihedral : 5.424 81.489 7670 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.53 % Favored : 95.35 % Rotamer: Outliers : 0.02 % Allowed : 0.89 % Favored : 99.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.10), residues: 7038 helix: 0.26 (0.09), residues: 3793 sheet: -0.65 (0.22), residues: 579 loop : -1.08 (0.12), residues: 2666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP Z 141 HIS 0.006 0.001 HIS Y 204 PHE 0.030 0.001 PHE U 203 TYR 0.016 0.001 TYR 2 180 ARG 0.007 0.000 ARG X 441 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 776 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 775 time to evaluate : 4.804 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 19 SER cc_start: 0.8727 (p) cc_final: 0.8471 (p) REVERT: 0 36 THR cc_start: 0.7131 (t) cc_final: 0.6903 (t) REVERT: 0 81 HIS cc_start: 0.7326 (m90) cc_final: 0.5202 (p90) REVERT: 1 566 ASP cc_start: 0.7618 (p0) cc_final: 0.7404 (p0) REVERT: 2 394 LYS cc_start: 0.8174 (mmmm) cc_final: 0.7757 (mttt) REVERT: 2 396 LEU cc_start: 0.8107 (mt) cc_final: 0.7734 (mp) REVERT: 3 108 TYR cc_start: 0.7726 (t80) cc_final: 0.6829 (t80) REVERT: 3 177 LEU cc_start: 0.9394 (mt) cc_final: 0.9165 (mt) REVERT: 4 231 ASP cc_start: 0.7961 (m-30) cc_final: 0.7485 (m-30) REVERT: 5 34 ILE cc_start: 0.9403 (mt) cc_final: 0.9163 (mt) REVERT: 5 35 MET cc_start: 0.8267 (mmp) cc_final: 0.7992 (mmp) REVERT: 5 107 ASN cc_start: 0.7696 (t0) cc_final: 0.7467 (t0) REVERT: 6 41 GLU cc_start: 0.8484 (pp20) cc_final: 0.7958 (pp20) REVERT: 6 104 ASN cc_start: 0.8351 (t0) cc_final: 0.8089 (t0) REVERT: 8 46 TYR cc_start: 0.8315 (m-80) cc_final: 0.8014 (m-80) REVERT: 9 1 MET cc_start: 0.2082 (ptt) cc_final: 0.1581 (mmt) REVERT: 9 80 GLN cc_start: 0.8081 (mm-40) cc_final: 0.7624 (mp10) REVERT: I 81 MET cc_start: 0.6488 (tmm) cc_final: 0.5880 (tmm) REVERT: M 244 MET cc_start: 0.8062 (mmm) cc_final: 0.7817 (mmm) REVERT: P 141 TYR cc_start: 0.8448 (t80) cc_final: 0.8053 (t80) REVERT: P 145 MET cc_start: 0.8567 (mmp) cc_final: 0.8074 (mmt) REVERT: R 75 TYR cc_start: 0.6591 (m-80) cc_final: 0.6210 (m-80) REVERT: R 133 PHE cc_start: 0.7808 (m-80) cc_final: 0.7396 (m-10) REVERT: T 98 TYR cc_start: 0.7502 (t80) cc_final: 0.7183 (t80) REVERT: T 452 GLN cc_start: 0.8232 (mm-40) cc_final: 0.7746 (mm-40) REVERT: U 57 TYR cc_start: 0.6430 (p90) cc_final: 0.6175 (p90) REVERT: U 112 ASP cc_start: 0.8565 (p0) cc_final: 0.8130 (p0) REVERT: V 73 TRP cc_start: 0.8133 (m-10) cc_final: 0.7790 (m-10) REVERT: V 326 ASP cc_start: 0.7742 (t0) cc_final: 0.7404 (t0) REVERT: X 187 VAL cc_start: 0.8266 (m) cc_final: 0.7990 (t) REVERT: Y 386 MET cc_start: 0.7994 (mmm) cc_final: 0.7329 (tpp) REVERT: Y 405 LYS cc_start: 0.8156 (mtmm) cc_final: 0.7630 (tptt) REVERT: Y 468 SER cc_start: 0.7112 (m) cc_final: 0.6468 (p) REVERT: Y 502 MET cc_start: 0.8042 (tpt) cc_final: 0.7297 (ptt) REVERT: Z 80 MET cc_start: 0.7482 (mmm) cc_final: 0.6866 (ttp) REVERT: Z 386 MET cc_start: 0.6622 (mtp) cc_final: 0.6420 (mtt) REVERT: Z 422 MET cc_start: 0.5577 (tmm) cc_final: 0.4040 (ttm) REVERT: Z 484 MET cc_start: 0.7060 (mmm) cc_final: 0.6607 (tpp) outliers start: 1 outliers final: 0 residues processed: 775 average time/residue: 0.4832 time to fit residues: 652.3230 Evaluate side-chains 545 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 545 time to evaluate : 4.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 611 optimal weight: 9.9990 chunk 644 optimal weight: 0.8980 chunk 588 optimal weight: 7.9990 chunk 626 optimal weight: 7.9990 chunk 377 optimal weight: 2.9990 chunk 273 optimal weight: 20.0000 chunk 492 optimal weight: 3.9990 chunk 192 optimal weight: 20.0000 chunk 566 optimal weight: 0.7980 chunk 592 optimal weight: 0.0670 chunk 624 optimal weight: 0.9990 overall best weight: 1.1522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 82 HIS ** 2 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 89 HIS G 92 ASN J 98 GLN ** M 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 66 GLN P 84 HIS ** Q 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 181 ASN ** T 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 441 GLN U 196 GLN ** U 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 539 ASN ** X 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.4048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.105 54686 Z= 0.169 Angle : 0.568 10.532 74161 Z= 0.284 Chirality : 0.042 0.198 8689 Planarity : 0.004 0.051 9510 Dihedral : 5.326 82.206 7670 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.56 % Favored : 95.35 % Rotamer: Outliers : 0.02 % Allowed : 0.75 % Favored : 99.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.45 (0.10), residues: 7038 helix: 0.35 (0.09), residues: 3791 sheet: -0.59 (0.22), residues: 589 loop : -1.04 (0.13), residues: 2658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP 9 73 HIS 0.007 0.001 HIS Y 204 PHE 0.035 0.001 PHE X 283 TYR 0.028 0.001 TYR 4 211 ARG 0.006 0.000 ARG X 441 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 752 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 751 time to evaluate : 4.970 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: 0 19 SER cc_start: 0.8777 (p) cc_final: 0.8512 (p) REVERT: 0 36 THR cc_start: 0.7409 (t) cc_final: 0.7200 (t) REVERT: 0 81 HIS cc_start: 0.7180 (m90) cc_final: 0.5182 (p90) REVERT: 1 273 GLU cc_start: 0.8311 (mp0) cc_final: 0.8023 (mt-10) REVERT: 1 566 ASP cc_start: 0.7667 (p0) cc_final: 0.7355 (p0) REVERT: 2 394 LYS cc_start: 0.8147 (mmmm) cc_final: 0.7743 (mttt) REVERT: 2 396 LEU cc_start: 0.8112 (mt) cc_final: 0.7729 (mp) REVERT: 3 108 TYR cc_start: 0.7701 (t80) cc_final: 0.6822 (t80) REVERT: 3 177 LEU cc_start: 0.9390 (mt) cc_final: 0.9175 (mt) REVERT: 4 231 ASP cc_start: 0.7967 (m-30) cc_final: 0.7526 (m-30) REVERT: 5 34 ILE cc_start: 0.9385 (mt) cc_final: 0.9156 (mt) REVERT: 5 35 MET cc_start: 0.8239 (mmp) cc_final: 0.8002 (mmp) REVERT: 5 107 ASN cc_start: 0.7757 (t0) cc_final: 0.7518 (t0) REVERT: 6 41 GLU cc_start: 0.8629 (pp20) cc_final: 0.8103 (pp20) REVERT: 7 20 PHE cc_start: 0.9061 (m-80) cc_final: 0.8546 (m-10) REVERT: 7 100 ARG cc_start: 0.8932 (mmt-90) cc_final: 0.8666 (mmt90) REVERT: 7 114 TYR cc_start: 0.7789 (m-80) cc_final: 0.7586 (m-80) REVERT: 8 46 TYR cc_start: 0.8319 (m-80) cc_final: 0.8022 (m-80) REVERT: 9 1 MET cc_start: 0.2098 (ptt) cc_final: 0.1513 (mmt) REVERT: 9 80 GLN cc_start: 0.8083 (mm-40) cc_final: 0.7402 (mp10) REVERT: 9 83 LYS cc_start: 0.7769 (tmtt) cc_final: 0.7375 (tttt) REVERT: C 61 MET cc_start: 0.6631 (mmt) cc_final: 0.5990 (mmt) REVERT: G 124 ILE cc_start: 0.5651 (tp) cc_final: 0.5165 (tt) REVERT: I 81 MET cc_start: 0.6446 (tmm) cc_final: 0.5969 (tmm) REVERT: M 244 MET cc_start: 0.8010 (mmm) cc_final: 0.7441 (mmm) REVERT: M 289 TYR cc_start: 0.9081 (m-80) cc_final: 0.8755 (m-80) REVERT: P 141 TYR cc_start: 0.8402 (t80) cc_final: 0.8056 (t80) REVERT: P 145 MET cc_start: 0.8548 (mmp) cc_final: 0.8052 (mmt) REVERT: Q 14 MET cc_start: 0.4219 (ppp) cc_final: 0.3911 (ppp) REVERT: R 75 TYR cc_start: 0.6617 (m-80) cc_final: 0.6202 (m-80) REVERT: R 133 PHE cc_start: 0.7767 (m-80) cc_final: 0.7367 (m-10) REVERT: S 92 PHE cc_start: 0.6257 (m-10) cc_final: 0.6011 (m-10) REVERT: S 144 ASP cc_start: 0.7470 (m-30) cc_final: 0.6719 (t0) REVERT: T 98 TYR cc_start: 0.7506 (t80) cc_final: 0.7198 (t80) REVERT: T 422 ASN cc_start: 0.7028 (m-40) cc_final: 0.6478 (t0) REVERT: T 452 GLN cc_start: 0.8239 (mm-40) cc_final: 0.7631 (tp40) REVERT: U 57 TYR cc_start: 0.6309 (p90) cc_final: 0.6027 (p90) REVERT: U 112 ASP cc_start: 0.8475 (p0) cc_final: 0.8059 (p0) REVERT: V 73 TRP cc_start: 0.8117 (m-10) cc_final: 0.7821 (m-10) REVERT: V 326 ASP cc_start: 0.7568 (t0) cc_final: 0.7211 (t0) REVERT: X 84 THR cc_start: 0.7735 (p) cc_final: 0.7462 (p) REVERT: X 187 VAL cc_start: 0.8268 (m) cc_final: 0.8042 (t) REVERT: Y 386 MET cc_start: 0.7998 (mmm) cc_final: 0.7351 (tpp) REVERT: Y 405 LYS cc_start: 0.8159 (mtmm) cc_final: 0.7648 (tptt) REVERT: Y 468 SER cc_start: 0.7172 (m) cc_final: 0.6641 (p) REVERT: Y 502 MET cc_start: 0.8109 (tpt) cc_final: 0.7434 (ptt) REVERT: Z 80 MET cc_start: 0.7440 (mmm) cc_final: 0.6834 (ttp) REVERT: Z 484 MET cc_start: 0.7013 (mmm) cc_final: 0.6626 (tpp) outliers start: 1 outliers final: 0 residues processed: 751 average time/residue: 0.4846 time to fit residues: 637.4299 Evaluate side-chains 544 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 544 time to evaluate : 4.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 411 optimal weight: 4.9990 chunk 662 optimal weight: 9.9990 chunk 404 optimal weight: 3.9990 chunk 314 optimal weight: 1.9990 chunk 460 optimal weight: 10.0000 chunk 695 optimal weight: 10.0000 chunk 640 optimal weight: 8.9990 chunk 553 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 427 optimal weight: 0.4980 chunk 339 optimal weight: 0.9980 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 90 GLN 7 91 ASN ** 7 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 92 ASN ** M 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 181 ASN ** T 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 441 GLN U 139 HIS U 196 GLN U 397 ASN ** U 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 539 ASN ** X 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.4163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 54686 Z= 0.203 Angle : 0.591 11.174 74161 Z= 0.296 Chirality : 0.042 0.190 8689 Planarity : 0.004 0.054 9510 Dihedral : 5.351 82.390 7670 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.16 % Favored : 94.76 % Rotamer: Outliers : 0.04 % Allowed : 0.25 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.43 (0.10), residues: 7038 helix: 0.36 (0.09), residues: 3775 sheet: -0.62 (0.21), residues: 608 loop : -1.01 (0.13), residues: 2655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP 9 73 HIS 0.006 0.001 HIS Y 204 PHE 0.044 0.002 PHE E 116 TYR 0.029 0.001 TYR T 312 ARG 0.006 0.000 ARG X 441 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 735 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 733 time to evaluate : 4.869 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: 0 19 SER cc_start: 0.8801 (p) cc_final: 0.8538 (p) REVERT: 0 81 HIS cc_start: 0.7173 (m90) cc_final: 0.5093 (p-80) REVERT: 1 273 GLU cc_start: 0.8341 (mp0) cc_final: 0.8133 (mp0) REVERT: 1 510 ILE cc_start: 0.9254 (tp) cc_final: 0.8988 (tt) REVERT: 1 566 ASP cc_start: 0.7743 (p0) cc_final: 0.7434 (p0) REVERT: 2 394 LYS cc_start: 0.8156 (mmmm) cc_final: 0.7749 (mttt) REVERT: 2 396 LEU cc_start: 0.8115 (mt) cc_final: 0.7737 (mp) REVERT: 3 108 TYR cc_start: 0.7718 (t80) cc_final: 0.6748 (t80) REVERT: 3 177 LEU cc_start: 0.9415 (mt) cc_final: 0.9190 (mt) REVERT: 4 231 ASP cc_start: 0.8040 (m-30) cc_final: 0.7633 (m-30) REVERT: 5 34 ILE cc_start: 0.9414 (mt) cc_final: 0.9186 (mt) REVERT: 5 35 MET cc_start: 0.8260 (mmp) cc_final: 0.8034 (mmp) REVERT: 6 41 GLU cc_start: 0.8691 (pp20) cc_final: 0.8161 (pp20) REVERT: 8 46 TYR cc_start: 0.8341 (m-80) cc_final: 0.8019 (m-80) REVERT: 9 1 MET cc_start: 0.2044 (ptt) cc_final: 0.1441 (mmt) REVERT: 9 80 GLN cc_start: 0.8057 (mm-40) cc_final: 0.7414 (mp10) REVERT: 9 83 LYS cc_start: 0.7819 (tmtt) cc_final: 0.7455 (tttt) REVERT: 9 85 LYS cc_start: 0.7908 (ptmm) cc_final: 0.7599 (ptmm) REVERT: G 124 ILE cc_start: 0.5492 (tp) cc_final: 0.4977 (tt) REVERT: I 81 MET cc_start: 0.6526 (tmm) cc_final: 0.6016 (tmm) REVERT: M 244 MET cc_start: 0.7844 (mmm) cc_final: 0.7483 (mmm) REVERT: M 278 CYS cc_start: 0.8066 (m) cc_final: 0.7786 (m) REVERT: P 141 TYR cc_start: 0.8463 (t80) cc_final: 0.8065 (t80) REVERT: P 145 MET cc_start: 0.8549 (mmp) cc_final: 0.8013 (mmt) REVERT: R 75 TYR cc_start: 0.6677 (m-80) cc_final: 0.6231 (m-80) REVERT: R 133 PHE cc_start: 0.7808 (m-80) cc_final: 0.7408 (m-10) REVERT: S 92 PHE cc_start: 0.6272 (m-10) cc_final: 0.6022 (m-10) REVERT: S 144 ASP cc_start: 0.7530 (m-30) cc_final: 0.6856 (t0) REVERT: T 98 TYR cc_start: 0.7514 (t80) cc_final: 0.7191 (t80) REVERT: T 282 MET cc_start: 0.6656 (tpp) cc_final: 0.6419 (tpp) REVERT: T 452 GLN cc_start: 0.8354 (mm-40) cc_final: 0.7713 (tp40) REVERT: U 57 TYR cc_start: 0.6449 (p90) cc_final: 0.6135 (p90) REVERT: V 73 TRP cc_start: 0.8131 (m-10) cc_final: 0.7824 (m-10) REVERT: V 326 ASP cc_start: 0.7769 (t0) cc_final: 0.7394 (t0) REVERT: V 484 LEU cc_start: 0.8776 (mt) cc_final: 0.8536 (mt) REVERT: X 84 THR cc_start: 0.7729 (p) cc_final: 0.7447 (p) REVERT: X 187 VAL cc_start: 0.8287 (m) cc_final: 0.8074 (t) REVERT: Y 386 MET cc_start: 0.8088 (mmm) cc_final: 0.7385 (tpp) REVERT: Y 405 LYS cc_start: 0.8190 (mtmm) cc_final: 0.7669 (tptt) REVERT: Y 410 TYR cc_start: 0.6306 (t80) cc_final: 0.5862 (t80) REVERT: Y 468 SER cc_start: 0.7196 (m) cc_final: 0.6649 (p) REVERT: Y 502 MET cc_start: 0.8041 (tpt) cc_final: 0.7398 (ptt) REVERT: Z 80 MET cc_start: 0.7475 (mmm) cc_final: 0.6899 (ttp) REVERT: Z 422 MET cc_start: 0.5458 (tmm) cc_final: 0.4022 (ttm) REVERT: Z 484 MET cc_start: 0.7018 (mmm) cc_final: 0.6701 (tpp) outliers start: 2 outliers final: 0 residues processed: 734 average time/residue: 0.5246 time to fit residues: 679.4794 Evaluate side-chains 528 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 528 time to evaluate : 4.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 439 optimal weight: 0.5980 chunk 589 optimal weight: 0.0070 chunk 169 optimal weight: 2.9990 chunk 510 optimal weight: 0.9980 chunk 81 optimal weight: 0.8980 chunk 153 optimal weight: 20.0000 chunk 554 optimal weight: 9.9990 chunk 232 optimal weight: 5.9990 chunk 569 optimal weight: 10.0000 chunk 70 optimal weight: 1.9990 chunk 102 optimal weight: 9.9990 overall best weight: 0.9000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 93 GLN 6 106 ASN ** 6 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 92 ASN ** M 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 40 GLN Q 67 ASN R 137 HIS R 181 ASN ** T 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 441 GLN U 196 GLN ** U 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 539 ASN ** X 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 357 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.111798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.093437 restraints weight = 165287.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.093131 restraints weight = 136652.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.093536 restraints weight = 106513.712| |-----------------------------------------------------------------------------| r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.4280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.067 54686 Z= 0.160 Angle : 0.572 12.273 74161 Z= 0.285 Chirality : 0.042 0.199 8689 Planarity : 0.004 0.051 9510 Dihedral : 5.221 84.345 7670 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.35 % Favored : 95.58 % Rotamer: Outliers : 0.02 % Allowed : 0.30 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.31 (0.10), residues: 7038 helix: 0.44 (0.09), residues: 3778 sheet: -0.53 (0.22), residues: 580 loop : -0.95 (0.13), residues: 2680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP 9 73 HIS 0.007 0.001 HIS Y 204 PHE 0.034 0.001 PHE E 116 TYR 0.029 0.001 TYR 4 211 ARG 0.006 0.000 ARG X 441 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11680.25 seconds wall clock time: 206 minutes 59.70 seconds (12419.70 seconds total)