Starting phenix.real_space_refine on Fri Apr 5 17:14:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6re2_4839/04_2024/6re2_4839_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6re2_4839/04_2024/6re2_4839.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6re2_4839/04_2024/6re2_4839.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6re2_4839/04_2024/6re2_4839.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6re2_4839/04_2024/6re2_4839_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6re2_4839/04_2024/6re2_4839_updated.pdb" } resolution = 3.2 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= 1.029 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 34282 2.51 5 N 9107 2.21 5 O 10163 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "0 ASP 73": "OD1" <-> "OD2" 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 34": "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 GLU 235": "OE1" <-> "OE2" Residue "1 ARG 259": "NH1" <-> "NH2" Residue "1 ASP 283": "OD1" <-> "OD2" Residue "1 GLU 341": "OE1" <-> "OE2" Residue "1 GLU 350": "OE1" <-> "OE2" Residue "1 ARG 359": "NH1" <-> "NH2" Residue "1 GLU 367": "OE1" <-> "OE2" Residue "1 ASP 373": "OD1" <-> "OD2" 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 PHE 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ASP 479": "OD1" <-> "OD2" Residue "1 GLU 496": "OE1" <-> "OE2" Residue "1 ASP 508": "OD1" <-> "OD2" Residue "1 GLU 516": "OE1" <-> "OE2" Residue "1 GLU 517": "OE1" <-> "OE2" Residue "1 ASP 573": "OD1" <-> "OD2" Residue "1 ARG 609": "NH1" <-> "NH2" Residue "1 ASP 613": "OD1" <-> "OD2" Residue "2 ASP 7": "OD1" <-> "OD2" Residue "2 GLU 14": "OE1" <-> "OE2" Residue "2 ASP 31": "OD1" <-> "OD2" 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 TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ARG 173": "NH1" <-> "NH2" Residue "2 GLU 205": "OE1" <-> "OE2" Residue "2 PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 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 GLU 422": "OE1" <-> "OE2" Residue "2 ASP 426": "OD1" <-> "OD2" 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 PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 GLU 126": "OE1" <-> "OE2" Residue "3 ARG 149": "NH1" <-> "NH2" 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 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 "3 PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 GLU 320": "OE1" <-> "OE2" Residue "4 GLU 10": "OE1" <-> "OE2" Residue "4 TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 43": "OE1" <-> "OE2" Residue "4 TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 64": "OE1" <-> "OE2" Residue "4 ARG 84": "NH1" <-> "NH2" Residue "4 TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 112": "OE1" <-> "OE2" Residue "4 TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ASP 156": "OD1" <-> "OD2" Residue "4 ARG 176": "NH1" <-> "NH2" Residue "4 TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 193": "OE1" <-> "OE2" Residue "4 ASP 194": "OD1" <-> "OD2" Residue "4 ASP 197": "OD1" <-> "OD2" Residue "4 GLU 202": "OE1" <-> "OE2" Residue "4 TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ASP 214": "OD1" <-> "OD2" Residue "4 GLU 225": "OE1" <-> "OE2" Residue "4 ASP 231": "OD1" <-> "OD2" Residue "4 ARG 232": "NH1" <-> "NH2" Residue "4 ARG 255": "NH1" <-> "NH2" Residue "4 TYR 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 270": "OE1" <-> "OE2" Residue "5 GLU 6": "OE1" <-> "OE2" Residue "5 ARG 36": "NH1" <-> "NH2" Residue "5 ARG 50": "NH1" <-> "NH2" Residue "5 ARG 112": "NH1" <-> "NH2" Residue "5 PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 TYR 131": "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 ARG 13": "NH1" <-> "NH2" Residue "8 ARG 65": "NH1" <-> "NH2" Residue "8 TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 GLU 12": "OE1" <-> "OE2" 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 GLU 22": "OE1" <-> "OE2" Residue "9 PHE 24": "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 "9 PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 ASP 82": "OD1" <-> "OD2" Residue "9 GLU 92": "OE1" <-> "OE2" Residue "B GLU 111": "OE1" <-> "OE2" Residue "C PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 115": "NH1" <-> "NH2" 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 GLU 288": "OE1" <-> "OE2" Residue "M PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 313": "OD1" <-> "OD2" Residue "P GLU 64": "OE1" <-> "OE2" Residue "P ASP 68": "OD1" <-> "OD2" Residue "P GLU 79": "OE1" <-> "OE2" Residue "P PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 142": "OE1" <-> "OE2" Residue "P TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 191": "OD1" <-> "OD2" Residue "P GLU 201": "OE1" <-> "OE2" Residue "P ARG 206": "NH1" <-> "NH2" 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 ASP 25": "OD1" <-> "OD2" Residue "Q ARG 42": "NH1" <-> "NH2" Residue "Q ARG 48": "NH1" <-> "NH2" Residue "Q TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 64": "OE1" <-> "OE2" Residue "R PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 148": "OE1" <-> "OE2" Residue "R ASP 174": "OD1" <-> "OD2" Residue "R PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 177": "OE1" <-> "OE2" Residue "S ARG 46": "NH1" <-> "NH2" Residue "S ASP 83": "OD1" <-> "OD2" Residue "S TYR 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 133": "OE1" <-> "OE2" 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 214": "OD1" <-> "OD2" Residue "S ASP 222": "OD1" <-> "OD2" Residue "S TYR 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 244": "NH1" <-> "NH2" Residue "S ASP 291": "OD1" <-> "OD2" Residue "S TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 306": "OE1" <-> "OE2" Residue "T ARG 49": "NH1" <-> "NH2" Residue "T TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 74": "OE1" <-> "OE2" Residue "T ARG 86": "NH1" <-> "NH2" Residue "T ASP 125": "OD1" <-> "OD2" Residue "T ASP 142": "OD1" <-> "OD2" Residue "T ARG 162": "NH1" <-> "NH2" Residue "T ARG 195": "NH1" <-> "NH2" Residue "T ARG 199": "NH1" <-> "NH2" Residue "T PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 237": "OD1" <-> "OD2" Residue "T TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 283": "NH1" <-> "NH2" Residue "T TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 325": "OD1" <-> "OD2" Residue "T ASP 353": "OD1" <-> "OD2" Residue "T PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 418": "NH1" <-> "NH2" Residue "T PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 454": "NH1" <-> "NH2" Residue "T PHE 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 510": "OD1" <-> "OD2" Residue "T GLU 522": "OE1" <-> "OE2" Residue "T ARG 555": "NH1" <-> "NH2" Residue "U ASP 41": "OD1" <-> "OD2" Residue "U ASP 46": "OD1" <-> "OD2" Residue "U ARG 49": "NH1" <-> "NH2" Residue "U PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 96": "NH1" <-> "NH2" Residue "U TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 227": "NH1" <-> "NH2" Residue "U ARG 254": "NH1" <-> "NH2" Residue "U PHE 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 283": "NH1" <-> "NH2" Residue "U TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 GLU 371": "OE1" <-> "OE2" Residue "U PHE 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 407": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 414": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 454": "NH1" <-> "NH2" Residue "U PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 465": "OD1" <-> "OD2" 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 ARG 49": "NH1" <-> "NH2" Residue "V PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 135": "OD1" <-> "OD2" 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 TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 266": "NH1" <-> "NH2" Residue "V PHE 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 314": "NH1" <-> "NH2" Residue "V ASP 326": "OD1" <-> "OD2" 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 ASP 389": "OD1" <-> "OD2" Residue "V PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 429": "NH1" <-> "NH2" Residue "V ARG 454": "NH1" <-> "NH2" Residue "V PHE 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 476": "NH1" <-> "NH2" Residue "V PHE 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 496": "NH1" <-> "NH2" Residue "V TYR 502": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 513": "NH1" <-> "NH2" Residue "V ARG 555": "NH1" <-> "NH2" Residue "X TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 51": "NH1" <-> "NH2" Residue "X ARG 71": "NH1" <-> "NH2" Residue "X ARG 86": "NH1" <-> "NH2" Residue "X ARG 98": "NH1" <-> "NH2" Residue "X ASP 104": "OD1" <-> "OD2" Residue "X ARG 120": "NH1" <-> "NH2" Residue "X ASP 130": "OD1" <-> "OD2" Residue "X GLU 131": "OE1" <-> "OE2" Residue "X PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 216": "NH1" <-> "NH2" Residue "X GLU 229": "OE1" <-> "OE2" Residue "X ARG 258": "NH1" <-> "NH2" Residue "X GLU 270": "OE1" <-> "OE2" Residue "X GLU 323": "OE1" <-> "OE2" Residue "X PHE 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 359": "OD1" <-> "OD2" Residue "X ASP 378": "OD1" <-> "OD2" Residue "X ARG 385": "NH1" <-> "NH2" Residue "X ARG 401": "NH1" <-> "NH2" Residue "X TYR 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 429": "OD1" <-> "OD2" Residue "X ARG 435": "NH1" <-> "NH2" Residue "X ARG 437": "NH1" <-> "NH2" Residue "X PHE 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 505": "OD1" <-> "OD2" Residue "X ARG 509": "NH1" <-> "NH2" Residue "X ASP 513": "OD1" <-> "OD2" Residue "X GLU 519": "OE1" <-> "OE2" Residue "X ASP 523": "OD1" <-> "OD2" Residue "X GLU 541": "OE1" <-> "OE2" Residue "X PHE 549": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 36": "OD1" <-> "OD2" Residue "Y TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 51": "NH1" <-> "NH2" Residue "Y ASP 82": "OD1" <-> "OD2" Residue "Y ASP 136": "OD1" <-> "OD2" Residue "Y PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 156": "OE1" <-> "OE2" Residue "Y ASP 168": "OD1" <-> "OD2" Residue "Y PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 218": "NH1" <-> "NH2" Residue "Y ARG 225": "NH1" <-> "NH2" Residue "Y ARG 239": "NH1" <-> "NH2" Residue "Y TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 296": "OE1" <-> "OE2" Residue "Y TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 385": "NH1" <-> "NH2" Residue "Y TYR 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 401": "NH1" <-> "NH2" Residue "Y ASP 429": "OD1" <-> "OD2" Residue "Y PHE 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 479": "OD1" <-> "OD2" Residue "Y GLU 494": "OE1" <-> "OE2" Residue "Y ASP 500": "OD1" <-> "OD2" Residue "Y ASP 505": "OD1" <-> "OD2" Residue "Y ARG 509": "NH1" <-> "NH2" Residue "Y GLU 533": "OE1" <-> "OE2" Residue "Y GLU 540": "OE1" <-> "OE2" Residue "Y GLU 541": "OE1" <-> "OE2" Residue "Y PHE 549": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 71": "NH1" <-> "NH2" Residue "Z ASP 82": "OD1" <-> "OD2" Residue "Z ARG 86": "NH1" <-> "NH2" Residue "Z ARG 115": "NH1" <-> "NH2" Residue "Z ARG 120": "NH1" <-> "NH2" Residue "Z GLU 127": "OE1" <-> "OE2" Residue "Z ARG 145": "NH1" <-> "NH2" Residue "Z PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 258": "NH1" <-> "NH2" Residue "Z GLU 270": "OE1" <-> "OE2" Residue "Z TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 317": "OD1" <-> "OD2" Residue "Z ASP 345": "OD1" <-> "OD2" Residue "Z ARG 366": "NH1" <-> "NH2" Residue "Z TYR 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 378": "OD1" <-> "OD2" Residue "Z ARG 385": "NH1" <-> "NH2" Residue "Z GLU 451": "OE1" <-> "OE2" Residue "Z PHE 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 460": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 478": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 513": "OD1" <-> "OD2" Residue "Z GLU 520": "OE1" <-> "OE2" Residue "Z ASP 523": "OD1" <-> "OD2" Residue "Z ASP 528": "OD1" <-> "OD2" Residue "Z ASP 542": "OD1" <-> "OD2" Residue "Z ASP 548": "OD1" <-> "OD2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 53720 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: 3978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 3978 Classifications: {'peptide': 523} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 497} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "V" Number of atoms: 3961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 3961 Classifications: {'peptide': 520} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 494} Chain: "X" 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: "Y" Number of atoms: 3952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 3952 Classifications: {'peptide': 520} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 497} Chain: "Z" Number of atoms: 4095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 539, 4095 Classifications: {'peptide': 539} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 514} 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: "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} Chain: "Z" 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: 20.29, per 1000 atoms: 0.38 Number of scatterers: 53720 At special positions: 0 Unit cell: (214.812, 129.519, 260.091, 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 10163 8.00 N 9107 7.00 C 34282 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: 15.19 Conformation dependent library (CDL) restraints added in 7.3 seconds 14068 Ramachandran restraints generated. 7034 Oldfield, 0 Emsley, 7034 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13076 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 283 helices and 32 sheets defined 51.3% alpha, 7.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.33 Creating SS restraints... Processing helix chain '0' and resid 4 through 7 No H-bonds generated for 'chain '0' and resid 4 through 7' Processing helix chain '0' and resid 18 through 30 Processing helix chain '0' and resid 44 through 48 Processing helix chain '1' and resid 46 through 74 removed outlier: 3.877A pdb=" N LYS 1 74 " --> pdb=" O ILE 1 70 " (cutoff:3.500A) 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 107 through 141 Processing helix chain '1' and resid 164 through 175 removed outlier: 3.964A pdb=" N THR 1 169 " --> pdb=" O GLU 1 165 " (cutoff:3.500A) Processing helix chain '1' and resid 191 through 203 removed outlier: 3.712A pdb=" N ALA 1 196 " --> pdb=" O GLY 1 192 " (cutoff:3.500A) Processing helix chain '1' and resid 207 through 223 removed outlier: 4.446A pdb=" N SER 1 211 " --> pdb=" O LYS 1 208 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU 1 215 " --> pdb=" O GLU 1 212 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU 1 216 " --> pdb=" O VAL 1 213 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N GLU 1 223 " --> pdb=" O SER 1 220 " (cutoff:3.500A) Processing helix chain '1' and resid 242 through 270 Processing helix chain '1' and resid 272 through 276 removed outlier: 3.817A pdb=" N ALA 1 275 " --> pdb=" O PRO 1 272 " (cutoff:3.500A) Processing helix chain '1' and resid 290 through 292 No H-bonds generated for 'chain '1' and resid 290 through 292' Processing helix chain '1' and resid 298 through 304 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 removed outlier: 3.665A pdb=" N GLU 1 352 " --> pdb=" O ALA 1 348 " (cutoff:3.500A) 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 removed outlier: 3.688A pdb=" N VAL 1 382 " --> pdb=" O GLU 1 378 " (cutoff:3.500A) Processing helix chain '1' and resid 393 through 416 Processing helix chain '1' and resid 426 through 431 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 514 removed outlier: 4.251A pdb=" N GLU 1 496 " --> pdb=" O GLN 1 492 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLU 1 501 " --> pdb=" O LEU 1 497 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASP 1 504 " --> pdb=" O LEU 1 500 " (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 19 Processing helix chain '2' and resid 26 through 39 removed outlier: 3.747A pdb=" N LEU 2 39 " --> pdb=" O ALA 2 35 " (cutoff:3.500A) 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: 3.504A pdb=" N LEU 2 87 " --> pdb=" O THR 2 83 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ALA 2 88 " --> pdb=" O VAL 2 84 " (cutoff:3.500A) removed outlier: 5.062A 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 113 removed outlier: 3.610A pdb=" N ALA 2 113 " --> pdb=" O ALA 2 109 " (cutoff:3.500A) Processing helix chain '2' and resid 118 through 130 Processing helix chain '2' and resid 137 through 149 Processing helix chain '2' and resid 155 through 167 removed outlier: 3.849A 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: 4.003A pdb=" N ALA 2 195 " --> pdb=" O ALA 2 191 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N SER 2 199 " --> pdb=" O ALA 2 195 " (cutoff:3.500A) Processing helix chain '2' and resid 208 through 219 Processing helix chain '2' and resid 229 through 234 Processing helix chain '2' and resid 241 through 253 removed outlier: 3.946A pdb=" N GLU 2 246 " --> pdb=" O ALA 2 242 " (cutoff:3.500A) Processing helix chain '2' and resid 259 through 275 removed outlier: 3.674A pdb=" N VAL 2 268 " --> pdb=" O ALA 2 264 " (cutoff:3.500A) removed outlier: 3.612A 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: 4.229A pdb=" N SER 2 305 " --> pdb=" O ALA 2 301 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N PHE 2 306 " --> pdb=" O ALA 2 302 " (cutoff:3.500A) removed outlier: 3.768A 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 353 Processing helix chain '2' and resid 397 through 409 removed outlier: 3.674A pdb=" N GLN 2 409 " --> pdb=" O VAL 2 405 " (cutoff:3.500A) Processing helix chain '2' and resid 418 through 421 No H-bonds generated for 'chain '2' and resid 418 through 421' Processing helix chain '2' and resid 427 through 441 Processing helix chain '3' and resid 78 through 86 Processing helix chain '3' and resid 92 through 98 removed outlier: 3.659A pdb=" N VAL 3 96 " --> pdb=" O GLU 3 92 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASN 3 97 " --> pdb=" O GLU 3 93 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N VAL 3 98 " --> pdb=" O ASN 3 94 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 92 through 98' Processing helix chain '3' and resid 103 through 112 Processing helix chain '3' and resid 118 through 127 removed outlier: 4.234A 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 169 through 171 No H-bonds generated for 'chain '3' and resid 169 through 171' Processing helix chain '3' and resid 174 through 186 removed outlier: 4.097A 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 229 removed outlier: 3.816A pdb=" N ASN 3 229 " --> pdb=" O TYR 3 225 " (cutoff:3.500A) Processing helix chain '3' and resid 234 through 240 Processing helix chain '3' and resid 246 through 250 Processing helix chain '3' and resid 254 through 271 removed outlier: 3.808A pdb=" N PHE 3 271 " --> pdb=" O ALA 3 267 " (cutoff:3.500A) Processing helix chain '3' and resid 276 through 283 removed outlier: 4.035A pdb=" N ALA 3 280 " --> pdb=" O SER 3 277 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE 3 282 " --> pdb=" O GLU 3 279 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLY 3 283 " --> pdb=" O ALA 3 280 " (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 Processing helix chain '4' and resid 20 through 34 removed outlier: 4.011A pdb=" N ALA 4 25 " --> pdb=" O GLU 4 21 " (cutoff:3.500A) Processing helix chain '4' and resid 48 through 68 removed outlier: 4.160A pdb=" N GLN 4 61 " --> pdb=" O TYR 4 57 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL 4 62 " --> pdb=" O LEU 4 58 " (cutoff:3.500A) Proline residue: 4 65 - end of helix removed outlier: 3.830A pdb=" N HIS 4 68 " --> pdb=" O GLU 4 64 " (cutoff:3.500A) Processing helix chain '4' and resid 79 through 95 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: 3.880A pdb=" N VAL 4 141 " --> pdb=" O ALA 4 137 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLU 4 148 " --> pdb=" O SER 4 144 " (cutoff:3.500A) Processing helix chain '4' and resid 160 through 176 removed outlier: 3.969A pdb=" N LYS 4 168 " --> pdb=" O LYS 4 164 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ALA 4 171 " --> pdb=" O ALA 4 167 " (cutoff:3.500A) Processing helix chain '4' and resid 180 through 187 Processing helix chain '4' and resid 193 through 233 removed outlier: 4.874A pdb=" N GLU 4 202 " --> pdb=" O LYS 4 198 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N THR 4 205 " --> pdb=" O LYS 4 201 " (cutoff:3.500A) Processing helix chain '4' and resid 238 through 258 removed outlier: 3.906A pdb=" N ALA 4 256 " --> pdb=" O LEU 4 252 " (cutoff:3.500A) Processing helix chain '4' and resid 263 through 284 Processing helix chain '5' and resid 8 through 29 Processing helix chain '5' and resid 31 through 58 removed outlier: 3.672A pdb=" N GLU 5 37 " --> pdb=" O THR 5 33 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N HIS 5 41 " --> pdb=" O GLU 5 37 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N LYS 5 49 " --> pdb=" O ALA 5 45 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N ARG 5 50 " --> pdb=" O ALA 5 46 " (cutoff:3.500A) Processing helix chain '5' and resid 64 through 66 No H-bonds generated for 'chain '5' and resid 64 through 66' Processing helix chain '5' and resid 73 through 80 Processing helix chain '5' and resid 88 through 106 removed outlier: 4.048A pdb=" N LEU 5 92 " --> pdb=" O PRO 5 88 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LYS 5 101 " --> pdb=" O SER 5 97 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA 5 105 " --> pdb=" O LYS 5 101 " (cutoff:3.500A) Processing helix chain '5' and resid 115 through 118 No H-bonds generated for 'chain '5' and resid 115 through 118' Processing helix chain '6' and resid 31 through 40 Processing helix chain '6' and resid 52 through 57 Processing helix chain '6' and resid 73 through 93 Processing helix chain '6' and resid 99 through 119 removed outlier: 3.657A pdb=" N VAL 6 107 " --> pdb=" O LEU 6 103 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N TRP 6 112 " --> pdb=" O LEU 6 108 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU 6 113 " --> pdb=" O GLN 6 109 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER 6 118 " --> pdb=" O ILE 6 114 " (cutoff:3.500A) Processing helix chain '6' and resid 122 through 129 Processing helix chain '6' and resid 134 through 137 No H-bonds generated for 'chain '6' and resid 134 through 137' Processing helix chain '7' and resid 63 through 67 removed outlier: 3.963A pdb=" N ARG 7 67 " --> pdb=" O ALA 7 63 " (cutoff:3.500A) No H-bonds generated for 'chain '7' and resid 63 through 67' Processing helix chain '7' and resid 84 through 104 removed outlier: 3.776A pdb=" N GLU 7 99 " --> pdb=" O SER 7 95 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU 7 103 " --> pdb=" O GLU 7 99 " (cutoff:3.500A) 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 165 removed outlier: 3.553A pdb=" N LEU 7 150 " --> pdb=" O PHE 7 147 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N SER 7 151 " --> pdb=" O ASP 7 148 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ALA 7 154 " --> pdb=" O SER 7 151 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N SER 7 155 " --> pdb=" O ALA 7 152 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL 7 157 " --> pdb=" O ALA 7 154 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N VAL 7 158 " --> pdb=" O SER 7 155 " (cutoff:3.500A) Proline residue: 7 159 - end of helix removed outlier: 3.584A pdb=" N ARG 7 165 " --> pdb=" O ALA 7 162 " (cutoff:3.500A) 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 40 through 79 removed outlier: 3.724A pdb=" N TRP 8 45 " --> pdb=" O ILE 8 41 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N TYR 8 46 " --> pdb=" O PRO 8 42 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N LEU 8 47 " --> pdb=" O ARG 8 43 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA 8 76 " --> pdb=" O ALA 8 72 " (cutoff:3.500A) removed outlier: 4.693A 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 34 through 56 removed outlier: 3.561A pdb=" N ALA 9 38 " --> pdb=" O GLY 9 34 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N VAL 9 42 " --> pdb=" O ALA 9 38 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ASN 9 56 " --> pdb=" O LEU 9 52 " (cutoff:3.500A) Processing helix chain '9' and resid 83 through 96 removed outlier: 3.708A pdb=" N GLU 9 88 " --> pdb=" O ALA 9 84 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N LYS 9 95 " --> pdb=" O LYS 9 91 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N SER 9 96 " --> pdb=" O GLU 9 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 91 removed outlier: 3.541A pdb=" N CYS A 66 " --> pdb=" O VAL A 62 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N THR A 68 " --> pdb=" O ALA A 64 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N ILE A 69 " --> pdb=" O GLY A 65 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N ALA A 70 " --> pdb=" O CYS A 66 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N LEU A 71 " --> pdb=" O ALA A 67 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ALA A 72 " --> pdb=" O THR A 68 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLY A 73 " --> pdb=" O ILE A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 125 removed outlier: 3.682A pdb=" N ALA A 96 " --> pdb=" O PRO A 93 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N LYS A 97 " --> pdb=" O ASN A 94 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N VAL A 100 " --> pdb=" O LYS A 97 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N LEU A 104 " --> pdb=" O GLY A 101 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU A 105 " --> pdb=" O TYR A 102 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N PHE A 107 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU A 111 " --> pdb=" O ALA A 108 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER A 112 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU A 115 " --> pdb=" O SER A 112 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N LEU A 118 " --> pdb=" O LEU A 115 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU A 119 " --> pdb=" O PHE A 116 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU A 125 " --> pdb=" O PHE A 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 91 removed outlier: 3.645A pdb=" N THR B 68 " --> pdb=" O ALA B 64 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ILE B 69 " --> pdb=" O GLY B 65 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N ALA B 70 " --> pdb=" O CYS B 66 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N LEU B 71 " --> pdb=" O ALA B 67 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ALA B 72 " --> pdb=" O THR B 68 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLY B 73 " --> pdb=" O ILE B 69 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE B 86 " --> pdb=" O PHE B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 125 removed outlier: 3.553A pdb=" N ALA B 96 " --> pdb=" O PRO B 93 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N LYS B 97 " --> pdb=" O ASN B 94 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLY B 106 " --> pdb=" O ALA B 103 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLU B 111 " --> pdb=" O ALA B 108 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N SER B 112 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N LEU B 115 " --> pdb=" O SER B 112 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU B 119 " --> pdb=" O PHE B 116 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LEU B 125 " --> pdb=" O PHE B 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 65 removed outlier: 4.000A pdb=" N MET C 61 " --> pdb=" O ALA C 57 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N VAL C 62 " --> pdb=" O ALA C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 91 removed outlier: 3.652A pdb=" N GLY C 73 " --> pdb=" O ALA C 70 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLY C 77 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU C 85 " --> pdb=" O PHE C 82 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG C 91 " --> pdb=" O GLY C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 125 removed outlier: 3.508A pdb=" N ALA C 96 " --> pdb=" O PRO C 93 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N LYS C 97 " --> pdb=" O ASN C 94 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL C 100 " --> pdb=" O LYS C 97 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N SER C 112 " --> pdb=" O LEU C 109 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LEU C 119 " --> pdb=" O PHE C 116 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU C 125 " --> pdb=" O PHE C 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 91 removed outlier: 4.385A pdb=" N MET D 61 " --> pdb=" O ALA D 57 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL D 62 " --> pdb=" O ALA D 58 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ILE D 69 " --> pdb=" O GLY D 65 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N ALA D 70 " --> pdb=" O CYS D 66 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N LEU D 71 " --> pdb=" O ALA D 67 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N ALA D 72 " --> pdb=" O THR D 68 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N GLY D 73 " --> pdb=" O ILE D 69 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL D 74 " --> pdb=" O ALA D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 125 removed outlier: 3.546A pdb=" N ALA D 96 " --> pdb=" O PRO D 93 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N LYS D 97 " --> pdb=" O ASN D 94 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N VAL D 100 " --> pdb=" O LYS D 97 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR D 110 " --> pdb=" O PHE D 107 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N SER D 112 " --> pdb=" O LEU D 109 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LEU D 125 " --> pdb=" O PHE D 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 91 removed outlier: 4.521A pdb=" N MET E 61 " --> pdb=" O ALA E 57 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N VAL E 62 " --> pdb=" O ALA E 58 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ILE E 69 " --> pdb=" O GLY E 65 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N ALA E 70 " --> pdb=" O CYS E 66 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N LEU E 71 " --> pdb=" O ALA E 67 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N ALA E 72 " --> pdb=" O THR E 68 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N GLY E 73 " --> pdb=" O ILE E 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 126 removed outlier: 3.552A pdb=" N ALA E 96 " --> pdb=" O PRO E 93 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N LYS E 97 " --> pdb=" O ASN E 94 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N VAL E 100 " --> pdb=" O LYS E 97 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR E 110 " --> pdb=" O PHE E 107 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N SER E 112 " --> pdb=" O LEU E 109 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LEU E 119 " --> pdb=" O PHE E 116 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ILE E 124 " --> pdb=" O VAL E 121 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LEU E 125 " --> pdb=" O PHE E 122 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N PHE E 126 " --> pdb=" O LEU E 123 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 91 removed outlier: 4.340A pdb=" N MET F 61 " --> pdb=" O ALA F 57 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VAL F 62 " --> pdb=" O ALA F 58 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ILE F 69 " --> pdb=" O GLY F 65 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N ALA F 70 " --> pdb=" O CYS F 66 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N LEU F 71 " --> pdb=" O ALA F 67 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N ALA F 72 " --> pdb=" O THR F 68 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N GLY F 73 " --> pdb=" O ILE F 69 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL F 74 " --> pdb=" O ALA F 70 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE F 86 " --> pdb=" O PHE F 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 126 removed outlier: 3.525A pdb=" N ALA F 96 " --> pdb=" O PRO F 93 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N LYS F 97 " --> pdb=" O ASN F 94 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N VAL F 100 " --> pdb=" O LYS F 97 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLU F 111 " --> pdb=" O ALA F 108 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N SER F 112 " --> pdb=" O LEU F 109 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE F 124 " --> pdb=" O VAL F 121 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N PHE F 126 " --> pdb=" O LEU F 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 89 removed outlier: 3.932A pdb=" N MET G 61 " --> pdb=" O ALA G 57 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N VAL G 62 " --> pdb=" O ALA G 58 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N THR G 68 " --> pdb=" O ALA G 64 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ILE G 69 " --> pdb=" O GLY G 65 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N ALA G 70 " --> pdb=" O CYS G 66 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N LEU G 71 " --> pdb=" O ALA G 67 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N ALA G 72 " --> pdb=" O THR G 68 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N GLY G 73 " --> pdb=" O ILE G 69 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL G 74 " --> pdb=" O ALA G 70 " (cutoff:3.500A) Processing helix chain 'G' and resid 93 through 125 removed outlier: 3.502A pdb=" N ALA G 96 " --> pdb=" O PRO G 93 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N LYS G 97 " --> pdb=" O ASN G 94 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N VAL G 100 " --> pdb=" O LYS G 97 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LEU G 104 " --> pdb=" O GLY G 101 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR G 110 " --> pdb=" O PHE G 107 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU G 111 " --> pdb=" O ALA G 108 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N SER G 112 " --> pdb=" O LEU G 109 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU G 118 " --> pdb=" O LEU G 115 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N LEU G 125 " --> pdb=" O PHE G 122 " (cutoff:3.500A) Processing helix chain 'H' and resid 56 through 67 removed outlier: 4.286A pdb=" N MET H 61 " --> pdb=" O ALA H 57 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ALA H 64 " --> pdb=" O LYS H 60 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLY H 65 " --> pdb=" O MET H 61 " (cutoff:3.500A) Processing helix chain 'H' and resid 71 through 91 removed outlier: 3.679A pdb=" N ARG H 91 " --> pdb=" O ASN H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 93 through 126 removed outlier: 5.146A pdb=" N LYS H 97 " --> pdb=" O ASN H 94 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N VAL H 100 " --> pdb=" O LYS H 97 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N PHE H 107 " --> pdb=" O LEU H 104 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU H 111 " --> pdb=" O ALA H 108 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N SER H 112 " --> pdb=" O LEU H 109 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE H 113 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N LEU H 125 " --> pdb=" O PHE H 122 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N PHE H 126 " --> pdb=" O LEU H 123 " (cutoff:3.500A) Processing helix chain 'I' and resid 55 through 67 removed outlier: 4.277A pdb=" N MET I 61 " --> pdb=" O ALA I 57 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL I 62 " --> pdb=" O ALA I 58 " (cutoff:3.500A) Processing helix chain 'I' and resid 70 through 91 removed outlier: 3.503A pdb=" N ILE I 86 " --> pdb=" O PHE I 82 " (cutoff:3.500A) Processing helix chain 'I' and resid 93 through 124 removed outlier: 3.932A pdb=" N ALA I 96 " --> pdb=" O PRO I 93 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N LYS I 97 " --> pdb=" O ASN I 94 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N VAL I 100 " --> pdb=" O LYS I 97 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N SER I 112 " --> pdb=" O LEU I 109 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE I 124 " --> pdb=" O VAL I 121 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 91 removed outlier: 3.668A pdb=" N MET J 61 " --> pdb=" O ALA J 57 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL J 62 " --> pdb=" O ALA J 58 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ILE J 69 " --> pdb=" O GLY J 65 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N ALA J 70 " --> pdb=" O CYS J 66 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N LEU J 71 " --> pdb=" O ALA J 67 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N ALA J 72 " --> pdb=" O THR J 68 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N GLY J 73 " --> pdb=" O ILE J 69 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL J 74 " --> pdb=" O ALA J 70 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE J 86 " --> pdb=" O PHE J 82 " (cutoff:3.500A) Processing helix chain 'J' and resid 96 through 125 removed outlier: 3.612A pdb=" N VAL J 100 " --> pdb=" O ALA J 96 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLY J 101 " --> pdb=" O LYS J 97 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ILE J 113 " --> pdb=" O LEU J 109 " (cutoff:3.500A) Processing helix chain 'M' and resid 105 through 119 Processing helix chain 'M' and resid 135 through 144 Processing helix chain 'M' and resid 148 through 167 removed outlier: 3.929A pdb=" N GLY M 166 " --> pdb=" O CYS M 162 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LEU M 167 " --> pdb=" O ASN M 163 " (cutoff:3.500A) Processing helix chain 'M' and resid 174 through 176 No H-bonds generated for 'chain 'M' and resid 174 through 176' Processing helix chain 'M' and resid 178 through 200 removed outlier: 3.844A pdb=" N THR M 200 " --> pdb=" O GLY M 196 " (cutoff:3.500A) Processing helix chain 'M' and resid 222 through 229 removed outlier: 3.915A pdb=" N SER M 228 " --> pdb=" O LEU M 224 " (cutoff:3.500A) Processing helix chain 'M' and resid 231 through 264 removed outlier: 4.201A pdb=" N GLY M 237 " --> pdb=" O ALA M 233 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N LEU M 240 " --> pdb=" O LEU M 236 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N GLY M 247 " --> pdb=" O ASN M 243 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N HIS M 248 " --> pdb=" O MET M 244 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA M 260 " --> pdb=" O GLY M 256 " (cutoff:3.500A) removed outlier: 4.250A 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: 3.793A pdb=" N VAL M 277 " --> pdb=" O ALA M 273 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU M 280 " --> pdb=" O GLY M 276 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N SER M 296 " --> pdb=" O ALA M 292 " (cutoff:3.500A) Processing helix chain 'P' and resid 51 through 63 removed outlier: 3.922A pdb=" N LYS P 63 " --> pdb=" O GLN P 59 " (cutoff:3.500A) Processing helix chain 'P' and resid 67 through 83 removed outlier: 3.609A pdb=" N PHE P 77 " --> pdb=" O GLU P 73 " (cutoff:3.500A) Processing helix chain 'P' and resid 85 through 92 removed outlier: 4.435A pdb=" N LEU P 90 " --> pdb=" O GLU P 86 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ALA P 91 " --> pdb=" O LEU P 87 " (cutoff:3.500A) Processing helix chain 'P' and resid 98 through 108 removed outlier: 3.579A pdb=" N THR P 102 " --> pdb=" O THR P 98 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER P 106 " --> pdb=" O THR P 102 " (cutoff:3.500A) Processing helix chain 'P' and resid 118 through 128 removed outlier: 3.870A pdb=" N GLU P 123 " --> pdb=" O LYS P 119 " (cutoff:3.500A) Processing helix chain 'P' and resid 130 through 148 removed outlier: 3.853A pdb=" N LEU P 135 " --> pdb=" O SER P 132 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N THR P 138 " --> pdb=" O LEU P 135 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N VAL P 139 " --> pdb=" O GLU P 136 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLU P 142 " --> pdb=" O VAL P 139 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLU P 143 " --> pdb=" O ASN P 140 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU P 144 " --> pdb=" O TYR P 141 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA P 147 " --> pdb=" O LEU P 144 " (cutoff:3.500A) Processing helix chain 'P' and resid 166 through 176 removed outlier: 3.669A pdb=" N LYS P 172 " --> pdb=" O VAL P 168 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N LYS P 176 " --> pdb=" O LYS P 172 " (cutoff:3.500A) Processing helix chain 'P' and resid 211 through 225 Processing helix chain 'Q' and resid 10 through 12 No H-bonds generated for 'chain 'Q' and resid 10 through 12' Processing helix chain 'Q' and resid 16 through 30 removed outlier: 3.738A pdb=" N VAL Q 30 " --> pdb=" O LEU Q 26 " (cutoff:3.500A) Processing helix chain 'Q' and resid 33 through 39 removed outlier: 3.686A pdb=" N ALA Q 37 " --> pdb=" O GLU Q 33 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N LYS Q 38 " --> pdb=" O PRO Q 34 " (cutoff:3.500A) Processing helix chain 'Q' and resid 41 through 43 No H-bonds generated for 'chain 'Q' and resid 41 through 43' Processing helix chain 'R' and resid 30 through 38 removed outlier: 3.668A pdb=" N THR R 34 " --> pdb=" O PRO R 30 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N GLU R 35 " --> pdb=" O LYS R 31 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL R 36 " --> pdb=" O GLU R 32 " (cutoff:3.500A) Processing helix chain 'R' and resid 51 through 53 No H-bonds generated for 'chain 'R' and resid 51 through 53' Processing helix chain 'R' and resid 152 through 154 No H-bonds generated for 'chain 'R' and resid 152 through 154' Processing helix chain 'R' and resid 159 through 169 removed outlier: 4.189A pdb=" N ALA R 166 " --> pdb=" O SER R 162 " (cutoff:3.500A) Processing helix chain 'R' and resid 175 through 193 removed outlier: 3.614A pdb=" N ALA R 190 " --> pdb=" O GLU R 186 " (cutoff:3.500A) Processing helix chain 'S' and resid 42 through 78 removed outlier: 3.523A pdb=" N LYS S 55 " --> pdb=" O LYS S 51 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N LYS S 58 " --> pdb=" O GLY S 54 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASN S 70 " --> pdb=" O SER S 66 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ILE S 73 " --> pdb=" O LYS S 69 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ALA S 74 " --> pdb=" O ASN S 70 " (cutoff:3.500A) Processing helix chain 'S' and resid 82 through 88 Processing helix chain 'S' and resid 116 through 130 Processing helix chain 'S' and resid 144 through 150 removed outlier: 3.819A pdb=" N GLN S 149 " --> pdb=" O LYS S 145 " (cutoff:3.500A) Processing helix chain 'S' and resid 172 through 182 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 273 removed outlier: 3.744A pdb=" N ASN S 263 " --> pdb=" O MET S 259 " (cutoff:3.500A) Processing helix chain 'S' and resid 277 through 312 Processing helix chain 'T' and resid 58 through 75 removed outlier: 3.641A pdb=" N ILE T 67 " --> pdb=" O SER T 63 " (cutoff:3.500A) Proline residue: T 68 - end of helix removed outlier: 3.823A 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 212 removed outlier: 3.508A pdb=" N ALA T 211 " --> pdb=" O LYS T 207 " (cutoff:3.500A) Processing helix chain 'T' and resid 231 through 247 removed outlier: 3.605A pdb=" N GLU T 247 " --> pdb=" O LYS T 243 " (cutoff:3.500A) Processing helix chain 'T' and resid 251 through 253 No H-bonds generated for 'chain 'T' and resid 251 through 253' 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 315 Proline residue: T 303 - end of helix removed outlier: 3.630A pdb=" N TYR T 312 " --> pdb=" O ALA T 308 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N PHE T 313 " --> pdb=" O MET T 309 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG T 314 " --> pdb=" O ALA T 310 " (cutoff:3.500A) Processing helix chain 'T' and resid 328 through 340 removed outlier: 3.663A pdb=" N VAL T 332 " --> pdb=" O SER T 328 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA T 333 " --> pdb=" O LYS T 329 " (cutoff:3.500A) Processing helix chain 'T' and resid 347 through 349 No H-bonds generated for 'chain 'T' and resid 347 through 349' Processing helix chain 'T' and resid 354 through 362 removed outlier: 3.834A pdb=" N HIS T 358 " --> pdb=" O VAL T 354 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LEU T 361 " --> pdb=" O LEU T 357 " (cutoff:3.500A) Processing helix chain 'T' and resid 393 through 399 Processing helix chain 'T' and resid 411 through 414 No H-bonds generated for 'chain 'T' and resid 411 through 414' Processing helix chain 'T' and resid 432 through 434 No H-bonds generated for 'chain 'T' and resid 432 through 434' Processing helix chain 'T' and resid 437 through 440 No H-bonds generated for 'chain 'T' and resid 437 through 440' Processing helix chain 'T' and resid 446 through 456 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 483 removed outlier: 3.815A pdb=" N GLU T 475 " --> pdb=" O GLN T 471 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ARG T 479 " --> pdb=" O GLU T 475 " (cutoff:3.500A) Processing helix chain 'T' and resid 494 through 505 removed outlier: 4.012A pdb=" N ALA T 500 " --> pdb=" O ARG T 496 " (cutoff:3.500A) Processing helix chain 'T' and resid 514 through 527 removed outlier: 3.887A pdb=" N ILE T 517 " --> pdb=" O VAL T 514 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N VAL T 518 " --> pdb=" O GLN T 515 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N GLU T 521 " --> pdb=" O VAL T 518 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLU T 522 " --> pdb=" O ALA T 519 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL T 524 " --> pdb=" O GLU T 521 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE T 525 " --> pdb=" O GLU T 522 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER T 526 " --> pdb=" O ALA T 523 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLN T 527 " --> pdb=" O VAL T 524 " (cutoff:3.500A) Processing helix chain 'T' and resid 530 through 539 removed outlier: 3.615A pdb=" N LYS T 534 " --> pdb=" O PRO T 530 " (cutoff:3.500A) Processing helix chain 'T' and resid 544 through 555 removed outlier: 3.859A pdb=" N ALA T 548 " --> pdb=" O PRO T 544 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N HIS T 549 " --> pdb=" O ALA T 545 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA T 552 " --> pdb=" O ALA T 548 " (cutoff:3.500A) Processing helix chain 'U' and resid 47 through 49 No H-bonds generated for 'chain 'U' and resid 47 through 49' Processing helix chain 'U' and resid 59 through 64 removed outlier: 3.975A pdb=" N SER U 63 " --> pdb=" O ILE U 59 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N GLN U 64 " --> pdb=" O GLN U 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 59 through 64' Processing helix chain 'U' and resid 66 through 71 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: 3.945A pdb=" N GLU U 247 " --> pdb=" O LYS U 243 " (cutoff:3.500A) removed outlier: 4.771A 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 314 Proline residue: U 303 - end of helix removed outlier: 3.669A pdb=" N TYR U 312 " --> pdb=" O ALA U 308 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N PHE U 313 " --> pdb=" O MET U 309 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG U 314 " --> pdb=" O ALA U 310 " (cutoff:3.500A) Processing helix chain 'U' and resid 327 through 340 removed outlier: 3.807A pdb=" N VAL U 332 " --> pdb=" O SER U 328 " (cutoff:3.500A) Processing helix chain 'U' and resid 347 through 349 No H-bonds generated for 'chain 'U' and resid 347 through 349' Processing helix chain 'U' and resid 354 through 364 removed outlier: 4.999A pdb=" N ARG U 364 " --> pdb=" O ARG U 360 " (cutoff:3.500A) Processing helix chain 'U' and resid 393 through 401 Processing helix chain 'U' and resid 410 through 413 No H-bonds generated for 'chain 'U' and resid 410 through 413' Processing helix chain 'U' and resid 437 through 456 removed outlier: 4.074A pdb=" N VAL U 442 " --> pdb=" O GLY U 438 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLY U 444 " --> pdb=" O LYS U 440 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N THR U 445 " --> pdb=" O GLN U 441 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLU U 455 " --> pdb=" O ALA U 451 " (cutoff:3.500A) Processing helix chain 'U' and resid 470 through 484 removed outlier: 3.534A pdb=" N GLU U 482 " --> pdb=" O ALA U 478 " (cutoff:3.500A) Processing helix chain 'U' and resid 494 through 505 Processing helix chain 'U' and resid 517 through 526 removed outlier: 4.096A pdb=" N GLU U 522 " --> pdb=" O VAL U 518 " (cutoff:3.500A) Processing helix chain 'U' and resid 531 through 539 removed outlier: 3.710A pdb=" N ILE U 535 " --> pdb=" O ALA U 531 " (cutoff:3.500A) Processing helix chain 'U' and resid 544 through 553 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 58 through 66 removed outlier: 3.993A pdb=" N GLN V 64 " --> pdb=" O GLN V 60 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LYS V 65 " --> pdb=" O HIS V 61 " (cutoff:3.500A) 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 210 No H-bonds generated for 'chain 'V' and resid 207 through 210' Processing helix chain 'V' and resid 231 through 246 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 315 Proline residue: V 303 - end of helix removed outlier: 3.728A pdb=" N TYR V 312 " --> pdb=" O ALA V 308 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N PHE V 313 " --> pdb=" O MET V 309 " (cutoff:3.500A) Processing helix chain 'V' and resid 327 through 340 Processing helix chain 'V' and resid 347 through 349 No H-bonds generated for 'chain 'V' and resid 347 through 349' Processing helix chain 'V' and resid 352 through 364 removed outlier: 4.348A pdb=" N PHE V 355 " --> pdb=" O GLY V 352 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU V 357 " --> pdb=" O VAL V 354 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ARG V 360 " --> pdb=" O LEU V 357 " (cutoff:3.500A) removed outlier: 4.498A 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: 3.953A 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 439 through 456 removed outlier: 3.714A pdb=" N GLY V 444 " --> pdb=" O LYS V 440 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N THR V 445 " --> pdb=" O GLN V 441 " (cutoff:3.500A) Processing helix chain 'V' and resid 470 through 483 Processing helix chain 'V' and resid 494 through 505 removed outlier: 3.663A pdb=" N ALA V 504 " --> pdb=" O ALA V 500 " (cutoff:3.500A) Processing helix chain 'V' and resid 514 through 516 No H-bonds generated for 'chain 'V' and resid 514 through 516' Processing helix chain 'V' and resid 520 through 527 Processing helix chain 'V' and resid 531 through 539 removed outlier: 3.801A pdb=" N ILE V 535 " --> pdb=" O ALA V 531 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA V 538 " --> pdb=" O LYS V 534 " (cutoff:3.500A) Processing helix chain 'V' and resid 549 through 553 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 Processing helix chain 'X' and resid 217 through 230 Processing helix chain 'X' and resid 236 through 241 removed outlier: 4.939A pdb=" N GLY X 240 " --> pdb=" O ALA X 237 " (cutoff:3.500A) Processing helix chain 'X' and resid 255 through 258 No H-bonds generated for 'chain 'X' and resid 255 through 258' Processing helix chain 'X' and resid 261 through 274 removed outlier: 3.555A pdb=" N PHE X 272 " --> pdb=" O VAL X 268 " (cutoff:3.500A) Processing helix chain 'X' and resid 287 through 300 Processing helix chain 'X' and resid 314 through 324 removed outlier: 4.468A pdb=" N ARG X 324 " --> pdb=" O GLY X 320 " (cutoff:3.500A) Processing helix chain 'X' and resid 342 through 344 No H-bonds generated for 'chain 'X' and resid 342 through 344' Processing helix chain 'X' and resid 349 through 354 Processing helix chain 'X' and resid 366 through 369 No H-bonds generated for 'chain 'X' and resid 366 through 369' Processing helix chain 'X' and resid 394 through 412 Processing helix chain 'X' and resid 427 through 442 Processing helix chain 'X' and resid 450 through 454 removed outlier: 3.510A pdb=" N PHE X 453 " --> pdb=" O ALA X 450 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N THR X 454 " --> pdb=" O GLU X 451 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 450 through 454' Processing helix chain 'X' and resid 463 through 474 removed outlier: 3.715A pdb=" N SER X 468 " --> pdb=" O ALA X 464 " (cutoff:3.500A) Processing helix chain 'X' and resid 492 through 500 removed outlier: 3.910A pdb=" N LYS X 496 " --> pdb=" O ILE X 492 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLU X 497 " --> pdb=" O LYS X 493 " (cutoff:3.500A) Processing helix chain 'X' and resid 527 through 532 Processing helix chain 'Y' and resid 150 through 152 No H-bonds generated for 'chain 'Y' and resid 150 through 152' Processing helix chain 'Y' and resid 165 through 170 Processing helix chain 'Y' and resid 191 through 203 removed outlier: 4.268A pdb=" N LYS Y 202 " --> pdb=" O ASN Y 198 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ALA Y 203 " --> pdb=" O ASN Y 199 " (cutoff:3.500A) Processing helix chain 'Y' and resid 217 through 229 Processing helix chain 'Y' and resid 236 through 241 removed outlier: 3.616A pdb=" N ARG Y 239 " --> pdb=" O GLY Y 236 " (cutoff:3.500A) removed outlier: 5.047A 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 removed outlier: 3.748A pdb=" N PHE Y 272 " --> pdb=" O VAL Y 268 " (cutoff:3.500A) Processing helix chain 'Y' and resid 287 through 297 removed outlier: 3.523A pdb=" N GLN Y 292 " --> pdb=" O ARG Y 289 " (cutoff:3.500A) Processing helix chain 'Y' and resid 314 through 324 removed outlier: 4.303A pdb=" N ARG Y 324 " --> pdb=" O GLY Y 320 " (cutoff:3.500A) Processing helix chain 'Y' and resid 342 through 344 No H-bonds generated for 'chain 'Y' and resid 342 through 344' Processing helix chain 'Y' and resid 349 through 357 removed outlier: 4.577A pdb=" N ALA Y 356 " --> pdb=" O ALA Y 352 " (cutoff:3.500A) removed outlier: 4.368A 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 395 through 419 removed outlier: 3.557A pdb=" N LEU Y 413 " --> pdb=" O ASP Y 409 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLN Y 414 " --> pdb=" O TYR Y 410 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N ASP Y 415 " --> pdb=" O LYS Y 411 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N ILE Y 416 " --> pdb=" O ASN Y 412 " (cutoff:3.500A) Processing helix chain 'Y' and resid 422 through 424 No H-bonds generated for 'chain 'Y' and resid 422 through 424' Processing helix chain 'Y' and resid 427 through 443 removed outlier: 3.585A pdb=" N ALA Y 434 " --> pdb=" O LYS Y 430 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG Y 441 " --> pdb=" O ARG Y 437 " (cutoff:3.500A) Processing helix chain 'Y' and resid 463 through 475 Processing helix chain 'Y' and resid 492 through 503 removed outlier: 4.099A pdb=" N LYS Y 496 " --> pdb=" O ILE Y 492 " (cutoff:3.500A) Processing helix chain 'Y' and resid 527 through 531 Processing helix chain 'Y' and resid 545 through 549 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 170 Processing helix chain 'Z' and resid 189 through 199 Processing helix chain 'Z' and resid 217 through 228 Processing helix chain 'Z' and resid 236 through 241 removed outlier: 3.531A pdb=" N ARG Z 239 " --> pdb=" O GLY Z 236 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N GLY Z 240 " --> pdb=" O ALA Z 237 " (cutoff:3.500A) Processing helix chain 'Z' and resid 255 through 274 removed outlier: 3.600A pdb=" N ARG Z 260 " --> pdb=" O GLY Z 256 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N ALA Z 262 " --> pdb=" O ARG Z 258 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N LEU Z 263 " --> pdb=" O ALA Z 259 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE Z 272 " --> pdb=" O VAL Z 268 " (cutoff:3.500A) Processing helix chain 'Z' and resid 288 through 298 removed outlier: 3.712A pdb=" N VAL Z 297 " --> pdb=" O ALA Z 293 " (cutoff:3.500A) Processing helix chain 'Z' and resid 314 through 324 removed outlier: 4.531A pdb=" N ARG Z 324 " --> pdb=" O GLY Z 320 " (cutoff:3.500A) Processing helix chain 'Z' and resid 342 through 344 No H-bonds generated for 'chain 'Z' and resid 342 through 344' Processing helix chain 'Z' and resid 349 through 353 Processing helix chain 'Z' and resid 366 through 369 No H-bonds generated for 'chain 'Z' and resid 366 through 369' Processing helix chain 'Z' and resid 394 through 417 removed outlier: 3.992A pdb=" N VAL Z 399 " --> pdb=" O GLU Z 395 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ASP Z 415 " --> pdb=" O LYS Z 411 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N ILE Z 416 " --> pdb=" O ASN Z 412 " (cutoff:3.500A) Processing helix chain 'Z' and resid 430 through 443 removed outlier: 3.694A pdb=" N LYS Z 438 " --> pdb=" O ALA Z 434 " (cutoff:3.500A) Processing helix chain 'Z' and resid 463 through 475 Processing helix chain 'Z' and resid 492 through 505 removed outlier: 4.043A pdb=" N LYS Z 496 " --> pdb=" O ILE Z 492 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LYS Z 501 " --> pdb=" O GLU Z 497 " (cutoff:3.500A) Processing helix chain 'Z' and resid 527 through 533 removed outlier: 3.899A pdb=" N VAL Z 531 " --> pdb=" O LEU Z 527 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N SER Z 532 " --> pdb=" O ASP Z 528 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain '2' and resid 369 through 372 Processing sheet with id= B, first strand: chain '7' and resid 36 through 41 removed outlier: 3.519A pdb=" N LYS 7 36 " --> pdb=" O ALA 7 51 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'P' and resid 151 through 153 removed outlier: 6.900A pdb=" N LYS P 183 " --> pdb=" O VAL P 152 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'P' and resid 188 through 190 removed outlier: 6.328A pdb=" N VAL P 156 " --> pdb=" O LYS P 189 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'Q' and resid 45 through 50 removed outlier: 3.602A 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: 6.883A pdb=" N THR R 142 " --> pdb=" O ASN R 73 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N TYR R 75 " --> pdb=" O THR R 142 " (cutoff:3.500A) removed outlier: 6.560A 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: 3.838A pdb=" N THR R 88 " --> pdb=" O HIS R 119 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N VAL R 115 " --> pdb=" O PRO R 92 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'S' and resid 203 through 211 removed outlier: 5.083A pdb=" N ASN S 195 " --> pdb=" O VAL S 105 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ASP S 136 " --> pdb=" O SER S 100 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N VAL S 102 " --> pdb=" O ASP S 136 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N VAL S 138 " --> pdb=" O VAL S 102 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N ALA S 104 " --> pdb=" O VAL S 138 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N VAL S 140 " --> pdb=" O ALA S 104 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N SER S 141 " --> pdb=" O GLN S 159 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N ALA S 161 " --> pdb=" O SER S 141 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'T' and resid 87 through 91 removed outlier: 6.491A pdb=" N ARG T 96 " --> pdb=" O LEU T 88 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N VAL T 90 " --> pdb=" O ILE T 94 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ILE T 94 " --> pdb=" O VAL T 90 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N VAL T 130 " --> pdb=" O ALA T 119 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N ALA T 119 " --> pdb=" O VAL T 130 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N PHE T 132 " --> pdb=" O GLY T 117 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N GLY T 117 " --> pdb=" O PHE T 132 " (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 404 through 408 removed outlier: 3.881A pdb=" N LEU T 222 " --> pdb=" O GLY T 404 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'T' and resid 285 through 290 removed outlier: 8.770A pdb=" N ILE T 286 " --> pdb=" O VAL T 255 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N CYS T 257 " --> pdb=" O ILE T 286 " (cutoff:3.500A) removed outlier: 8.168A pdb=" N VAL T 288 " --> pdb=" O CYS T 257 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N TYR T 259 " --> pdb=" O VAL T 288 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ALA T 290 " --> pdb=" O TYR T 259 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N ALA T 261 " --> pdb=" O ALA T 290 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N HIS T 319 " --> pdb=" O TYR T 256 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N VAL T 258 " --> pdb=" O HIS T 319 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N LEU T 321 " --> pdb=" O VAL T 258 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N VAL T 260 " --> pdb=" O LEU T 321 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N ILE T 323 " --> pdb=" O VAL T 260 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N VAL T 262 " --> pdb=" O ILE T 323 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ASP T 325 " --> pdb=" O VAL T 262 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N SER T 376 " --> pdb=" O GLY T 320 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N ILE T 322 " --> pdb=" O SER T 376 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N THR T 378 " --> pdb=" O ILE T 322 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N TYR T 324 " --> pdb=" O THR T 378 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N PHE T 380 " --> pdb=" O TYR T 324 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'U' and resid 85 through 91 removed outlier: 6.666A pdb=" N ARG U 96 " --> pdb=" O LEU U 88 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N VAL U 90 " --> pdb=" O ILE U 94 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ILE U 94 " --> pdb=" O VAL U 90 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASN U 121 " --> pdb=" O GLY U 128 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N VAL U 130 " --> pdb=" O ALA U 119 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N ALA U 119 " --> pdb=" O VAL U 130 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'U' and resid 152 through 155 Processing sheet with id= O, first strand: chain 'U' and resid 163 through 165 removed outlier: 8.246A pdb=" N THR U 164 " --> pdb=" O THR U 285 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N MET U 287 " --> pdb=" O THR U 164 " (cutoff:3.500A) removed outlier: 8.925A pdb=" N ILE U 286 " --> pdb=" O VAL U 255 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N CYS U 257 " --> pdb=" O ILE U 286 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N VAL U 288 " --> pdb=" O CYS U 257 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N TYR U 259 " --> pdb=" O VAL U 288 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N ALA U 290 " --> pdb=" O TYR U 259 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N ALA U 261 " --> pdb=" O ALA U 290 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N HIS U 319 " --> pdb=" O TYR U 256 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N VAL U 258 " --> pdb=" O HIS U 319 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N LEU U 321 " --> pdb=" O VAL U 258 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N VAL U 260 " --> pdb=" O LEU U 321 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N ILE U 323 " --> pdb=" O VAL U 260 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N VAL U 262 " --> pdb=" O ILE U 323 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ASP U 325 " --> pdb=" O VAL U 262 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N SER U 376 " --> pdb=" O GLY U 320 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N ILE U 322 " --> pdb=" O SER U 376 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N THR U 378 " --> pdb=" O ILE U 322 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N TYR U 324 " --> pdb=" O THR U 378 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N PHE U 380 " --> pdb=" O TYR U 324 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'U' and resid 405 through 408 removed outlier: 6.433A pdb=" N LEU U 222 " --> pdb=" O ILE U 406 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N LEU U 408 " --> pdb=" O LEU U 222 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N ILE U 224 " --> pdb=" O LEU U 408 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'U' and resid 107 through 111 removed outlier: 4.586A pdb=" N GLN U 149 " --> pdb=" O LEU U 108 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N CYS U 110 " --> pdb=" O THR U 147 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N THR U 147 " --> pdb=" O CYS U 110 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'V' and resid 143 through 145 removed outlier: 6.505A pdb=" N ARG V 96 " --> pdb=" O LEU V 88 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N VAL V 130 " --> pdb=" O ALA V 119 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N ALA V 119 " --> pdb=" O VAL V 130 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLU V 107 " --> pdb=" O ALA V 119 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N GLN V 149 " --> pdb=" O LEU V 108 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N CYS V 110 " --> pdb=" O THR V 147 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N THR V 147 " --> pdb=" O CYS V 110 " (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 404 through 407 Processing sheet with id= U, first strand: chain 'V' and resid 285 through 290 removed outlier: 8.914A pdb=" N ILE V 286 " --> pdb=" O VAL V 255 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N CYS V 257 " --> pdb=" O ILE V 286 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N VAL V 288 " --> pdb=" O CYS V 257 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N TYR V 259 " --> pdb=" O VAL V 288 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N ALA V 290 " --> pdb=" O TYR V 259 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N ALA V 261 " --> pdb=" O ALA V 290 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N HIS V 319 " --> pdb=" O TYR V 256 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N VAL V 258 " --> pdb=" O HIS V 319 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N LEU V 321 " --> pdb=" O VAL V 258 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N VAL V 260 " --> pdb=" O LEU V 321 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ILE V 323 " --> pdb=" O VAL V 260 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N VAL V 262 " --> pdb=" O ILE V 323 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ASP V 325 " --> pdb=" O VAL V 262 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N SER V 376 " --> pdb=" O GLY V 320 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N ILE V 322 " --> pdb=" O SER V 376 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N THR V 378 " --> pdb=" O ILE V 322 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N TYR V 324 " --> pdb=" O THR V 378 " (cutoff:3.500A) No H-bonds generated for sheet with id= U Processing sheet with id= V, first strand: chain 'X' and resid 38 through 44 removed outlier: 6.339A pdb=" N ASP X 49 " --> pdb=" O SER X 41 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N VAL X 43 " --> pdb=" O VAL X 47 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL X 47 " --> pdb=" O VAL X 43 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N ILE X 88 " --> pdb=" O VAL X 76 " (cutoff:3.500A) removed outlier: 5.302A 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: 8.519A pdb=" N ILE X 179 " --> pdb=" O ILE X 333 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N SER X 335 " --> pdb=" O ILE X 179 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N LEU X 181 " --> pdb=" O SER X 335 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N GLN X 337 " --> pdb=" O LEU X 181 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL X 213 " --> pdb=" O ASP X 285 " (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 37 through 39 removed outlier: 6.554A pdb=" N ARG Y 86 " --> pdb=" O ALA Y 77 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N HIS Y 79 " --> pdb=" O THR Y 84 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N THR Y 84 " --> pdb=" O HIS Y 79 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N ARG Y 51 " --> pdb=" O VAL Y 40 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N VAL Y 40 " --> pdb=" O ARG Y 51 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'Y' and resid 110 through 113 Processing sheet with id= AB, first strand: chain 'Y' and resid 360 through 363 removed outlier: 7.380A pdb=" N ILE Y 179 " --> pdb=" O ILE Y 333 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N SER Y 335 " --> pdb=" O ILE Y 179 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N LEU Y 181 " --> pdb=" O SER Y 335 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N GLN Y 337 " --> pdb=" O LEU Y 181 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N GLY Y 183 " --> pdb=" O GLN Y 337 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N VAL Y 339 " --> pdb=" O GLY Y 183 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N PHE Y 207 " --> pdb=" O LEU Y 281 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N PHE Y 283 " --> pdb=" O PHE Y 207 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N VAL Y 209 " --> pdb=" O PHE Y 283 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N ASP Y 285 " --> pdb=" O VAL Y 209 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N ALA Y 211 " --> pdb=" O ASP Y 285 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'Z' and resid 38 through 44 removed outlier: 6.468A pdb=" N ASP Z 49 " --> pdb=" O SER Z 41 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N VAL Z 43 " --> pdb=" O VAL Z 47 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N VAL Z 47 " --> pdb=" O VAL Z 43 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N ILE Z 88 " --> pdb=" O VAL Z 76 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N VAL Z 76 " --> pdb=" O ILE Z 88 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'Z' and resid 110 through 113 removed outlier: 3.709A pdb=" N ASP Z 139 " --> pdb=" O VAL Z 113 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'Z' and resid 360 through 363 removed outlier: 7.346A pdb=" N ILE Z 179 " --> pdb=" O ILE Z 333 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N SER Z 335 " --> pdb=" O ILE Z 179 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N LEU Z 181 " --> pdb=" O SER Z 335 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N GLN Z 337 " --> pdb=" O LEU Z 181 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N GLY Z 183 " --> pdb=" O GLN Z 337 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N VAL Z 339 " --> pdb=" O GLY Z 183 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU Z 282 " --> pdb=" O THR Z 334 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N THR Z 245 " --> pdb=" O PHE Z 210 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N GLY Z 212 " --> pdb=" O THR Z 245 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N VAL Z 247 " --> pdb=" O GLY Z 212 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'Z' and resid 559 through 561 2408 hydrogen bonds defined for protein. 6363 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: 15.58 Time building geometry restraints manager: 17.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 9120 1.31 - 1.44: 13370 1.44 - 1.56: 31893 1.56 - 1.69: 21 1.69 - 1.81: 254 Bond restraints: 54658 Sorted by residual: bond pdb=" C4 ATP U1001 " pdb=" C5 ATP U1001 " ideal model delta sigma weight residual 1.388 1.458 -0.070 1.00e-02 1.00e+04 4.92e+01 bond pdb=" C4 ATP T1001 " pdb=" C5 ATP T1001 " ideal model delta sigma weight residual 1.388 1.458 -0.070 1.00e-02 1.00e+04 4.84e+01 bond pdb=" C4 ATP V1001 " pdb=" C5 ATP V1001 " ideal model delta sigma weight residual 1.388 1.457 -0.069 1.00e-02 1.00e+04 4.73e+01 bond pdb=" C5 ATP V1001 " pdb=" C6 ATP V1001 " ideal model delta sigma weight residual 1.409 1.471 -0.062 1.00e-02 1.00e+04 3.81e+01 bond pdb=" C5 ATP T1001 " pdb=" C6 ATP T1001 " ideal model delta sigma weight residual 1.409 1.468 -0.059 1.00e-02 1.00e+04 3.48e+01 ... (remaining 54653 not shown) Histogram of bond angle deviations from ideal: 94.89 - 103.21: 532 103.21 - 111.52: 23908 111.52 - 119.83: 25584 119.83 - 128.15: 23759 128.15 - 136.46: 338 Bond angle restraints: 74121 Sorted by residual: angle pdb=" PB ATP U1001 " pdb=" O3B ATP U1001 " pdb=" PG ATP U1001 " ideal model delta sigma weight residual 139.87 120.46 19.41 1.00e+00 1.00e+00 3.77e+02 angle pdb=" PB ATP T1001 " pdb=" O3B ATP T1001 " pdb=" PG ATP T1001 " ideal model delta sigma weight residual 139.87 121.84 18.03 1.00e+00 1.00e+00 3.25e+02 angle pdb=" PA ATP V1001 " pdb=" O3A ATP V1001 " pdb=" PB ATP V1001 " ideal model delta sigma weight residual 136.83 120.37 16.46 1.00e+00 1.00e+00 2.71e+02 angle pdb=" PB ATP V1001 " pdb=" O3B ATP V1001 " pdb=" PG ATP V1001 " ideal model delta sigma weight residual 139.87 123.51 16.36 1.00e+00 1.00e+00 2.68e+02 angle pdb=" PA ATP T1001 " pdb=" O3A ATP T1001 " pdb=" PB ATP T1001 " ideal model delta sigma weight residual 136.83 120.53 16.30 1.00e+00 1.00e+00 2.66e+02 ... (remaining 74116 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.09: 32082 31.09 - 62.18: 851 62.18 - 93.27: 70 93.27 - 124.36: 0 124.36 - 155.44: 2 Dihedral angle restraints: 33005 sinusoidal: 12661 harmonic: 20344 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 -128.57 -51.43 0 5.00e+00 4.00e-02 1.06e+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 -130.66 -49.34 0 5.00e+00 4.00e-02 9.74e+01 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 -132.37 -47.63 0 5.00e+00 4.00e-02 9.07e+01 ... (remaining 33002 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 6391 0.066 - 0.132: 1952 0.132 - 0.197: 307 0.197 - 0.263: 27 0.263 - 0.329: 6 Chirality restraints: 8683 Sorted by residual: chirality pdb=" CB VAL T 180 " pdb=" CA VAL T 180 " pdb=" CG1 VAL T 180 " pdb=" CG2 VAL T 180 " 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=" CG LEU Y 266 " pdb=" CB LEU Y 266 " pdb=" CD1 LEU Y 266 " pdb=" CD2 LEU Y 266 " both_signs ideal model delta sigma weight residual False -2.59 -2.29 -0.30 2.00e-01 2.50e+01 2.28e+00 chirality pdb=" CB THR Z 334 " pdb=" CA THR Z 334 " pdb=" OG1 THR Z 334 " pdb=" CG2 THR Z 334 " both_signs ideal model delta sigma weight residual False 2.55 2.25 0.30 2.00e-01 2.50e+01 2.26e+00 ... (remaining 8680 not shown) Planarity restraints: 9504 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA Y 503 " 0.031 2.00e-02 2.50e+03 6.06e-02 3.68e+01 pdb=" C ALA Y 503 " -0.105 2.00e-02 2.50e+03 pdb=" O ALA Y 503 " 0.039 2.00e-02 2.50e+03 pdb=" N LYS Y 504 " 0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA Z 503 " 0.031 2.00e-02 2.50e+03 5.97e-02 3.56e+01 pdb=" C ALA Z 503 " -0.103 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 THR T 543 " -0.052 5.00e-02 4.00e+02 7.88e-02 9.93e+00 pdb=" N PRO T 544 " 0.136 5.00e-02 4.00e+02 pdb=" CA PRO T 544 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO T 544 " -0.043 5.00e-02 4.00e+02 ... (remaining 9501 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.58: 484 2.58 - 3.16: 43255 3.16 - 3.74: 86237 3.74 - 4.32: 125209 4.32 - 4.90: 204886 Nonbonded interactions: 460071 Sorted by model distance: nonbonded pdb=" O ALA X 499 " pdb=" N ALA X 503 " model vdw 1.994 2.520 nonbonded pdb=" O ASN Z 514 " pdb=" CG2 VAL Z 517 " model vdw 2.031 3.460 nonbonded pdb=" O1G ATP T1001 " pdb="MG MG T1002 " model vdw 2.083 2.170 nonbonded pdb=" CD1 LEU E 78 " pdb=" OE2 GLU E 111 " model vdw 2.178 3.460 nonbonded pdb=" OH TYR 5 62 " pdb=" O PHE 6 146 " model vdw 2.205 2.440 ... (remaining 460066 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 562 or resid 1001 through 1002)) selection = chain 'V' } ncs_group { reference = (chain 'X' and resid 37 through 552) selection = (chain 'Y' and resid 37 through 552) selection = (chain 'Z' and resid 37 through 552) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.290 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: 23.770 Check model and map are aligned: 0.660 Set scattering table: 0.380 Process input model: 103.420 Find NCS groups from input model: 2.760 Set up NCS constraints: 0.330 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: 0.010 Load rotamer database and sin/cos tables:2.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 137.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 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 : 0.012 0.153 54658 Z= 0.749 Angle : 1.019 19.408 74121 Z= 0.573 Chirality : 0.062 0.329 8683 Planarity : 0.008 0.079 9504 Dihedral : 14.083 155.445 19929 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.89 % Favored : 94.91 % Rotamer: Outliers : 0.43 % Allowed : 6.36 % Favored : 93.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.34 % 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: -3.96 (0.08), residues: 7034 helix: -2.89 (0.06), residues: 3785 sheet: -1.49 (0.20), residues: 593 loop : -2.20 (0.10), residues: 2656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP 4 206 HIS 0.012 0.002 HIS 4 233 PHE 0.037 0.003 PHE S 249 TYR 0.035 0.003 TYR 4 211 ARG 0.011 0.001 ARG X 98 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14068 Ramachandran restraints generated. 7034 Oldfield, 0 Emsley, 7034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14068 Ramachandran restraints generated. 7034 Oldfield, 0 Emsley, 7034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 994 residues out of total 5633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 970 time to evaluate : 4.485 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: 1 539 ASP cc_start: 0.8648 (p0) cc_final: 0.8447 (p0) REVERT: 1 614 LEU cc_start: 0.8687 (mt) cc_final: 0.8413 (mt) REVERT: 5 115 ILE cc_start: 0.8647 (tp) cc_final: 0.8233 (tp) REVERT: 7 184 ASN cc_start: 0.8415 (t0) cc_final: 0.8061 (t0) REVERT: 8 69 LYS cc_start: 0.8668 (mttt) cc_final: 0.7032 (tmtt) REVERT: 9 35 GLN cc_start: 0.8109 (tt0) cc_final: 0.7775 (mt0) REVERT: 9 74 GLU cc_start: 0.7920 (mp0) cc_final: 0.7238 (mp0) REVERT: A 86 ILE cc_start: 0.8363 (mt) cc_final: 0.8155 (mt) REVERT: F 61 MET cc_start: 0.7783 (mmt) cc_final: 0.7379 (mmt) REVERT: G 71 LEU cc_start: 0.8822 (mt) cc_final: 0.8590 (mt) REVERT: G 124 ILE cc_start: 0.8253 (mm) cc_final: 0.7967 (mt) REVERT: I 87 ASN cc_start: 0.8241 (t0) cc_final: 0.7922 (t0) REVERT: P 219 ASN cc_start: 0.9189 (m-40) cc_final: 0.8838 (m-40) REVERT: P 220 ASN cc_start: 0.9007 (m110) cc_final: 0.8805 (m-40) REVERT: Q 42 ARG cc_start: 0.8512 (ptp90) cc_final: 0.8294 (ptp-170) REVERT: R 31 LYS cc_start: 0.8133 (tmtt) cc_final: 0.7904 (pttp) REVERT: R 40 LYS cc_start: 0.8203 (ttmt) cc_final: 0.7991 (mtpt) REVERT: R 164 LEU cc_start: 0.6127 (pp) cc_final: 0.5506 (tp) REVERT: S 180 GLU cc_start: 0.7443 (mt-10) cc_final: 0.7231 (mt-10) REVERT: S 291 ASP cc_start: 0.7641 (t70) cc_final: 0.7441 (t0) REVERT: T 483 MET cc_start: 0.7688 (tmm) cc_final: 0.7460 (tmm) REVERT: U 482 GLU cc_start: 0.7425 (mm-30) cc_final: 0.7197 (mm-30) REVERT: U 521 GLU cc_start: 0.6412 (pt0) cc_final: 0.6074 (pt0) REVERT: U 546 LEU cc_start: 0.8802 (tp) cc_final: 0.8365 (tp) REVERT: V 67 ILE cc_start: 0.8845 (pt) cc_final: 0.8433 (mp) REVERT: V 134 ASN cc_start: 0.8187 (t0) cc_final: 0.7961 (t0) REVERT: V 448 LEU cc_start: 0.7550 (tp) cc_final: 0.7247 (tp) REVERT: V 471 GLN cc_start: 0.7873 (tt0) cc_final: 0.7448 (mm110) REVERT: X 465 ASP cc_start: 0.7530 (m-30) cc_final: 0.7260 (m-30) REVERT: Z 90 MET cc_start: 0.9025 (mmp) cc_final: 0.8797 (mmt) REVERT: Z 430 LYS cc_start: 0.7629 (ttmt) cc_final: 0.7362 (mtpp) REVERT: Z 437 ARG cc_start: 0.8423 (mtt-85) cc_final: 0.8112 (mtp85) REVERT: Z 483 GLU cc_start: 0.6921 (tt0) cc_final: 0.6669 (tt0) REVERT: Z 488 MET cc_start: 0.8720 (mmt) cc_final: 0.8317 (mmm) outliers start: 24 outliers final: 10 residues processed: 991 average time/residue: 0.5468 time to fit residues: 881.6258 Evaluate side-chains 677 residues out of total 5633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 667 time to evaluate : 4.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 240 VAL Chi-restraints excluded: chain 7 residue 157 VAL Chi-restraints excluded: chain P residue 152 VAL Chi-restraints excluded: chain P residue 185 VAL Chi-restraints excluded: chain Q residue 69 ILE Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain S residue 140 VAL Chi-restraints excluded: chain T residue 94 ILE Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain Z residue 559 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 697 random chunks: chunk 588 optimal weight: 2.9990 chunk 528 optimal weight: 4.9990 chunk 293 optimal weight: 0.8980 chunk 180 optimal weight: 7.9990 chunk 356 optimal weight: 2.9990 chunk 282 optimal weight: 0.1980 chunk 546 optimal weight: 2.9990 chunk 211 optimal weight: 0.7980 chunk 332 optimal weight: 0.3980 chunk 406 optimal weight: 0.9980 chunk 632 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 60 GLN 0 79 HIS 1 65 GLN 1 100 GLN 1 285 GLN 1 298 GLN 1 316 ASN ** 1 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 482 ASN 1 562 ASN 1 587 ASN 1 590 HIS 1 606 ASN 2 102 GLN 2 243 GLN 2 289 HIS ** 3 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 189 HIS 3 206 ASN 3 229 ASN 4 240 GLN 5 29 GLN 5 107 ASN 6 40 ASN 7 86 HIS 7 91 ASN 7 123 HIS 7 170 HIS 8 26 HIS 8 29 GLN A 87 ASN ** B 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 GLN D 98 GLN F 98 GLN G 98 GLN I 98 GLN J 87 ASN J 98 GLN M 108 ASN M 121 ASN M 127 HIS M 163 ASN M 243 ASN P 66 GLN P 76 GLN P 140 ASN P 220 ASN ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 46 HIS R 83 GLN R 137 HIS R 154 GLN ** S 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 262 ASN S 267 HIS T 64 GLN T 152 ASN ** T 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 241 HIS T 264 GLN T 358 HIS T 441 GLN U 64 GLN U 179 ASN U 196 GLN U 242 GLN U 246 ASN U 248 GLN U 264 GLN U 319 HIS U 386 GLN U 539 ASN V 78 GLN V 152 ASN V 179 ASN V 241 HIS V 244 ASN V 386 GLN V 486 GLN V 488 GLN V 497 GLN X 144 HIS X 199 ASN X 250 GLN X 278 GLN X 294 ASN X 414 GLN Y 174 GLN Y 199 ASN Y 278 GLN Y 412 ASN Z 157 GLN Z 174 GLN Z 398 ASN Z 408 GLN Total number of N/Q/H flips: 90 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 54658 Z= 0.169 Angle : 0.550 11.362 74121 Z= 0.287 Chirality : 0.041 0.170 8683 Planarity : 0.005 0.062 9504 Dihedral : 6.431 136.907 7676 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.13 % Favored : 96.74 % Rotamer: Outliers : 1.71 % Allowed : 10.50 % Favored : 87.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -2.15 (0.09), residues: 7034 helix: -1.18 (0.08), residues: 3822 sheet: -1.11 (0.20), residues: 602 loop : -1.63 (0.11), residues: 2610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP 9 93 HIS 0.006 0.001 HIS V 83 PHE 0.019 0.001 PHE C 82 TYR 0.027 0.001 TYR 4 211 ARG 0.005 0.000 ARG 1 387 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14068 Ramachandran restraints generated. 7034 Oldfield, 0 Emsley, 7034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14068 Ramachandran restraints generated. 7034 Oldfield, 0 Emsley, 7034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 911 residues out of total 5633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 815 time to evaluate : 4.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 539 ASP cc_start: 0.8593 (p0) cc_final: 0.8381 (p0) REVERT: 2 427 GLN cc_start: 0.8071 (tt0) cc_final: 0.7675 (tp40) REVERT: 4 218 GLU cc_start: 0.6984 (OUTLIER) cc_final: 0.6570 (mp0) REVERT: 5 100 SER cc_start: 0.8729 (t) cc_final: 0.8435 (p) REVERT: 5 115 ILE cc_start: 0.8634 (tp) cc_final: 0.8206 (tp) REVERT: 7 138 TYR cc_start: 0.8735 (m-80) cc_final: 0.8531 (m-80) REVERT: 8 69 LYS cc_start: 0.8613 (mttt) cc_final: 0.7097 (tmtt) REVERT: C 81 MET cc_start: 0.7640 (ttp) cc_final: 0.7430 (ttp) REVERT: E 60 LYS cc_start: 0.8107 (ptmt) cc_final: 0.7887 (mtpt) REVERT: F 61 MET cc_start: 0.7735 (mmt) cc_final: 0.7413 (mmt) REVERT: F 81 MET cc_start: 0.8553 (ttp) cc_final: 0.8264 (ttt) REVERT: G 124 ILE cc_start: 0.8144 (mm) cc_final: 0.7908 (mt) REVERT: H 92 ASN cc_start: 0.8628 (p0) cc_final: 0.8025 (p0) REVERT: I 104 LEU cc_start: 0.8172 (mt) cc_final: 0.7954 (mp) REVERT: J 124 ILE cc_start: 0.8710 (mm) cc_final: 0.8508 (tp) REVERT: P 49 THR cc_start: 0.8539 (OUTLIER) cc_final: 0.8284 (m) REVERT: P 78 ILE cc_start: 0.8952 (mm) cc_final: 0.8656 (mt) REVERT: P 220 ASN cc_start: 0.9012 (m-40) cc_final: 0.8802 (m-40) REVERT: R 127 PHE cc_start: 0.8596 (m-80) cc_final: 0.8284 (m-80) REVERT: R 164 LEU cc_start: 0.5881 (pp) cc_final: 0.5589 (tp) REVERT: T 407 PHE cc_start: 0.7753 (t80) cc_final: 0.7419 (t80) REVERT: T 483 MET cc_start: 0.7626 (tmm) cc_final: 0.7410 (tmm) REVERT: U 467 ASP cc_start: 0.6439 (t0) cc_final: 0.6217 (t0) REVERT: U 482 GLU cc_start: 0.7405 (mm-30) cc_final: 0.7176 (mm-30) REVERT: V 66 LEU cc_start: 0.8463 (mm) cc_final: 0.8240 (mt) REVERT: V 67 ILE cc_start: 0.8782 (pt) cc_final: 0.8518 (mm) REVERT: V 407 PHE cc_start: 0.7786 (t80) cc_final: 0.7507 (m-80) REVERT: V 471 GLN cc_start: 0.7756 (tt0) cc_final: 0.7340 (mm110) REVERT: Z 430 LYS cc_start: 0.7501 (ttmt) cc_final: 0.7081 (tppt) REVERT: Z 488 MET cc_start: 0.8651 (mmt) cc_final: 0.8319 (mmm) outliers start: 96 outliers final: 61 residues processed: 877 average time/residue: 0.5106 time to fit residues: 754.1086 Evaluate side-chains 730 residues out of total 5633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 667 time to evaluate : 4.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 43 SER Chi-restraints excluded: chain 1 residue 240 VAL Chi-restraints excluded: chain 1 residue 308 ASN Chi-restraints excluded: chain 1 residue 486 ASP Chi-restraints excluded: chain 2 residue 374 ASP Chi-restraints excluded: chain 2 residue 422 GLU Chi-restraints excluded: chain 4 residue 218 GLU Chi-restraints excluded: chain 5 residue 61 SER Chi-restraints excluded: chain 6 residue 101 VAL Chi-restraints excluded: chain 7 residue 35 ILE Chi-restraints excluded: chain 7 residue 79 VAL Chi-restraints excluded: chain 7 residue 144 VAL Chi-restraints excluded: chain 7 residue 157 VAL Chi-restraints excluded: chain 8 residue 55 ILE Chi-restraints excluded: chain 9 residue 29 PHE Chi-restraints excluded: chain 9 residue 65 THR Chi-restraints excluded: chain C residue 59 SER Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain E residue 84 SER Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain F residue 94 ASN Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain J residue 84 SER Chi-restraints excluded: chain J residue 87 ASN Chi-restraints excluded: chain J residue 121 VAL Chi-restraints excluded: chain M residue 313 ASP Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 152 VAL Chi-restraints excluded: chain P residue 185 VAL Chi-restraints excluded: chain P residue 207 VAL Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain Q residue 69 ILE Chi-restraints excluded: chain R residue 82 SER Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain R residue 153 ASP Chi-restraints excluded: chain S residue 140 VAL Chi-restraints excluded: chain T residue 76 SER Chi-restraints excluded: chain T residue 94 ILE Chi-restraints excluded: chain T residue 428 SER Chi-restraints excluded: chain T residue 514 VAL Chi-restraints excluded: chain T residue 543 THR Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 514 VAL Chi-restraints excluded: chain U residue 516 ASP Chi-restraints excluded: chain U residue 528 VAL Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 410 THR Chi-restraints excluded: chain X residue 226 GLU Chi-restraints excluded: chain X residue 232 VAL Chi-restraints excluded: chain X residue 502 MET Chi-restraints excluded: chain X residue 511 GLU Chi-restraints excluded: chain Y residue 80 MET Chi-restraints excluded: chain Y residue 266 LEU Chi-restraints excluded: chain Y residue 381 ASP Chi-restraints excluded: chain Y residue 451 GLU Chi-restraints excluded: chain Y residue 524 ILE Chi-restraints excluded: chain Z residue 308 VAL Chi-restraints excluded: chain Z residue 334 THR Chi-restraints excluded: chain Z residue 416 ILE Chi-restraints excluded: chain Z residue 545 LEU Chi-restraints excluded: chain Z residue 559 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 697 random chunks: chunk 351 optimal weight: 2.9990 chunk 196 optimal weight: 0.2980 chunk 526 optimal weight: 6.9990 chunk 431 optimal weight: 5.9990 chunk 174 optimal weight: 4.9990 chunk 634 optimal weight: 0.0770 chunk 685 optimal weight: 0.0570 chunk 564 optimal weight: 3.9990 chunk 628 optimal weight: 5.9990 chunk 216 optimal weight: 0.2980 chunk 508 optimal weight: 0.7980 overall best weight: 0.3056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 394 GLN 1 531 HIS 2 68 ASN 2 102 GLN 3 97 ASN 3 231 HIS 4 276 GLN 9 56 ASN B 87 ASN C 87 ASN M 127 HIS ** M 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 76 GLN P 140 ASN ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 149 GLN U 179 ASN U 241 HIS U 539 ASN V 228 GLN ** X 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 414 GLN ** Y 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 241 ASN Z 440 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 54658 Z= 0.132 Angle : 0.497 9.615 74121 Z= 0.256 Chirality : 0.040 0.159 8683 Planarity : 0.004 0.049 9504 Dihedral : 5.712 129.738 7676 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.40 % Favored : 96.50 % Rotamer: Outliers : 1.81 % Allowed : 13.13 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.10), residues: 7034 helix: -0.38 (0.08), residues: 3839 sheet: -0.80 (0.21), residues: 618 loop : -1.19 (0.12), residues: 2577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP 9 93 HIS 0.006 0.001 HIS M 127 PHE 0.027 0.001 PHE 3 115 TYR 0.026 0.001 TYR 4 211 ARG 0.005 0.000 ARG Z 401 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14068 Ramachandran restraints generated. 7034 Oldfield, 0 Emsley, 7034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14068 Ramachandran restraints generated. 7034 Oldfield, 0 Emsley, 7034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 905 residues out of total 5633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 803 time to evaluate : 4.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 37 LYS cc_start: 0.8559 (tptm) cc_final: 0.8348 (tptp) REVERT: 1 219 LYS cc_start: 0.8084 (mttp) cc_final: 0.7872 (mmtt) REVERT: 2 322 ARG cc_start: 0.8114 (ttm170) cc_final: 0.7894 (ttm170) REVERT: 4 218 GLU cc_start: 0.6848 (OUTLIER) cc_final: 0.6408 (mp0) REVERT: 5 100 SER cc_start: 0.8683 (t) cc_final: 0.8431 (p) REVERT: 5 115 ILE cc_start: 0.8544 (tp) cc_final: 0.8125 (tp) REVERT: 8 69 LYS cc_start: 0.8590 (mttt) cc_final: 0.7123 (tmtt) REVERT: A 92 ASN cc_start: 0.8407 (t0) cc_final: 0.8132 (t0) REVERT: E 60 LYS cc_start: 0.8120 (ptmt) cc_final: 0.7855 (mtpt) REVERT: F 61 MET cc_start: 0.7581 (mmt) cc_final: 0.7308 (mmt) REVERT: F 81 MET cc_start: 0.8479 (ttp) cc_final: 0.8160 (ttt) REVERT: G 61 MET cc_start: 0.8058 (mmt) cc_final: 0.7825 (mmm) REVERT: G 124 ILE cc_start: 0.8128 (mm) cc_final: 0.7912 (mt) REVERT: H 92 ASN cc_start: 0.8497 (p0) cc_final: 0.7970 (p0) REVERT: J 115 LEU cc_start: 0.7299 (OUTLIER) cc_final: 0.6944 (mt) REVERT: J 124 ILE cc_start: 0.8675 (mm) cc_final: 0.8474 (tp) REVERT: M 288 GLU cc_start: 0.7403 (OUTLIER) cc_final: 0.7135 (mt-10) REVERT: P 49 THR cc_start: 0.8383 (OUTLIER) cc_final: 0.8081 (m) REVERT: P 78 ILE cc_start: 0.8984 (mm) cc_final: 0.8700 (mt) REVERT: P 220 ASN cc_start: 0.8993 (m-40) cc_final: 0.8723 (m-40) REVERT: Q 16 TYR cc_start: 0.8442 (t80) cc_final: 0.8221 (t80) REVERT: Q 20 SER cc_start: 0.8817 (t) cc_final: 0.8477 (p) REVERT: R 127 PHE cc_start: 0.8491 (m-80) cc_final: 0.8270 (m-80) REVERT: S 232 ASP cc_start: 0.7713 (m-30) cc_final: 0.7506 (m-30) REVERT: S 260 LEU cc_start: 0.9284 (OUTLIER) cc_final: 0.8937 (mp) REVERT: T 407 PHE cc_start: 0.7872 (t80) cc_final: 0.7518 (t80) REVERT: T 549 HIS cc_start: 0.6349 (t70) cc_final: 0.6045 (t70) REVERT: U 49 ARG cc_start: 0.7291 (mtm-85) cc_final: 0.6961 (mtm-85) REVERT: V 112 ASP cc_start: 0.8332 (p0) cc_final: 0.8054 (p0) REVERT: V 471 GLN cc_start: 0.7721 (tt0) cc_final: 0.7324 (mm110) REVERT: X 497 GLU cc_start: 0.7266 (OUTLIER) cc_final: 0.6978 (mp0) REVERT: Z 195 GLU cc_start: 0.7793 (tp30) cc_final: 0.7577 (tp30) REVERT: Z 385 ARG cc_start: 0.7297 (mpt180) cc_final: 0.7020 (mmt90) outliers start: 102 outliers final: 53 residues processed: 872 average time/residue: 0.5176 time to fit residues: 757.3755 Evaluate side-chains 735 residues out of total 5633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 676 time to evaluate : 4.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 43 SER Chi-restraints excluded: chain 1 residue 226 VAL Chi-restraints excluded: chain 1 residue 240 VAL Chi-restraints excluded: chain 2 residue 377 VAL Chi-restraints excluded: chain 3 residue 156 ASP Chi-restraints excluded: chain 3 residue 309 ASN Chi-restraints excluded: chain 4 residue 44 THR Chi-restraints excluded: chain 4 residue 218 GLU Chi-restraints excluded: chain 6 residue 31 SER Chi-restraints excluded: chain 6 residue 79 LEU Chi-restraints excluded: chain 6 residue 101 VAL Chi-restraints excluded: chain 7 residue 79 VAL Chi-restraints excluded: chain 8 residue 3 LEU Chi-restraints excluded: chain 9 residue 29 PHE Chi-restraints excluded: chain 9 residue 56 ASN Chi-restraints excluded: chain 9 residue 65 THR Chi-restraints excluded: chain E residue 84 SER Chi-restraints excluded: chain F residue 94 ASN Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 121 VAL Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain I residue 118 LEU Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain J residue 115 LEU Chi-restraints excluded: chain J residue 121 VAL Chi-restraints excluded: chain M residue 288 GLU Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 152 VAL Chi-restraints excluded: chain P residue 185 VAL Chi-restraints excluded: chain P residue 195 LEU Chi-restraints excluded: chain P residue 207 VAL Chi-restraints excluded: chain P residue 227 LEU Chi-restraints excluded: chain Q residue 69 ILE Chi-restraints excluded: chain R residue 82 SER Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain S residue 140 VAL Chi-restraints excluded: chain S residue 260 LEU Chi-restraints excluded: chain T residue 94 ILE Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 428 SER Chi-restraints excluded: chain T residue 514 VAL Chi-restraints excluded: chain T residue 543 THR Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 465 ASP Chi-restraints excluded: chain U residue 483 MET Chi-restraints excluded: chain U residue 514 VAL Chi-restraints excluded: chain U residue 516 ASP Chi-restraints excluded: chain U residue 528 VAL Chi-restraints excluded: chain U residue 546 LEU Chi-restraints excluded: chain V residue 70 VAL Chi-restraints excluded: chain V residue 410 THR Chi-restraints excluded: chain X residue 226 GLU Chi-restraints excluded: chain X residue 497 GLU Chi-restraints excluded: chain X residue 524 ILE Chi-restraints excluded: chain Y residue 266 LEU Chi-restraints excluded: chain Y residue 451 GLU Chi-restraints excluded: chain Y residue 524 ILE Chi-restraints excluded: chain Z residue 334 THR Chi-restraints excluded: chain Z residue 559 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 697 random chunks: chunk 626 optimal weight: 3.9990 chunk 476 optimal weight: 6.9990 chunk 329 optimal weight: 4.9990 chunk 70 optimal weight: 0.6980 chunk 302 optimal weight: 4.9990 chunk 425 optimal weight: 10.0000 chunk 636 optimal weight: 3.9990 chunk 673 optimal weight: 4.9990 chunk 332 optimal weight: 2.9990 chunk 603 optimal weight: 3.9990 chunk 181 optimal weight: 2.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 430 GLN 2 102 GLN 3 309 ASN 4 276 GLN 5 29 GLN 6 74 GLN B 87 ASN C 87 ASN F 98 GLN M 127 HIS M 243 ASN P 59 GLN P 140 ASN ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 267 HIS T 61 HIS T 121 ASN T 471 GLN U 241 HIS U 539 ASN U 549 HIS V 64 GLN ** V 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 241 ASN X 414 GLN X 574 ASN ** Y 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.1917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.097 54658 Z= 0.396 Angle : 0.608 12.897 74121 Z= 0.312 Chirality : 0.045 0.179 8683 Planarity : 0.004 0.049 9504 Dihedral : 6.107 121.304 7674 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.18 % Favored : 95.69 % Rotamer: Outliers : 2.79 % Allowed : 14.29 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.02 (0.10), residues: 7034 helix: -0.25 (0.08), residues: 3832 sheet: -0.87 (0.21), residues: 631 loop : -1.08 (0.12), residues: 2571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP 9 93 HIS 0.008 0.001 HIS 7 123 PHE 0.036 0.002 PHE I 122 TYR 0.026 0.002 TYR 7 101 ARG 0.006 0.001 ARG Z 435 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14068 Ramachandran restraints generated. 7034 Oldfield, 0 Emsley, 7034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14068 Ramachandran restraints generated. 7034 Oldfield, 0 Emsley, 7034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 836 residues out of total 5633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 679 time to evaluate : 4.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 37 LYS cc_start: 0.8678 (tptm) cc_final: 0.8453 (tptp) REVERT: 5 115 ILE cc_start: 0.8623 (tp) cc_final: 0.8235 (tp) REVERT: 8 69 LYS cc_start: 0.8626 (mttt) cc_final: 0.7049 (tmtt) REVERT: C 81 MET cc_start: 0.7722 (ttp) cc_final: 0.7438 (ttp) REVERT: E 61 MET cc_start: 0.7667 (mtm) cc_final: 0.7337 (mtm) REVERT: F 61 MET cc_start: 0.7693 (mmt) cc_final: 0.7449 (mmt) REVERT: F 81 MET cc_start: 0.8560 (ttp) cc_final: 0.8259 (ttt) REVERT: G 116 PHE cc_start: 0.7443 (OUTLIER) cc_final: 0.7029 (m-10) REVERT: H 92 ASN cc_start: 0.8586 (p0) cc_final: 0.7959 (p0) REVERT: I 123 LEU cc_start: 0.8078 (OUTLIER) cc_final: 0.7873 (mp) REVERT: M 288 GLU cc_start: 0.7546 (OUTLIER) cc_final: 0.7346 (mt-10) REVERT: P 49 THR cc_start: 0.8551 (OUTLIER) cc_final: 0.8310 (m) REVERT: P 140 ASN cc_start: 0.8723 (m-40) cc_final: 0.8427 (m110) REVERT: P 220 ASN cc_start: 0.8990 (m-40) cc_final: 0.8759 (m-40) REVERT: R 127 PHE cc_start: 0.8599 (m-80) cc_final: 0.8338 (m-80) REVERT: R 188 TYR cc_start: 0.7432 (m-80) cc_final: 0.7213 (m-80) REVERT: S 260 LEU cc_start: 0.9334 (OUTLIER) cc_final: 0.8947 (mp) REVERT: V 471 GLN cc_start: 0.7889 (tt0) cc_final: 0.7383 (mm110) REVERT: Z 430 LYS cc_start: 0.7591 (ttmt) cc_final: 0.7183 (mtpp) outliers start: 157 outliers final: 123 residues processed: 786 average time/residue: 0.5045 time to fit residues: 672.4274 Evaluate side-chains 759 residues out of total 5633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 631 time to evaluate : 4.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 19 SER Chi-restraints excluded: chain 0 residue 32 THR Chi-restraints excluded: chain 0 residue 36 THR Chi-restraints excluded: chain 0 residue 43 SER Chi-restraints excluded: chain 1 residue 226 VAL Chi-restraints excluded: chain 1 residue 240 VAL Chi-restraints excluded: chain 1 residue 486 ASP Chi-restraints excluded: chain 1 residue 530 LYS Chi-restraints excluded: chain 2 residue 209 ASP Chi-restraints excluded: chain 2 residue 238 ASP Chi-restraints excluded: chain 2 residue 377 VAL Chi-restraints excluded: chain 3 residue 156 ASP Chi-restraints excluded: chain 3 residue 159 THR Chi-restraints excluded: chain 3 residue 258 LYS Chi-restraints excluded: chain 3 residue 309 ASN Chi-restraints excluded: chain 4 residue 44 THR Chi-restraints excluded: chain 4 residue 77 SER Chi-restraints excluded: chain 5 residue 61 SER Chi-restraints excluded: chain 5 residue 110 SER Chi-restraints excluded: chain 5 residue 113 VAL Chi-restraints excluded: chain 6 residue 31 SER Chi-restraints excluded: chain 6 residue 57 GLN Chi-restraints excluded: chain 6 residue 73 THR Chi-restraints excluded: chain 6 residue 79 LEU Chi-restraints excluded: chain 6 residue 101 VAL Chi-restraints excluded: chain 6 residue 118 SER Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 7 residue 15 LEU Chi-restraints excluded: chain 7 residue 35 ILE Chi-restraints excluded: chain 7 residue 79 VAL Chi-restraints excluded: chain 7 residue 144 VAL Chi-restraints excluded: chain 8 residue 3 LEU Chi-restraints excluded: chain 8 residue 55 ILE Chi-restraints excluded: chain 8 residue 67 SER Chi-restraints excluded: chain 8 residue 82 THR Chi-restraints excluded: chain 9 residue 29 PHE Chi-restraints excluded: chain 9 residue 56 ASN Chi-restraints excluded: chain 9 residue 65 THR Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 59 SER Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain E residue 84 SER Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain F residue 94 ASN Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 121 VAL Chi-restraints excluded: chain G residue 113 ILE Chi-restraints excluded: chain G residue 116 PHE Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain I residue 118 LEU Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 123 LEU Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 115 LEU Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain J residue 121 VAL Chi-restraints excluded: chain M residue 161 SER Chi-restraints excluded: chain M residue 274 THR Chi-restraints excluded: chain M residue 288 GLU Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 107 SER Chi-restraints excluded: chain P residue 146 LEU Chi-restraints excluded: chain P residue 152 VAL Chi-restraints excluded: chain P residue 185 VAL Chi-restraints excluded: chain P residue 195 LEU Chi-restraints excluded: chain P residue 199 VAL Chi-restraints excluded: chain P residue 200 ILE Chi-restraints excluded: chain P residue 207 VAL Chi-restraints excluded: chain P residue 227 LEU Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain Q residue 69 ILE Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain R residue 82 SER Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain R residue 146 VAL Chi-restraints excluded: chain R residue 162 SER Chi-restraints excluded: chain S residue 140 VAL Chi-restraints excluded: chain S residue 243 LEU Chi-restraints excluded: chain S residue 260 LEU Chi-restraints excluded: chain T residue 75 LYS Chi-restraints excluded: chain T residue 94 ILE Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 359 SER Chi-restraints excluded: chain T residue 410 THR Chi-restraints excluded: chain T residue 428 SER Chi-restraints excluded: chain T residue 430 VAL Chi-restraints excluded: chain T residue 514 VAL Chi-restraints excluded: chain T residue 532 VAL Chi-restraints excluded: chain U residue 53 PHE Chi-restraints excluded: chain U residue 448 LEU Chi-restraints excluded: chain U residue 465 ASP Chi-restraints excluded: chain U residue 514 VAL Chi-restraints excluded: chain U residue 516 ASP Chi-restraints excluded: chain U residue 546 LEU Chi-restraints excluded: chain V residue 70 VAL Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain V residue 187 VAL Chi-restraints excluded: chain V residue 410 THR Chi-restraints excluded: chain V residue 421 LEU Chi-restraints excluded: chain V residue 430 VAL Chi-restraints excluded: chain V residue 465 ASP Chi-restraints excluded: chain V residue 475 GLU Chi-restraints excluded: chain V residue 518 VAL Chi-restraints excluded: chain X residue 49 ASP Chi-restraints excluded: chain X residue 62 SER Chi-restraints excluded: chain X residue 232 VAL Chi-restraints excluded: chain X residue 308 VAL Chi-restraints excluded: chain X residue 425 LEU Chi-restraints excluded: chain X residue 524 ILE Chi-restraints excluded: chain X residue 531 VAL Chi-restraints excluded: chain X residue 554 LEU Chi-restraints excluded: chain Y residue 84 THR Chi-restraints excluded: chain Y residue 266 LEU Chi-restraints excluded: chain Y residue 280 VAL Chi-restraints excluded: chain Y residue 383 THR Chi-restraints excluded: chain Y residue 420 LEU Chi-restraints excluded: chain Y residue 547 GLU Chi-restraints excluded: chain Z residue 103 VAL Chi-restraints excluded: chain Z residue 113 VAL Chi-restraints excluded: chain Z residue 217 THR Chi-restraints excluded: chain Z residue 334 THR Chi-restraints excluded: chain Z residue 489 VAL Chi-restraints excluded: chain Z residue 545 LEU Chi-restraints excluded: chain Z residue 554 LEU Chi-restraints excluded: chain Z residue 559 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 697 random chunks: chunk 561 optimal weight: 0.9990 chunk 382 optimal weight: 3.9990 chunk 9 optimal weight: 0.0770 chunk 501 optimal weight: 0.7980 chunk 277 optimal weight: 0.0030 chunk 574 optimal weight: 4.9990 chunk 465 optimal weight: 7.9990 chunk 0 optimal weight: 2.9990 chunk 344 optimal weight: 4.9990 chunk 604 optimal weight: 2.9990 chunk 170 optimal weight: 0.9980 overall best weight: 0.5750 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 102 GLN 4 276 GLN ** 7 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 56 ASN J 87 ASN M 127 HIS M 243 ASN ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 441 GLN U 179 ASN U 241 HIS ** U 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 539 ASN ** V 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 440 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 54658 Z= 0.145 Angle : 0.497 10.069 74121 Z= 0.255 Chirality : 0.040 0.158 8683 Planarity : 0.004 0.046 9504 Dihedral : 5.620 123.454 7674 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.27 % Favored : 96.62 % Rotamer: Outliers : 2.31 % Allowed : 15.17 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.10), residues: 7034 helix: 0.17 (0.09), residues: 3835 sheet: -0.57 (0.21), residues: 617 loop : -0.89 (0.12), residues: 2582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP 9 93 HIS 0.004 0.001 HIS M 127 PHE 0.038 0.001 PHE I 122 TYR 0.024 0.001 TYR 4 211 ARG 0.004 0.000 ARG Y 385 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14068 Ramachandran restraints generated. 7034 Oldfield, 0 Emsley, 7034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14068 Ramachandran restraints generated. 7034 Oldfield, 0 Emsley, 7034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 833 residues out of total 5633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 703 time to evaluate : 4.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 267 ARG cc_start: 0.8417 (mpt180) cc_final: 0.8037 (mpt180) REVERT: 2 177 GLN cc_start: 0.6963 (tt0) cc_final: 0.5991 (tt0) REVERT: 3 258 LYS cc_start: 0.7186 (OUTLIER) cc_final: 0.6864 (ttpt) REVERT: 3 279 GLU cc_start: 0.8190 (pt0) cc_final: 0.7919 (pt0) REVERT: 5 115 ILE cc_start: 0.8569 (tp) cc_final: 0.8149 (tp) REVERT: 6 146 PHE cc_start: 0.8567 (OUTLIER) cc_final: 0.7904 (t80) REVERT: 8 69 LYS cc_start: 0.8587 (mttt) cc_final: 0.7083 (tmtt) REVERT: B 78 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8108 (mp) REVERT: E 60 LYS cc_start: 0.8040 (ptmt) cc_final: 0.7290 (ptmm) REVERT: F 61 MET cc_start: 0.7583 (mmt) cc_final: 0.7368 (mmt) REVERT: F 81 MET cc_start: 0.8486 (ttp) cc_final: 0.8163 (ttt) REVERT: G 71 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8423 (mp) REVERT: G 116 PHE cc_start: 0.7368 (OUTLIER) cc_final: 0.6951 (m-10) REVERT: H 92 ASN cc_start: 0.8514 (p0) cc_final: 0.7969 (p0) REVERT: J 115 LEU cc_start: 0.7422 (OUTLIER) cc_final: 0.6988 (mt) REVERT: P 49 THR cc_start: 0.8393 (OUTLIER) cc_final: 0.8159 (m) REVERT: P 78 ILE cc_start: 0.9077 (mm) cc_final: 0.8848 (mt) REVERT: P 83 GLN cc_start: 0.6748 (OUTLIER) cc_final: 0.5726 (mp10) REVERT: P 220 ASN cc_start: 0.8941 (m-40) cc_final: 0.8689 (m-40) REVERT: Q 20 SER cc_start: 0.8850 (OUTLIER) cc_final: 0.8486 (p) REVERT: R 127 PHE cc_start: 0.8538 (m-80) cc_final: 0.8311 (m-80) REVERT: S 260 LEU cc_start: 0.9311 (OUTLIER) cc_final: 0.8950 (mp) REVERT: U 49 ARG cc_start: 0.7386 (mtm-85) cc_final: 0.6650 (mtm-85) REVERT: U 482 GLU cc_start: 0.7431 (mm-30) cc_final: 0.7143 (mm-30) REVERT: V 112 ASP cc_start: 0.8447 (p0) cc_final: 0.8239 (p0) REVERT: V 471 GLN cc_start: 0.7721 (tt0) cc_final: 0.7341 (mm110) REVERT: X 497 GLU cc_start: 0.7377 (OUTLIER) cc_final: 0.7039 (mp0) REVERT: X 550 LYS cc_start: 0.7721 (pttt) cc_final: 0.7436 (mmmt) outliers start: 130 outliers final: 90 residues processed: 799 average time/residue: 0.5048 time to fit residues: 681.9540 Evaluate side-chains 748 residues out of total 5633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 647 time to evaluate : 4.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 47 VAL Chi-restraints excluded: chain 1 residue 226 VAL Chi-restraints excluded: chain 1 residue 234 VAL Chi-restraints excluded: chain 1 residue 240 VAL Chi-restraints excluded: chain 1 residue 310 THR Chi-restraints excluded: chain 1 residue 486 ASP Chi-restraints excluded: chain 2 residue 209 ASP Chi-restraints excluded: chain 2 residue 238 ASP Chi-restraints excluded: chain 2 residue 303 VAL Chi-restraints excluded: chain 3 residue 156 ASP Chi-restraints excluded: chain 3 residue 258 LYS Chi-restraints excluded: chain 4 residue 44 THR Chi-restraints excluded: chain 4 residue 77 SER Chi-restraints excluded: chain 4 residue 122 VAL Chi-restraints excluded: chain 6 residue 73 THR Chi-restraints excluded: chain 6 residue 79 LEU Chi-restraints excluded: chain 6 residue 101 VAL Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 7 residue 15 LEU Chi-restraints excluded: chain 7 residue 35 ILE Chi-restraints excluded: chain 7 residue 79 VAL Chi-restraints excluded: chain 7 residue 144 VAL Chi-restraints excluded: chain 8 residue 3 LEU Chi-restraints excluded: chain 9 residue 29 PHE Chi-restraints excluded: chain 9 residue 56 ASN Chi-restraints excluded: chain 9 residue 65 THR Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain E residue 84 SER Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain F residue 94 ASN Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 121 VAL Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 111 GLU Chi-restraints excluded: chain G residue 113 ILE Chi-restraints excluded: chain G residue 116 PHE Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain I residue 118 LEU Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain J residue 84 SER Chi-restraints excluded: chain J residue 87 ASN Chi-restraints excluded: chain J residue 115 LEU Chi-restraints excluded: chain J residue 121 VAL Chi-restraints excluded: chain J residue 124 ILE Chi-restraints excluded: chain M residue 128 ASP Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 83 GLN Chi-restraints excluded: chain P residue 107 SER Chi-restraints excluded: chain P residue 146 LEU Chi-restraints excluded: chain P residue 152 VAL Chi-restraints excluded: chain P residue 185 VAL Chi-restraints excluded: chain P residue 195 LEU Chi-restraints excluded: chain P residue 199 VAL Chi-restraints excluded: chain P residue 207 VAL Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain Q residue 69 ILE Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain R residue 60 VAL Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain R residue 82 SER Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain S residue 140 VAL Chi-restraints excluded: chain S residue 260 LEU Chi-restraints excluded: chain T residue 75 LYS Chi-restraints excluded: chain T residue 76 SER Chi-restraints excluded: chain T residue 94 ILE Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 359 SER Chi-restraints excluded: chain T residue 428 SER Chi-restraints excluded: chain T residue 543 THR Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 465 ASP Chi-restraints excluded: chain U residue 514 VAL Chi-restraints excluded: chain U residue 516 ASP Chi-restraints excluded: chain U residue 528 VAL Chi-restraints excluded: chain U residue 546 LEU Chi-restraints excluded: chain V residue 70 VAL Chi-restraints excluded: chain V residue 410 THR Chi-restraints excluded: chain X residue 62 SER Chi-restraints excluded: chain X residue 226 GLU Chi-restraints excluded: chain X residue 232 VAL Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 308 VAL Chi-restraints excluded: chain X residue 344 ASP Chi-restraints excluded: chain X residue 425 LEU Chi-restraints excluded: chain X residue 497 GLU Chi-restraints excluded: chain X residue 524 ILE Chi-restraints excluded: chain Y residue 84 THR Chi-restraints excluded: chain Y residue 266 LEU Chi-restraints excluded: chain Y residue 420 LEU Chi-restraints excluded: chain Y residue 524 ILE Chi-restraints excluded: chain Y residue 547 GLU Chi-restraints excluded: chain Z residue 113 VAL Chi-restraints excluded: chain Z residue 193 ILE Chi-restraints excluded: chain Z residue 334 THR Chi-restraints excluded: chain Z residue 489 VAL Chi-restraints excluded: chain Z residue 554 LEU Chi-restraints excluded: chain Z residue 559 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 697 random chunks: chunk 226 optimal weight: 0.0370 chunk 606 optimal weight: 3.9990 chunk 133 optimal weight: 3.9990 chunk 395 optimal weight: 0.9980 chunk 166 optimal weight: 0.8980 chunk 674 optimal weight: 0.9980 chunk 559 optimal weight: 5.9990 chunk 312 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 223 optimal weight: 5.9990 chunk 354 optimal weight: 1.9990 overall best weight: 0.9860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 68 ASN 2 102 GLN 4 276 GLN 6 74 GLN ** 7 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 87 ASN M 127 HIS M 243 ASN P 140 ASN Q 29 ASN ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 178 GLN ** S 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 267 HIS U 179 ASN ** U 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 539 ASN ** U 549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 78 GLN ** X 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 54658 Z= 0.178 Angle : 0.508 11.417 74121 Z= 0.258 Chirality : 0.041 0.199 8683 Planarity : 0.004 0.046 9504 Dihedral : 5.498 119.347 7674 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.68 % Favored : 96.20 % Rotamer: Outliers : 2.72 % Allowed : 15.41 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.30 (0.10), residues: 7034 helix: 0.33 (0.09), residues: 3841 sheet: -0.45 (0.21), residues: 615 loop : -0.78 (0.12), residues: 2578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP 9 93 HIS 0.005 0.001 HIS M 127 PHE 0.028 0.001 PHE H 122 TYR 0.024 0.001 TYR 4 211 ARG 0.005 0.000 ARG Y 385 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14068 Ramachandran restraints generated. 7034 Oldfield, 0 Emsley, 7034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14068 Ramachandran restraints generated. 7034 Oldfield, 0 Emsley, 7034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 842 residues out of total 5633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 689 time to evaluate : 4.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 267 ARG cc_start: 0.8482 (mpt180) cc_final: 0.8131 (mpt180) REVERT: 2 177 GLN cc_start: 0.6991 (tt0) cc_final: 0.6059 (tt0) REVERT: 3 258 LYS cc_start: 0.7182 (OUTLIER) cc_final: 0.6857 (ttpt) REVERT: 3 265 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8661 (mm) REVERT: 3 279 GLU cc_start: 0.8185 (pt0) cc_final: 0.7923 (pt0) REVERT: 5 115 ILE cc_start: 0.8572 (tp) cc_final: 0.8166 (tp) REVERT: 6 146 PHE cc_start: 0.8599 (OUTLIER) cc_final: 0.7931 (t80) REVERT: 8 69 LYS cc_start: 0.8590 (mttt) cc_final: 0.7110 (tmtt) REVERT: A 92 ASN cc_start: 0.8393 (t0) cc_final: 0.8050 (t0) REVERT: E 60 LYS cc_start: 0.8044 (ptmt) cc_final: 0.7261 (ptmm) REVERT: G 71 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8413 (mp) REVERT: G 116 PHE cc_start: 0.7368 (OUTLIER) cc_final: 0.6893 (m-10) REVERT: H 92 ASN cc_start: 0.8509 (p0) cc_final: 0.7958 (p0) REVERT: J 115 LEU cc_start: 0.7412 (OUTLIER) cc_final: 0.6984 (mt) REVERT: P 49 THR cc_start: 0.8395 (OUTLIER) cc_final: 0.8175 (m) REVERT: P 78 ILE cc_start: 0.9128 (mm) cc_final: 0.8894 (mt) REVERT: P 83 GLN cc_start: 0.6620 (OUTLIER) cc_final: 0.5607 (mp10) REVERT: P 220 ASN cc_start: 0.8947 (m-40) cc_final: 0.8703 (m-40) REVERT: Q 20 SER cc_start: 0.8832 (OUTLIER) cc_final: 0.8475 (p) REVERT: R 107 THR cc_start: 0.7964 (OUTLIER) cc_final: 0.7668 (t) REVERT: R 127 PHE cc_start: 0.8548 (m-80) cc_final: 0.8321 (m-80) REVERT: S 260 LEU cc_start: 0.9323 (OUTLIER) cc_final: 0.8980 (mp) REVERT: T 407 PHE cc_start: 0.7981 (t80) cc_final: 0.7606 (t80) REVERT: V 112 ASP cc_start: 0.8460 (p0) cc_final: 0.8244 (p0) REVERT: V 471 GLN cc_start: 0.7737 (tt0) cc_final: 0.7343 (mm110) REVERT: X 497 GLU cc_start: 0.7395 (OUTLIER) cc_final: 0.7042 (mp0) REVERT: X 550 LYS cc_start: 0.7838 (pttt) cc_final: 0.7495 (mmmt) REVERT: Z 430 LYS cc_start: 0.7605 (ttmt) cc_final: 0.7151 (tppt) REVERT: Z 563 GLU cc_start: 0.7245 (tp30) cc_final: 0.7024 (tp30) outliers start: 153 outliers final: 110 residues processed: 801 average time/residue: 0.5096 time to fit residues: 691.1606 Evaluate side-chains 768 residues out of total 5633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 646 time to evaluate : 4.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 32 THR Chi-restraints excluded: chain 1 residue 47 VAL Chi-restraints excluded: chain 1 residue 226 VAL Chi-restraints excluded: chain 1 residue 234 VAL Chi-restraints excluded: chain 1 residue 240 VAL Chi-restraints excluded: chain 1 residue 249 ILE Chi-restraints excluded: chain 1 residue 310 THR Chi-restraints excluded: chain 1 residue 486 ASP Chi-restraints excluded: chain 1 residue 568 ASP Chi-restraints excluded: chain 2 residue 209 ASP Chi-restraints excluded: chain 2 residue 238 ASP Chi-restraints excluded: chain 2 residue 245 VAL Chi-restraints excluded: chain 2 residue 303 VAL Chi-restraints excluded: chain 2 residue 377 VAL Chi-restraints excluded: chain 3 residue 156 ASP Chi-restraints excluded: chain 3 residue 258 LYS Chi-restraints excluded: chain 3 residue 265 LEU Chi-restraints excluded: chain 4 residue 44 THR Chi-restraints excluded: chain 4 residue 77 SER Chi-restraints excluded: chain 4 residue 122 VAL Chi-restraints excluded: chain 4 residue 218 GLU Chi-restraints excluded: chain 5 residue 100 SER Chi-restraints excluded: chain 5 residue 112 ARG Chi-restraints excluded: chain 5 residue 113 VAL Chi-restraints excluded: chain 6 residue 31 SER Chi-restraints excluded: chain 6 residue 53 THR Chi-restraints excluded: chain 6 residue 73 THR Chi-restraints excluded: chain 6 residue 79 LEU Chi-restraints excluded: chain 6 residue 101 VAL Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 7 residue 15 LEU Chi-restraints excluded: chain 7 residue 35 ILE Chi-restraints excluded: chain 7 residue 79 VAL Chi-restraints excluded: chain 7 residue 144 VAL Chi-restraints excluded: chain 7 residue 157 VAL Chi-restraints excluded: chain 8 residue 3 LEU Chi-restraints excluded: chain 8 residue 67 SER Chi-restraints excluded: chain 9 residue 29 PHE Chi-restraints excluded: chain 9 residue 65 THR Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain E residue 84 SER Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain F residue 94 ASN Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 121 VAL Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 111 GLU Chi-restraints excluded: chain G residue 113 ILE Chi-restraints excluded: chain G residue 116 PHE Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain I residue 71 LEU Chi-restraints excluded: chain I residue 118 LEU Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 84 SER Chi-restraints excluded: chain J residue 87 ASN Chi-restraints excluded: chain J residue 115 LEU Chi-restraints excluded: chain J residue 121 VAL Chi-restraints excluded: chain M residue 128 ASP Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 83 GLN Chi-restraints excluded: chain P residue 146 LEU Chi-restraints excluded: chain P residue 152 VAL Chi-restraints excluded: chain P residue 185 VAL Chi-restraints excluded: chain P residue 195 LEU Chi-restraints excluded: chain P residue 199 VAL Chi-restraints excluded: chain P residue 200 ILE Chi-restraints excluded: chain P residue 207 VAL Chi-restraints excluded: chain P residue 227 LEU Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain Q residue 69 ILE Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain R residue 60 VAL Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain R residue 82 SER Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain R residue 107 THR Chi-restraints excluded: chain R residue 178 GLN Chi-restraints excluded: chain S residue 140 VAL Chi-restraints excluded: chain S residue 238 GLU Chi-restraints excluded: chain S residue 260 LEU Chi-restraints excluded: chain T residue 75 LYS Chi-restraints excluded: chain T residue 94 ILE Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 300 PHE Chi-restraints excluded: chain T residue 359 SER Chi-restraints excluded: chain T residue 410 THR Chi-restraints excluded: chain T residue 428 SER Chi-restraints excluded: chain T residue 514 VAL Chi-restraints excluded: chain T residue 543 THR Chi-restraints excluded: chain U residue 465 ASP Chi-restraints excluded: chain U residue 514 VAL Chi-restraints excluded: chain U residue 516 ASP Chi-restraints excluded: chain U residue 528 VAL Chi-restraints excluded: chain U residue 546 LEU Chi-restraints excluded: chain V residue 70 VAL Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain V residue 187 VAL Chi-restraints excluded: chain V residue 410 THR Chi-restraints excluded: chain V residue 430 VAL Chi-restraints excluded: chain X residue 62 SER Chi-restraints excluded: chain X residue 190 THR Chi-restraints excluded: chain X residue 226 GLU Chi-restraints excluded: chain X residue 232 VAL Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 308 VAL Chi-restraints excluded: chain X residue 425 LEU Chi-restraints excluded: chain X residue 497 GLU Chi-restraints excluded: chain X residue 524 ILE Chi-restraints excluded: chain X residue 531 VAL Chi-restraints excluded: chain Y residue 84 THR Chi-restraints excluded: chain Y residue 266 LEU Chi-restraints excluded: chain Y residue 383 THR Chi-restraints excluded: chain Y residue 420 LEU Chi-restraints excluded: chain Y residue 524 ILE Chi-restraints excluded: chain Y residue 547 GLU Chi-restraints excluded: chain Z residue 113 VAL Chi-restraints excluded: chain Z residue 193 ILE Chi-restraints excluded: chain Z residue 334 THR Chi-restraints excluded: chain Z residue 554 LEU Chi-restraints excluded: chain Z residue 557 GLU Chi-restraints excluded: chain Z residue 559 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 697 random chunks: chunk 650 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 384 optimal weight: 5.9990 chunk 492 optimal weight: 2.9990 chunk 381 optimal weight: 3.9990 chunk 567 optimal weight: 2.9990 chunk 376 optimal weight: 6.9990 chunk 671 optimal weight: 0.7980 chunk 420 optimal weight: 5.9990 chunk 409 optimal weight: 1.9990 chunk 310 optimal weight: 0.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 102 GLN 4 276 GLN ** 7 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 98 GLN J 87 ASN M 127 HIS M 243 ASN P 140 ASN ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 241 HIS U 539 ASN ** U 549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.2339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 54658 Z= 0.236 Angle : 0.532 11.166 74121 Z= 0.270 Chirality : 0.042 0.247 8683 Planarity : 0.004 0.047 9504 Dihedral : 5.568 115.922 7674 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.78 % Favored : 96.10 % Rotamer: Outliers : 2.81 % Allowed : 16.13 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.26 (0.10), residues: 7034 helix: 0.37 (0.09), residues: 3849 sheet: -0.58 (0.21), residues: 613 loop : -0.72 (0.12), residues: 2572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP 9 93 HIS 0.005 0.001 HIS 4 233 PHE 0.029 0.001 PHE H 122 TYR 0.024 0.001 TYR 4 211 ARG 0.006 0.000 ARG Y 385 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14068 Ramachandran restraints generated. 7034 Oldfield, 0 Emsley, 7034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14068 Ramachandran restraints generated. 7034 Oldfield, 0 Emsley, 7034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 826 residues out of total 5633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 668 time to evaluate : 4.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 267 ARG cc_start: 0.8509 (mpt180) cc_final: 0.8174 (mpt180) REVERT: 1 414 GLU cc_start: 0.7001 (pt0) cc_final: 0.6763 (pt0) REVERT: 2 177 GLN cc_start: 0.7024 (tt0) cc_final: 0.6116 (tt0) REVERT: 3 258 LYS cc_start: 0.7152 (OUTLIER) cc_final: 0.6826 (ttpt) REVERT: 3 265 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8707 (mm) REVERT: 3 279 GLU cc_start: 0.8191 (pt0) cc_final: 0.7931 (pt0) REVERT: 5 115 ILE cc_start: 0.8595 (tp) cc_final: 0.8196 (tp) REVERT: 6 146 PHE cc_start: 0.8527 (OUTLIER) cc_final: 0.7843 (t80) REVERT: 8 69 LYS cc_start: 0.8610 (mttt) cc_final: 0.7096 (tmtt) REVERT: A 92 ASN cc_start: 0.8505 (t0) cc_final: 0.8111 (t0) REVERT: B 78 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8156 (mp) REVERT: E 60 LYS cc_start: 0.8063 (ptmt) cc_final: 0.7282 (ptmm) REVERT: F 81 MET cc_start: 0.8403 (ttp) cc_final: 0.8112 (ttt) REVERT: F 107 PHE cc_start: 0.8562 (t80) cc_final: 0.8331 (t80) REVERT: G 71 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8420 (mp) REVERT: G 97 LYS cc_start: 0.6950 (OUTLIER) cc_final: 0.6650 (tmtt) REVERT: G 116 PHE cc_start: 0.7407 (OUTLIER) cc_final: 0.6945 (m-10) REVERT: G 124 ILE cc_start: 0.8202 (mm) cc_final: 0.7951 (mt) REVERT: H 92 ASN cc_start: 0.8550 (p0) cc_final: 0.7972 (p0) REVERT: J 115 LEU cc_start: 0.7455 (OUTLIER) cc_final: 0.7006 (mt) REVERT: P 49 THR cc_start: 0.8373 (OUTLIER) cc_final: 0.8145 (m) REVERT: P 78 ILE cc_start: 0.9141 (mm) cc_final: 0.8912 (mt) REVERT: P 220 ASN cc_start: 0.8925 (m-40) cc_final: 0.8690 (m-40) REVERT: Q 20 SER cc_start: 0.8847 (OUTLIER) cc_final: 0.8481 (p) REVERT: R 127 PHE cc_start: 0.8564 (m-80) cc_final: 0.8327 (m-80) REVERT: S 260 LEU cc_start: 0.9334 (OUTLIER) cc_final: 0.8978 (mp) REVERT: V 471 GLN cc_start: 0.7783 (tt0) cc_final: 0.7364 (mm110) REVERT: X 497 GLU cc_start: 0.7403 (OUTLIER) cc_final: 0.7033 (mp0) REVERT: X 550 LYS cc_start: 0.7788 (pttt) cc_final: 0.7488 (mmmt) REVERT: Z 395 GLU cc_start: 0.7899 (OUTLIER) cc_final: 0.7522 (tt0) outliers start: 158 outliers final: 123 residues processed: 780 average time/residue: 0.5068 time to fit residues: 669.7955 Evaluate side-chains 779 residues out of total 5633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 643 time to evaluate : 4.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 19 SER Chi-restraints excluded: chain 0 residue 32 THR Chi-restraints excluded: chain 1 residue 47 VAL Chi-restraints excluded: chain 1 residue 226 VAL Chi-restraints excluded: chain 1 residue 234 VAL Chi-restraints excluded: chain 1 residue 240 VAL Chi-restraints excluded: chain 1 residue 249 ILE Chi-restraints excluded: chain 1 residue 486 ASP Chi-restraints excluded: chain 1 residue 568 ASP Chi-restraints excluded: chain 2 residue 209 ASP Chi-restraints excluded: chain 2 residue 238 ASP Chi-restraints excluded: chain 2 residue 245 VAL Chi-restraints excluded: chain 2 residue 303 VAL Chi-restraints excluded: chain 2 residue 377 VAL Chi-restraints excluded: chain 3 residue 156 ASP Chi-restraints excluded: chain 3 residue 258 LYS Chi-restraints excluded: chain 3 residue 265 LEU Chi-restraints excluded: chain 3 residue 309 ASN Chi-restraints excluded: chain 4 residue 44 THR Chi-restraints excluded: chain 4 residue 77 SER Chi-restraints excluded: chain 4 residue 122 VAL Chi-restraints excluded: chain 5 residue 37 GLU Chi-restraints excluded: chain 5 residue 100 SER Chi-restraints excluded: chain 5 residue 112 ARG Chi-restraints excluded: chain 5 residue 113 VAL Chi-restraints excluded: chain 6 residue 31 SER Chi-restraints excluded: chain 6 residue 53 THR Chi-restraints excluded: chain 6 residue 73 THR Chi-restraints excluded: chain 6 residue 79 LEU Chi-restraints excluded: chain 6 residue 101 VAL Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 7 residue 15 LEU Chi-restraints excluded: chain 7 residue 35 ILE Chi-restraints excluded: chain 7 residue 39 VAL Chi-restraints excluded: chain 7 residue 79 VAL Chi-restraints excluded: chain 7 residue 144 VAL Chi-restraints excluded: chain 7 residue 157 VAL Chi-restraints excluded: chain 8 residue 3 LEU Chi-restraints excluded: chain 8 residue 55 ILE Chi-restraints excluded: chain 8 residue 67 SER Chi-restraints excluded: chain 8 residue 82 THR Chi-restraints excluded: chain 9 residue 29 PHE Chi-restraints excluded: chain 9 residue 65 THR Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain E residue 84 SER Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain F residue 61 MET Chi-restraints excluded: chain F residue 94 ASN Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 121 VAL Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 97 LYS Chi-restraints excluded: chain G residue 111 GLU Chi-restraints excluded: chain G residue 113 ILE Chi-restraints excluded: chain G residue 116 PHE Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain I residue 71 LEU Chi-restraints excluded: chain I residue 118 LEU Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 84 SER Chi-restraints excluded: chain J residue 87 ASN Chi-restraints excluded: chain J residue 115 LEU Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain J residue 121 VAL Chi-restraints excluded: chain M residue 128 ASP Chi-restraints excluded: chain M residue 161 SER Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 146 LEU Chi-restraints excluded: chain P residue 152 VAL Chi-restraints excluded: chain P residue 185 VAL Chi-restraints excluded: chain P residue 195 LEU Chi-restraints excluded: chain P residue 199 VAL Chi-restraints excluded: chain P residue 200 ILE Chi-restraints excluded: chain P residue 207 VAL Chi-restraints excluded: chain P residue 227 LEU Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain Q residue 69 ILE Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain R residue 60 VAL Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain R residue 82 SER Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain S residue 140 VAL Chi-restraints excluded: chain S residue 238 GLU Chi-restraints excluded: chain S residue 260 LEU Chi-restraints excluded: chain S residue 303 GLU Chi-restraints excluded: chain T residue 75 LYS Chi-restraints excluded: chain T residue 76 SER Chi-restraints excluded: chain T residue 94 ILE Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 300 PHE Chi-restraints excluded: chain T residue 359 SER Chi-restraints excluded: chain T residue 410 THR Chi-restraints excluded: chain T residue 428 SER Chi-restraints excluded: chain T residue 514 VAL Chi-restraints excluded: chain T residue 521 GLU Chi-restraints excluded: chain T residue 532 VAL Chi-restraints excluded: chain T residue 543 THR Chi-restraints excluded: chain T residue 549 HIS Chi-restraints excluded: chain U residue 287 MET Chi-restraints excluded: chain U residue 465 ASP Chi-restraints excluded: chain U residue 514 VAL Chi-restraints excluded: chain U residue 516 ASP Chi-restraints excluded: chain U residue 546 LEU Chi-restraints excluded: chain V residue 70 VAL Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain V residue 187 VAL Chi-restraints excluded: chain V residue 410 THR Chi-restraints excluded: chain V residue 430 VAL Chi-restraints excluded: chain X residue 62 SER Chi-restraints excluded: chain X residue 158 GLU Chi-restraints excluded: chain X residue 190 THR Chi-restraints excluded: chain X residue 232 VAL Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 308 VAL Chi-restraints excluded: chain X residue 497 GLU Chi-restraints excluded: chain X residue 524 ILE Chi-restraints excluded: chain X residue 531 VAL Chi-restraints excluded: chain Y residue 84 THR Chi-restraints excluded: chain Y residue 266 LEU Chi-restraints excluded: chain Y residue 383 THR Chi-restraints excluded: chain Y residue 420 LEU Chi-restraints excluded: chain Y residue 524 ILE Chi-restraints excluded: chain Y residue 547 GLU Chi-restraints excluded: chain Z residue 103 VAL Chi-restraints excluded: chain Z residue 113 VAL Chi-restraints excluded: chain Z residue 193 ILE Chi-restraints excluded: chain Z residue 217 THR Chi-restraints excluded: chain Z residue 334 THR Chi-restraints excluded: chain Z residue 395 GLU Chi-restraints excluded: chain Z residue 554 LEU Chi-restraints excluded: chain Z residue 557 GLU Chi-restraints excluded: chain Z residue 559 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 697 random chunks: chunk 415 optimal weight: 3.9990 chunk 268 optimal weight: 4.9990 chunk 401 optimal weight: 4.9990 chunk 202 optimal weight: 0.8980 chunk 132 optimal weight: 0.3980 chunk 130 optimal weight: 5.9990 chunk 427 optimal weight: 2.9990 chunk 457 optimal weight: 4.9990 chunk 332 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 528 optimal weight: 8.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 102 GLN 4 276 GLN ** 7 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 87 ASN M 127 HIS M 243 ASN P 140 ASN Q 29 ASN ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 405 GLN U 539 ASN ** U 549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 179 ASN ** Y 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 54658 Z= 0.292 Angle : 0.559 12.168 74121 Z= 0.284 Chirality : 0.043 0.202 8683 Planarity : 0.004 0.051 9504 Dihedral : 5.747 114.295 7674 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.09 % Favored : 95.79 % Rotamer: Outliers : 2.95 % Allowed : 16.44 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.29 (0.10), residues: 7034 helix: 0.33 (0.09), residues: 3846 sheet: -0.64 (0.21), residues: 615 loop : -0.71 (0.13), residues: 2573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP 9 93 HIS 0.006 0.001 HIS 4 233 PHE 0.032 0.001 PHE H 122 TYR 0.023 0.001 TYR 4 211 ARG 0.007 0.000 ARG J 91 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14068 Ramachandran restraints generated. 7034 Oldfield, 0 Emsley, 7034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14068 Ramachandran restraints generated. 7034 Oldfield, 0 Emsley, 7034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 827 residues out of total 5633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 661 time to evaluate : 4.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 414 GLU cc_start: 0.7003 (pt0) cc_final: 0.6771 (pt0) REVERT: 3 265 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8739 (mm) REVERT: 3 279 GLU cc_start: 0.8210 (pt0) cc_final: 0.7945 (pt0) REVERT: 5 115 ILE cc_start: 0.8598 (tp) cc_final: 0.8191 (tp) REVERT: 8 69 LYS cc_start: 0.8655 (mttt) cc_final: 0.7113 (tmtt) REVERT: A 92 ASN cc_start: 0.8558 (t0) cc_final: 0.8231 (t0) REVERT: B 78 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8181 (mp) REVERT: G 71 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8425 (mp) REVERT: G 111 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.7666 (mm-30) REVERT: G 116 PHE cc_start: 0.7465 (OUTLIER) cc_final: 0.6984 (m-10) REVERT: G 124 ILE cc_start: 0.8163 (mm) cc_final: 0.7911 (mt) REVERT: H 92 ASN cc_start: 0.8578 (p0) cc_final: 0.7987 (p0) REVERT: P 49 THR cc_start: 0.8448 (OUTLIER) cc_final: 0.8222 (m) REVERT: P 78 ILE cc_start: 0.9161 (mm) cc_final: 0.8942 (mt) REVERT: P 83 GLN cc_start: 0.6581 (OUTLIER) cc_final: 0.5605 (mp10) REVERT: P 220 ASN cc_start: 0.8940 (m-40) cc_final: 0.8702 (m-40) REVERT: Q 20 SER cc_start: 0.8892 (OUTLIER) cc_final: 0.8521 (p) REVERT: R 127 PHE cc_start: 0.8526 (m-80) cc_final: 0.8298 (m-80) REVERT: S 260 LEU cc_start: 0.9349 (OUTLIER) cc_final: 0.8962 (mp) REVERT: T 407 PHE cc_start: 0.7885 (t80) cc_final: 0.7592 (t80) REVERT: V 471 GLN cc_start: 0.7798 (tt0) cc_final: 0.7447 (mm110) REVERT: X 497 GLU cc_start: 0.7423 (OUTLIER) cc_final: 0.7046 (mp0) REVERT: X 550 LYS cc_start: 0.7827 (pttt) cc_final: 0.7527 (mmmt) REVERT: Z 395 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7508 (tt0) REVERT: Z 430 LYS cc_start: 0.7622 (ttmt) cc_final: 0.7206 (mtpp) outliers start: 166 outliers final: 133 residues processed: 774 average time/residue: 0.5085 time to fit residues: 668.9675 Evaluate side-chains 775 residues out of total 5633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 631 time to evaluate : 4.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 19 SER Chi-restraints excluded: chain 0 residue 32 THR Chi-restraints excluded: chain 0 residue 36 THR Chi-restraints excluded: chain 1 residue 47 VAL Chi-restraints excluded: chain 1 residue 234 VAL Chi-restraints excluded: chain 1 residue 240 VAL Chi-restraints excluded: chain 1 residue 249 ILE Chi-restraints excluded: chain 1 residue 486 ASP Chi-restraints excluded: chain 1 residue 568 ASP Chi-restraints excluded: chain 2 residue 209 ASP Chi-restraints excluded: chain 2 residue 238 ASP Chi-restraints excluded: chain 2 residue 303 VAL Chi-restraints excluded: chain 2 residue 377 VAL Chi-restraints excluded: chain 3 residue 156 ASP Chi-restraints excluded: chain 3 residue 180 ILE Chi-restraints excluded: chain 3 residue 265 LEU Chi-restraints excluded: chain 3 residue 309 ASN Chi-restraints excluded: chain 4 residue 44 THR Chi-restraints excluded: chain 4 residue 77 SER Chi-restraints excluded: chain 4 residue 122 VAL Chi-restraints excluded: chain 5 residue 37 GLU Chi-restraints excluded: chain 5 residue 100 SER Chi-restraints excluded: chain 5 residue 110 SER Chi-restraints excluded: chain 5 residue 113 VAL Chi-restraints excluded: chain 6 residue 31 SER Chi-restraints excluded: chain 6 residue 53 THR Chi-restraints excluded: chain 6 residue 73 THR Chi-restraints excluded: chain 6 residue 79 LEU Chi-restraints excluded: chain 6 residue 101 VAL Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 7 residue 15 LEU Chi-restraints excluded: chain 7 residue 35 ILE Chi-restraints excluded: chain 7 residue 39 VAL Chi-restraints excluded: chain 7 residue 79 VAL Chi-restraints excluded: chain 7 residue 82 ILE Chi-restraints excluded: chain 7 residue 117 ASP Chi-restraints excluded: chain 7 residue 144 VAL Chi-restraints excluded: chain 7 residue 157 VAL Chi-restraints excluded: chain 8 residue 3 LEU Chi-restraints excluded: chain 8 residue 55 ILE Chi-restraints excluded: chain 8 residue 67 SER Chi-restraints excluded: chain 8 residue 82 THR Chi-restraints excluded: chain 9 residue 29 PHE Chi-restraints excluded: chain 9 residue 65 THR Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain E residue 84 SER Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain F residue 61 MET Chi-restraints excluded: chain F residue 94 ASN Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 121 VAL Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 111 GLU Chi-restraints excluded: chain G residue 113 ILE Chi-restraints excluded: chain G residue 116 PHE Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain I residue 71 LEU Chi-restraints excluded: chain I residue 118 LEU Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 84 SER Chi-restraints excluded: chain J residue 87 ASN Chi-restraints excluded: chain J residue 115 LEU Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain J residue 121 VAL Chi-restraints excluded: chain M residue 128 ASP Chi-restraints excluded: chain M residue 161 SER Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 83 GLN Chi-restraints excluded: chain P residue 146 LEU Chi-restraints excluded: chain P residue 152 VAL Chi-restraints excluded: chain P residue 185 VAL Chi-restraints excluded: chain P residue 195 LEU Chi-restraints excluded: chain P residue 199 VAL Chi-restraints excluded: chain P residue 200 ILE Chi-restraints excluded: chain P residue 207 VAL Chi-restraints excluded: chain P residue 227 LEU Chi-restraints excluded: chain Q residue 20 SER Chi-restraints excluded: chain Q residue 69 ILE Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain R residue 60 VAL Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain R residue 82 SER Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain R residue 162 SER Chi-restraints excluded: chain S residue 140 VAL Chi-restraints excluded: chain S residue 238 GLU Chi-restraints excluded: chain S residue 260 LEU Chi-restraints excluded: chain S residue 303 GLU Chi-restraints excluded: chain T residue 70 VAL Chi-restraints excluded: chain T residue 75 LYS Chi-restraints excluded: chain T residue 76 SER Chi-restraints excluded: chain T residue 94 ILE Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 300 PHE Chi-restraints excluded: chain T residue 359 SER Chi-restraints excluded: chain T residue 410 THR Chi-restraints excluded: chain T residue 428 SER Chi-restraints excluded: chain T residue 514 VAL Chi-restraints excluded: chain T residue 521 GLU Chi-restraints excluded: chain T residue 532 VAL Chi-restraints excluded: chain T residue 549 HIS Chi-restraints excluded: chain U residue 53 PHE Chi-restraints excluded: chain U residue 287 MET Chi-restraints excluded: chain U residue 448 LEU Chi-restraints excluded: chain U residue 465 ASP Chi-restraints excluded: chain U residue 492 ILE Chi-restraints excluded: chain U residue 514 VAL Chi-restraints excluded: chain U residue 516 ASP Chi-restraints excluded: chain U residue 546 LEU Chi-restraints excluded: chain V residue 70 VAL Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 187 VAL Chi-restraints excluded: chain V residue 410 THR Chi-restraints excluded: chain V residue 430 VAL Chi-restraints excluded: chain V residue 559 LEU Chi-restraints excluded: chain X residue 49 ASP Chi-restraints excluded: chain X residue 62 SER Chi-restraints excluded: chain X residue 190 THR Chi-restraints excluded: chain X residue 232 VAL Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 308 VAL Chi-restraints excluded: chain X residue 425 LEU Chi-restraints excluded: chain X residue 497 GLU Chi-restraints excluded: chain X residue 524 ILE Chi-restraints excluded: chain X residue 531 VAL Chi-restraints excluded: chain Y residue 84 THR Chi-restraints excluded: chain Y residue 266 LEU Chi-restraints excluded: chain Y residue 383 THR Chi-restraints excluded: chain Y residue 524 ILE Chi-restraints excluded: chain Y residue 547 GLU Chi-restraints excluded: chain Z residue 103 VAL Chi-restraints excluded: chain Z residue 113 VAL Chi-restraints excluded: chain Z residue 217 THR Chi-restraints excluded: chain Z residue 334 THR Chi-restraints excluded: chain Z residue 395 GLU Chi-restraints excluded: chain Z residue 554 LEU Chi-restraints excluded: chain Z residue 557 GLU Chi-restraints excluded: chain Z residue 559 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 697 random chunks: chunk 611 optimal weight: 2.9990 chunk 643 optimal weight: 0.9980 chunk 587 optimal weight: 8.9990 chunk 626 optimal weight: 0.0000 chunk 376 optimal weight: 6.9990 chunk 272 optimal weight: 0.9990 chunk 491 optimal weight: 0.6980 chunk 192 optimal weight: 9.9990 chunk 565 optimal weight: 0.3980 chunk 592 optimal weight: 0.4980 chunk 623 optimal weight: 3.9990 overall best weight: 0.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 276 GLN 7 184 ASN J 87 ASN M 127 HIS M 243 ASN P 140 ASN ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 241 HIS U 271 GLN U 539 ASN ** U 549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 414 GLN ** Y 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 157 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.2592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 54658 Z= 0.139 Angle : 0.502 11.944 74121 Z= 0.254 Chirality : 0.040 0.196 8683 Planarity : 0.004 0.049 9504 Dihedral : 5.334 114.140 7674 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.21 % Favored : 96.69 % Rotamer: Outliers : 2.31 % Allowed : 17.34 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.04 (0.10), residues: 7034 helix: 0.61 (0.09), residues: 3824 sheet: -0.38 (0.22), residues: 614 loop : -0.59 (0.13), residues: 2596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP 9 93 HIS 0.004 0.001 HIS Z 396 PHE 0.032 0.001 PHE 3 115 TYR 0.025 0.001 TYR 4 211 ARG 0.007 0.000 ARG Y 385 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14068 Ramachandran restraints generated. 7034 Oldfield, 0 Emsley, 7034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14068 Ramachandran restraints generated. 7034 Oldfield, 0 Emsley, 7034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 828 residues out of total 5633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 698 time to evaluate : 4.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 267 ARG cc_start: 0.8389 (mpt180) cc_final: 0.8063 (mpt180) REVERT: 1 414 GLU cc_start: 0.6963 (pt0) cc_final: 0.6728 (pt0) REVERT: 2 31 ASP cc_start: 0.7261 (m-30) cc_final: 0.7052 (m-30) REVERT: 2 177 GLN cc_start: 0.6726 (tt0) cc_final: 0.5775 (tt0) REVERT: 3 258 LYS cc_start: 0.7343 (OUTLIER) cc_final: 0.6997 (ttpt) REVERT: 3 279 GLU cc_start: 0.8197 (pt0) cc_final: 0.7969 (pt0) REVERT: 5 115 ILE cc_start: 0.8494 (tp) cc_final: 0.8095 (tp) REVERT: 6 146 PHE cc_start: 0.8564 (OUTLIER) cc_final: 0.7934 (t80) REVERT: 8 69 LYS cc_start: 0.8598 (mttt) cc_final: 0.7150 (tmtt) REVERT: 9 9 LYS cc_start: 0.8220 (mttp) cc_final: 0.7990 (mttm) REVERT: A 59 SER cc_start: 0.8558 (OUTLIER) cc_final: 0.7981 (p) REVERT: A 92 ASN cc_start: 0.8473 (t0) cc_final: 0.8069 (t0) REVERT: B 78 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8114 (mp) REVERT: E 60 LYS cc_start: 0.7947 (ptmt) cc_final: 0.7223 (pttp) REVERT: F 81 MET cc_start: 0.8114 (ttp) cc_final: 0.7842 (ttt) REVERT: G 97 LYS cc_start: 0.6926 (OUTLIER) cc_final: 0.6689 (tmtt) REVERT: G 116 PHE cc_start: 0.7359 (OUTLIER) cc_final: 0.6879 (m-10) REVERT: H 92 ASN cc_start: 0.8469 (p0) cc_final: 0.7923 (p0) REVERT: J 87 ASN cc_start: 0.8044 (OUTLIER) cc_final: 0.7809 (t0) REVERT: J 115 LEU cc_start: 0.7170 (OUTLIER) cc_final: 0.6878 (mt) REVERT: P 49 THR cc_start: 0.8246 (OUTLIER) cc_final: 0.8038 (m) REVERT: P 78 ILE cc_start: 0.9131 (mm) cc_final: 0.8913 (mt) REVERT: P 83 GLN cc_start: 0.6452 (OUTLIER) cc_final: 0.5471 (mp10) REVERT: P 220 ASN cc_start: 0.8941 (m-40) cc_final: 0.8733 (m-40) REVERT: Q 20 SER cc_start: 0.8748 (t) cc_final: 0.8411 (p) REVERT: S 48 ARG cc_start: 0.7286 (ptm160) cc_final: 0.6891 (mtp-110) REVERT: S 260 LEU cc_start: 0.9313 (OUTLIER) cc_final: 0.8949 (mp) REVERT: T 407 PHE cc_start: 0.8042 (t80) cc_final: 0.7682 (t80) REVERT: T 475 GLU cc_start: 0.6904 (pt0) cc_final: 0.6650 (pt0) REVERT: V 112 ASP cc_start: 0.8410 (p0) cc_final: 0.8164 (p0) REVERT: V 471 GLN cc_start: 0.7640 (tt0) cc_final: 0.7256 (mm110) REVERT: X 250 GLN cc_start: 0.8373 (OUTLIER) cc_final: 0.7913 (mm-40) REVERT: X 497 GLU cc_start: 0.7417 (OUTLIER) cc_final: 0.7085 (mp0) REVERT: X 550 LYS cc_start: 0.7672 (pttt) cc_final: 0.7459 (mmmt) REVERT: Z 395 GLU cc_start: 0.7913 (OUTLIER) cc_final: 0.7498 (tt0) outliers start: 130 outliers final: 93 residues processed: 790 average time/residue: 0.5215 time to fit residues: 697.2685 Evaluate side-chains 745 residues out of total 5633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 638 time to evaluate : 4.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 19 SER Chi-restraints excluded: chain 0 residue 32 THR Chi-restraints excluded: chain 1 residue 47 VAL Chi-restraints excluded: chain 1 residue 234 VAL Chi-restraints excluded: chain 1 residue 240 VAL Chi-restraints excluded: chain 2 residue 209 ASP Chi-restraints excluded: chain 2 residue 238 ASP Chi-restraints excluded: chain 2 residue 245 VAL Chi-restraints excluded: chain 2 residue 303 VAL Chi-restraints excluded: chain 2 residue 319 ARG Chi-restraints excluded: chain 2 residue 377 VAL Chi-restraints excluded: chain 3 residue 156 ASP Chi-restraints excluded: chain 3 residue 258 LYS Chi-restraints excluded: chain 3 residue 309 ASN Chi-restraints excluded: chain 4 residue 44 THR Chi-restraints excluded: chain 4 residue 77 SER Chi-restraints excluded: chain 4 residue 122 VAL Chi-restraints excluded: chain 5 residue 100 SER Chi-restraints excluded: chain 6 residue 53 THR Chi-restraints excluded: chain 6 residue 73 THR Chi-restraints excluded: chain 6 residue 79 LEU Chi-restraints excluded: chain 6 residue 101 VAL Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 7 residue 15 LEU Chi-restraints excluded: chain 7 residue 35 ILE Chi-restraints excluded: chain 7 residue 39 VAL Chi-restraints excluded: chain 7 residue 79 VAL Chi-restraints excluded: chain 7 residue 117 ASP Chi-restraints excluded: chain 7 residue 144 VAL Chi-restraints excluded: chain 7 residue 184 ASN Chi-restraints excluded: chain 8 residue 3 LEU Chi-restraints excluded: chain 8 residue 82 THR Chi-restraints excluded: chain 9 residue 29 PHE Chi-restraints excluded: chain 9 residue 65 THR Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain E residue 84 SER Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain F residue 61 MET Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain G residue 97 LYS Chi-restraints excluded: chain G residue 111 GLU Chi-restraints excluded: chain G residue 113 ILE Chi-restraints excluded: chain G residue 116 PHE Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain I residue 118 LEU Chi-restraints excluded: chain J residue 84 SER Chi-restraints excluded: chain J residue 87 ASN Chi-restraints excluded: chain J residue 115 LEU Chi-restraints excluded: chain J residue 121 VAL Chi-restraints excluded: chain M residue 128 ASP Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 83 GLN Chi-restraints excluded: chain P residue 152 VAL Chi-restraints excluded: chain P residue 185 VAL Chi-restraints excluded: chain P residue 195 LEU Chi-restraints excluded: chain P residue 200 ILE Chi-restraints excluded: chain P residue 207 VAL Chi-restraints excluded: chain Q residue 69 ILE Chi-restraints excluded: chain R residue 60 VAL Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain R residue 82 SER Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain S residue 140 VAL Chi-restraints excluded: chain S residue 260 LEU Chi-restraints excluded: chain S residue 303 GLU Chi-restraints excluded: chain T residue 75 LYS Chi-restraints excluded: chain T residue 94 ILE Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 300 PHE Chi-restraints excluded: chain T residue 410 THR Chi-restraints excluded: chain T residue 428 SER Chi-restraints excluded: chain T residue 514 VAL Chi-restraints excluded: chain T residue 521 GLU Chi-restraints excluded: chain T residue 549 HIS Chi-restraints excluded: chain U residue 287 MET Chi-restraints excluded: chain U residue 465 ASP Chi-restraints excluded: chain U residue 514 VAL Chi-restraints excluded: chain U residue 516 ASP Chi-restraints excluded: chain U residue 546 LEU Chi-restraints excluded: chain V residue 70 VAL Chi-restraints excluded: chain V residue 84 LEU Chi-restraints excluded: chain V residue 410 THR Chi-restraints excluded: chain V residue 430 VAL Chi-restraints excluded: chain V residue 464 SER Chi-restraints excluded: chain X residue 62 SER Chi-restraints excluded: chain X residue 190 THR Chi-restraints excluded: chain X residue 250 GLN Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 308 VAL Chi-restraints excluded: chain X residue 425 LEU Chi-restraints excluded: chain X residue 497 GLU Chi-restraints excluded: chain X residue 524 ILE Chi-restraints excluded: chain X residue 531 VAL Chi-restraints excluded: chain Y residue 84 THR Chi-restraints excluded: chain Y residue 266 LEU Chi-restraints excluded: chain Y residue 383 THR Chi-restraints excluded: chain Y residue 524 ILE Chi-restraints excluded: chain Z residue 103 VAL Chi-restraints excluded: chain Z residue 334 THR Chi-restraints excluded: chain Z residue 395 GLU Chi-restraints excluded: chain Z residue 554 LEU Chi-restraints excluded: chain Z residue 557 GLU Chi-restraints excluded: chain Z residue 559 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 697 random chunks: chunk 411 optimal weight: 2.9990 chunk 661 optimal weight: 6.9990 chunk 404 optimal weight: 0.7980 chunk 314 optimal weight: 3.9990 chunk 460 optimal weight: 0.0970 chunk 694 optimal weight: 7.9990 chunk 639 optimal weight: 4.9990 chunk 552 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 427 optimal weight: 2.9990 chunk 339 optimal weight: 10.0000 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 276 GLN 5 79 ASN 6 106 ASN ** 7 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 87 ASN M 127 HIS M 243 ASN P 140 ASN ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 241 HIS U 539 ASN ** U 549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 471 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 54658 Z= 0.216 Angle : 0.530 10.668 74121 Z= 0.268 Chirality : 0.041 0.209 8683 Planarity : 0.004 0.049 9504 Dihedral : 5.390 110.674 7674 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.64 % Favored : 96.26 % Rotamer: Outliers : 2.17 % Allowed : 17.79 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.05 (0.10), residues: 7034 helix: 0.60 (0.09), residues: 3831 sheet: -0.33 (0.22), residues: 606 loop : -0.58 (0.13), residues: 2597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP 9 93 HIS 0.004 0.001 HIS 4 233 PHE 0.028 0.001 PHE 3 115 TYR 0.024 0.001 TYR 4 211 ARG 0.007 0.000 ARG Y 385 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14068 Ramachandran restraints generated. 7034 Oldfield, 0 Emsley, 7034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14068 Ramachandran restraints generated. 7034 Oldfield, 0 Emsley, 7034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 772 residues out of total 5633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 650 time to evaluate : 4.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 267 ARG cc_start: 0.8490 (mpt180) cc_final: 0.8154 (mpt180) REVERT: 1 352 GLU cc_start: 0.7516 (mm-30) cc_final: 0.7316 (mm-30) REVERT: 1 414 GLU cc_start: 0.6951 (pt0) cc_final: 0.6689 (pt0) REVERT: 2 31 ASP cc_start: 0.7213 (m-30) cc_final: 0.7004 (m-30) REVERT: 2 177 GLN cc_start: 0.6747 (tt0) cc_final: 0.5805 (tt0) REVERT: 3 258 LYS cc_start: 0.7330 (OUTLIER) cc_final: 0.6999 (ttmt) REVERT: 3 279 GLU cc_start: 0.8236 (pt0) cc_final: 0.7992 (pt0) REVERT: 5 115 ILE cc_start: 0.8491 (tp) cc_final: 0.8096 (tp) REVERT: 6 146 PHE cc_start: 0.8550 (OUTLIER) cc_final: 0.7882 (t80) REVERT: 8 69 LYS cc_start: 0.8614 (mttt) cc_final: 0.7145 (tmtt) REVERT: 9 9 LYS cc_start: 0.8275 (mttp) cc_final: 0.8050 (mttm) REVERT: A 59 SER cc_start: 0.8568 (OUTLIER) cc_final: 0.8004 (p) REVERT: A 92 ASN cc_start: 0.8410 (t0) cc_final: 0.8117 (t0) REVERT: E 60 LYS cc_start: 0.8037 (ptmt) cc_final: 0.7240 (ptmm) REVERT: F 81 MET cc_start: 0.8267 (ttp) cc_final: 0.8036 (ttt) REVERT: G 97 LYS cc_start: 0.6964 (OUTLIER) cc_final: 0.6683 (tmtt) REVERT: G 116 PHE cc_start: 0.7392 (OUTLIER) cc_final: 0.6947 (m-10) REVERT: G 124 ILE cc_start: 0.8208 (mm) cc_final: 0.7995 (mt) REVERT: H 92 ASN cc_start: 0.8509 (p0) cc_final: 0.7951 (p0) REVERT: J 87 ASN cc_start: 0.8207 (OUTLIER) cc_final: 0.7981 (t0) REVERT: J 115 LEU cc_start: 0.7321 (OUTLIER) cc_final: 0.6946 (mt) REVERT: P 49 THR cc_start: 0.8332 (OUTLIER) cc_final: 0.8104 (m) REVERT: P 78 ILE cc_start: 0.9155 (mm) cc_final: 0.8927 (mt) REVERT: P 83 GLN cc_start: 0.6452 (OUTLIER) cc_final: 0.5486 (mp10) REVERT: P 220 ASN cc_start: 0.8962 (m-40) cc_final: 0.8751 (m-40) REVERT: Q 20 SER cc_start: 0.8820 (t) cc_final: 0.8472 (p) REVERT: S 48 ARG cc_start: 0.7304 (ptm160) cc_final: 0.6866 (mtp-110) REVERT: S 260 LEU cc_start: 0.9336 (OUTLIER) cc_final: 0.8978 (mp) REVERT: T 407 PHE cc_start: 0.7957 (t80) cc_final: 0.7596 (t80) REVERT: T 475 GLU cc_start: 0.6985 (pt0) cc_final: 0.6710 (pt0) REVERT: V 112 ASP cc_start: 0.8474 (p0) cc_final: 0.8227 (p0) REVERT: V 471 GLN cc_start: 0.7653 (tt0) cc_final: 0.7284 (mm110) REVERT: X 250 GLN cc_start: 0.8447 (OUTLIER) cc_final: 0.7865 (mm-40) REVERT: X 497 GLU cc_start: 0.7386 (OUTLIER) cc_final: 0.7041 (mp0) REVERT: X 550 LYS cc_start: 0.7711 (pttt) cc_final: 0.7466 (mmmt) REVERT: Z 414 GLN cc_start: 0.8077 (mm110) cc_final: 0.7866 (mm-40) outliers start: 122 outliers final: 100 residues processed: 739 average time/residue: 0.5165 time to fit residues: 648.0021 Evaluate side-chains 746 residues out of total 5633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 634 time to evaluate : 4.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 19 SER Chi-restraints excluded: chain 0 residue 32 THR Chi-restraints excluded: chain 1 residue 47 VAL Chi-restraints excluded: chain 1 residue 234 VAL Chi-restraints excluded: chain 1 residue 240 VAL Chi-restraints excluded: chain 2 residue 209 ASP Chi-restraints excluded: chain 2 residue 238 ASP Chi-restraints excluded: chain 2 residue 245 VAL Chi-restraints excluded: chain 2 residue 303 VAL Chi-restraints excluded: chain 2 residue 377 VAL Chi-restraints excluded: chain 3 residue 156 ASP Chi-restraints excluded: chain 3 residue 258 LYS Chi-restraints excluded: chain 3 residue 309 ASN Chi-restraints excluded: chain 4 residue 44 THR Chi-restraints excluded: chain 4 residue 77 SER Chi-restraints excluded: chain 4 residue 122 VAL Chi-restraints excluded: chain 5 residue 100 SER Chi-restraints excluded: chain 6 residue 53 THR Chi-restraints excluded: chain 6 residue 73 THR Chi-restraints excluded: chain 6 residue 79 LEU Chi-restraints excluded: chain 6 residue 101 VAL Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 7 residue 15 LEU Chi-restraints excluded: chain 7 residue 35 ILE Chi-restraints excluded: chain 7 residue 39 VAL Chi-restraints excluded: chain 7 residue 79 VAL Chi-restraints excluded: chain 7 residue 117 ASP Chi-restraints excluded: chain 7 residue 144 VAL Chi-restraints excluded: chain 7 residue 157 VAL Chi-restraints excluded: chain 8 residue 3 LEU Chi-restraints excluded: chain 8 residue 67 SER Chi-restraints excluded: chain 8 residue 82 THR Chi-restraints excluded: chain 9 residue 29 PHE Chi-restraints excluded: chain 9 residue 65 THR Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain E residue 84 SER Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain F residue 61 MET Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain G residue 97 LYS Chi-restraints excluded: chain G residue 111 GLU Chi-restraints excluded: chain G residue 113 ILE Chi-restraints excluded: chain G residue 116 PHE Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain I residue 118 LEU Chi-restraints excluded: chain J residue 84 SER Chi-restraints excluded: chain J residue 87 ASN Chi-restraints excluded: chain J residue 115 LEU Chi-restraints excluded: chain J residue 121 VAL Chi-restraints excluded: chain M residue 128 ASP Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 83 GLN Chi-restraints excluded: chain P residue 146 LEU Chi-restraints excluded: chain P residue 152 VAL Chi-restraints excluded: chain P residue 185 VAL Chi-restraints excluded: chain P residue 195 LEU Chi-restraints excluded: chain P residue 200 ILE Chi-restraints excluded: chain P residue 207 VAL Chi-restraints excluded: chain Q residue 69 ILE Chi-restraints excluded: chain R residue 60 VAL Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain R residue 82 SER Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain S residue 140 VAL Chi-restraints excluded: chain S residue 260 LEU Chi-restraints excluded: chain S residue 303 GLU Chi-restraints excluded: chain T residue 70 VAL Chi-restraints excluded: chain T residue 75 LYS Chi-restraints excluded: chain T residue 76 SER Chi-restraints excluded: chain T residue 94 ILE Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 300 PHE Chi-restraints excluded: chain T residue 359 SER Chi-restraints excluded: chain T residue 410 THR Chi-restraints excluded: chain T residue 428 SER Chi-restraints excluded: chain T residue 514 VAL Chi-restraints excluded: chain T residue 521 GLU Chi-restraints excluded: chain T residue 532 VAL Chi-restraints excluded: chain T residue 549 HIS Chi-restraints excluded: chain U residue 287 MET Chi-restraints excluded: chain U residue 465 ASP Chi-restraints excluded: chain U residue 514 VAL Chi-restraints excluded: chain U residue 516 ASP Chi-restraints excluded: chain U residue 546 LEU Chi-restraints excluded: chain V residue 70 VAL Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 410 THR Chi-restraints excluded: chain V residue 430 VAL Chi-restraints excluded: chain V residue 464 SER Chi-restraints excluded: chain X residue 62 SER Chi-restraints excluded: chain X residue 190 THR Chi-restraints excluded: chain X residue 250 GLN Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 308 VAL Chi-restraints excluded: chain X residue 425 LEU Chi-restraints excluded: chain X residue 497 GLU Chi-restraints excluded: chain X residue 524 ILE Chi-restraints excluded: chain X residue 531 VAL Chi-restraints excluded: chain Y residue 84 THR Chi-restraints excluded: chain Y residue 266 LEU Chi-restraints excluded: chain Y residue 383 THR Chi-restraints excluded: chain Y residue 471 GLN Chi-restraints excluded: chain Y residue 524 ILE Chi-restraints excluded: chain Z residue 103 VAL Chi-restraints excluded: chain Z residue 334 THR Chi-restraints excluded: chain Z residue 344 ASP Chi-restraints excluded: chain Z residue 554 LEU Chi-restraints excluded: chain Z residue 557 GLU Chi-restraints excluded: chain Z residue 559 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 697 random chunks: chunk 439 optimal weight: 0.7980 chunk 589 optimal weight: 0.0970 chunk 169 optimal weight: 0.7980 chunk 509 optimal weight: 0.8980 chunk 81 optimal weight: 4.9990 chunk 153 optimal weight: 10.0000 chunk 553 optimal weight: 5.9990 chunk 231 optimal weight: 0.9990 chunk 568 optimal weight: 0.1980 chunk 70 optimal weight: 3.9990 chunk 102 optimal weight: 10.0000 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 276 GLN 5 79 ASN ** 7 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 127 HIS M 243 ASN P 140 ASN ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 241 HIS U 539 ASN ** U 549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 179 ASN X 132 GLN ** Y 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.129510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.102857 restraints weight = 83370.990| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 1.68 r_work: 0.3058 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.2721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 54658 Z= 0.147 Angle : 0.505 10.472 74121 Z= 0.256 Chirality : 0.040 0.199 8683 Planarity : 0.004 0.049 9504 Dihedral : 5.216 109.665 7674 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.26 % Favored : 96.64 % Rotamer: Outliers : 2.04 % Allowed : 17.96 % Favored : 79.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.19 (0.10), residues: 7034 helix: 0.72 (0.09), residues: 3830 sheet: -0.23 (0.22), residues: 612 loop : -0.54 (0.13), residues: 2592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP 9 93 HIS 0.004 0.001 HIS Z 396 PHE 0.028 0.001 PHE 3 115 TYR 0.024 0.001 TYR 4 211 ARG 0.012 0.000 ARG J 91 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12641.87 seconds wall clock time: 222 minutes 5.04 seconds (13325.04 seconds total)