Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 20 09:39:33 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rdw_4833/04_2023/6rdw_4833_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rdw_4833/04_2023/6rdw_4833.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rdw_4833/04_2023/6rdw_4833.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rdw_4833/04_2023/6rdw_4833.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rdw_4833/04_2023/6rdw_4833_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rdw_4833/04_2023/6rdw_4833_updated.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 1.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 13 5.49 5 Mg 5 5.21 5 S 149 5.16 5 C 34297 2.51 5 N 9112 2.21 5 O 10171 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "0 ASP 73": "OD1" <-> "OD2" Residue "1 ARG 28": "NH1" <-> "NH2" Residue "1 PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 GLU 33": "OE1" <-> "OE2" Residue "1 GLU 34": "OE1" <-> "OE2" Residue "1 GLU 49": "OE1" <-> "OE2" Residue "1 ASP 69": "OD1" <-> "OD2" Residue "1 GLU 138": "OE1" <-> "OE2" Residue "1 ARG 150": "NH1" <-> "NH2" Residue "1 ASP 172": "OD1" <-> "OD2" Residue "1 ARG 182": "NH1" <-> "NH2" Residue "1 GLU 215": "OE1" <-> "OE2" Residue "1 GLU 229": "OE1" <-> "OE2" Residue "1 ARG 259": "NH1" <-> "NH2" Residue "1 GLU 281": "OE1" <-> "OE2" Residue "1 GLU 343": "OE1" <-> "OE2" Residue "1 GLU 350": "OE1" <-> "OE2" Residue "1 ASP 353": "OD1" <-> "OD2" Residue "1 ARG 359": "NH1" <-> "NH2" Residue "1 ASP 373": "OD1" <-> "OD2" Residue "1 ARG 387": "NH1" <-> "NH2" Residue "1 GLU 409": "OE1" <-> "OE2" Residue "1 GLU 414": "OE1" <-> "OE2" Residue "1 ARG 434": "NH1" <-> "NH2" Residue "1 ASP 479": "OD1" <-> "OD2" Residue "1 ASP 486": "OD1" <-> "OD2" Residue "1 GLU 496": "OE1" <-> "OE2" Residue "1 GLU 513": "OE1" <-> "OE2" Residue "1 ASP 549": "OD1" <-> "OD2" Residue "1 ASP 573": "OD1" <-> "OD2" Residue "1 GLU 586": "OE1" <-> "OE2" Residue "1 ARG 609": "NH1" <-> "NH2" Residue "1 ASP 613": "OD1" <-> "OD2" Residue "2 ASP 16": "OD1" <-> "OD2" 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 TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ARG 173": "NH1" <-> "NH2" Residue "2 PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 ARG 346": "NH1" <-> "NH2" Residue "2 TYR 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 TYR 411": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 TYR 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ASP 102": "OD1" <-> "OD2" Residue "3 ASP 119": "OD1" <-> "OD2" Residue "3 PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 GLU 126": "OE1" <-> "OE2" Residue "3 ARG 149": "NH1" <-> "NH2" Residue "3 ASP 154": "OD1" <-> "OD2" Residue "3 PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 GLU 173": "OE1" <-> "OE2" Residue "3 GLU 175": "OE1" <-> "OE2" Residue "3 PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ASP 197": "OD1" <-> "OD2" Residue "3 ARG 213": "NH1" <-> "NH2" 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 GLU 295": "OE1" <-> "OE2" Residue "3 GLU 301": "OE1" <-> "OE2" Residue "3 GLU 320": "OE1" <-> "OE2" Residue "4 ASP 19": "OD1" <-> "OD2" Residue "4 TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ASP 45": "OD1" <-> "OD2" 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 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ASP 133": "OD1" <-> "OD2" Residue "4 TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ARG 176": "NH1" <-> "NH2" Residue "4 ASP 181": "OD1" <-> "OD2" Residue "4 TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 193": "OE1" <-> "OE2" Residue "4 TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ASP 214": "OD1" <-> "OD2" Residue "4 GLU 218": "OE1" <-> "OE2" Residue "4 GLU 225": "OE1" <-> "OE2" Residue "4 ARG 232": "NH1" <-> "NH2" Residue "4 GLU 244": "OE1" <-> "OE2" Residue "4 ARG 255": "NH1" <-> "NH2" Residue "4 TYR 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 "7 PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ASP 25": "OD1" <-> "OD2" Residue "7 GLU 47": "OE1" <-> "OE2" Residue "7 ARG 81": "NH1" <-> "NH2" Residue "7 GLU 99": "OE1" <-> "OE2" Residue "7 ASP 109": "OD1" <-> "OD2" Residue "7 PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 "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 ARG 28": "NH1" <-> "NH2" Residue "9 PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 "B GLU 111": "OE1" <-> "OE2" Residue "C GLU 111": "OE1" <-> "OE2" Residue "C PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 111": "OE1" <-> "OE2" Residue "F GLU 111": "OE1" <-> "OE2" Residue "H GLU 111": "OE1" <-> "OE2" Residue "H PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 115": "NH1" <-> "NH2" Residue "M ASP 143": "OD1" <-> "OD2" Residue "M ARG 145": "NH1" <-> "NH2" Residue "M PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 232": "NH1" <-> "NH2" Residue "M ARG 239": "NH1" <-> "NH2" Residue "M TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 64": "OE1" <-> "OE2" Residue "P ASP 68": "OD1" <-> "OD2" Residue "P ASP 72": "OD1" <-> "OD2" Residue "P PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 86": "OE1" <-> "OE2" Residue "P PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 127": "OD1" <-> "OD2" Residue "P GLU 166": "OE1" <-> "OE2" Residue "P GLU 169": "OE1" <-> "OE2" Residue "P PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 204": "OD1" <-> "OD2" Residue "P ARG 206": "NH1" <-> "NH2" Residue "P GLU 216": "OE1" <-> "OE2" Residue "P GLU 217": "OE1" <-> "OE2" 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 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 ASP 95": "OD1" <-> "OD2" Residue "R GLU 117": "OE1" <-> "OE2" Residue "R ASP 143": "OD1" <-> "OD2" Residue "S ARG 46": "NH1" <-> "NH2" Residue "S ASP 91": "OD1" <-> "OD2" 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 GLU 180": "OE1" <-> "OE2" Residue "S GLU 181": "OE1" <-> "OE2" Residue "S TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 222": "OD1" <-> "OD2" Residue "S TYR 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 241": "OD1" <-> "OD2" Residue "S ARG 244": "NH1" <-> "NH2" Residue "S GLU 248": "OE1" <-> "OE2" Residue "S GLU 283": "OE1" <-> "OE2" Residue "S TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 306": "OE1" <-> "OE2" Residue "T ARG 49": "NH1" <-> "NH2" Residue "T GLU 72": "OE1" <-> "OE2" Residue "T ARG 86": "NH1" <-> "NH2" Residue "T ASP 92": "OD1" <-> "OD2" Residue "T ASP 125": "OD1" <-> "OD2" Residue "T ASP 135": "OD1" <-> "OD2" Residue "T ASP 142": "OD1" <-> "OD2" Residue "T ARG 162": "NH1" <-> "NH2" Residue "T ASP 172": "OD1" <-> "OD2" Residue "T ARG 195": "NH1" <-> "NH2" Residue "T ARG 199": "NH1" <-> "NH2" Residue "T PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 283": "NH1" <-> "NH2" Residue "T TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 294": "OD1" <-> "OD2" Residue "T TYR 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 403": "OD1" <-> "OD2" Residue "T PHE 407": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 429": "NH1" <-> "NH2" Residue "T PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 454": "NH1" <-> "NH2" Residue "T GLU 475": "OE1" <-> "OE2" Residue "T PHE 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 502": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 516": "OD1" <-> "OD2" Residue "T GLU 521": "OE1" <-> "OE2" Residue "T ASP 547": "OD1" <-> "OD2" Residue "T ARG 555": "NH1" <-> "NH2" Residue "U ASP 41": "OD1" <-> "OD2" Residue "U GLU 47": "OE1" <-> "OE2" Residue "U ARG 49": "NH1" <-> "NH2" Residue "U PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 92": "OD1" <-> "OD2" Residue "U ARG 96": "NH1" <-> "NH2" Residue "U TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 125": "OD1" <-> "OD2" Residue "U TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 146": "NH1" <-> "NH2" Residue "U ARG 162": "NH1" <-> "NH2" Residue "U ASP 165": "OD1" <-> "OD2" Residue "U ARG 181": "NH1" <-> "NH2" Residue "U ARG 199": "NH1" <-> "NH2" Residue "U ASP 210": "OD1" <-> "OD2" Residue "U ARG 227": "NH1" <-> "NH2" Residue "U ASP 237": "OD1" <-> "OD2" Residue "U ARG 254": "NH1" <-> "NH2" Residue "U TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 283": "NH1" <-> "NH2" Residue "U TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U 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 ASP 389": "OD1" <-> "OD2" Residue "U PHE 407": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 449": "OE1" <-> "OE2" Residue "U ARG 454": "NH1" <-> "NH2" Residue "U GLU 455": "OE1" <-> "OE2" Residue "U PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 475": "OE1" <-> "OE2" Residue "U ARG 479": "NH1" <-> "NH2" Residue "U ARG 496": "NH1" <-> "NH2" Residue "U ARG 513": "NH1" <-> "NH2" Residue "U ASP 516": "OD1" <-> "OD2" Residue "U PHE 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 547": "OD1" <-> "OD2" Residue "V GLU 47": "OE1" <-> "OE2" Residue "V ARG 49": "NH1" <-> "NH2" Residue "V PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 74": "OE1" <-> "OE2" Residue "V PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 135": "OD1" <-> "OD2" Residue "V ARG 181": "NH1" <-> "NH2" Residue "V ARG 217": "NH1" <-> "NH2" Residue "V ARG 220": "NH1" <-> "NH2" Residue "V GLU 247": "OE1" <-> "OE2" Residue "V TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 266": "NH1" <-> "NH2" Residue "V TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 314": "NH1" <-> "NH2" Residue "V ARG 335": "NH1" <-> "NH2" Residue "V ARG 342": "NH1" <-> "NH2" Residue "V ARG 343": "NH1" <-> "NH2" Residue "V ARG 347": "NH1" <-> "NH2" Residue "V ARG 360": "NH1" <-> "NH2" Residue "V GLU 384": "OE1" <-> "OE2" Residue "V PHE 407": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 409": "OE1" <-> "OE2" 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 ARG 513": "NH1" <-> "NH2" Residue "V GLU 521": "OE1" <-> "OE2" Residue "V GLU 522": "OE1" <-> "OE2" Residue "V GLU 553": "OE1" <-> "OE2" Residue "V ARG 555": "NH1" <-> "NH2" Residue "X ARG 51": "NH1" <-> "NH2" Residue "X PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 75": "OE1" <-> "OE2" Residue "X ASP 82": "OD1" <-> "OD2" Residue "X GLU 146": "OE1" <-> "OE2" Residue "X PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 156": "OE1" <-> "OE2" Residue "X GLU 158": "OE1" <-> "OE2" Residue "X ASP 168": "OD1" <-> "OD2" Residue "X PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 218": "NH1" <-> "NH2" Residue "X ARG 225": "NH1" <-> "NH2" Residue "X ARG 239": "NH1" <-> "NH2" Residue "X TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 253": "OE1" <-> "OE2" Residue "X ASP 274": "OD1" <-> "OD2" Residue "X GLU 296": "OE1" <-> "OE2" Residue "X ASP 317": "OD1" <-> "OD2" Residue "X TYR 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 378": "OD1" <-> "OD2" Residue "X ASP 381": "OD1" <-> "OD2" Residue "X ARG 385": "NH1" <-> "NH2" Residue "X TYR 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 401": "NH1" <-> "NH2" Residue "X ASP 409": "OD1" <-> "OD2" Residue "X GLU 424": "OE1" <-> "OE2" Residue "X GLU 427": "OE1" <-> "OE2" Residue "X ASP 465": "OD1" <-> "OD2" Residue "X ASP 479": "OD1" <-> "OD2" Residue "X ASP 480": "OD1" <-> "OD2" Residue "X GLU 483": "OE1" <-> "OE2" Residue "X PHE 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 494": "OE1" <-> "OE2" Residue "X GLU 497": "OE1" <-> "OE2" Residue "X ARG 509": "NH1" <-> "NH2" Residue "X GLU 511": "OE1" <-> "OE2" Residue "X ASP 543": "OD1" <-> "OD2" Residue "X ASP 548": "OD1" <-> "OD2" Residue "X GLU 552": "OE1" <-> "OE2" Residue "Y ASP 36": "OD1" <-> "OD2" Residue "Y ARG 71": "NH1" <-> "NH2" Residue "Y GLU 75": "OE1" <-> "OE2" Residue "Y ARG 86": "NH1" <-> "NH2" Residue "Y ASP 91": "OD1" <-> "OD2" Residue "Y ASP 94": "OD1" <-> "OD2" Residue "Y ARG 115": "NH1" <-> "NH2" Residue "Y ARG 120": "NH1" <-> "NH2" Residue "Y ASP 139": "OD1" <-> "OD2" Residue "Y ARG 145": "NH1" <-> "NH2" Residue "Y PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 195": "OE1" <-> "OE2" Residue "Y PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 215": "OE1" <-> "OE2" Residue "Y ASP 222": "OD1" <-> "OD2" Residue "Y ARG 258": "NH1" <-> "NH2" Residue "Y GLU 270": "OE1" <-> "OE2" Residue "Y ASP 285": "OD1" <-> "OD2" Residue "Y TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 344": "OD1" <-> "OD2" Residue "Y ARG 366": "NH1" <-> "NH2" Residue "Y ASP 381": "OD1" <-> "OD2" Residue "Y ARG 385": "NH1" <-> "NH2" Residue "Y ASP 409": "OD1" <-> "OD2" Residue "Y ASP 415": "OD1" <-> "OD2" Residue "Y PHE 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 497": "OE1" <-> "OE2" Residue "Y GLU 511": "OE1" <-> "OE2" Residue "Y GLU 519": "OE1" <-> "OE2" Residue "Y GLU 520": "OE1" <-> "OE2" Residue "Y GLU 540": "OE1" <-> "OE2" Residue "Y PHE 549": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 49": "OD1" <-> "OD2" Residue "Z ARG 51": "NH1" <-> "NH2" Residue "Z ARG 71": "NH1" <-> "NH2" Residue "Z GLU 75": "OE1" <-> "OE2" Residue "Z ARG 86": "NH1" <-> "NH2" Residue "Z ASP 94": "OD1" <-> "OD2" Residue "Z ARG 98": "NH1" <-> "NH2" Residue "Z ARG 120": "NH1" <-> "NH2" Residue "Z GLU 156": "OE1" <-> "OE2" Residue "Z PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 215": "OE1" <-> "OE2" Residue "Z ARG 216": "NH1" <-> "NH2" Residue "Z GLU 238": "OE1" <-> "OE2" Residue "Z ARG 258": "NH1" <-> "NH2" Residue "Z GLU 270": "OE1" <-> "OE2" Residue "Z ASP 285": "OD1" <-> "OD2" Residue "Z ARG 289": "NH1" <-> "NH2" Residue "Z GLU 296": "OE1" <-> "OE2" Residue "Z ASP 317": "OD1" <-> "OD2" Residue "Z GLU 323": "OE1" <-> "OE2" Residue "Z ASP 344": "OD1" <-> "OD2" Residue "Z ASP 345": "OD1" <-> "OD2" Residue "Z ASP 348": "OD1" <-> "OD2" Residue "Z PHE 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 370": "OE1" <-> "OE2" Residue "Z ASP 378": "OD1" <-> "OD2" Residue "Z ARG 385": "NH1" <-> "NH2" Residue "Z GLU 395": "OE1" <-> "OE2" Residue "Z ARG 401": "NH1" <-> "NH2" Residue "Z ASP 409": "OD1" <-> "OD2" Residue "Z TYR 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 424": "OE1" <-> "OE2" Residue "Z GLU 427": "OE1" <-> "OE2" Residue "Z ASP 429": "OD1" <-> "OD2" Residue "Z ARG 435": "NH1" <-> "NH2" Residue "Z ARG 437": "NH1" <-> "NH2" Residue "Z ASP 505": "OD1" <-> "OD2" Residue "Z ARG 509": "NH1" <-> "NH2" Residue "Z ASP 513": "OD1" <-> "OD2" Residue "Z GLU 519": "OE1" <-> "OE2" Residue "Z PHE 549": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 563": "OE1" <-> "OE2" Residue "Z GLU 564": "OE1" <-> "OE2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 53748 Number of models: 1 Model: "" Number of chains: 37 Chain: "0" Number of atoms: 607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 607 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 8, 'TRANS': 72} Chain: "1" Number of atoms: 4661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4661 Classifications: {'peptide': 595} Link IDs: {'PTRANS': 31, 'TRANS': 563} Chain: "2" Number of atoms: 3163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3163 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 17, 'TRANS': 423} Chain: "3" Number of atoms: 1874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1874 Classifications: {'peptide': 245} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 239} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 7 Chain: "4" Number of atoms: 2177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2177 Classifications: {'peptide': 290} Link IDs: {'PTRANS': 9, 'TRANS': 280} Chain: "5" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 986 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 7, 'TRANS': 115} Chain: "6" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 926 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "7" Number of atoms: 1347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1347 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 5, 'TRANS': 170} Chain: "8" Number of atoms: 692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 692 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 7, 'TRANS': 80} Chain: "9" Number of atoms: 776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 776 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 5, 'TRANS': 91} Chain: "A" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "B" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "C" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain breaks: 1 Chain: "D" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "E" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "F" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "G" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "H" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "I" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "J" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "M" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1640 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 12, 'TRANS': 204} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "P" Number of atoms: 1532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1532 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 5, 'TRANS': 187} Chain: "Q" Number of atoms: 561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 561 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 5, 'TRANS': 66} Chain: "R" Number of atoms: 1303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1303 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 13, 'TRANS': 163} Chain: "S" Number of atoms: 2130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2130 Classifications: {'peptide': 277} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 271} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "T" Number of atoms: 3979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 3979 Classifications: {'peptide': 523} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 497} Chain breaks: 1 Chain: "U" Number of atoms: 3980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 3980 Classifications: {'peptide': 523} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 497} Chain: "V" Number of atoms: 3962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 3962 Classifications: {'peptide': 520} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 494} Chain: "X" Number of atoms: 4115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 542, 4115 Classifications: {'peptide': 542} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 517} Chain: "Y" Number of atoms: 3957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 521, 3957 Classifications: {'peptide': 521} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 498} Chain: "Z" Number of atoms: 4087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 538, 4087 Classifications: {'peptide': 538} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 513} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "U" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "V" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 21.39, per 1000 atoms: 0.40 Number of scatterers: 53748 At special positions: 0 Unit cell: (211.653, 134.784, 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 10171 8.00 N 9112 7.00 C 34297 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 16.68 Conformation dependent library (CDL) restraints added in 6.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN M 600 " pdb="ZN ZN M 600 " - pdb=" NE2 HIS M 248 " 14072 Ramachandran restraints generated. 7036 Oldfield, 0 Emsley, 7036 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13086 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 290 helices and 33 sheets defined 50.9% alpha, 6.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.77 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 49 Processing helix chain '0' and resid 52 through 55 No H-bonds generated for 'chain '0' and resid 52 through 55' Processing helix chain '1' and resid 46 through 71 Processing helix chain '1' and resid 79 through 82 No H-bonds generated for 'chain '1' and resid 79 through 82' 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 142 removed outlier: 3.916A pdb=" N GLU 1 136 " --> pdb=" O GLY 1 132 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ALA 1 142 " --> pdb=" O GLU 1 138 " (cutoff:3.500A) Processing helix chain '1' and resid 164 through 175 removed outlier: 3.787A pdb=" N THR 1 169 " --> pdb=" O GLU 1 165 " (cutoff:3.500A) Processing helix chain '1' and resid 191 through 202 removed outlier: 3.730A pdb=" N ALA 1 196 " --> pdb=" O GLY 1 192 " (cutoff:3.500A) Processing helix chain '1' and resid 210 through 222 Processing helix chain '1' and resid 242 through 270 Processing helix chain '1' and resid 272 through 276 removed outlier: 4.035A pdb=" N ALA 1 275 " --> pdb=" O PRO 1 272 " (cutoff:3.500A) Processing helix chain '1' and resid 280 through 285 removed outlier: 4.096A pdb=" N ASP 1 283 " --> pdb=" O ASN 1 280 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ALA 1 284 " --> pdb=" O GLU 1 281 " (cutoff:3.500A) Processing helix chain '1' and resid 298 through 306 removed outlier: 3.920A pdb=" N GLN 1 306 " --> pdb=" O SER 1 302 " (cutoff:3.500A) Processing helix chain '1' and resid 311 through 316 Processing helix chain '1' and resid 324 through 326 No H-bonds generated for 'chain '1' and resid 324 through 326' Processing helix chain '1' and resid 331 through 333 No H-bonds generated for 'chain '1' and resid 331 through 333' Processing helix chain '1' and resid 339 through 350 Processing helix chain '1' and resid 354 through 361 Processing helix chain '1' and resid 376 through 387 Processing helix chain '1' and resid 393 through 420 removed outlier: 5.016A pdb=" N VAL 1 418 " --> pdb=" O GLU 1 414 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N ILE 1 419 " --> pdb=" O GLU 1 415 " (cutoff:3.500A) Processing helix chain '1' and resid 426 through 431 Processing helix chain '1' and resid 436 through 444 Processing helix chain '1' and resid 447 through 459 removed outlier: 3.838A pdb=" N ARG 1 453 " --> pdb=" O ALA 1 449 " (cutoff:3.500A) Processing helix chain '1' and resid 464 through 478 Processing helix chain '1' and resid 480 through 482 No H-bonds generated for 'chain '1' and resid 480 through 482' Processing helix chain '1' and resid 486 through 489 No H-bonds generated for 'chain '1' and resid 486 through 489' Processing helix chain '1' and resid 491 through 515 removed outlier: 3.781A pdb=" N GLU 1 501 " --> pdb=" O LEU 1 497 " (cutoff:3.500A) removed outlier: 3.562A 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 605 removed outlier: 5.432A pdb=" N HIS 1 590 " --> pdb=" O GLU 1 586 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N HIS 1 591 " --> pdb=" O ASN 1 587 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N PHE 1 592 " --> pdb=" O LEU 1 588 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N LEU 1 593 " --> pdb=" O SER 1 589 " (cutoff:3.500A) Proline residue: 1 594 - end of helix Processing helix chain '2' and resid 8 through 16 Processing helix chain '2' and resid 26 through 37 Processing helix chain '2' and resid 46 through 57 Processing helix chain '2' and resid 63 through 76 Processing helix chain '2' and resid 81 through 93 removed outlier: 3.639A pdb=" N LEU 2 87 " --> pdb=" O THR 2 83 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ALA 2 88 " --> pdb=" O VAL 2 84 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N GLY 2 89 " --> pdb=" O ALA 2 85 " (cutoff:3.500A) Proline residue: 2 90 - end of helix Processing helix chain '2' and resid 100 through 112 Processing helix chain '2' and resid 118 through 130 removed outlier: 4.184A pdb=" N VAL 2 127 " --> pdb=" O LYS 2 123 " (cutoff:3.500A) Processing helix chain '2' and resid 137 through 149 Processing helix chain '2' and resid 156 through 167 removed outlier: 3.648A 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: 4.794A pdb=" N ALA 2 195 " --> pdb=" O ALA 2 191 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LYS 2 198 " --> pdb=" O ASP 2 194 " (cutoff:3.500A) removed outlier: 4.130A 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 228 through 233 Processing helix chain '2' and resid 241 through 253 removed outlier: 3.778A pdb=" N GLU 2 246 " --> pdb=" O ALA 2 242 " (cutoff:3.500A) Processing helix chain '2' and resid 259 through 275 removed outlier: 3.839A pdb=" N VAL 2 268 " --> pdb=" O ALA 2 264 " (cutoff:3.500A) removed outlier: 3.743A 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: 4.062A pdb=" N SER 2 305 " --> pdb=" O ALA 2 301 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N PHE 2 306 " --> pdb=" O ALA 2 302 " (cutoff:3.500A) removed outlier: 3.537A 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 355 Processing helix chain '2' and resid 397 through 409 removed outlier: 3.924A pdb=" N GLN 2 409 " --> pdb=" O VAL 2 405 " (cutoff:3.500A) Processing helix chain '2' and resid 418 through 423 removed outlier: 3.688A pdb=" N GLU 2 422 " --> pdb=" O ALA 2 418 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N ALA 2 423 " --> pdb=" O ASN 2 419 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 418 through 423' Processing helix chain '2' and resid 427 through 441 removed outlier: 3.912A pdb=" N VAL 2 441 " --> pdb=" O ALA 2 437 " (cutoff:3.500A) Processing helix chain '3' and resid 78 through 87 Processing helix chain '3' and resid 103 through 112 removed outlier: 3.910A pdb=" N TYR 3 108 " --> pdb=" O PRO 3 104 " (cutoff:3.500A) Processing helix chain '3' and resid 118 through 124 removed outlier: 3.961A 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 removed outlier: 4.279A pdb=" N GLY 3 160 " --> pdb=" O ASP 3 156 " (cutoff:3.500A) Processing helix chain '3' and resid 174 through 186 removed outlier: 3.751A pdb=" N GLN 3 179 " --> pdb=" O GLU 3 175 " (cutoff:3.500A) Processing helix chain '3' and resid 192 through 203 Processing helix chain '3' and resid 212 through 214 No H-bonds generated for 'chain '3' and resid 212 through 214' Processing helix chain '3' and resid 216 through 229 removed outlier: 3.892A pdb=" N THR 3 221 " --> pdb=" O ASP 3 217 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ASN 3 229 " --> pdb=" O TYR 3 225 " (cutoff:3.500A) Processing helix chain '3' and resid 234 through 242 removed outlier: 4.063A pdb=" N ARG 3 242 " --> pdb=" O ALA 3 238 " (cutoff:3.500A) Processing helix chain '3' and resid 246 through 249 No H-bonds generated for 'chain '3' and resid 246 through 249' Processing helix chain '3' and resid 254 through 271 removed outlier: 3.539A pdb=" N PHE 3 271 " --> pdb=" O ALA 3 267 " (cutoff:3.500A) Processing helix chain '3' and resid 276 through 283 removed outlier: 3.658A pdb=" N GLU 3 279 " --> pdb=" O GLU 3 276 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ALA 3 280 " --> pdb=" O SER 3 277 " (cutoff:3.500A) Processing helix chain '3' and resid 294 through 311 removed outlier: 3.917A pdb=" N VAL 3 303 " --> pdb=" O GLU 3 299 " (cutoff:3.500A) Processing helix chain '4' and resid 20 through 34 Processing helix chain '4' and resid 48 through 68 removed outlier: 3.596A pdb=" N ALA 4 60 " --> pdb=" O LYS 4 56 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N GLN 4 61 " --> pdb=" O TYR 4 57 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N VAL 4 62 " --> pdb=" O LEU 4 58 " (cutoff:3.500A) Proline residue: 4 65 - end of helix removed outlier: 3.991A pdb=" N HIS 4 68 " --> pdb=" O GLU 4 64 " (cutoff:3.500A) Processing helix chain '4' and resid 80 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: 4.011A pdb=" N ALA 4 137 " --> pdb=" O ASP 4 133 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VAL 4 141 " --> pdb=" O ALA 4 137 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU 4 148 " --> pdb=" O SER 4 144 " (cutoff:3.500A) Processing helix chain '4' and resid 160 through 176 removed outlier: 3.629A pdb=" N LYS 4 168 " --> pdb=" O LYS 4 164 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA 4 171 " --> pdb=" O ALA 4 167 " (cutoff:3.500A) Processing helix chain '4' and resid 180 through 188 Processing helix chain '4' and resid 193 through 233 removed outlier: 4.739A pdb=" N LYS 4 198 " --> pdb=" O ASP 4 194 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N VAL 4 199 " --> pdb=" O ALA 4 195 " (cutoff:3.500A) Processing helix chain '4' and resid 238 through 258 Processing helix chain '4' and resid 263 through 284 Processing helix chain '5' and resid 8 through 58 removed outlier: 5.041A pdb=" N LEU 5 31 " --> pdb=" O ASP 5 27 " (cutoff:3.500A) Proline residue: 5 32 - end of helix removed outlier: 3.841A pdb=" N GLU 5 37 " --> pdb=" O THR 5 33 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N HIS 5 41 " --> pdb=" O GLU 5 37 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N LYS 5 49 " --> pdb=" O ALA 5 45 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N ARG 5 50 " --> pdb=" O ALA 5 46 " (cutoff:3.500A) Processing helix chain '5' and resid 64 through 67 No H-bonds generated for 'chain '5' and resid 64 through 67' Processing helix chain '5' and resid 73 through 79 Processing helix chain '5' and resid 88 through 105 removed outlier: 3.736A pdb=" N LEU 5 92 " --> pdb=" O PRO 5 88 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LYS 5 101 " --> pdb=" O SER 5 97 " (cutoff:3.500A) removed outlier: 3.624A 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 49 through 57 removed outlier: 4.518A pdb=" N LYS 6 52 " --> pdb=" O SER 6 49 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N THR 6 53 " --> pdb=" O SER 6 50 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA 6 56 " --> pdb=" O THR 6 53 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLN 6 57 " --> pdb=" O ILE 6 54 " (cutoff:3.500A) Processing helix chain '6' and resid 73 through 93 Processing helix chain '6' and resid 99 through 117 removed outlier: 4.403A pdb=" N VAL 6 107 " --> pdb=" O LEU 6 103 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N TRP 6 112 " --> pdb=" O LEU 6 108 " (cutoff:3.500A) Processing helix chain '6' and resid 122 through 129 Processing helix chain '7' and resid 63 through 66 No H-bonds generated for 'chain '7' and resid 63 through 66' Processing helix chain '7' and resid 84 through 104 removed outlier: 3.731A pdb=" N GLU 7 99 " --> pdb=" O SER 7 95 " (cutoff:3.500A) removed outlier: 3.869A 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 117 through 120 No H-bonds generated for 'chain '7' and resid 117 through 120' Processing helix chain '7' and resid 124 through 144 Processing helix chain '7' and resid 150 through 156 removed outlier: 4.334A pdb=" N SER 7 155 " --> pdb=" O SER 7 151 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLN 7 156 " --> pdb=" O ALA 7 152 " (cutoff:3.500A) Processing helix chain '7' and resid 158 through 165 Processing helix chain '7' and resid 175 through 187 Processing helix chain '8' and resid 27 through 30 No H-bonds generated for 'chain '8' and resid 27 through 30' Processing helix chain '8' and resid 32 through 38 Processing helix chain '8' and resid 41 through 79 removed outlier: 3.712A pdb=" N TRP 8 45 " --> pdb=" O ILE 8 41 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N TYR 8 46 " --> pdb=" O PRO 8 42 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N LEU 8 47 " --> pdb=" O ARG 8 43 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA 8 76 " --> pdb=" O ALA 8 72 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ALA 8 79 " --> pdb=" O GLU 8 75 " (cutoff:3.500A) Processing helix chain '9' and resid 5 through 16 Processing helix chain '9' and resid 20 through 23 No H-bonds generated for 'chain '9' and resid 20 through 23' Processing helix chain '9' and resid 37 through 56 removed outlier: 4.256A pdb=" N VAL 9 42 " --> pdb=" O ALA 9 38 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ASN 9 56 " --> pdb=" O LEU 9 52 " (cutoff:3.500A) Processing helix chain '9' and resid 77 through 79 No H-bonds generated for 'chain '9' and resid 77 through 79' Processing helix chain '9' and resid 83 through 94 Processing helix chain 'A' and resid 56 through 91 removed outlier: 4.500A pdb=" N MET A 61 " --> pdb=" O ALA A 57 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ILE A 69 " --> pdb=" O GLY A 65 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N ALA A 70 " --> pdb=" O CYS A 66 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N LEU A 71 " --> pdb=" O ALA A 67 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N ALA A 72 " --> pdb=" O THR A 68 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N GLY A 73 " --> pdb=" O ILE A 69 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL A 74 " --> pdb=" O ALA A 70 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE A 86 " --> pdb=" O PHE A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 95 No H-bonds generated for 'chain 'A' and resid 93 through 95' Processing helix chain 'A' and resid 98 through 110 Processing helix chain 'A' and resid 112 through 126 removed outlier: 3.634A pdb=" N PHE A 126 " --> pdb=" O PHE A 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 67 removed outlier: 3.766A pdb=" N MET B 61 " --> pdb=" O ALA B 57 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N CYS B 66 " --> pdb=" O VAL B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 91 removed outlier: 3.558A pdb=" N VAL B 80 " --> pdb=" O ALA B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 126 removed outlier: 4.086A pdb=" N GLY B 101 " --> pdb=" O LYS B 97 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU B 109 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ILE B 113 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LEU B 125 " --> pdb=" O VAL B 121 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N PHE B 126 " --> pdb=" O PHE B 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 89 removed outlier: 4.096A pdb=" N MET C 61 " --> pdb=" O ALA C 57 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL C 62 " --> pdb=" O ALA C 58 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ILE C 69 " --> pdb=" O GLY C 65 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N ALA C 70 " --> pdb=" O CYS C 66 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N LEU C 71 " --> pdb=" O ALA C 67 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N ALA C 72 " --> pdb=" O THR C 68 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N GLY C 73 " --> pdb=" O ILE C 69 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL C 74 " --> pdb=" O ALA C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 125 removed outlier: 4.861A pdb=" N LYS C 97 " --> pdb=" O ASN C 94 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU C 99 " --> pdb=" O ALA C 96 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N VAL C 100 " --> pdb=" O LYS C 97 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N LEU C 104 " --> pdb=" O GLY C 101 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA C 108 " --> pdb=" O LEU C 105 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N SER C 112 " --> pdb=" O LEU C 109 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE C 113 " --> pdb=" O THR C 110 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE C 124 " --> pdb=" O VAL C 121 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU C 125 " --> pdb=" O PHE C 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 65 removed outlier: 3.532A pdb=" N SER D 59 " --> pdb=" O VAL D 55 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N MET D 61 " --> pdb=" O ALA D 57 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL D 62 " --> pdb=" O ALA D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 91 removed outlier: 3.811A pdb=" N GLY D 79 " --> pdb=" O ALA D 76 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N LEU D 85 " --> pdb=" O PHE D 82 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASN D 87 " --> pdb=" O SER D 84 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG D 91 " --> pdb=" O GLY D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 126 removed outlier: 3.558A pdb=" N ALA D 96 " --> pdb=" O PRO D 93 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N LYS D 97 " --> pdb=" O ASN D 94 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N VAL D 100 " --> pdb=" O LYS D 97 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N LEU D 104 " --> pdb=" O GLY D 101 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N SER D 112 " --> pdb=" O LEU D 109 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU D 119 " --> pdb=" O PHE D 116 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU D 125 " --> pdb=" O PHE D 122 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N PHE D 126 " --> pdb=" O LEU D 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 65 removed outlier: 3.742A pdb=" N LYS E 60 " --> pdb=" O LEU E 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 89 removed outlier: 3.539A pdb=" N ILE E 86 " --> pdb=" O PHE E 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 95 No H-bonds generated for 'chain 'E' and resid 93 through 95' Processing helix chain 'E' and resid 98 through 125 removed outlier: 4.249A pdb=" N LEU E 105 " --> pdb=" O GLY E 101 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N SER E 112 " --> pdb=" O ALA E 108 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N ILE E 113 " --> pdb=" O LEU E 109 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ALA E 114 " --> pdb=" O THR E 110 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N PHE E 122 " --> pdb=" O LEU E 118 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU E 125 " --> pdb=" O VAL E 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 67 removed outlier: 3.971A pdb=" N MET F 61 " --> pdb=" O ALA F 57 " (cutoff:3.500A) Processing helix chain 'F' and resid 70 through 91 Processing helix chain 'F' and resid 93 through 126 removed outlier: 4.909A pdb=" N LYS F 97 " --> pdb=" O ASN F 94 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N VAL F 100 " --> pdb=" O LYS F 97 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU F 104 " --> pdb=" O GLY F 101 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA F 108 " --> pdb=" O LEU F 105 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N GLU F 111 " --> pdb=" O ALA F 108 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER F 112 " --> pdb=" O LEU F 109 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU F 119 " --> pdb=" O PHE F 116 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL F 121 " --> pdb=" O LEU F 118 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU F 123 " --> pdb=" O VAL F 120 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N ILE F 124 " --> pdb=" O VAL F 121 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N PHE F 126 " --> pdb=" O LEU F 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 91 removed outlier: 4.178A pdb=" N ILE G 69 " --> pdb=" O GLY G 65 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N ALA G 70 " --> pdb=" O CYS G 66 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N LEU G 71 " --> pdb=" O ALA G 67 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N ALA G 72 " --> pdb=" O THR G 68 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N GLY G 73 " --> pdb=" O ILE G 69 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL G 74 " --> pdb=" O ALA G 70 " (cutoff:3.500A) Processing helix chain 'G' and resid 93 through 125 removed outlier: 4.868A pdb=" N LYS G 97 " --> pdb=" O ASN G 94 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N LEU G 104 " --> pdb=" O GLY G 101 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU G 109 " --> pdb=" O GLY G 106 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N SER G 112 " --> pdb=" O LEU G 109 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ILE G 124 " --> pdb=" O VAL G 121 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LEU G 125 " --> pdb=" O PHE G 122 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 91 removed outlier: 4.029A pdb=" N THR H 68 " --> pdb=" O ALA H 64 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ILE H 69 " --> pdb=" O GLY H 65 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N ALA H 70 " --> pdb=" O CYS H 66 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N LEU H 71 " --> pdb=" O ALA H 67 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N ALA H 72 " --> pdb=" O THR H 68 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N GLY H 73 " --> pdb=" O ILE H 69 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL H 74 " --> pdb=" O ALA H 70 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ILE H 86 " --> pdb=" O PHE H 82 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASN H 87 " --> pdb=" O GLY H 83 " (cutoff:3.500A) Processing helix chain 'H' and resid 93 through 125 removed outlier: 5.528A pdb=" N LYS H 97 " --> pdb=" O ASN H 94 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N VAL H 100 " --> pdb=" O LYS H 97 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA H 108 " --> pdb=" O LEU H 105 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR H 110 " --> pdb=" O PHE H 107 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU H 111 " --> pdb=" O ALA H 108 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N SER H 112 " --> pdb=" O LEU H 109 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N VAL H 120 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N VAL H 121 " --> pdb=" O LEU H 118 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N LEU H 125 " --> pdb=" O PHE H 122 " (cutoff:3.500A) Processing helix chain 'I' and resid 55 through 91 removed outlier: 3.974A pdb=" N MET I 61 " --> pdb=" O ALA I 57 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N THR I 68 " --> pdb=" O ALA I 64 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N ILE I 69 " --> pdb=" O GLY I 65 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N ALA I 70 " --> pdb=" O CYS I 66 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N LEU I 71 " --> pdb=" O ALA I 67 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ALA I 72 " --> pdb=" O THR I 68 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLY I 73 " --> pdb=" O ILE I 69 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLY I 75 " --> pdb=" O LEU I 71 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE I 86 " --> pdb=" O PHE I 82 " (cutoff:3.500A) Processing helix chain 'I' and resid 93 through 95 No H-bonds generated for 'chain 'I' and resid 93 through 95' Processing helix chain 'I' and resid 98 through 125 removed outlier: 3.677A pdb=" N SER I 112 " --> pdb=" O ALA I 108 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N ILE I 113 " --> pdb=" O LEU I 109 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA I 114 " --> pdb=" O THR I 110 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 89 removed outlier: 4.367A pdb=" N MET J 61 " --> pdb=" O ALA J 57 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL J 62 " --> pdb=" O ALA J 58 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ILE J 69 " --> pdb=" O GLY J 65 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N ALA J 70 " --> pdb=" O CYS J 66 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N LEU J 71 " --> pdb=" O ALA J 67 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N ALA J 72 " --> pdb=" O THR J 68 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N GLY J 73 " --> pdb=" O ILE J 69 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL J 74 " --> pdb=" O ALA J 70 " (cutoff:3.500A) Processing helix chain 'J' and resid 93 through 126 removed outlier: 4.940A pdb=" N LYS J 97 " --> pdb=" O ASN J 94 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N LEU J 99 " --> pdb=" O ALA J 96 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LEU J 104 " --> pdb=" O GLY J 101 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR J 110 " --> pdb=" O PHE J 107 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLU J 111 " --> pdb=" O ALA J 108 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N SER J 112 " --> pdb=" O LEU J 109 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE J 113 " --> pdb=" O THR J 110 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU J 115 " --> pdb=" O SER J 112 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU J 118 " --> pdb=" O LEU J 115 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU J 125 " --> pdb=" O PHE J 122 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N PHE J 126 " --> pdb=" O LEU J 123 " (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 165 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: 3.897A pdb=" N THR M 200 " --> pdb=" O GLY M 196 " (cutoff:3.500A) Processing helix chain 'M' and resid 222 through 264 removed outlier: 4.315A pdb=" N SER M 228 " --> pdb=" O LEU M 224 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ARG M 232 " --> pdb=" O SER M 228 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ALA M 233 " --> pdb=" O TYR M 229 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N VAL M 234 " --> pdb=" O THR M 230 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLY M 237 " --> pdb=" O ALA M 233 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LEU M 240 " --> pdb=" O LEU M 236 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLY M 247 " --> pdb=" O ASN M 243 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N HIS M 248 " --> pdb=" O MET M 244 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA M 260 " --> pdb=" O GLY M 256 " (cutoff:3.500A) removed outlier: 4.101A 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: 3.999A pdb=" N VAL M 277 " --> pdb=" O ALA M 273 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N LEU M 280 " --> pdb=" O GLY M 276 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N SER M 296 " --> pdb=" O ALA M 292 " (cutoff:3.500A) Processing helix chain 'P' and resid 51 through 64 removed outlier: 3.721A pdb=" N LEU P 56 " --> pdb=" O GLN P 52 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LYS P 63 " --> pdb=" O GLN P 59 " (cutoff:3.500A) Processing helix chain 'P' and resid 67 through 83 removed outlier: 3.691A pdb=" N GLN P 71 " --> pdb=" O LEU P 67 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASP P 72 " --> pdb=" O ASP P 68 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLU P 73 " --> pdb=" O LYS P 69 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLN P 76 " --> pdb=" O ASP P 72 " (cutoff:3.500A) Processing helix chain 'P' and resid 88 through 92 removed outlier: 4.058A pdb=" N THR P 92 " --> pdb=" O ARG P 89 " (cutoff:3.500A) Processing helix chain 'P' and resid 98 through 101 No H-bonds generated for 'chain 'P' and resid 98 through 101' Processing helix chain 'P' and resid 105 through 108 No H-bonds generated for 'chain 'P' and resid 105 through 108' Processing helix chain 'P' and resid 118 through 128 removed outlier: 3.645A pdb=" N GLU P 123 " --> pdb=" O LYS P 119 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA P 126 " --> pdb=" O PHE P 122 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASP P 127 " --> pdb=" O GLU P 123 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU P 128 " --> pdb=" O ALA P 124 " (cutoff:3.500A) Processing helix chain 'P' and resid 130 through 145 removed outlier: 3.529A pdb=" N LEU P 134 " --> pdb=" O LEU P 131 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N LEU P 135 " --> pdb=" O SER P 132 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N GLU P 136 " --> pdb=" O ALA P 133 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N THR P 138 " --> pdb=" O LEU P 135 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N VAL P 139 " --> pdb=" O GLU P 136 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASN P 140 " --> pdb=" O VAL P 137 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLU P 143 " --> pdb=" O ASN P 140 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LEU P 144 " --> pdb=" O TYR P 141 " (cutoff:3.500A) Processing helix chain 'P' and resid 164 through 177 removed outlier: 3.629A pdb=" N VAL P 168 " --> pdb=" O LYS P 164 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LYS P 176 " --> pdb=" O LYS P 172 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N PHE P 177 " --> pdb=" O LYS P 173 " (cutoff:3.500A) Processing helix chain 'P' and resid 211 through 226 Processing helix chain 'Q' and resid 8 through 11 No H-bonds generated for 'chain 'Q' and resid 8 through 11' Processing helix chain 'Q' and resid 16 through 30 removed outlier: 3.995A pdb=" N VAL Q 30 " --> pdb=" O LEU Q 26 " (cutoff:3.500A) Processing helix chain 'Q' and resid 33 through 39 removed outlier: 3.868A pdb=" N ALA Q 37 " --> pdb=" O GLU Q 33 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N LYS Q 38 " --> pdb=" O PRO Q 34 " (cutoff:3.500A) Processing helix chain 'R' and resid 32 through 40 removed outlier: 3.632A pdb=" N VAL R 36 " --> pdb=" O GLU R 32 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N LYS R 39 " --> pdb=" O GLU R 35 " (cutoff:3.500A) Processing helix chain 'R' and resid 51 through 54 removed outlier: 3.782A pdb=" N TYR R 54 " --> pdb=" O PRO R 51 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 51 through 54' 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 167 removed outlier: 3.982A pdb=" N ALA R 166 " --> pdb=" O SER R 162 " (cutoff:3.500A) Processing helix chain 'R' and resid 175 through 196 Processing helix chain 'S' and resid 42 through 69 removed outlier: 3.620A pdb=" N MET S 62 " --> pdb=" O LYS S 58 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS S 69 " --> pdb=" O ALA S 65 " (cutoff:3.500A) Processing helix chain 'S' and resid 82 through 88 removed outlier: 3.595A pdb=" N VAL S 86 " --> pdb=" O VAL S 82 " (cutoff:3.500A) Processing helix chain 'S' and resid 116 through 127 Processing helix chain 'S' and resid 144 through 150 removed outlier: 3.818A pdb=" N SER S 148 " --> pdb=" O ASP S 144 " (cutoff:3.500A) removed outlier: 4.484A 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 213 through 221 removed outlier: 6.304A pdb=" N LYS S 218 " --> pdb=" O ASP S 214 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N GLN S 219 " --> pdb=" O LEU S 215 " (cutoff:3.500A) Processing helix chain 'S' and resid 239 through 241 No H-bonds generated for 'chain 'S' and resid 239 through 241' Processing helix chain 'S' and resid 243 through 311 removed outlier: 4.129A pdb=" N GLU S 248 " --> pdb=" O ARG S 244 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ASN S 263 " --> pdb=" O MET S 259 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N SER S 272 " --> pdb=" O ALA S 268 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N THR S 278 " --> pdb=" O MET S 274 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU S 285 " --> pdb=" O ALA S 281 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE S 307 " --> pdb=" O GLU S 303 " (cutoff:3.500A) Processing helix chain 'T' and resid 58 through 64 Processing helix chain 'T' and resid 67 through 74 removed outlier: 4.207A pdb=" N GLU T 72 " --> pdb=" O PRO T 68 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N TRP T 73 " --> pdb=" O ALA T 69 " (cutoff:3.500A) Processing helix chain 'T' and resid 135 through 137 No H-bonds generated for 'chain 'T' and resid 135 through 137' Processing helix chain 'T' and resid 157 through 159 No H-bonds generated for 'chain 'T' and resid 157 through 159' Processing helix chain 'T' and resid 207 through 210 No H-bonds generated for 'chain 'T' and resid 207 through 210' Processing helix chain 'T' and resid 231 through 246 removed outlier: 3.809A pdb=" N GLN T 242 " --> pdb=" O ALA T 238 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LYS T 243 " --> pdb=" O ILE T 239 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ASN T 244 " --> pdb=" O ILE T 240 " (cutoff:3.500A) Processing helix chain 'T' and resid 266 through 279 removed outlier: 3.549A pdb=" N GLN T 278 " --> pdb=" O LYS T 274 " (cutoff:3.500A) Processing helix chain 'T' and resid 281 through 284 Processing helix chain 'T' and resid 296 through 300 Processing helix chain 'T' and resid 302 through 310 Processing helix chain 'T' and resid 312 through 315 No H-bonds generated for 'chain 'T' and resid 312 through 315' Processing helix chain 'T' and resid 327 through 340 removed outlier: 3.701A pdb=" N ALA T 333 " --> pdb=" O LYS T 329 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N MET T 337 " --> pdb=" O ALA T 333 " (cutoff:3.500A) Processing helix chain 'T' and resid 352 through 364 removed outlier: 4.167A pdb=" N PHE T 355 " --> pdb=" O GLY T 352 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER T 359 " --> pdb=" O TYR T 356 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ARG T 360 " --> pdb=" O LEU T 357 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N LEU T 361 " --> pdb=" O HIS T 358 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU T 362 " --> pdb=" O SER T 359 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N GLU T 363 " --> pdb=" O ARG T 360 " (cutoff:3.500A) Processing helix chain 'T' and resid 393 through 399 removed outlier: 3.513A pdb=" N ASN T 397 " --> pdb=" O TYR T 393 " (cutoff:3.500A) Processing helix chain 'T' and resid 410 through 414 removed outlier: 3.868A pdb=" N TYR T 414 " --> pdb=" O THR T 410 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 410 through 414' Processing helix chain 'T' and resid 431 through 434 removed outlier: 3.644A pdb=" N ALA T 434 " --> pdb=" O GLY T 431 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 431 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 444 through 449 removed outlier: 3.964A pdb=" N LEU T 448 " --> pdb=" O GLY T 444 " (cutoff:3.500A) Processing helix chain 'T' and resid 451 through 459 removed outlier: 4.185A pdb=" N GLU T 455 " --> pdb=" O ALA T 451 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N VAL T 456 " --> pdb=" O GLN T 452 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA T 458 " --> pdb=" O ARG T 454 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N PHE T 459 " --> pdb=" O GLU T 455 " (cutoff:3.500A) Processing helix chain 'T' and resid 470 through 483 removed outlier: 3.742A pdb=" N ALA T 478 " --> pdb=" O LEU T 474 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR T 481 " --> pdb=" O GLY T 477 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLU T 482 " --> pdb=" O ALA T 478 " (cutoff:3.500A) Processing helix chain 'T' and resid 495 through 498 No H-bonds generated for 'chain 'T' and resid 495 through 498' Processing helix chain 'T' and resid 502 through 505 No H-bonds generated for 'chain 'T' and resid 502 through 505' Processing helix chain 'T' and resid 518 through 526 removed outlier: 4.452A pdb=" N GLU T 522 " --> pdb=" O VAL T 518 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ALA T 523 " --> pdb=" O ALA T 519 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL T 524 " --> pdb=" O ALA T 520 " (cutoff:3.500A) Processing helix chain 'T' and resid 531 through 539 removed outlier: 3.532A pdb=" N ILE T 535 " --> pdb=" O ALA T 531 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ALA T 538 " --> pdb=" O LYS T 534 " (cutoff:3.500A) Processing helix chain 'T' and resid 544 through 551 removed outlier: 4.360A pdb=" N ALA T 548 " --> pdb=" O PRO T 544 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N HIS T 549 " --> pdb=" O ALA T 545 " (cutoff:3.500A) Processing helix chain 'U' and resid 42 through 49 removed outlier: 3.800A pdb=" N GLU U 47 " --> pdb=" O LYS U 43 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N LEU U 48 " --> pdb=" O ALA U 44 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N ARG U 49 " --> pdb=" O LEU U 45 " (cutoff:3.500A) Processing helix chain 'U' and resid 59 through 70 removed outlier: 5.375A pdb=" N ILE U 67 " --> pdb=" O SER U 63 " (cutoff:3.500A) Proline residue: U 68 - end of helix 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 157 through 159 No H-bonds generated for 'chain 'U' and resid 157 through 159' Processing helix chain 'U' and resid 207 through 212 Processing helix chain 'U' and resid 231 through 248 removed outlier: 3.799A pdb=" N ALA U 235 " --> pdb=" O LYS U 231 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLU U 247 " --> pdb=" O LYS U 243 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N GLN U 248 " --> pdb=" O ASN U 244 " (cutoff:3.500A) Processing helix chain 'U' and resid 266 through 278 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: 3.998A pdb=" N TYR U 312 " --> pdb=" O ALA U 308 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N PHE U 313 " --> pdb=" O MET U 309 " (cutoff:3.500A) Processing helix chain 'U' and resid 327 through 341 removed outlier: 3.975A pdb=" N LEU U 341 " --> pdb=" O MET U 337 " (cutoff:3.500A) Processing helix chain 'U' and resid 354 through 364 removed outlier: 3.536A pdb=" N HIS U 358 " --> pdb=" O VAL U 354 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LEU U 361 " --> pdb=" O LEU U 357 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N ARG U 364 " --> pdb=" O ARG U 360 " (cutoff:3.500A) Processing helix chain 'U' and resid 393 through 399 Processing helix chain 'U' and resid 410 through 414 Processing helix chain 'U' and resid 437 through 459 removed outlier: 4.055A pdb=" N GLY U 444 " --> pdb=" O LYS U 440 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N THR U 445 " --> pdb=" O GLN U 441 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU U 446 " --> pdb=" O VAL U 442 " (cutoff:3.500A) Processing helix chain 'U' and resid 471 through 484 removed outlier: 4.262A pdb=" N ALA U 478 " --> pdb=" O LEU U 474 " (cutoff:3.500A) Processing helix chain 'U' and resid 494 through 496 No H-bonds generated for 'chain 'U' and resid 494 through 496' Processing helix chain 'U' and resid 498 through 505 removed outlier: 4.233A pdb=" N ALA U 504 " --> pdb=" O ALA U 500 " (cutoff:3.500A) Processing helix chain 'U' and resid 515 through 527 removed outlier: 4.195A pdb=" N VAL U 518 " --> pdb=" O GLN U 515 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU U 522 " --> pdb=" O ALA U 519 " (cutoff:3.500A) Processing helix chain 'U' and resid 530 through 539 removed outlier: 3.929A pdb=" N LYS U 534 " --> pdb=" O ALA U 531 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU U 536 " --> pdb=" O PHE U 533 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ASN U 539 " --> pdb=" O LEU U 536 " (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 59 through 66 removed outlier: 4.214A pdb=" N GLN V 64 " --> pdb=" O GLN V 60 " (cutoff:3.500A) removed outlier: 3.773A 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 207 through 212 Processing helix chain 'V' and resid 231 through 248 removed outlier: 3.815A pdb=" N GLU V 247 " --> pdb=" O LYS V 243 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N GLN V 248 " --> pdb=" O ASN V 244 " (cutoff:3.500A) Processing helix chain 'V' and resid 251 through 253 No H-bonds generated for 'chain 'V' and resid 251 through 253' Processing helix chain 'V' and resid 266 through 278 Processing helix chain 'V' and resid 296 through 315 Proline residue: V 303 - end of helix removed outlier: 3.703A pdb=" N TYR V 312 " --> pdb=" O ALA V 308 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N PHE V 313 " --> pdb=" O MET V 309 " (cutoff:3.500A) Processing helix chain 'V' and resid 327 through 341 Processing helix chain 'V' and resid 352 through 364 removed outlier: 3.972A pdb=" N PHE V 355 " --> pdb=" O GLY V 352 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LEU V 357 " --> pdb=" O VAL V 354 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER V 359 " --> pdb=" O TYR V 356 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N GLU V 363 " --> pdb=" O ARG V 360 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ARG V 364 " --> pdb=" O LEU V 361 " (cutoff:3.500A) Processing helix chain 'V' and resid 370 through 372 No H-bonds generated for 'chain 'V' and resid 370 through 372' Processing helix chain 'V' and resid 393 through 401 Processing helix chain 'V' and resid 431 through 434 removed outlier: 4.081A 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 455 removed outlier: 4.276A pdb=" N THR V 445 " --> pdb=" O GLN V 441 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LEU V 448 " --> pdb=" O GLY V 444 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLU V 455 " --> pdb=" O ALA V 451 " (cutoff:3.500A) Processing helix chain 'V' and resid 470 through 481 Processing helix chain 'V' and resid 494 through 505 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 522 through 525 No H-bonds generated for 'chain 'V' and resid 522 through 525' Processing helix chain 'V' and resid 531 through 539 removed outlier: 3.563A pdb=" N ILE V 535 " --> pdb=" O ALA V 531 " (cutoff:3.500A) Processing helix chain 'V' and resid 544 through 553 removed outlier: 4.028A pdb=" N ALA V 552 " --> pdb=" O ALA V 548 " (cutoff:3.500A) Processing helix chain 'X' and resid 115 through 117 No H-bonds generated for 'chain 'X' and resid 115 through 117' Processing helix chain 'X' and resid 150 through 152 No H-bonds generated for 'chain 'X' and resid 150 through 152' Processing helix chain 'X' and resid 165 through 170 Processing helix chain 'X' and resid 189 through 203 removed outlier: 4.839A pdb=" N LYS X 202 " --> pdb=" O ASN X 198 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ALA X 203 " --> pdb=" O ASN X 199 " (cutoff:3.500A) Processing helix chain 'X' and resid 217 through 229 removed outlier: 3.625A pdb=" N GLU X 229 " --> pdb=" O ARG X 225 " (cutoff:3.500A) Processing helix chain 'X' and resid 239 through 241 No H-bonds generated for 'chain 'X' and resid 239 through 241' Processing helix chain 'X' and resid 255 through 259 removed outlier: 3.779A pdb=" N ALA X 259 " --> pdb=" O PRO X 255 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 255 through 259' Processing helix chain 'X' and resid 261 through 274 removed outlier: 3.786A pdb=" N PHE X 272 " --> pdb=" O VAL X 268 " (cutoff:3.500A) Processing helix chain 'X' and resid 288 through 299 removed outlier: 3.897A pdb=" N ALA X 299 " --> pdb=" O SER X 295 " (cutoff:3.500A) Processing helix chain 'X' and resid 314 through 324 removed outlier: 4.502A pdb=" N ARG X 324 " --> pdb=" O GLY X 320 " (cutoff:3.500A) Processing helix chain 'X' and resid 349 through 352 No H-bonds generated for 'chain 'X' and resid 349 through 352' Processing helix chain 'X' and resid 366 through 371 removed outlier: 3.841A pdb=" N LEU X 371 " --> pdb=" O SER X 367 " (cutoff:3.500A) Processing helix chain 'X' and resid 389 through 420 removed outlier: 7.663A pdb=" N ALA X 394 " --> pdb=" O ASN X 390 " (cutoff:3.500A) removed outlier: 9.044A pdb=" N GLU X 395 " --> pdb=" O VAL X 391 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N HIS X 396 " --> pdb=" O ILE X 392 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N ASP X 415 " --> pdb=" O LYS X 411 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N ILE X 416 " --> pdb=" O ASN X 412 " (cutoff:3.500A) Processing helix chain 'X' and resid 422 through 424 No H-bonds generated for 'chain 'X' and resid 422 through 424' Processing helix chain 'X' and resid 427 through 441 removed outlier: 3.543A pdb=" N THR X 432 " --> pdb=" O GLU X 428 " (cutoff:3.500A) Processing helix chain 'X' and resid 451 through 454 No H-bonds generated for 'chain 'X' and resid 451 through 454' Processing helix chain 'X' and resid 463 through 475 Processing helix chain 'X' and resid 484 through 486 No H-bonds generated for 'chain 'X' and resid 484 through 486' Processing helix chain 'X' and resid 492 through 506 removed outlier: 3.847A pdb=" N LYS X 496 " --> pdb=" O ILE X 492 " (cutoff:3.500A) Processing helix chain 'X' and resid 527 through 533 removed outlier: 3.871A pdb=" N VAL X 531 " --> pdb=" O LEU X 527 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N SER X 532 " --> pdb=" O ASP X 528 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLU X 533 " --> pdb=" O LYS X 529 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 527 through 533' Processing helix chain 'Y' and resid 115 through 117 No H-bonds generated for 'chain 'Y' and resid 115 through 117' Processing helix chain 'Y' and resid 165 through 170 Processing helix chain 'Y' and resid 189 through 200 Processing helix chain 'Y' and resid 217 through 229 Processing helix chain 'Y' and resid 236 through 241 removed outlier: 4.530A pdb=" N GLY Y 240 " --> pdb=" O ALA Y 237 " (cutoff:3.500A) Processing helix chain 'Y' and resid 255 through 274 removed outlier: 3.556A pdb=" N ALA Y 259 " --> pdb=" O PRO Y 255 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ARG Y 260 " --> pdb=" O GLY Y 256 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL Y 261 " --> pdb=" O ALA Y 257 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N ALA Y 262 " --> pdb=" O ARG Y 258 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N LEU Y 263 " --> pdb=" O ALA Y 259 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N THR Y 264 " --> pdb=" O ARG Y 260 " (cutoff:3.500A) Processing helix chain 'Y' and resid 288 through 296 Processing helix chain 'Y' and resid 314 through 324 removed outlier: 4.884A pdb=" N ARG Y 324 " --> pdb=" O GLY Y 320 " (cutoff:3.500A) Processing helix chain 'Y' and resid 349 through 352 No H-bonds generated for 'chain 'Y' and resid 349 through 352' Processing helix chain 'Y' and resid 355 through 357 No H-bonds generated for 'chain 'Y' and resid 355 through 357' Processing helix chain 'Y' and resid 367 through 370 No H-bonds generated for 'chain 'Y' and resid 367 through 370' Processing helix chain 'Y' and resid 394 through 420 removed outlier: 3.726A pdb=" N VAL Y 399 " --> pdb=" O GLU Y 395 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N ASP Y 415 " --> pdb=" O LYS Y 411 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N ILE Y 416 " --> pdb=" O ASN Y 412 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA Y 418 " --> pdb=" O GLN Y 414 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N ILE Y 419 " --> pdb=" O ASP Y 415 " (cutoff:3.500A) Processing helix chain 'Y' and resid 429 through 442 Processing helix chain 'Y' and resid 449 through 451 No H-bonds generated for 'chain 'Y' and resid 449 through 451' Processing helix chain 'Y' and resid 463 through 475 removed outlier: 3.600A pdb=" N GLY Y 472 " --> pdb=" O SER Y 468 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N THR Y 475 " --> pdb=" O GLN Y 471 " (cutoff:3.500A) Processing helix chain 'Y' and resid 492 through 508 removed outlier: 3.708A pdb=" N LYS Y 496 " --> pdb=" O ILE Y 492 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASP Y 500 " --> pdb=" O LYS Y 496 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LYS Y 501 " --> pdb=" O GLU Y 497 " (cutoff:3.500A) Processing helix chain 'Y' and resid 527 through 531 Processing helix chain 'Y' and resid 545 through 554 removed outlier: 4.220A pdb=" N LYS Y 550 " --> pdb=" O GLU Y 546 " (cutoff:3.500A) Processing helix chain 'Z' and resid 115 through 117 No H-bonds generated for 'chain 'Z' and resid 115 through 117' Processing helix chain 'Z' and resid 165 through 169 Processing helix chain 'Z' and resid 189 through 203 Processing helix chain 'Z' and resid 217 through 228 Processing helix chain 'Z' and resid 236 through 241 removed outlier: 3.797A pdb=" N ARG Z 239 " --> pdb=" O GLY Z 236 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N GLY Z 240 " --> pdb=" O ALA Z 237 " (cutoff:3.500A) Processing helix chain 'Z' and resid 255 through 258 No H-bonds generated for 'chain 'Z' and resid 255 through 258' Processing helix chain 'Z' and resid 261 through 274 Processing helix chain 'Z' and resid 287 through 300 Processing helix chain 'Z' and resid 314 through 322 removed outlier: 4.417A pdb=" N LEU Z 321 " --> pdb=" O ASP Z 317 " (cutoff:3.500A) Processing helix chain 'Z' and resid 349 through 354 Processing helix chain 'Z' and resid 368 through 371 Processing helix chain 'Z' and resid 389 through 392 No H-bonds generated for 'chain 'Z' and resid 389 through 392' Processing helix chain 'Z' and resid 394 through 413 removed outlier: 4.202A pdb=" N LEU Z 413 " --> pdb=" O ASP Z 409 " (cutoff:3.500A) Processing helix chain 'Z' and resid 427 through 440 removed outlier: 3.576A pdb=" N LEU Z 431 " --> pdb=" O GLU Z 427 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N THR Z 432 " --> pdb=" O GLU Z 428 " (cutoff:3.500A) Processing helix chain 'Z' and resid 451 through 454 No H-bonds generated for 'chain 'Z' and resid 451 through 454' Processing helix chain 'Z' and resid 463 through 475 removed outlier: 3.906A pdb=" N GLY Z 472 " --> pdb=" O SER Z 468 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL Z 473 " --> pdb=" O GLY Z 469 " (cutoff:3.500A) Processing helix chain 'Z' and resid 483 through 485 No H-bonds generated for 'chain 'Z' and resid 483 through 485' Processing helix chain 'Z' and resid 492 through 501 removed outlier: 3.737A pdb=" N LYS Z 496 " --> pdb=" O ILE Z 492 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N GLU Z 497 " --> pdb=" O LYS Z 493 " (cutoff:3.500A) Processing helix chain 'Z' and resid 527 through 531 Processing sheet with id= A, first strand: chain '1' and resid 183 through 185 removed outlier: 4.338A pdb=" N VAL 1 226 " --> pdb=" O ALA 1 185 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain '2' and resid 368 through 372 removed outlier: 4.361A pdb=" N ILE 2 368 " --> pdb=" O VAL 2 379 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA 2 375 " --> pdb=" O LYS 2 372 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain '7' and resid 36 through 41 Processing sheet with id= D, first strand: chain 'P' and resid 156 through 158 Processing sheet with id= E, first strand: chain 'P' and resid 199 through 201 Processing sheet with id= F, first strand: chain 'Q' and resid 45 through 48 Processing sheet with id= G, first strand: chain 'R' and resid 72 through 76 removed outlier: 6.582A pdb=" N THR R 142 " --> pdb=" O ASN R 73 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N TYR R 75 " --> pdb=" O THR R 142 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N ILE R 144 " --> pdb=" O TYR R 75 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLY R 132 " --> pdb=" O LEU R 111 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'R' and resid 96 through 100 removed outlier: 6.751A pdb=" N VAL R 115 " --> pdb=" O PRO R 92 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU R 125 " --> pdb=" O LEU R 118 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'S' and resid 203 through 211 removed outlier: 3.509A pdb=" N SER S 189 " --> pdb=" O LYS S 99 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N ASN S 195 " --> pdb=" O VAL S 105 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ASP S 136 " --> pdb=" O SER S 100 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N VAL S 102 " --> pdb=" O ASP S 136 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N VAL S 138 " --> pdb=" O VAL S 102 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N ALA S 104 " --> pdb=" O VAL S 138 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N VAL S 140 " --> pdb=" O ALA S 104 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N SER S 141 " --> pdb=" O GLN S 159 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ALA S 161 " --> pdb=" O SER S 141 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'T' and resid 85 through 91 removed outlier: 6.716A pdb=" N ARG T 96 " --> pdb=" O LEU T 88 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N VAL T 90 " --> pdb=" O ILE T 94 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ILE T 94 " --> pdb=" O VAL T 90 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ASN T 121 " --> pdb=" O GLY T 128 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N VAL T 130 " --> pdb=" O ALA T 119 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N ALA T 119 " --> pdb=" O VAL T 130 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N PHE T 132 " --> pdb=" O GLY T 117 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N GLY T 117 " --> pdb=" O PHE T 132 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'T' and resid 109 through 111 Processing sheet with id= L, first strand: chain 'T' and resid 152 through 155 Processing sheet with id= M, first strand: chain 'T' and resid 404 through 407 removed outlier: 3.860A pdb=" N LEU T 222 " --> pdb=" O GLY T 404 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'T' and resid 286 through 290 removed outlier: 6.866A pdb=" N HIS T 319 " --> pdb=" O TYR T 256 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N VAL T 258 " --> pdb=" O HIS T 319 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N LEU T 321 " --> pdb=" O VAL T 258 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N VAL T 260 " --> pdb=" O LEU T 321 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ILE T 323 " --> pdb=" O VAL T 260 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N VAL T 262 " --> pdb=" O ILE T 323 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ASP T 325 " --> pdb=" O VAL T 262 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N SER T 376 " --> pdb=" O GLY T 320 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N ILE T 322 " --> pdb=" O SER T 376 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N THR T 378 " --> pdb=" O ILE T 322 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N TYR T 324 " --> pdb=" O THR T 378 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'U' and resid 85 through 91 removed outlier: 6.628A pdb=" N ARG U 96 " --> pdb=" O LEU U 88 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N VAL U 90 " --> pdb=" O ILE U 94 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ILE U 94 " --> pdb=" O VAL U 90 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASN U 121 " --> pdb=" O GLY U 128 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N VAL U 130 " --> pdb=" O ALA U 119 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N ALA U 119 " --> pdb=" O VAL U 130 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N PHE U 132 " --> pdb=" O GLY U 117 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N GLY U 117 " --> pdb=" O PHE U 132 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'U' and resid 152 through 155 Processing sheet with id= Q, first strand: chain 'U' and resid 404 through 408 removed outlier: 3.721A pdb=" N LEU U 222 " --> pdb=" O GLY U 404 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'U' and resid 319 through 325 Processing sheet with id= S, first strand: chain 'V' and resid 84 through 86 removed outlier: 3.816A pdb=" N GLU V 107 " --> pdb=" O ALA V 119 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N GLY V 128 " --> pdb=" O LEU V 120 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N LEU V 122 " --> pdb=" O HIS V 126 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N HIS V 126 " --> pdb=" O LEU V 122 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'V' and resid 152 through 155 Processing sheet with id= U, first strand: chain 'V' and resid 382 through 384 removed outlier: 6.451A pdb=" N ILE V 223 " --> pdb=" O ILE V 383 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N ILE V 406 " --> pdb=" O ILE V 224 " (cutoff:3.500A) No H-bonds generated for sheet with id= U Processing sheet with id= V, first strand: chain 'V' and resid 286 through 290 removed outlier: 6.615A pdb=" N HIS V 319 " --> pdb=" O TYR V 256 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N VAL V 258 " --> pdb=" O HIS V 319 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N LEU V 321 " --> pdb=" O VAL V 258 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N VAL V 260 " --> pdb=" O LEU V 321 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ILE V 323 " --> pdb=" O VAL V 260 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N VAL V 262 " --> pdb=" O ILE V 323 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ASP V 325 " --> pdb=" O VAL V 262 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N SER V 376 " --> pdb=" O GLY V 320 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N ILE V 322 " --> pdb=" O SER V 376 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N THR V 378 " --> pdb=" O ILE V 322 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N TYR V 324 " --> pdb=" O THR V 378 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N PHE V 380 " --> pdb=" O TYR V 324 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'X' and resid 37 through 39 removed outlier: 4.732A pdb=" N LEU X 72 " --> pdb=" O VAL X 65 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ARG X 86 " --> pdb=" O ALA X 77 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N HIS X 79 " --> pdb=" O THR X 84 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N THR X 84 " --> pdb=" O HIS X 79 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N ARG X 51 " --> pdb=" O VAL X 40 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N VAL X 40 " --> pdb=" O ARG X 51 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'X' and resid 110 through 113 Processing sheet with id= Y, first strand: chain 'X' and resid 360 through 363 removed outlier: 7.606A pdb=" N ILE X 179 " --> pdb=" O ILE X 333 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N SER X 335 " --> pdb=" O ILE X 179 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N LEU X 181 " --> pdb=" O SER X 335 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N GLN X 337 " --> pdb=" O LEU X 181 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N GLY X 183 " --> pdb=" O GLN X 337 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N VAL X 339 " --> pdb=" O GLY X 183 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'X' and resid 208 through 212 Processing sheet with id= AA, first strand: chain 'X' and resid 559 through 561 Processing sheet with id= AB, first strand: chain 'Y' and resid 39 through 44 removed outlier: 6.569A pdb=" N ASP Y 49 " --> pdb=" O SER Y 41 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N VAL Y 43 " --> pdb=" O VAL Y 47 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N VAL Y 47 " --> pdb=" O VAL Y 43 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ILE Y 88 " --> pdb=" O VAL Y 76 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N VAL Y 76 " --> pdb=" O ILE Y 88 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N LEU Y 72 " --> pdb=" O VAL Y 65 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'Y' and resid 360 through 362 removed outlier: 3.826A pdb=" N ALA Y 360 " --> pdb=" O LYS Y 178 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N ILE Y 179 " --> pdb=" O ILE Y 333 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N SER Y 335 " --> pdb=" O ILE Y 179 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N LEU Y 181 " --> pdb=" O SER Y 335 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N GLN Y 337 " --> pdb=" O LEU Y 181 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N GLY Y 183 " --> pdb=" O GLN Y 337 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N VAL Y 339 " --> pdb=" O GLY Y 183 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N PHE Y 207 " --> pdb=" O LEU Y 281 " (cutoff:3.500A) removed outlier: 8.384A pdb=" N PHE Y 283 " --> pdb=" O PHE Y 207 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N VAL Y 209 " --> pdb=" O PHE Y 283 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N ASP Y 285 " --> pdb=" O VAL Y 209 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N ALA Y 211 " --> pdb=" O ASP Y 285 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N THR Y 245 " --> pdb=" O PHE Y 210 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N GLY Y 212 " --> pdb=" O THR Y 245 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N VAL Y 247 " --> pdb=" O GLY Y 212 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'Z' and resid 39 through 44 removed outlier: 6.590A pdb=" N ASP Z 49 " --> pdb=" O SER Z 41 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N VAL Z 43 " --> pdb=" O VAL Z 47 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL Z 47 " --> pdb=" O VAL Z 43 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ILE Z 88 " --> pdb=" O VAL Z 76 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N VAL Z 76 " --> pdb=" O ILE Z 88 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N LEU Z 72 " --> pdb=" O VAL Z 65 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'Z' and resid 110 through 113 Processing sheet with id= AF, first strand: chain 'Z' and resid 178 through 181 removed outlier: 8.516A pdb=" N ILE Z 179 " --> pdb=" O ILE Z 333 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N SER Z 335 " --> pdb=" O ILE Z 179 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N LEU Z 181 " --> pdb=" O SER Z 335 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N GLN Z 337 " --> pdb=" O LEU Z 181 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL Z 284 " --> pdb=" O VAL Z 336 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'Z' and resid 559 through 561 2343 hydrogen bonds defined for protein. 6420 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: 15.05 Time building geometry restraints manager: 18.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 15806 1.33 - 1.46: 11117 1.46 - 1.58: 27487 1.58 - 1.70: 21 1.70 - 1.83: 254 Bond restraints: 54685 Sorted by residual: bond pdb=" C4 ATP U1001 " pdb=" C5 ATP U1001 " ideal model delta sigma weight residual 1.388 1.459 -0.071 1.00e-02 1.00e+04 5.07e+01 bond pdb=" C4 ATP V1001 " pdb=" C5 ATP V1001 " 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 1.454 -0.066 1.00e-02 1.00e+04 4.37e+01 bond pdb=" C4 ATP T1001 " pdb=" N9 ATP T1001 " ideal model delta sigma weight residual 1.374 1.313 0.061 1.00e-02 1.00e+04 3.77e+01 bond pdb=" C5 ATP U1001 " pdb=" N7 ATP U1001 " ideal model delta sigma weight residual 1.387 1.326 0.061 1.00e-02 1.00e+04 3.75e+01 ... (remaining 54680 not shown) Histogram of bond angle deviations from ideal: 97.47 - 105.46: 1091 105.46 - 113.44: 31173 113.44 - 121.43: 30003 121.43 - 129.42: 11656 129.42 - 137.40: 234 Bond angle restraints: 74157 Sorted by residual: angle pdb=" PB ATP U1001 " pdb=" O3B ATP U1001 " pdb=" PG ATP U1001 " ideal model delta sigma weight residual 139.87 118.14 21.73 1.00e+00 1.00e+00 4.72e+02 angle pdb=" PB ATP V1001 " pdb=" O3B ATP V1001 " pdb=" PG ATP V1001 " ideal model delta sigma weight residual 139.87 118.49 21.38 1.00e+00 1.00e+00 4.57e+02 angle pdb=" PB ATP T1001 " pdb=" O3B ATP T1001 " pdb=" PG ATP T1001 " ideal model delta sigma weight residual 139.87 118.96 20.91 1.00e+00 1.00e+00 4.37e+02 angle pdb=" PA ATP V1001 " pdb=" O3A ATP V1001 " pdb=" PB ATP V1001 " ideal model delta sigma weight residual 136.83 119.81 17.02 1.00e+00 1.00e+00 2.90e+02 angle pdb=" PA ATP T1001 " pdb=" O3A ATP T1001 " pdb=" PB ATP T1001 " ideal model delta sigma weight residual 136.83 122.47 14.36 1.00e+00 1.00e+00 2.06e+02 ... (remaining 74152 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.67: 31331 26.67 - 53.35: 1440 53.35 - 80.02: 131 80.02 - 106.69: 28 106.69 - 133.37: 1 Dihedral angle restraints: 32931 sinusoidal: 12574 harmonic: 20357 Sorted by residual: 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 -125.01 -54.99 0 5.00e+00 4.00e-02 1.21e+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 -126.64 -53.36 0 5.00e+00 4.00e-02 1.14e+02 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 -126.85 -53.15 0 5.00e+00 4.00e-02 1.13e+02 ... (remaining 32928 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 7023 0.075 - 0.150: 1497 0.150 - 0.225: 151 0.225 - 0.301: 14 0.301 - 0.376: 4 Chirality restraints: 8689 Sorted by residual: chirality pdb=" CB VAL 2 357 " pdb=" CA VAL 2 357 " pdb=" CG1 VAL 2 357 " pdb=" CG2 VAL 2 357 " both_signs ideal model delta sigma weight residual False -2.63 -2.25 -0.38 2.00e-01 2.50e+01 3.53e+00 chirality pdb=" CB ILE D 95 " pdb=" CA ILE D 95 " pdb=" CG1 ILE D 95 " pdb=" CG2 ILE D 95 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.35 2.00e-01 2.50e+01 3.08e+00 chirality pdb=" CB ILE E 95 " pdb=" CA ILE E 95 " pdb=" CG1 ILE E 95 " pdb=" CG2 ILE E 95 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.32 2.00e-01 2.50e+01 2.57e+00 ... (remaining 8686 not shown) Planarity restraints: 9508 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA Z 503 " 0.030 2.00e-02 2.50e+03 5.92e-02 3.50e+01 pdb=" C ALA Z 503 " -0.102 2.00e-02 2.50e+03 pdb=" O ALA Z 503 " 0.038 2.00e-02 2.50e+03 pdb=" N LYS Z 504 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA X 350 " -0.060 5.00e-02 4.00e+02 9.06e-02 1.31e+01 pdb=" N PRO X 351 " 0.157 5.00e-02 4.00e+02 pdb=" CA PRO X 351 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO X 351 " -0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE U 203 " 0.026 2.00e-02 2.50e+03 2.54e-02 1.13e+01 pdb=" CG PHE U 203 " -0.059 2.00e-02 2.50e+03 pdb=" CD1 PHE U 203 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 PHE U 203 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE U 203 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE U 203 " 0.008 2.00e-02 2.50e+03 pdb=" CZ PHE U 203 " 0.003 2.00e-02 2.50e+03 ... (remaining 9505 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 750 2.62 - 3.19: 46996 3.19 - 3.76: 85788 3.76 - 4.33: 118555 4.33 - 4.90: 194102 Nonbonded interactions: 446191 Sorted by model distance: nonbonded pdb=" OE1 GLU Y 215 " pdb="MG MG Y 602 " model vdw 2.050 2.170 nonbonded pdb=" OE2 GLU X 215 " pdb="MG MG X 602 " model vdw 2.060 2.170 nonbonded pdb=" O2B ATP T1001 " pdb="MG MG T1002 " model vdw 2.138 2.170 nonbonded pdb=" OH TYR 5 62 " pdb=" O PHE 6 146 " model vdw 2.205 2.440 nonbonded pdb=" O SER 1 29 " pdb=" OG SER 1 29 " model vdw 2.230 2.440 ... (remaining 446186 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = (chain 'T' and (resid 43 through 562 or resid 1001 through 1002)) selection = (chain 'U' and (resid 43 through 561 or (resid 562 and (name N or name CA or nam \ e C or name O or name CB )) or resid 1001 through 1002)) selection = (chain 'V' and (resid 43 through 561 or (resid 562 and (name N or name CA or nam \ e C or name O or name CB )) or resid 1001 through 1002)) } ncs_group { reference = (chain 'X' and resid 37 through 556) selection = (chain 'Y' and resid 37 through 556) selection = (chain 'Z' and resid 37 through 556) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.320 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: 0.040 Extract box with map and model: 25.180 Check model and map are aligned: 0.680 Set scattering table: 0.370 Process input model: 106.810 Find NCS groups from input model: 2.540 Set up NCS constraints: 0.280 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 143.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 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 : 0.010 0.130 54685 Z= 0.677 Angle : 1.050 21.732 74157 Z= 0.593 Chirality : 0.061 0.376 8689 Planarity : 0.008 0.091 9508 Dihedral : 15.029 133.367 19845 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.77 % Favored : 94.02 % Rotamer Outliers : 0.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.32 (0.08), residues: 7036 helix: -3.08 (0.06), residues: 3747 sheet: -2.12 (0.19), residues: 618 loop : -2.43 (0.10), residues: 2671 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14072 Ramachandran restraints generated. 7036 Oldfield, 0 Emsley, 7036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14072 Ramachandran restraints generated. 7036 Oldfield, 0 Emsley, 7036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1166 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 1135 time to evaluate : 5.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 19 residues processed: 1163 average time/residue: 0.5578 time to fit residues: 1056.7276 Evaluate side-chains 775 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 756 time to evaluate : 4.834 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.3710 time to fit residues: 19.9616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 589 optimal weight: 6.9990 chunk 529 optimal weight: 4.9990 chunk 293 optimal weight: 0.8980 chunk 180 optimal weight: 4.9990 chunk 356 optimal weight: 4.9990 chunk 282 optimal weight: 5.9990 chunk 547 optimal weight: 0.9980 chunk 211 optimal weight: 0.9990 chunk 332 optimal weight: 2.9990 chunk 407 optimal weight: 0.6980 chunk 633 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 60 GLN 1 51 ASN 1 81 ASN 1 285 GLN ** 1 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 527 GLN 1 590 HIS 1 606 ASN 2 122 ASN 2 153 ASN 2 243 GLN 2 289 HIS 2 380 GLN 3 80 ASN 3 188 ASN 3 189 HIS 3 206 ASN 4 68 HIS 5 79 ASN 6 74 GLN ** 6 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 60 GLN 7 98 ASN 7 102 GLN 7 123 HIS ** 7 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 184 ASN ** 8 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 9 60 ASN B 87 ASN F 98 GLN G 98 GLN J 98 GLN M 108 ASN M 163 ASN P 65 ASN P 223 ASN ** Q 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 67 ASN R 38 ASN ** R 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 137 HIS R 171 GLN S 195 ASN S 250 HIS S 267 HIS S 297 GLN T 61 HIS ** T 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 169 GLN T 241 HIS T 271 GLN T 386 GLN T 405 GLN ** T 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 497 GLN U 241 HIS U 246 ASN U 319 HIS U 386 GLN U 441 GLN U 497 GLN U 529 ASN V 196 GLN V 242 GLN V 244 ASN V 271 GLN V 486 GLN ** V 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 497 GLN V 539 ASN X 199 ASN X 337 GLN X 408 GLN X 412 ASN ** Y 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 198 ASN Y 388 ASN Y 390 ASN Y 514 ASN ** Z 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 252 ASN Z 278 GLN Z 414 GLN Total number of N/Q/H flips: 73 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 54685 Z= 0.169 Angle : 0.586 11.729 74157 Z= 0.302 Chirality : 0.042 0.182 8689 Planarity : 0.005 0.064 9508 Dihedral : 6.100 105.522 7576 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.79 % Favored : 96.01 % Rotamer Outliers : 2.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.34 % Twisted General : 0.12 % 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: -2.48 (0.09), residues: 7036 helix: -1.37 (0.08), residues: 3768 sheet: -1.76 (0.20), residues: 585 loop : -1.80 (0.11), residues: 2683 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14072 Ramachandran restraints generated. 7036 Oldfield, 0 Emsley, 7036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14072 Ramachandran restraints generated. 7036 Oldfield, 0 Emsley, 7036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1101 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 972 time to evaluate : 4.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 129 outliers final: 73 residues processed: 1053 average time/residue: 0.5246 time to fit residues: 931.6340 Evaluate side-chains 848 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 775 time to evaluate : 4.924 Switching outliers to nearest non-outliers outliers start: 73 outliers final: 0 residues processed: 73 average time/residue: 0.3899 time to fit residues: 60.4073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 352 optimal weight: 0.0370 chunk 196 optimal weight: 4.9990 chunk 527 optimal weight: 0.9990 chunk 431 optimal weight: 0.9980 chunk 174 optimal weight: 9.9990 chunk 635 optimal weight: 0.0370 chunk 685 optimal weight: 1.9990 chunk 565 optimal weight: 1.9990 chunk 629 optimal weight: 0.9990 chunk 216 optimal weight: 9.9990 chunk 509 optimal weight: 9.9990 overall best weight: 0.6140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 316 ASN 2 122 ASN 4 135 ASN 5 79 ASN ** 7 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 GLN C 92 ASN E 87 ASN G 94 ASN G 98 GLN ** M 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 49 GLN T 61 HIS T 405 GLN T 422 ASN ** U 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 134 ASN ** U 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 488 GLN X 412 ASN Y 42 GLN ** Y 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 144 HIS ** Z 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.042 54685 Z= 0.148 Angle : 0.553 10.883 74157 Z= 0.281 Chirality : 0.041 0.185 8689 Planarity : 0.004 0.055 9508 Dihedral : 5.540 101.604 7576 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.14 % Favored : 95.74 % Rotamer Outliers : 1.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.10), residues: 7036 helix: -0.58 (0.08), residues: 3788 sheet: -1.47 (0.21), residues: 603 loop : -1.54 (0.11), residues: 2645 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14072 Ramachandran restraints generated. 7036 Oldfield, 0 Emsley, 7036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14072 Ramachandran restraints generated. 7036 Oldfield, 0 Emsley, 7036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 991 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 895 time to evaluate : 4.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 96 outliers final: 49 residues processed: 963 average time/residue: 0.5165 time to fit residues: 846.8121 Evaluate side-chains 827 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 778 time to evaluate : 4.912 Switching outliers to nearest non-outliers outliers start: 49 outliers final: 0 residues processed: 49 average time/residue: 0.4016 time to fit residues: 43.2717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 627 optimal weight: 0.9980 chunk 477 optimal weight: 9.9990 chunk 329 optimal weight: 9.9990 chunk 70 optimal weight: 5.9990 chunk 303 optimal weight: 7.9990 chunk 426 optimal weight: 2.9990 chunk 637 optimal weight: 0.0020 chunk 674 optimal weight: 9.9990 chunk 332 optimal weight: 7.9990 chunk 603 optimal weight: 10.0000 chunk 181 optimal weight: 10.0000 overall best weight: 3.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 65 GLN 1 438 GLN 2 122 ASN 2 344 GLN 3 309 ASN ** 5 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 GLN G 98 GLN ** Q 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 104 GLN ** T 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 549 HIS ** U 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 134 ASN ** U 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 134 ASN V 488 GLN X 204 HIS ** Y 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 408 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.2170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.072 54685 Z= 0.339 Angle : 0.630 11.184 74157 Z= 0.320 Chirality : 0.044 0.189 8689 Planarity : 0.005 0.056 9508 Dihedral : 5.605 100.269 7576 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.06 % Favored : 94.77 % Rotamer Outliers : 2.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.34 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.10), residues: 7036 helix: -0.38 (0.08), residues: 3790 sheet: -1.36 (0.21), residues: 599 loop : -1.39 (0.12), residues: 2647 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14072 Ramachandran restraints generated. 7036 Oldfield, 0 Emsley, 7036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14072 Ramachandran restraints generated. 7036 Oldfield, 0 Emsley, 7036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 936 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 784 time to evaluate : 5.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 152 outliers final: 104 residues processed: 882 average time/residue: 0.5234 time to fit residues: 794.3669 Evaluate side-chains 838 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 734 time to evaluate : 4.920 Switching outliers to nearest non-outliers outliers start: 104 outliers final: 0 residues processed: 104 average time/residue: 0.4209 time to fit residues: 87.5380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 561 optimal weight: 1.9990 chunk 382 optimal weight: 4.9990 chunk 9 optimal weight: 9.9990 chunk 502 optimal weight: 6.9990 chunk 278 optimal weight: 9.9990 chunk 575 optimal weight: 3.9990 chunk 466 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 344 optimal weight: 7.9990 chunk 605 optimal weight: 1.9990 chunk 170 optimal weight: 0.9980 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 438 GLN ** 5 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 98 GLN ** Q 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 61 HIS T 549 HIS ** U 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 134 ASN ** U 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 529 ASN V 64 GLN V 134 ASN V 539 ASN ** Y 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.2301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.056 54685 Z= 0.260 Angle : 0.587 11.040 74157 Z= 0.297 Chirality : 0.043 0.255 8689 Planarity : 0.004 0.053 9508 Dihedral : 5.476 97.099 7576 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.60 % Favored : 95.24 % Rotamer Outliers : 1.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.10), residues: 7036 helix: -0.12 (0.09), residues: 3769 sheet: -1.25 (0.21), residues: 597 loop : -1.31 (0.12), residues: 2670 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14072 Ramachandran restraints generated. 7036 Oldfield, 0 Emsley, 7036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14072 Ramachandran restraints generated. 7036 Oldfield, 0 Emsley, 7036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 891 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 800 time to evaluate : 5.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 91 outliers final: 49 residues processed: 862 average time/residue: 0.5181 time to fit residues: 763.1598 Evaluate side-chains 797 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 748 time to evaluate : 5.155 Switching outliers to nearest non-outliers outliers start: 49 outliers final: 0 residues processed: 49 average time/residue: 0.4001 time to fit residues: 44.3805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 226 optimal weight: 2.9990 chunk 607 optimal weight: 2.9990 chunk 133 optimal weight: 2.9990 chunk 396 optimal weight: 2.9990 chunk 166 optimal weight: 4.9990 chunk 675 optimal weight: 0.0370 chunk 560 optimal weight: 6.9990 chunk 312 optimal weight: 0.1980 chunk 56 optimal weight: 0.8980 chunk 223 optimal weight: 0.9980 chunk 354 optimal weight: 10.0000 overall best weight: 1.0260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 107 ASN ** 7 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 GLN D 98 GLN G 98 GLN ** Q 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 61 HIS T 461 GLN T 549 HIS ** U 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 134 ASN U 358 HIS ** U 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 529 ASN ** Y 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.2553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 54685 Z= 0.163 Angle : 0.550 11.125 74157 Z= 0.276 Chirality : 0.041 0.174 8689 Planarity : 0.004 0.048 9508 Dihedral : 5.193 92.516 7576 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.55 % Favored : 95.34 % Rotamer Outliers : 1.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.34 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.10), residues: 7036 helix: 0.17 (0.09), residues: 3777 sheet: -1.05 (0.22), residues: 600 loop : -1.20 (0.12), residues: 2659 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14072 Ramachandran restraints generated. 7036 Oldfield, 0 Emsley, 7036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14072 Ramachandran restraints generated. 7036 Oldfield, 0 Emsley, 7036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 905 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 831 time to evaluate : 5.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 74 outliers final: 40 residues processed: 878 average time/residue: 0.5222 time to fit residues: 783.7243 Evaluate side-chains 792 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 752 time to evaluate : 4.845 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 0 residues processed: 40 average time/residue: 0.4010 time to fit residues: 36.7603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 651 optimal weight: 10.0000 chunk 76 optimal weight: 0.0970 chunk 384 optimal weight: 2.9990 chunk 493 optimal weight: 4.9990 chunk 382 optimal weight: 6.9990 chunk 568 optimal weight: 3.9990 chunk 377 optimal weight: 0.6980 chunk 672 optimal weight: 4.9990 chunk 421 optimal weight: 0.9990 chunk 410 optimal weight: 7.9990 chunk 310 optimal weight: 0.8980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 438 GLN ** 7 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 87 ASN C 98 GLN ** Q 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 61 HIS T 441 GLN T 549 HIS ** U 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 134 ASN ** U 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 529 ASN ** V 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 134 ASN ** Y 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 54685 Z= 0.170 Angle : 0.556 15.476 74157 Z= 0.277 Chirality : 0.041 0.206 8689 Planarity : 0.004 0.046 9508 Dihedral : 5.059 94.297 7576 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.25 % Favored : 95.64 % Rotamer Outliers : 1.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.10), residues: 7036 helix: 0.33 (0.09), residues: 3766 sheet: -0.92 (0.22), residues: 592 loop : -1.09 (0.12), residues: 2678 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14072 Ramachandran restraints generated. 7036 Oldfield, 0 Emsley, 7036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14072 Ramachandran restraints generated. 7036 Oldfield, 0 Emsley, 7036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 871 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 809 time to evaluate : 4.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 62 outliers final: 35 residues processed: 851 average time/residue: 0.5254 time to fit residues: 768.3222 Evaluate side-chains 797 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 762 time to evaluate : 4.823 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 0 residues processed: 35 average time/residue: 0.4075 time to fit residues: 33.6962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 416 optimal weight: 10.0000 chunk 268 optimal weight: 0.7980 chunk 401 optimal weight: 4.9990 chunk 202 optimal weight: 0.9980 chunk 132 optimal weight: 4.9990 chunk 130 optimal weight: 0.5980 chunk 427 optimal weight: 2.9990 chunk 458 optimal weight: 1.9990 chunk 332 optimal weight: 0.5980 chunk 62 optimal weight: 0.9990 chunk 528 optimal weight: 8.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 438 GLN ** 7 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 87 ASN ** Q 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 78 HIS ** S 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 61 HIS T 549 HIS ** U 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 134 ASN ** U 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 529 ASN ** V 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.038 54685 Z= 0.154 Angle : 0.558 13.245 74157 Z= 0.277 Chirality : 0.041 0.227 8689 Planarity : 0.004 0.046 9508 Dihedral : 4.930 91.129 7576 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.22 % Favored : 95.68 % Rotamer Outliers : 0.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -0.39 (0.10), residues: 7036 helix: 0.43 (0.09), residues: 3792 sheet: -0.80 (0.22), residues: 609 loop : -1.00 (0.12), residues: 2635 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14072 Ramachandran restraints generated. 7036 Oldfield, 0 Emsley, 7036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14072 Ramachandran restraints generated. 7036 Oldfield, 0 Emsley, 7036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 890 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 848 time to evaluate : 4.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 42 outliers final: 18 residues processed: 877 average time/residue: 0.5353 time to fit residues: 805.5342 Evaluate side-chains 802 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 784 time to evaluate : 4.904 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.4243 time to fit residues: 20.8601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 611 optimal weight: 8.9990 chunk 644 optimal weight: 0.9990 chunk 588 optimal weight: 6.9990 chunk 626 optimal weight: 6.9990 chunk 377 optimal weight: 0.9990 chunk 273 optimal weight: 6.9990 chunk 492 optimal weight: 5.9990 chunk 192 optimal weight: 0.0980 chunk 566 optimal weight: 3.9990 chunk 592 optimal weight: 0.0980 chunk 624 optimal weight: 7.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 398 HIS ** 7 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 87 ASN P 65 ASN ** Q 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 191 GLN ** S 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 61 HIS T 549 HIS ** U 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 134 ASN ** U 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 134 ASN ** Y 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 157 GLN ** Z 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.2977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 54685 Z= 0.177 Angle : 0.566 13.312 74157 Z= 0.281 Chirality : 0.042 0.420 8689 Planarity : 0.004 0.057 9508 Dihedral : 4.891 90.226 7576 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.21 % Favored : 95.69 % Rotamer Outliers : 0.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -0.33 (0.10), residues: 7036 helix: 0.48 (0.09), residues: 3795 sheet: -0.81 (0.22), residues: 604 loop : -0.98 (0.12), residues: 2637 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14072 Ramachandran restraints generated. 7036 Oldfield, 0 Emsley, 7036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14072 Ramachandran restraints generated. 7036 Oldfield, 0 Emsley, 7036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 826 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 793 time to evaluate : 5.057 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 17 residues processed: 815 average time/residue: 0.5215 time to fit residues: 733.7559 Evaluate side-chains 788 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 771 time to evaluate : 4.878 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.4155 time to fit residues: 19.6705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 411 optimal weight: 0.8980 chunk 662 optimal weight: 5.9990 chunk 404 optimal weight: 3.9990 chunk 314 optimal weight: 1.9990 chunk 460 optimal weight: 8.9990 chunk 695 optimal weight: 3.9990 chunk 640 optimal weight: 7.9990 chunk 553 optimal weight: 0.3980 chunk 57 optimal weight: 0.8980 chunk 427 optimal weight: 5.9990 chunk 339 optimal weight: 20.0000 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 111 GLN ** 7 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 61 HIS T 441 GLN T 549 HIS ** U 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 134 ASN ** U 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 132 GLN Z 157 GLN ** Z 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.3006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 54685 Z= 0.202 Angle : 0.582 12.724 74157 Z= 0.289 Chirality : 0.042 0.205 8689 Planarity : 0.004 0.065 9508 Dihedral : 4.898 90.752 7576 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.52 % Favored : 95.38 % Rotamer Outliers : 0.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.10), residues: 7036 helix: 0.51 (0.09), residues: 3793 sheet: -0.83 (0.22), residues: 602 loop : -0.98 (0.12), residues: 2641 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14072 Ramachandran restraints generated. 7036 Oldfield, 0 Emsley, 7036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14072 Ramachandran restraints generated. 7036 Oldfield, 0 Emsley, 7036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 810 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 789 time to evaluate : 4.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 12 residues processed: 798 average time/residue: 0.5410 time to fit residues: 743.8689 Evaluate side-chains 775 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 763 time to evaluate : 4.910 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.4470 time to fit residues: 16.2884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 439 optimal weight: 0.9990 chunk 589 optimal weight: 0.5980 chunk 169 optimal weight: 0.8980 chunk 510 optimal weight: 5.9990 chunk 81 optimal weight: 5.9990 chunk 153 optimal weight: 20.0000 chunk 554 optimal weight: 7.9990 chunk 232 optimal weight: 6.9990 chunk 569 optimal weight: 6.9990 chunk 70 optimal weight: 4.9990 chunk 102 optimal weight: 0.0670 overall best weight: 1.5122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 65 ASN ** Q 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 61 HIS T 441 GLN T 549 HIS ** U 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 134 ASN ** U 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 414 GLN ** Z 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.114554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.096400 restraints weight = 105128.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.098166 restraints weight = 62877.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.099300 restraints weight = 44516.307| |-----------------------------------------------------------------------------| r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.3050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 54685 Z= 0.193 Angle : 0.575 12.441 74157 Z= 0.286 Chirality : 0.042 0.188 8689 Planarity : 0.004 0.069 9508 Dihedral : 4.864 89.863 7576 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.43 % Favored : 95.45 % Rotamer Outliers : 0.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -0.25 (0.10), residues: 7036 helix: 0.56 (0.09), residues: 3793 sheet: -0.77 (0.22), residues: 577 loop : -0.96 (0.12), residues: 2666 =============================================================================== Job complete usr+sys time: 12420.44 seconds wall clock time: 219 minutes 26.07 seconds (13166.07 seconds total)