Starting phenix.real_space_refine on Tue Feb 20 17:13:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yew_10796/02_2024/6yew_10796.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yew_10796/02_2024/6yew_10796.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yew_10796/02_2024/6yew_10796.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yew_10796/02_2024/6yew_10796.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yew_10796/02_2024/6yew_10796.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yew_10796/02_2024/6yew_10796.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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: 4 Type Number sf(0) Gaussians S 305 5.16 5 C 55970 2.51 5 N 15350 2.21 5 O 17075 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 33": "OE1" <-> "OE2" Residue "A ARG 41": "NH1" <-> "NH2" Residue "A ARG 44": "NH1" <-> "NH2" Residue "A GLU 45": "OE1" <-> "OE2" Residue "A ARG 137": "NH1" <-> "NH2" Residue "A ASP 154": "OD1" <-> "OD2" Residue "A ASP 157": "OD1" <-> "OD2" Residue "A GLU 159": "OE1" <-> "OE2" Residue "A ASP 182": "OD1" <-> "OD2" Residue "A ARG 194": "NH1" <-> "NH2" Residue "A ASP 221": "OD1" <-> "OD2" Residue "A ASP 259": "OD1" <-> "OD2" Residue "A GLU 261": "OE1" <-> "OE2" Residue "A ARG 266": "NH1" <-> "NH2" Residue "A PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 280": "OD1" <-> "OD2" Residue "A GLU 287": "OE1" <-> "OE2" Residue "A ASP 291": "OD1" <-> "OD2" Residue "A GLU 300": "OE1" <-> "OE2" Residue "A ARG 304": "NH1" <-> "NH2" Residue "A TYR 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 339": "OD1" <-> "OD2" Residue "A ASP 344": "OD1" <-> "OD2" Residue "A ASP 347": "OD1" <-> "OD2" Residue "A ASP 368": "OD1" <-> "OD2" Residue "A PHE 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 427": "OE1" <-> "OE2" Residue "A ARG 449": "NH1" <-> "NH2" Residue "A GLU 466": "OE1" <-> "OE2" Residue "A ARG 493": "NH1" <-> "NH2" Residue "A ASP 517": "OD1" <-> "OD2" Residue "A PHE 523": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 542": "OD1" <-> "OD2" Residue "A GLU 547": "OE1" <-> "OE2" Residue "A ASP 549": "OD1" <-> "OD2" Residue "A ASP 552": "OD1" <-> "OD2" Residue "A GLU 556": "OE1" <-> "OE2" Residue "A ARG 578": "NH1" <-> "NH2" Residue "A GLU 586": "OE1" <-> "OE2" Residue "A GLU 673": "OE1" <-> "OE2" Residue "A ASP 679": "OD1" <-> "OD2" Residue "A ARG 682": "NH1" <-> "NH2" Residue "A GLU 715": "OE1" <-> "OE2" Residue "A ASP 722": "OD1" <-> "OD2" Residue "A ARG 736": "NH1" <-> "NH2" Residue "A ASP 796": "OD1" <-> "OD2" Residue "A ASP 813": "OD1" <-> "OD2" Residue "A GLU 833": "OE1" <-> "OE2" Residue "A GLU 834": "OE1" <-> "OE2" Residue "A ARG 861": "NH1" <-> "NH2" Residue "A ASP 866": "OD1" <-> "OD2" Residue "A GLU 883": "OE1" <-> "OE2" Residue "A ARG 886": "NH1" <-> "NH2" Residue "A GLU 905": "OE1" <-> "OE2" Residue "A GLU 916": "OE1" <-> "OE2" Residue "A ASP 940": "OD1" <-> "OD2" Residue "A ASP 963": "OD1" <-> "OD2" Residue "A ASP 997": "OD1" <-> "OD2" Residue "A ASP 1047": "OD1" <-> "OD2" Residue "A PHE 1060": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1096": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1118": "OD1" <-> "OD2" Residue "A ASP 1131": "OD1" <-> "OD2" Residue "A PHE 1163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1205": "OD1" <-> "OD2" Residue "A TYR 1213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1231": "OD1" <-> "OD2" Residue "A TYR 1291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1470": "OE1" <-> "OE2" Residue "A GLU 1490": "OE1" <-> "OE2" Residue "A PHE 1494": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1520": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1532": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1561": "OD1" <-> "OD2" Residue "A GLU 1590": "OE1" <-> "OE2" Residue "A TYR 1627": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1640": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1695": "NH1" <-> "NH2" Residue "A PHE 1734": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1760": "OE1" <-> "OE2" Residue "A ARG 1785": "NH1" <-> "NH2" Residue "A ASP 1792": "OD1" <-> "OD2" Residue "A ASP 1842": "OD1" <-> "OD2" Residue "A ASP 1860": "OD1" <-> "OD2" Residue "A PHE 1866": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1880": "OD1" <-> "OD2" Residue "A ASP 1889": "OD1" <-> "OD2" Residue "A GLU 1890": "OE1" <-> "OE2" Residue "A PHE 1913": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1914": "NH1" <-> "NH2" Residue "A GLU 1929": "OE1" <-> "OE2" Residue "A PHE 1951": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1956": "OD1" <-> "OD2" Residue "A ASP 2013": "OD1" <-> "OD2" Residue "A GLU 2037": "OE1" <-> "OE2" Residue "A GLU 2051": "OE1" <-> "OE2" Residue "A ARG 2054": "NH1" <-> "NH2" Residue "A ASP 2062": "OD1" <-> "OD2" Residue "A ASP 2081": "OD1" <-> "OD2" Residue "A ASP 2142": "OD1" <-> "OD2" Residue "A ARG 2151": "NH1" <-> "NH2" Residue "A GLU 2204": "OE1" <-> "OE2" Residue "A ARG 2208": "NH1" <-> "NH2" Residue "A PHE 2230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 2255": "NH1" <-> "NH2" Residue "A TYR 2256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2315": "OE1" <-> "OE2" Residue "A ASP 2319": "OD1" <-> "OD2" Residue "A ASP 2340": "OD1" <-> "OD2" Residue "A ASP 2356": "OD1" <-> "OD2" Residue "A ASP 2357": "OD1" <-> "OD2" Residue "A TYR 2358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 2384": "OD1" <-> "OD2" Residue "A ASP 2411": "OD1" <-> "OD2" Residue "A ASP 2418": "OD1" <-> "OD2" Residue "A ASP 2459": "OD1" <-> "OD2" Residue "A TYR 2466": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 33": "OE1" <-> "OE2" Residue "B ARG 41": "NH1" <-> "NH2" Residue "B ARG 44": "NH1" <-> "NH2" Residue "B GLU 45": "OE1" <-> "OE2" Residue "B ARG 137": "NH1" <-> "NH2" Residue "B ASP 154": "OD1" <-> "OD2" Residue "B ASP 157": "OD1" <-> "OD2" Residue "B GLU 159": "OE1" <-> "OE2" Residue "B ASP 182": "OD1" <-> "OD2" Residue "B ARG 194": "NH1" <-> "NH2" Residue "B ASP 221": "OD1" <-> "OD2" Residue "B ASP 259": "OD1" <-> "OD2" Residue "B GLU 261": "OE1" <-> "OE2" Residue "B ARG 266": "NH1" <-> "NH2" Residue "B PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 280": "OD1" <-> "OD2" Residue "B GLU 287": "OE1" <-> "OE2" Residue "B ASP 291": "OD1" <-> "OD2" Residue "B GLU 300": "OE1" <-> "OE2" Residue "B ARG 304": "NH1" <-> "NH2" Residue "B TYR 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 339": "OD1" <-> "OD2" Residue "B ASP 344": "OD1" <-> "OD2" Residue "B ASP 347": "OD1" <-> "OD2" Residue "B ASP 368": "OD1" <-> "OD2" Residue "B PHE 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 427": "OE1" <-> "OE2" Residue "B ARG 449": "NH1" <-> "NH2" Residue "B GLU 466": "OE1" <-> "OE2" Residue "B ARG 493": "NH1" <-> "NH2" Residue "B ASP 517": "OD1" <-> "OD2" Residue "B PHE 523": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 542": "OD1" <-> "OD2" Residue "B GLU 547": "OE1" <-> "OE2" Residue "B ASP 549": "OD1" <-> "OD2" Residue "B ASP 552": "OD1" <-> "OD2" Residue "B GLU 556": "OE1" <-> "OE2" Residue "B ARG 578": "NH1" <-> "NH2" Residue "B GLU 586": "OE1" <-> "OE2" Residue "B GLU 673": "OE1" <-> "OE2" Residue "B ASP 679": "OD1" <-> "OD2" Residue "B ARG 682": "NH1" <-> "NH2" Residue "B GLU 715": "OE1" <-> "OE2" Residue "B ASP 722": "OD1" <-> "OD2" Residue "B ARG 736": "NH1" <-> "NH2" Residue "B ASP 796": "OD1" <-> "OD2" Residue "B ASP 813": "OD1" <-> "OD2" Residue "B GLU 833": "OE1" <-> "OE2" Residue "B GLU 834": "OE1" <-> "OE2" Residue "B ARG 861": "NH1" <-> "NH2" Residue "B ASP 866": "OD1" <-> "OD2" Residue "B GLU 883": "OE1" <-> "OE2" Residue "B ARG 886": "NH1" <-> "NH2" Residue "B GLU 905": "OE1" <-> "OE2" Residue "B GLU 916": "OE1" <-> "OE2" Residue "B ASP 940": "OD1" <-> "OD2" Residue "B ASP 963": "OD1" <-> "OD2" Residue "B ASP 997": "OD1" <-> "OD2" Residue "B ASP 1047": "OD1" <-> "OD2" Residue "B PHE 1060": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1096": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1118": "OD1" <-> "OD2" Residue "B ASP 1131": "OD1" <-> "OD2" Residue "B PHE 1163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1205": "OD1" <-> "OD2" Residue "B TYR 1213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1231": "OD1" <-> "OD2" Residue "B TYR 1291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1470": "OE1" <-> "OE2" Residue "B GLU 1490": "OE1" <-> "OE2" Residue "B PHE 1494": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1520": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1532": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1561": "OD1" <-> "OD2" Residue "B GLU 1590": "OE1" <-> "OE2" Residue "B TYR 1627": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1640": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1695": "NH1" <-> "NH2" Residue "B PHE 1734": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1760": "OE1" <-> "OE2" Residue "B ARG 1785": "NH1" <-> "NH2" Residue "B ASP 1792": "OD1" <-> "OD2" Residue "B ASP 1842": "OD1" <-> "OD2" Residue "B ASP 1860": "OD1" <-> "OD2" Residue "B PHE 1866": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1880": "OD1" <-> "OD2" Residue "B ASP 1889": "OD1" <-> "OD2" Residue "B GLU 1890": "OE1" <-> "OE2" Residue "B PHE 1913": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1914": "NH1" <-> "NH2" Residue "B GLU 1929": "OE1" <-> "OE2" Residue "B PHE 1951": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1956": "OD1" <-> "OD2" Residue "B ASP 2013": "OD1" <-> "OD2" Residue "B GLU 2037": "OE1" <-> "OE2" Residue "B GLU 2051": "OE1" <-> "OE2" Residue "B ARG 2054": "NH1" <-> "NH2" Residue "B ASP 2062": "OD1" <-> "OD2" Residue "B ASP 2081": "OD1" <-> "OD2" Residue "B ASP 2142": "OD1" <-> "OD2" Residue "B ARG 2151": "NH1" <-> "NH2" Residue "B GLU 2204": "OE1" <-> "OE2" Residue "B ARG 2208": "NH1" <-> "NH2" Residue "B PHE 2230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 2255": "NH1" <-> "NH2" Residue "B TYR 2256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 2315": "OE1" <-> "OE2" Residue "B ASP 2319": "OD1" <-> "OD2" Residue "B ASP 2340": "OD1" <-> "OD2" Residue "B ASP 2356": "OD1" <-> "OD2" Residue "B ASP 2357": "OD1" <-> "OD2" Residue "B TYR 2358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 2384": "OD1" <-> "OD2" Residue "B ASP 2411": "OD1" <-> "OD2" Residue "B ASP 2418": "OD1" <-> "OD2" Residue "B ASP 2459": "OD1" <-> "OD2" Residue "B TYR 2466": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 33": "OE1" <-> "OE2" Residue "C ARG 41": "NH1" <-> "NH2" Residue "C ARG 44": "NH1" <-> "NH2" Residue "C GLU 45": "OE1" <-> "OE2" Residue "C ARG 137": "NH1" <-> "NH2" Residue "C ASP 154": "OD1" <-> "OD2" Residue "C ASP 157": "OD1" <-> "OD2" Residue "C GLU 159": "OE1" <-> "OE2" Residue "C ASP 182": "OD1" <-> "OD2" Residue "C ARG 194": "NH1" <-> "NH2" Residue "C ASP 221": "OD1" <-> "OD2" Residue "C ASP 259": "OD1" <-> "OD2" Residue "C GLU 261": "OE1" <-> "OE2" Residue "C ARG 266": "NH1" <-> "NH2" Residue "C PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 280": "OD1" <-> "OD2" Residue "C GLU 287": "OE1" <-> "OE2" Residue "C ASP 291": "OD1" <-> "OD2" Residue "C GLU 300": "OE1" <-> "OE2" Residue "C ARG 304": "NH1" <-> "NH2" Residue "C TYR 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 339": "OD1" <-> "OD2" Residue "C ASP 344": "OD1" <-> "OD2" Residue "C ASP 347": "OD1" <-> "OD2" Residue "C ASP 368": "OD1" <-> "OD2" Residue "C PHE 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 427": "OE1" <-> "OE2" Residue "C ARG 449": "NH1" <-> "NH2" Residue "C GLU 466": "OE1" <-> "OE2" Residue "C ARG 493": "NH1" <-> "NH2" Residue "C ASP 517": "OD1" <-> "OD2" Residue "C PHE 523": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 542": "OD1" <-> "OD2" Residue "C GLU 547": "OE1" <-> "OE2" Residue "C ASP 549": "OD1" <-> "OD2" Residue "C ASP 552": "OD1" <-> "OD2" Residue "C GLU 556": "OE1" <-> "OE2" Residue "C ARG 578": "NH1" <-> "NH2" Residue "C GLU 586": "OE1" <-> "OE2" Residue "C GLU 673": "OE1" <-> "OE2" Residue "C ASP 679": "OD1" <-> "OD2" Residue "C ARG 682": "NH1" <-> "NH2" Residue "C GLU 715": "OE1" <-> "OE2" Residue "C ASP 722": "OD1" <-> "OD2" Residue "C ARG 736": "NH1" <-> "NH2" Residue "C ASP 796": "OD1" <-> "OD2" Residue "C ASP 813": "OD1" <-> "OD2" Residue "C GLU 833": "OE1" <-> "OE2" Residue "C GLU 834": "OE1" <-> "OE2" Residue "C ARG 861": "NH1" <-> "NH2" Residue "C ASP 866": "OD1" <-> "OD2" Residue "C GLU 883": "OE1" <-> "OE2" Residue "C ARG 886": "NH1" <-> "NH2" Residue "C GLU 905": "OE1" <-> "OE2" Residue "C GLU 916": "OE1" <-> "OE2" Residue "C ASP 940": "OD1" <-> "OD2" Residue "C ASP 963": "OD1" <-> "OD2" Residue "C ASP 997": "OD1" <-> "OD2" Residue "C ASP 1047": "OD1" <-> "OD2" Residue "C PHE 1060": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1096": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1118": "OD1" <-> "OD2" Residue "C ASP 1131": "OD1" <-> "OD2" Residue "C PHE 1163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1205": "OD1" <-> "OD2" Residue "C TYR 1213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1231": "OD1" <-> "OD2" Residue "C TYR 1291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1470": "OE1" <-> "OE2" Residue "C GLU 1490": "OE1" <-> "OE2" Residue "C PHE 1494": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1520": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1532": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1561": "OD1" <-> "OD2" Residue "C GLU 1590": "OE1" <-> "OE2" Residue "C TYR 1627": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1640": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 1695": "NH1" <-> "NH2" Residue "C PHE 1734": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1760": "OE1" <-> "OE2" Residue "C ARG 1785": "NH1" <-> "NH2" Residue "C ASP 1792": "OD1" <-> "OD2" Residue "C ASP 1842": "OD1" <-> "OD2" Residue "C ASP 1860": "OD1" <-> "OD2" Residue "C PHE 1866": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1880": "OD1" <-> "OD2" Residue "C ASP 1889": "OD1" <-> "OD2" Residue "C GLU 1890": "OE1" <-> "OE2" Residue "C PHE 1913": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 1914": "NH1" <-> "NH2" Residue "C GLU 1929": "OE1" <-> "OE2" Residue "C PHE 1951": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1956": "OD1" <-> "OD2" Residue "C ASP 2013": "OD1" <-> "OD2" Residue "C GLU 2037": "OE1" <-> "OE2" Residue "C GLU 2051": "OE1" <-> "OE2" Residue "C ARG 2054": "NH1" <-> "NH2" Residue "C ASP 2062": "OD1" <-> "OD2" Residue "C ASP 2081": "OD1" <-> "OD2" Residue "C ASP 2142": "OD1" <-> "OD2" Residue "C ARG 2151": "NH1" <-> "NH2" Residue "C GLU 2204": "OE1" <-> "OE2" Residue "C ARG 2208": "NH1" <-> "NH2" Residue "C PHE 2230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 2255": "NH1" <-> "NH2" Residue "C TYR 2256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 2315": "OE1" <-> "OE2" Residue "C ASP 2319": "OD1" <-> "OD2" Residue "C ASP 2340": "OD1" <-> "OD2" Residue "C ASP 2356": "OD1" <-> "OD2" Residue "C ASP 2357": "OD1" <-> "OD2" Residue "C TYR 2358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 2384": "OD1" <-> "OD2" Residue "C ASP 2411": "OD1" <-> "OD2" Residue "C ASP 2418": "OD1" <-> "OD2" Residue "C ASP 2459": "OD1" <-> "OD2" Residue "C TYR 2466": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 33": "OE1" <-> "OE2" Residue "D ARG 41": "NH1" <-> "NH2" Residue "D ARG 44": "NH1" <-> "NH2" Residue "D GLU 45": "OE1" <-> "OE2" Residue "D ARG 137": "NH1" <-> "NH2" Residue "D ASP 154": "OD1" <-> "OD2" Residue "D ASP 157": "OD1" <-> "OD2" Residue "D GLU 159": "OE1" <-> "OE2" Residue "D ASP 182": "OD1" <-> "OD2" Residue "D ARG 194": "NH1" <-> "NH2" Residue "D ASP 221": "OD1" <-> "OD2" Residue "D ASP 259": "OD1" <-> "OD2" Residue "D GLU 261": "OE1" <-> "OE2" Residue "D ARG 266": "NH1" <-> "NH2" Residue "D PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 280": "OD1" <-> "OD2" Residue "D GLU 287": "OE1" <-> "OE2" Residue "D ASP 291": "OD1" <-> "OD2" Residue "D GLU 300": "OE1" <-> "OE2" Residue "D ARG 304": "NH1" <-> "NH2" Residue "D TYR 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 339": "OD1" <-> "OD2" Residue "D ASP 344": "OD1" <-> "OD2" Residue "D ASP 347": "OD1" <-> "OD2" Residue "D ASP 368": "OD1" <-> "OD2" Residue "D PHE 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 427": "OE1" <-> "OE2" Residue "D ARG 449": "NH1" <-> "NH2" Residue "D GLU 466": "OE1" <-> "OE2" Residue "D ARG 493": "NH1" <-> "NH2" Residue "D ASP 517": "OD1" <-> "OD2" Residue "D PHE 523": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 542": "OD1" <-> "OD2" Residue "D GLU 547": "OE1" <-> "OE2" Residue "D ASP 549": "OD1" <-> "OD2" Residue "D ASP 552": "OD1" <-> "OD2" Residue "D GLU 556": "OE1" <-> "OE2" Residue "D ARG 578": "NH1" <-> "NH2" Residue "D GLU 586": "OE1" <-> "OE2" Residue "D GLU 673": "OE1" <-> "OE2" Residue "D ASP 679": "OD1" <-> "OD2" Residue "D ARG 682": "NH1" <-> "NH2" Residue "D GLU 715": "OE1" <-> "OE2" Residue "D ASP 722": "OD1" <-> "OD2" Residue "D ARG 736": "NH1" <-> "NH2" Residue "D ASP 796": "OD1" <-> "OD2" Residue "D ASP 813": "OD1" <-> "OD2" Residue "D GLU 833": "OE1" <-> "OE2" Residue "D GLU 834": "OE1" <-> "OE2" Residue "D ARG 861": "NH1" <-> "NH2" Residue "D ASP 866": "OD1" <-> "OD2" Residue "D GLU 883": "OE1" <-> "OE2" Residue "D ARG 886": "NH1" <-> "NH2" Residue "D GLU 905": "OE1" <-> "OE2" Residue "D GLU 916": "OE1" <-> "OE2" Residue "D ASP 940": "OD1" <-> "OD2" Residue "D ASP 963": "OD1" <-> "OD2" Residue "D ASP 997": "OD1" <-> "OD2" Residue "D ASP 1047": "OD1" <-> "OD2" Residue "D PHE 1060": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1096": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 1118": "OD1" <-> "OD2" Residue "D ASP 1131": "OD1" <-> "OD2" Residue "D PHE 1163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 1205": "OD1" <-> "OD2" Residue "D TYR 1213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 1231": "OD1" <-> "OD2" Residue "D TYR 1291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1470": "OE1" <-> "OE2" Residue "D GLU 1490": "OE1" <-> "OE2" Residue "D PHE 1494": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1520": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1532": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 1561": "OD1" <-> "OD2" Residue "D GLU 1590": "OE1" <-> "OE2" Residue "D TYR 1627": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1640": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 1695": "NH1" <-> "NH2" Residue "D PHE 1734": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1760": "OE1" <-> "OE2" Residue "D ARG 1785": "NH1" <-> "NH2" Residue "D ASP 1792": "OD1" <-> "OD2" Residue "D ASP 1842": "OD1" <-> "OD2" Residue "D ASP 1860": "OD1" <-> "OD2" Residue "D PHE 1866": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 1880": "OD1" <-> "OD2" Residue "D ASP 1889": "OD1" <-> "OD2" Residue "D GLU 1890": "OE1" <-> "OE2" Residue "D PHE 1913": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 1914": "NH1" <-> "NH2" Residue "D GLU 1929": "OE1" <-> "OE2" Residue "D PHE 1951": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 1956": "OD1" <-> "OD2" Residue "D ASP 2013": "OD1" <-> "OD2" Residue "D GLU 2037": "OE1" <-> "OE2" Residue "D GLU 2051": "OE1" <-> "OE2" Residue "D ARG 2054": "NH1" <-> "NH2" Residue "D ASP 2062": "OD1" <-> "OD2" Residue "D ASP 2081": "OD1" <-> "OD2" Residue "D ASP 2142": "OD1" <-> "OD2" Residue "D ARG 2151": "NH1" <-> "NH2" Residue "D GLU 2204": "OE1" <-> "OE2" Residue "D ARG 2208": "NH1" <-> "NH2" Residue "D PHE 2230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 2255": "NH1" <-> "NH2" Residue "D TYR 2256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 2315": "OE1" <-> "OE2" Residue "D ASP 2319": "OD1" <-> "OD2" Residue "D ASP 2340": "OD1" <-> "OD2" Residue "D ASP 2356": "OD1" <-> "OD2" Residue "D ASP 2357": "OD1" <-> "OD2" Residue "D TYR 2358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 2384": "OD1" <-> "OD2" Residue "D ASP 2411": "OD1" <-> "OD2" Residue "D ASP 2418": "OD1" <-> "OD2" Residue "D ASP 2459": "OD1" <-> "OD2" Residue "D TYR 2466": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 33": "OE1" <-> "OE2" Residue "E ARG 41": "NH1" <-> "NH2" Residue "E ARG 44": "NH1" <-> "NH2" Residue "E GLU 45": "OE1" <-> "OE2" Residue "E ARG 137": "NH1" <-> "NH2" Residue "E ASP 154": "OD1" <-> "OD2" Residue "E ASP 157": "OD1" <-> "OD2" Residue "E GLU 159": "OE1" <-> "OE2" Residue "E ASP 182": "OD1" <-> "OD2" Residue "E ARG 194": "NH1" <-> "NH2" Residue "E ASP 221": "OD1" <-> "OD2" Residue "E ASP 259": "OD1" <-> "OD2" Residue "E GLU 261": "OE1" <-> "OE2" Residue "E ARG 266": "NH1" <-> "NH2" Residue "E PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 280": "OD1" <-> "OD2" Residue "E GLU 287": "OE1" <-> "OE2" Residue "E ASP 291": "OD1" <-> "OD2" Residue "E GLU 300": "OE1" <-> "OE2" Residue "E ARG 304": "NH1" <-> "NH2" Residue "E TYR 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 339": "OD1" <-> "OD2" Residue "E ASP 344": "OD1" <-> "OD2" Residue "E ASP 347": "OD1" <-> "OD2" Residue "E ASP 368": "OD1" <-> "OD2" Residue "E PHE 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 427": "OE1" <-> "OE2" Residue "E ARG 449": "NH1" <-> "NH2" Residue "E GLU 466": "OE1" <-> "OE2" Residue "E ARG 493": "NH1" <-> "NH2" Residue "E ASP 517": "OD1" <-> "OD2" Residue "E PHE 523": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 542": "OD1" <-> "OD2" Residue "E GLU 547": "OE1" <-> "OE2" Residue "E ASP 549": "OD1" <-> "OD2" Residue "E ASP 552": "OD1" <-> "OD2" Residue "E GLU 556": "OE1" <-> "OE2" Residue "E ARG 578": "NH1" <-> "NH2" Residue "E GLU 586": "OE1" <-> "OE2" Residue "E GLU 673": "OE1" <-> "OE2" Residue "E ASP 679": "OD1" <-> "OD2" Residue "E ARG 682": "NH1" <-> "NH2" Residue "E GLU 715": "OE1" <-> "OE2" Residue "E ASP 722": "OD1" <-> "OD2" Residue "E ARG 736": "NH1" <-> "NH2" Residue "E ASP 796": "OD1" <-> "OD2" Residue "E ASP 813": "OD1" <-> "OD2" Residue "E GLU 833": "OE1" <-> "OE2" Residue "E GLU 834": "OE1" <-> "OE2" Residue "E ARG 861": "NH1" <-> "NH2" Residue "E ASP 866": "OD1" <-> "OD2" Residue "E GLU 883": "OE1" <-> "OE2" Residue "E ARG 886": "NH1" <-> "NH2" Residue "E GLU 905": "OE1" <-> "OE2" Residue "E GLU 916": "OE1" <-> "OE2" Residue "E ASP 940": "OD1" <-> "OD2" Residue "E ASP 963": "OD1" <-> "OD2" Residue "E ASP 997": "OD1" <-> "OD2" Residue "E ASP 1047": "OD1" <-> "OD2" Residue "E PHE 1060": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1096": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 1118": "OD1" <-> "OD2" Residue "E ASP 1131": "OD1" <-> "OD2" Residue "E PHE 1163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 1205": "OD1" <-> "OD2" Residue "E TYR 1213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 1231": "OD1" <-> "OD2" Residue "E TYR 1291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 1470": "OE1" <-> "OE2" Residue "E GLU 1490": "OE1" <-> "OE2" Residue "E PHE 1494": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1520": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1532": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 1561": "OD1" <-> "OD2" Residue "E GLU 1590": "OE1" <-> "OE2" Residue "E TYR 1627": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1640": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 1695": "NH1" <-> "NH2" Residue "E PHE 1734": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 1760": "OE1" <-> "OE2" Residue "E ARG 1785": "NH1" <-> "NH2" Residue "E ASP 1792": "OD1" <-> "OD2" Residue "E ASP 1842": "OD1" <-> "OD2" Residue "E ASP 1860": "OD1" <-> "OD2" Residue "E PHE 1866": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 1880": "OD1" <-> "OD2" Residue "E ASP 1889": "OD1" <-> "OD2" Residue "E GLU 1890": "OE1" <-> "OE2" Residue "E PHE 1913": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 1914": "NH1" <-> "NH2" Residue "E GLU 1929": "OE1" <-> "OE2" Residue "E PHE 1951": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 1956": "OD1" <-> "OD2" Residue "E ASP 2013": "OD1" <-> "OD2" Residue "E GLU 2037": "OE1" <-> "OE2" Residue "E GLU 2051": "OE1" <-> "OE2" Residue "E ARG 2054": "NH1" <-> "NH2" Residue "E ASP 2062": "OD1" <-> "OD2" Residue "E ASP 2081": "OD1" <-> "OD2" Residue "E ASP 2142": "OD1" <-> "OD2" Residue "E ARG 2151": "NH1" <-> "NH2" Residue "E GLU 2204": "OE1" <-> "OE2" Residue "E ARG 2208": "NH1" <-> "NH2" Residue "E PHE 2230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 2255": "NH1" <-> "NH2" Residue "E TYR 2256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 2315": "OE1" <-> "OE2" Residue "E ASP 2319": "OD1" <-> "OD2" Residue "E ASP 2340": "OD1" <-> "OD2" Residue "E ASP 2356": "OD1" <-> "OD2" Residue "E ASP 2357": "OD1" <-> "OD2" Residue "E TYR 2358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 2384": "OD1" <-> "OD2" Residue "E ASP 2411": "OD1" <-> "OD2" Residue "E ASP 2418": "OD1" <-> "OD2" Residue "E ASP 2459": "OD1" <-> "OD2" Residue "E TYR 2466": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.21s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 88700 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 17740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2285, 17740 Classifications: {'peptide': 2285} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 57} Link IDs: {'CIS': 4, 'PCIS': 6, 'PTRANS': 93, 'TRANS': 2181} Chain breaks: 5 Unresolved non-hydrogen bonds: 202 Unresolved non-hydrogen angles: 240 Unresolved non-hydrogen dihedrals: 164 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 12, 'ARG:plan': 1, 'ASN:plan1': 4, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 101 Chain: "B" Number of atoms: 17740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2285, 17740 Classifications: {'peptide': 2285} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 57} Link IDs: {'CIS': 4, 'PCIS': 6, 'PTRANS': 93, 'TRANS': 2181} Chain breaks: 5 Unresolved non-hydrogen bonds: 202 Unresolved non-hydrogen angles: 240 Unresolved non-hydrogen dihedrals: 164 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 12, 'ARG:plan': 1, 'ASN:plan1': 4, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 101 Chain: "C" Number of atoms: 17740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2285, 17740 Classifications: {'peptide': 2285} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 57} Link IDs: {'CIS': 4, 'PCIS': 6, 'PTRANS': 93, 'TRANS': 2181} Chain breaks: 5 Unresolved non-hydrogen bonds: 202 Unresolved non-hydrogen angles: 240 Unresolved non-hydrogen dihedrals: 164 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 12, 'ARG:plan': 1, 'ASN:plan1': 4, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 101 Chain: "D" Number of atoms: 17740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2285, 17740 Classifications: {'peptide': 2285} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 57} Link IDs: {'CIS': 4, 'PCIS': 6, 'PTRANS': 93, 'TRANS': 2181} Chain breaks: 5 Unresolved non-hydrogen bonds: 202 Unresolved non-hydrogen angles: 240 Unresolved non-hydrogen dihedrals: 164 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 12, 'ARG:plan': 1, 'ASN:plan1': 4, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 101 Chain: "E" Number of atoms: 17740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2285, 17740 Classifications: {'peptide': 2285} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 57} Link IDs: {'CIS': 4, 'PCIS': 6, 'PTRANS': 93, 'TRANS': 2181} Chain breaks: 5 Unresolved non-hydrogen bonds: 202 Unresolved non-hydrogen angles: 240 Unresolved non-hydrogen dihedrals: 164 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 12, 'ARG:plan': 1, 'ASN:plan1': 4, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 101 Time building chain proxies: 33.24, per 1000 atoms: 0.37 Number of scatterers: 88700 At special positions: 0 Unit cell: (186.48, 189.81, 255.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 305 16.00 O 17075 8.00 N 15350 7.00 C 55970 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: 27.38 Conformation dependent library (CDL) restraints added in 12.2 seconds 22730 Ramachandran restraints generated. 11365 Oldfield, 0 Emsley, 11365 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 21550 Finding SS restraints... Secondary structure from input PDB file: 425 helices and 95 sheets defined 49.9% alpha, 10.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.29 Creating SS restraints... Processing helix chain 'A' and resid 21 through 26 removed outlier: 3.703A pdb=" N PHE A 26 " --> pdb=" O THR A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 30 through 37 Processing helix chain 'A' and resid 45 through 70 Processing helix chain 'A' and resid 71 through 80 Proline residue: A 74 - end of helix removed outlier: 4.534A pdb=" N LYS A 78 " --> pdb=" O LEU A 75 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N MET A 80 " --> pdb=" O LYS A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 128 Processing helix chain 'A' and resid 138 through 143 Processing helix chain 'A' and resid 152 through 158 Processing helix chain 'A' and resid 162 through 179 removed outlier: 3.695A pdb=" N ALA A 173 " --> pdb=" O GLN A 169 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA A 176 " --> pdb=" O THR A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 191 Processing helix chain 'A' and resid 202 through 215 Processing helix chain 'A' and resid 218 through 222 Processing helix chain 'A' and resid 226 through 228 No H-bonds generated for 'chain 'A' and resid 226 through 228' Processing helix chain 'A' and resid 229 through 239 Processing helix chain 'A' and resid 241 through 249 Processing helix chain 'A' and resid 257 through 268 removed outlier: 3.594A pdb=" N GLU A 261 " --> pdb=" O GLY A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 277 Processing helix chain 'A' and resid 278 through 286 Processing helix chain 'A' and resid 289 through 302 Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.523A pdb=" N LEU A 408 " --> pdb=" O ASP A 404 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LYS A 410 " --> pdb=" O LYS A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 461 removed outlier: 3.582A pdb=" N LEU A 447 " --> pdb=" O PRO A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 470 Processing helix chain 'A' and resid 478 through 495 Processing helix chain 'A' and resid 499 through 507 Processing helix chain 'A' and resid 521 through 528 Processing helix chain 'A' and resid 531 through 535 Processing helix chain 'A' and resid 552 through 562 removed outlier: 3.919A pdb=" N GLU A 556 " --> pdb=" O ASP A 552 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N VAL A 557 " --> pdb=" O PRO A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 577 removed outlier: 3.634A pdb=" N TRP A 570 " --> pdb=" O ASN A 566 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASN A 577 " --> pdb=" O LEU A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 605 removed outlier: 3.892A pdb=" N LEU A 592 " --> pdb=" O LYS A 588 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA A 602 " --> pdb=" O VAL A 598 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N HIS A 605 " --> pdb=" O LEU A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 618 removed outlier: 3.548A pdb=" N GLN A 617 " --> pdb=" O ASP A 613 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ILE A 618 " --> pdb=" O ALA A 614 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 629 Processing helix chain 'A' and resid 630 through 651 Processing helix chain 'A' and resid 654 through 663 Processing helix chain 'A' and resid 671 through 683 Processing helix chain 'A' and resid 693 through 707 Proline residue: A 700 - end of helix Processing helix chain 'A' and resid 710 through 724 removed outlier: 3.509A pdb=" N ARG A 719 " --> pdb=" O GLU A 715 " (cutoff:3.500A) Processing helix chain 'A' and resid 731 through 740 Processing helix chain 'A' and resid 749 through 770 removed outlier: 3.543A pdb=" N PHE A 769 " --> pdb=" O VAL A 765 " (cutoff:3.500A) Processing helix chain 'A' and resid 772 through 780 Processing helix chain 'A' and resid 787 through 805 removed outlier: 4.006A pdb=" N ASN A 793 " --> pdb=" O THR A 789 " (cutoff:3.500A) Processing helix chain 'A' and resid 807 through 817 Processing helix chain 'A' and resid 821 through 830 Processing helix chain 'A' and resid 832 through 842 removed outlier: 4.674A pdb=" N GLN A 838 " --> pdb=" O GLU A 834 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR A 841 " --> pdb=" O THR A 837 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU A 842 " --> pdb=" O GLN A 838 " (cutoff:3.500A) Processing helix chain 'A' and resid 851 through 855 Processing helix chain 'A' and resid 857 through 868 removed outlier: 3.849A pdb=" N ARG A 861 " --> pdb=" O VAL A 857 " (cutoff:3.500A) Processing helix chain 'A' and resid 871 through 884 removed outlier: 3.577A pdb=" N THR A 876 " --> pdb=" O PRO A 872 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N THR A 877 " --> pdb=" O LYS A 873 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU A 878 " --> pdb=" O ASP A 874 " (cutoff:3.500A) Processing helix chain 'A' and resid 888 through 902 removed outlier: 3.868A pdb=" N GLY A 902 " --> pdb=" O LEU A 898 " (cutoff:3.500A) Processing helix chain 'A' and resid 904 through 931 Proline residue: A 917 - end of helix Processing helix chain 'A' and resid 938 through 947 removed outlier: 3.935A pdb=" N ILE A 942 " --> pdb=" O ASP A 938 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TRP A 943 " --> pdb=" O ARG A 939 " (cutoff:3.500A) Processing helix chain 'A' and resid 959 through 977 removed outlier: 3.511A pdb=" N ASP A 963 " --> pdb=" O THR A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 984 through 989 Processing helix chain 'A' and resid 990 through 995 Processing helix chain 'A' and resid 1002 through 1015 removed outlier: 3.761A pdb=" N LEU A1012 " --> pdb=" O GLY A1008 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N VAL A1013 " --> pdb=" O VAL A1009 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N TYR A1014 " --> pdb=" O SER A1010 " (cutoff:3.500A) Processing helix chain 'A' and resid 1016 through 1019 Processing helix chain 'A' and resid 1029 through 1039 Processing helix chain 'A' and resid 1045 through 1065 removed outlier: 3.739A pdb=" N PHE A1053 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing helix chain 'A' and resid 1113 through 1116 removed outlier: 3.932A pdb=" N TRP A1116 " --> pdb=" O ALA A1113 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1113 through 1116' Processing helix chain 'A' and resid 1242 through 1247 removed outlier: 3.946A pdb=" N THR A1246 " --> pdb=" O GLY A1242 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL A1247 " --> pdb=" O ILE A1243 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1242 through 1247' Processing helix chain 'A' and resid 1248 through 1251 removed outlier: 3.559A pdb=" N LEU A1251 " --> pdb=" O THR A1248 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1248 through 1251' Processing helix chain 'A' and resid 1474 through 1476 No H-bonds generated for 'chain 'A' and resid 1474 through 1476' Processing helix chain 'A' and resid 1571 through 1579 removed outlier: 3.650A pdb=" N ILE A1576 " --> pdb=" O THR A1572 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N GLU A1577 " --> pdb=" O ARG A1573 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ARG A1578 " --> pdb=" O GLN A1574 " (cutoff:3.500A) Processing helix chain 'A' and resid 1582 through 1587 Processing helix chain 'A' and resid 1588 through 1593 removed outlier: 3.715A pdb=" N GLN A1592 " --> pdb=" O SER A1588 " (cutoff:3.500A) Processing helix chain 'A' and resid 1738 through 1747 Processing helix chain 'A' and resid 1747 through 1759 Processing helix chain 'A' and resid 1762 through 1771 removed outlier: 3.724A pdb=" N ARG A1768 " --> pdb=" O THR A1764 " (cutoff:3.500A) Processing helix chain 'A' and resid 1786 through 1791 Processing helix chain 'A' and resid 1798 through 1802 removed outlier: 4.117A pdb=" N ASP A1801 " --> pdb=" O ASP A1798 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N SER A1802 " --> pdb=" O PRO A1799 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1798 through 1802' Processing helix chain 'A' and resid 1804 through 1812 removed outlier: 3.912A pdb=" N VAL A1808 " --> pdb=" O ASP A1804 " (cutoff:3.500A) Processing helix chain 'A' and resid 1813 through 1838 Processing helix chain 'A' and resid 1840 through 1859 Processing helix chain 'A' and resid 1874 through 1879 Processing helix chain 'A' and resid 1880 through 1896 removed outlier: 3.597A pdb=" N PHE A1887 " --> pdb=" O GLN A1883 " (cutoff:3.500A) Processing helix chain 'A' and resid 1918 through 1937 Processing helix chain 'A' and resid 1983 through 2070 removed outlier: 3.807A pdb=" N ASP A1989 " --> pdb=" O PRO A1985 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N SER A2031 " --> pdb=" O GLU A2027 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLN A2038 " --> pdb=" O ARG A2034 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N LEU A2043 " --> pdb=" O ALA A2039 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASP A2044 " --> pdb=" O LEU A2040 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LYS A2048 " --> pdb=" O ASP A2044 " (cutoff:3.500A) Processing helix chain 'A' and resid 2073 through 2092 Processing helix chain 'A' and resid 2093 through 2105 Processing helix chain 'A' and resid 2120 through 2209 Processing helix chain 'A' and resid 2212 through 2249 removed outlier: 3.596A pdb=" N ASP A2232 " --> pdb=" O TYR A2228 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N LEU A2233 " --> pdb=" O ARG A2229 " (cutoff:3.500A) Processing helix chain 'A' and resid 2263 through 2267 Processing helix chain 'A' and resid 2270 through 2290 removed outlier: 3.809A pdb=" N SER A2274 " --> pdb=" O MET A2270 " (cutoff:3.500A) Processing helix chain 'A' and resid 2302 through 2308 Processing helix chain 'A' and resid 2312 through 2319 removed outlier: 4.201A pdb=" N ALA A2318 " --> pdb=" O ALA A2314 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ASP A2319 " --> pdb=" O GLU A2315 " (cutoff:3.500A) Processing helix chain 'A' and resid 2348 through 2353 removed outlier: 3.512A pdb=" N ASN A2353 " --> pdb=" O LYS A2350 " (cutoff:3.500A) Processing helix chain 'A' and resid 2354 through 2358 removed outlier: 3.593A pdb=" N TYR A2358 " --> pdb=" O LYS A2355 " (cutoff:3.500A) Processing helix chain 'A' and resid 2449 through 2457 removed outlier: 4.015A pdb=" N LEU A2453 " --> pdb=" O LYS A2449 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 26 removed outlier: 3.703A pdb=" N PHE B 26 " --> pdb=" O THR B 22 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 22 through 26' Processing helix chain 'B' and resid 30 through 37 Processing helix chain 'B' and resid 45 through 70 Processing helix chain 'B' and resid 71 through 80 Proline residue: B 74 - end of helix removed outlier: 4.534A pdb=" N LYS B 78 " --> pdb=" O LEU B 75 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET B 80 " --> pdb=" O LYS B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 128 Processing helix chain 'B' and resid 138 through 143 Processing helix chain 'B' and resid 152 through 158 Processing helix chain 'B' and resid 162 through 179 removed outlier: 3.695A pdb=" N ALA B 173 " --> pdb=" O GLN B 169 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA B 176 " --> pdb=" O THR B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 191 Processing helix chain 'B' and resid 202 through 215 Processing helix chain 'B' and resid 218 through 222 Processing helix chain 'B' and resid 226 through 228 No H-bonds generated for 'chain 'B' and resid 226 through 228' Processing helix chain 'B' and resid 229 through 239 Processing helix chain 'B' and resid 241 through 249 Processing helix chain 'B' and resid 257 through 268 removed outlier: 3.594A pdb=" N GLU B 261 " --> pdb=" O GLY B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 277 Processing helix chain 'B' and resid 278 through 286 Processing helix chain 'B' and resid 289 through 302 Processing helix chain 'B' and resid 404 through 410 removed outlier: 3.522A pdb=" N LEU B 408 " --> pdb=" O ASP B 404 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LYS B 410 " --> pdb=" O LYS B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 461 removed outlier: 3.582A pdb=" N LEU B 447 " --> pdb=" O PRO B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 470 Processing helix chain 'B' and resid 478 through 495 Processing helix chain 'B' and resid 499 through 507 Processing helix chain 'B' and resid 521 through 528 Processing helix chain 'B' and resid 531 through 535 Processing helix chain 'B' and resid 552 through 562 removed outlier: 3.919A pdb=" N GLU B 556 " --> pdb=" O ASP B 552 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N VAL B 557 " --> pdb=" O PRO B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 565 through 577 removed outlier: 3.633A pdb=" N TRP B 570 " --> pdb=" O ASN B 566 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASN B 577 " --> pdb=" O LEU B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 588 through 605 removed outlier: 3.892A pdb=" N LEU B 592 " --> pdb=" O LYS B 588 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA B 602 " --> pdb=" O VAL B 598 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N HIS B 605 " --> pdb=" O LEU B 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 618 removed outlier: 3.548A pdb=" N GLN B 617 " --> pdb=" O ASP B 613 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ILE B 618 " --> pdb=" O ALA B 614 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 629 Processing helix chain 'B' and resid 630 through 651 Processing helix chain 'B' and resid 654 through 663 Processing helix chain 'B' and resid 671 through 683 Processing helix chain 'B' and resid 693 through 707 Proline residue: B 700 - end of helix Processing helix chain 'B' and resid 710 through 724 removed outlier: 3.509A pdb=" N ARG B 719 " --> pdb=" O GLU B 715 " (cutoff:3.500A) Processing helix chain 'B' and resid 731 through 740 Processing helix chain 'B' and resid 749 through 770 removed outlier: 3.543A pdb=" N PHE B 769 " --> pdb=" O VAL B 765 " (cutoff:3.500A) Processing helix chain 'B' and resid 772 through 780 Processing helix chain 'B' and resid 787 through 805 removed outlier: 4.005A pdb=" N ASN B 793 " --> pdb=" O THR B 789 " (cutoff:3.500A) Processing helix chain 'B' and resid 807 through 817 Processing helix chain 'B' and resid 821 through 830 Processing helix chain 'B' and resid 832 through 842 removed outlier: 4.675A pdb=" N GLN B 838 " --> pdb=" O GLU B 834 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR B 841 " --> pdb=" O THR B 837 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU B 842 " --> pdb=" O GLN B 838 " (cutoff:3.500A) Processing helix chain 'B' and resid 851 through 855 Processing helix chain 'B' and resid 857 through 868 removed outlier: 3.848A pdb=" N ARG B 861 " --> pdb=" O VAL B 857 " (cutoff:3.500A) Processing helix chain 'B' and resid 871 through 884 removed outlier: 3.579A pdb=" N THR B 876 " --> pdb=" O PRO B 872 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N THR B 877 " --> pdb=" O LYS B 873 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU B 878 " --> pdb=" O ASP B 874 " (cutoff:3.500A) Processing helix chain 'B' and resid 888 through 902 removed outlier: 3.868A pdb=" N GLY B 902 " --> pdb=" O LEU B 898 " (cutoff:3.500A) Processing helix chain 'B' and resid 904 through 931 Proline residue: B 917 - end of helix Processing helix chain 'B' and resid 938 through 947 removed outlier: 3.935A pdb=" N ILE B 942 " --> pdb=" O ASP B 938 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TRP B 943 " --> pdb=" O ARG B 939 " (cutoff:3.500A) Processing helix chain 'B' and resid 959 through 977 removed outlier: 3.512A pdb=" N ASP B 963 " --> pdb=" O THR B 959 " (cutoff:3.500A) Processing helix chain 'B' and resid 984 through 989 Processing helix chain 'B' and resid 990 through 995 Processing helix chain 'B' and resid 1002 through 1015 removed outlier: 3.761A pdb=" N LEU B1012 " --> pdb=" O GLY B1008 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N VAL B1013 " --> pdb=" O VAL B1009 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N TYR B1014 " --> pdb=" O SER B1010 " (cutoff:3.500A) Processing helix chain 'B' and resid 1016 through 1019 Processing helix chain 'B' and resid 1029 through 1039 Processing helix chain 'B' and resid 1045 through 1065 removed outlier: 3.739A pdb=" N PHE B1053 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing helix chain 'B' and resid 1113 through 1116 removed outlier: 3.932A pdb=" N TRP B1116 " --> pdb=" O ALA B1113 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1113 through 1116' Processing helix chain 'B' and resid 1242 through 1247 removed outlier: 3.947A pdb=" N THR B1246 " --> pdb=" O GLY B1242 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL B1247 " --> pdb=" O ILE B1243 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1242 through 1247' Processing helix chain 'B' and resid 1248 through 1251 removed outlier: 3.558A pdb=" N LEU B1251 " --> pdb=" O THR B1248 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1248 through 1251' Processing helix chain 'B' and resid 1474 through 1476 No H-bonds generated for 'chain 'B' and resid 1474 through 1476' Processing helix chain 'B' and resid 1571 through 1579 removed outlier: 3.649A pdb=" N ILE B1576 " --> pdb=" O THR B1572 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N GLU B1577 " --> pdb=" O ARG B1573 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ARG B1578 " --> pdb=" O GLN B1574 " (cutoff:3.500A) Processing helix chain 'B' and resid 1582 through 1587 Processing helix chain 'B' and resid 1588 through 1593 removed outlier: 3.715A pdb=" N GLN B1592 " --> pdb=" O SER B1588 " (cutoff:3.500A) Processing helix chain 'B' and resid 1738 through 1747 Processing helix chain 'B' and resid 1747 through 1759 Processing helix chain 'B' and resid 1762 through 1771 removed outlier: 3.723A pdb=" N ARG B1768 " --> pdb=" O THR B1764 " (cutoff:3.500A) Processing helix chain 'B' and resid 1786 through 1791 Processing helix chain 'B' and resid 1798 through 1802 removed outlier: 4.116A pdb=" N ASP B1801 " --> pdb=" O ASP B1798 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N SER B1802 " --> pdb=" O PRO B1799 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1798 through 1802' Processing helix chain 'B' and resid 1804 through 1812 removed outlier: 3.912A pdb=" N VAL B1808 " --> pdb=" O ASP B1804 " (cutoff:3.500A) Processing helix chain 'B' and resid 1813 through 1838 Processing helix chain 'B' and resid 1840 through 1859 Processing helix chain 'B' and resid 1874 through 1879 Processing helix chain 'B' and resid 1880 through 1896 removed outlier: 3.597A pdb=" N PHE B1887 " --> pdb=" O GLN B1883 " (cutoff:3.500A) Processing helix chain 'B' and resid 1918 through 1937 Processing helix chain 'B' and resid 1983 through 2070 removed outlier: 3.807A pdb=" N ASP B1989 " --> pdb=" O PRO B1985 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N SER B2031 " --> pdb=" O GLU B2027 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLN B2038 " --> pdb=" O ARG B2034 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N LEU B2043 " --> pdb=" O ALA B2039 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASP B2044 " --> pdb=" O LEU B2040 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LYS B2048 " --> pdb=" O ASP B2044 " (cutoff:3.500A) Processing helix chain 'B' and resid 2073 through 2092 Processing helix chain 'B' and resid 2093 through 2105 Processing helix chain 'B' and resid 2120 through 2209 Processing helix chain 'B' and resid 2212 through 2249 removed outlier: 3.596A pdb=" N ASP B2232 " --> pdb=" O TYR B2228 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N LEU B2233 " --> pdb=" O ARG B2229 " (cutoff:3.500A) Processing helix chain 'B' and resid 2263 through 2267 Processing helix chain 'B' and resid 2270 through 2290 removed outlier: 3.809A pdb=" N SER B2274 " --> pdb=" O MET B2270 " (cutoff:3.500A) Processing helix chain 'B' and resid 2302 through 2308 Processing helix chain 'B' and resid 2312 through 2319 removed outlier: 4.202A pdb=" N ALA B2318 " --> pdb=" O ALA B2314 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ASP B2319 " --> pdb=" O GLU B2315 " (cutoff:3.500A) Processing helix chain 'B' and resid 2348 through 2353 removed outlier: 3.512A pdb=" N ASN B2353 " --> pdb=" O LYS B2350 " (cutoff:3.500A) Processing helix chain 'B' and resid 2354 through 2358 removed outlier: 3.593A pdb=" N TYR B2358 " --> pdb=" O LYS B2355 " (cutoff:3.500A) Processing helix chain 'B' and resid 2449 through 2457 removed outlier: 4.014A pdb=" N LEU B2453 " --> pdb=" O LYS B2449 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 26 removed outlier: 3.703A pdb=" N PHE C 26 " --> pdb=" O THR C 22 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 22 through 26' Processing helix chain 'C' and resid 30 through 37 Processing helix chain 'C' and resid 45 through 70 Processing helix chain 'C' and resid 71 through 80 Proline residue: C 74 - end of helix removed outlier: 4.535A pdb=" N LYS C 78 " --> pdb=" O LEU C 75 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N MET C 80 " --> pdb=" O LYS C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 128 Processing helix chain 'C' and resid 138 through 143 Processing helix chain 'C' and resid 152 through 158 Processing helix chain 'C' and resid 162 through 179 removed outlier: 3.694A pdb=" N ALA C 173 " --> pdb=" O GLN C 169 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA C 176 " --> pdb=" O THR C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 191 Processing helix chain 'C' and resid 202 through 215 Processing helix chain 'C' and resid 218 through 222 Processing helix chain 'C' and resid 226 through 228 No H-bonds generated for 'chain 'C' and resid 226 through 228' Processing helix chain 'C' and resid 229 through 239 Processing helix chain 'C' and resid 241 through 249 Processing helix chain 'C' and resid 257 through 268 removed outlier: 3.593A pdb=" N GLU C 261 " --> pdb=" O GLY C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 277 Processing helix chain 'C' and resid 278 through 286 Processing helix chain 'C' and resid 289 through 302 Processing helix chain 'C' and resid 404 through 410 removed outlier: 3.523A pdb=" N LEU C 408 " --> pdb=" O ASP C 404 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LYS C 410 " --> pdb=" O LYS C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 443 through 461 removed outlier: 3.582A pdb=" N LEU C 447 " --> pdb=" O PRO C 443 " (cutoff:3.500A) Processing helix chain 'C' and resid 463 through 470 Processing helix chain 'C' and resid 478 through 495 Processing helix chain 'C' and resid 499 through 507 Processing helix chain 'C' and resid 521 through 528 Processing helix chain 'C' and resid 531 through 535 Processing helix chain 'C' and resid 552 through 562 removed outlier: 3.919A pdb=" N GLU C 556 " --> pdb=" O ASP C 552 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N VAL C 557 " --> pdb=" O PRO C 553 " (cutoff:3.500A) Processing helix chain 'C' and resid 565 through 577 removed outlier: 3.634A pdb=" N TRP C 570 " --> pdb=" O ASN C 566 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASN C 577 " --> pdb=" O LEU C 573 " (cutoff:3.500A) Processing helix chain 'C' and resid 588 through 605 removed outlier: 3.892A pdb=" N LEU C 592 " --> pdb=" O LYS C 588 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA C 602 " --> pdb=" O VAL C 598 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N HIS C 605 " --> pdb=" O LEU C 601 " (cutoff:3.500A) Processing helix chain 'C' and resid 608 through 618 removed outlier: 3.548A pdb=" N GLN C 617 " --> pdb=" O ASP C 613 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ILE C 618 " --> pdb=" O ALA C 614 " (cutoff:3.500A) Processing helix chain 'C' and resid 625 through 629 Processing helix chain 'C' and resid 630 through 651 Processing helix chain 'C' and resid 654 through 663 Processing helix chain 'C' and resid 671 through 683 Processing helix chain 'C' and resid 693 through 707 Proline residue: C 700 - end of helix Processing helix chain 'C' and resid 710 through 724 removed outlier: 3.509A pdb=" N ARG C 719 " --> pdb=" O GLU C 715 " (cutoff:3.500A) Processing helix chain 'C' and resid 731 through 740 Processing helix chain 'C' and resid 749 through 770 removed outlier: 3.543A pdb=" N PHE C 769 " --> pdb=" O VAL C 765 " (cutoff:3.500A) Processing helix chain 'C' and resid 772 through 780 Processing helix chain 'C' and resid 787 through 805 removed outlier: 4.005A pdb=" N ASN C 793 " --> pdb=" O THR C 789 " (cutoff:3.500A) Processing helix chain 'C' and resid 807 through 817 Processing helix chain 'C' and resid 821 through 830 Processing helix chain 'C' and resid 832 through 842 removed outlier: 4.675A pdb=" N GLN C 838 " --> pdb=" O GLU C 834 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR C 841 " --> pdb=" O THR C 837 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU C 842 " --> pdb=" O GLN C 838 " (cutoff:3.500A) Processing helix chain 'C' and resid 851 through 855 Processing helix chain 'C' and resid 857 through 868 removed outlier: 3.848A pdb=" N ARG C 861 " --> pdb=" O VAL C 857 " (cutoff:3.500A) Processing helix chain 'C' and resid 871 through 884 removed outlier: 3.578A pdb=" N THR C 876 " --> pdb=" O PRO C 872 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N THR C 877 " --> pdb=" O LYS C 873 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU C 878 " --> pdb=" O ASP C 874 " (cutoff:3.500A) Processing helix chain 'C' and resid 888 through 902 removed outlier: 3.867A pdb=" N GLY C 902 " --> pdb=" O LEU C 898 " (cutoff:3.500A) Processing helix chain 'C' and resid 904 through 931 Proline residue: C 917 - end of helix Processing helix chain 'C' and resid 938 through 947 removed outlier: 3.934A pdb=" N ILE C 942 " --> pdb=" O ASP C 938 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TRP C 943 " --> pdb=" O ARG C 939 " (cutoff:3.500A) Processing helix chain 'C' and resid 959 through 977 removed outlier: 3.511A pdb=" N ASP C 963 " --> pdb=" O THR C 959 " (cutoff:3.500A) Processing helix chain 'C' and resid 984 through 989 Processing helix chain 'C' and resid 990 through 995 Processing helix chain 'C' and resid 1002 through 1015 removed outlier: 3.761A pdb=" N LEU C1012 " --> pdb=" O GLY C1008 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N VAL C1013 " --> pdb=" O VAL C1009 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N TYR C1014 " --> pdb=" O SER C1010 " (cutoff:3.500A) Processing helix chain 'C' and resid 1016 through 1019 Processing helix chain 'C' and resid 1029 through 1039 Processing helix chain 'C' and resid 1045 through 1065 removed outlier: 3.739A pdb=" N PHE C1053 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing helix chain 'C' and resid 1113 through 1116 removed outlier: 3.933A pdb=" N TRP C1116 " --> pdb=" O ALA C1113 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1113 through 1116' Processing helix chain 'C' and resid 1242 through 1247 removed outlier: 3.948A pdb=" N THR C1246 " --> pdb=" O GLY C1242 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL C1247 " --> pdb=" O ILE C1243 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1242 through 1247' Processing helix chain 'C' and resid 1248 through 1251 removed outlier: 3.558A pdb=" N LEU C1251 " --> pdb=" O THR C1248 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1248 through 1251' Processing helix chain 'C' and resid 1474 through 1476 No H-bonds generated for 'chain 'C' and resid 1474 through 1476' Processing helix chain 'C' and resid 1571 through 1579 removed outlier: 3.649A pdb=" N ILE C1576 " --> pdb=" O THR C1572 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N GLU C1577 " --> pdb=" O ARG C1573 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ARG C1578 " --> pdb=" O GLN C1574 " (cutoff:3.500A) Processing helix chain 'C' and resid 1582 through 1587 Processing helix chain 'C' and resid 1588 through 1593 removed outlier: 3.714A pdb=" N GLN C1592 " --> pdb=" O SER C1588 " (cutoff:3.500A) Processing helix chain 'C' and resid 1738 through 1747 Processing helix chain 'C' and resid 1747 through 1759 Processing helix chain 'C' and resid 1762 through 1771 removed outlier: 3.724A pdb=" N ARG C1768 " --> pdb=" O THR C1764 " (cutoff:3.500A) Processing helix chain 'C' and resid 1786 through 1791 Processing helix chain 'C' and resid 1798 through 1802 removed outlier: 4.115A pdb=" N ASP C1801 " --> pdb=" O ASP C1798 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N SER C1802 " --> pdb=" O PRO C1799 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1798 through 1802' Processing helix chain 'C' and resid 1804 through 1812 removed outlier: 3.912A pdb=" N VAL C1808 " --> pdb=" O ASP C1804 " (cutoff:3.500A) Processing helix chain 'C' and resid 1813 through 1838 Processing helix chain 'C' and resid 1840 through 1859 Processing helix chain 'C' and resid 1874 through 1879 Processing helix chain 'C' and resid 1880 through 1896 removed outlier: 3.596A pdb=" N PHE C1887 " --> pdb=" O GLN C1883 " (cutoff:3.500A) Processing helix chain 'C' and resid 1918 through 1937 Processing helix chain 'C' and resid 1983 through 2070 removed outlier: 3.806A pdb=" N ASP C1989 " --> pdb=" O PRO C1985 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N SER C2031 " --> pdb=" O GLU C2027 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLN C2038 " --> pdb=" O ARG C2034 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N LEU C2043 " --> pdb=" O ALA C2039 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASP C2044 " --> pdb=" O LEU C2040 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LYS C2048 " --> pdb=" O ASP C2044 " (cutoff:3.500A) Processing helix chain 'C' and resid 2073 through 2092 Processing helix chain 'C' and resid 2093 through 2105 Processing helix chain 'C' and resid 2120 through 2209 Processing helix chain 'C' and resid 2212 through 2249 removed outlier: 3.595A pdb=" N ASP C2232 " --> pdb=" O TYR C2228 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N LEU C2233 " --> pdb=" O ARG C2229 " (cutoff:3.500A) Processing helix chain 'C' and resid 2263 through 2267 Processing helix chain 'C' and resid 2270 through 2290 removed outlier: 3.810A pdb=" N SER C2274 " --> pdb=" O MET C2270 " (cutoff:3.500A) Processing helix chain 'C' and resid 2302 through 2308 Processing helix chain 'C' and resid 2312 through 2319 removed outlier: 4.202A pdb=" N ALA C2318 " --> pdb=" O ALA C2314 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ASP C2319 " --> pdb=" O GLU C2315 " (cutoff:3.500A) Processing helix chain 'C' and resid 2348 through 2353 removed outlier: 3.512A pdb=" N ASN C2353 " --> pdb=" O LYS C2350 " (cutoff:3.500A) Processing helix chain 'C' and resid 2354 through 2358 removed outlier: 3.593A pdb=" N TYR C2358 " --> pdb=" O LYS C2355 " (cutoff:3.500A) Processing helix chain 'C' and resid 2449 through 2457 removed outlier: 4.014A pdb=" N LEU C2453 " --> pdb=" O LYS C2449 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 26 removed outlier: 3.702A pdb=" N PHE D 26 " --> pdb=" O THR D 22 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 22 through 26' Processing helix chain 'D' and resid 30 through 37 Processing helix chain 'D' and resid 45 through 70 Processing helix chain 'D' and resid 71 through 80 Proline residue: D 74 - end of helix removed outlier: 4.534A pdb=" N LYS D 78 " --> pdb=" O LEU D 75 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N MET D 80 " --> pdb=" O LYS D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 128 Processing helix chain 'D' and resid 138 through 143 Processing helix chain 'D' and resid 152 through 158 Processing helix chain 'D' and resid 162 through 179 removed outlier: 3.695A pdb=" N ALA D 173 " --> pdb=" O GLN D 169 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA D 176 " --> pdb=" O THR D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 191 Processing helix chain 'D' and resid 202 through 215 Processing helix chain 'D' and resid 218 through 222 Processing helix chain 'D' and resid 226 through 228 No H-bonds generated for 'chain 'D' and resid 226 through 228' Processing helix chain 'D' and resid 229 through 239 Processing helix chain 'D' and resid 241 through 249 Processing helix chain 'D' and resid 257 through 268 removed outlier: 3.594A pdb=" N GLU D 261 " --> pdb=" O GLY D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 272 through 277 Processing helix chain 'D' and resid 278 through 286 Processing helix chain 'D' and resid 289 through 302 Processing helix chain 'D' and resid 404 through 410 removed outlier: 3.522A pdb=" N LEU D 408 " --> pdb=" O ASP D 404 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LYS D 410 " --> pdb=" O LYS D 406 " (cutoff:3.500A) Processing helix chain 'D' and resid 443 through 461 removed outlier: 3.581A pdb=" N LEU D 447 " --> pdb=" O PRO D 443 " (cutoff:3.500A) Processing helix chain 'D' and resid 463 through 470 Processing helix chain 'D' and resid 478 through 495 Processing helix chain 'D' and resid 499 through 507 Processing helix chain 'D' and resid 521 through 528 Processing helix chain 'D' and resid 531 through 535 Processing helix chain 'D' and resid 552 through 562 removed outlier: 3.919A pdb=" N GLU D 556 " --> pdb=" O ASP D 552 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N VAL D 557 " --> pdb=" O PRO D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 577 removed outlier: 3.633A pdb=" N TRP D 570 " --> pdb=" O ASN D 566 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASN D 577 " --> pdb=" O LEU D 573 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 605 removed outlier: 3.892A pdb=" N LEU D 592 " --> pdb=" O LYS D 588 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA D 602 " --> pdb=" O VAL D 598 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N HIS D 605 " --> pdb=" O LEU D 601 " (cutoff:3.500A) Processing helix chain 'D' and resid 608 through 618 removed outlier: 3.549A pdb=" N GLN D 617 " --> pdb=" O ASP D 613 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ILE D 618 " --> pdb=" O ALA D 614 " (cutoff:3.500A) Processing helix chain 'D' and resid 625 through 629 Processing helix chain 'D' and resid 630 through 651 Processing helix chain 'D' and resid 654 through 663 Processing helix chain 'D' and resid 671 through 683 Processing helix chain 'D' and resid 693 through 707 Proline residue: D 700 - end of helix Processing helix chain 'D' and resid 710 through 724 removed outlier: 3.510A pdb=" N ARG D 719 " --> pdb=" O GLU D 715 " (cutoff:3.500A) Processing helix chain 'D' and resid 731 through 740 Processing helix chain 'D' and resid 749 through 770 removed outlier: 3.543A pdb=" N PHE D 769 " --> pdb=" O VAL D 765 " (cutoff:3.500A) Processing helix chain 'D' and resid 772 through 780 Processing helix chain 'D' and resid 787 through 805 removed outlier: 4.005A pdb=" N ASN D 793 " --> pdb=" O THR D 789 " (cutoff:3.500A) Processing helix chain 'D' and resid 807 through 817 Processing helix chain 'D' and resid 821 through 830 Processing helix chain 'D' and resid 832 through 842 removed outlier: 4.674A pdb=" N GLN D 838 " --> pdb=" O GLU D 834 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N THR D 841 " --> pdb=" O THR D 837 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU D 842 " --> pdb=" O GLN D 838 " (cutoff:3.500A) Processing helix chain 'D' and resid 851 through 855 Processing helix chain 'D' and resid 857 through 868 removed outlier: 3.848A pdb=" N ARG D 861 " --> pdb=" O VAL D 857 " (cutoff:3.500A) Processing helix chain 'D' and resid 871 through 884 removed outlier: 3.578A pdb=" N THR D 876 " --> pdb=" O PRO D 872 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N THR D 877 " --> pdb=" O LYS D 873 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU D 878 " --> pdb=" O ASP D 874 " (cutoff:3.500A) Processing helix chain 'D' and resid 888 through 902 removed outlier: 3.867A pdb=" N GLY D 902 " --> pdb=" O LEU D 898 " (cutoff:3.500A) Processing helix chain 'D' and resid 904 through 931 Proline residue: D 917 - end of helix Processing helix chain 'D' and resid 938 through 947 removed outlier: 3.934A pdb=" N ILE D 942 " --> pdb=" O ASP D 938 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TRP D 943 " --> pdb=" O ARG D 939 " (cutoff:3.500A) Processing helix chain 'D' and resid 959 through 977 removed outlier: 3.512A pdb=" N ASP D 963 " --> pdb=" O THR D 959 " (cutoff:3.500A) Processing helix chain 'D' and resid 984 through 989 Processing helix chain 'D' and resid 990 through 995 Processing helix chain 'D' and resid 1002 through 1015 removed outlier: 3.761A pdb=" N LEU D1012 " --> pdb=" O GLY D1008 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N VAL D1013 " --> pdb=" O VAL D1009 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N TYR D1014 " --> pdb=" O SER D1010 " (cutoff:3.500A) Processing helix chain 'D' and resid 1016 through 1019 Processing helix chain 'D' and resid 1029 through 1039 Processing helix chain 'D' and resid 1045 through 1065 removed outlier: 3.739A pdb=" N PHE D1053 " --> pdb=" O LEU D1049 " (cutoff:3.500A) Processing helix chain 'D' and resid 1113 through 1116 removed outlier: 3.932A pdb=" N TRP D1116 " --> pdb=" O ALA D1113 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1113 through 1116' Processing helix chain 'D' and resid 1242 through 1247 removed outlier: 3.947A pdb=" N THR D1246 " --> pdb=" O GLY D1242 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL D1247 " --> pdb=" O ILE D1243 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1242 through 1247' Processing helix chain 'D' and resid 1248 through 1251 removed outlier: 3.557A pdb=" N LEU D1251 " --> pdb=" O THR D1248 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1248 through 1251' Processing helix chain 'D' and resid 1474 through 1476 No H-bonds generated for 'chain 'D' and resid 1474 through 1476' Processing helix chain 'D' and resid 1571 through 1579 removed outlier: 3.649A pdb=" N ILE D1576 " --> pdb=" O THR D1572 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N GLU D1577 " --> pdb=" O ARG D1573 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ARG D1578 " --> pdb=" O GLN D1574 " (cutoff:3.500A) Processing helix chain 'D' and resid 1582 through 1587 Processing helix chain 'D' and resid 1588 through 1593 removed outlier: 3.715A pdb=" N GLN D1592 " --> pdb=" O SER D1588 " (cutoff:3.500A) Processing helix chain 'D' and resid 1738 through 1747 Processing helix chain 'D' and resid 1747 through 1759 Processing helix chain 'D' and resid 1762 through 1771 removed outlier: 3.724A pdb=" N ARG D1768 " --> pdb=" O THR D1764 " (cutoff:3.500A) Processing helix chain 'D' and resid 1786 through 1791 Processing helix chain 'D' and resid 1798 through 1802 removed outlier: 4.117A pdb=" N ASP D1801 " --> pdb=" O ASP D1798 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N SER D1802 " --> pdb=" O PRO D1799 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1798 through 1802' Processing helix chain 'D' and resid 1804 through 1812 removed outlier: 3.912A pdb=" N VAL D1808 " --> pdb=" O ASP D1804 " (cutoff:3.500A) Processing helix chain 'D' and resid 1813 through 1838 Processing helix chain 'D' and resid 1840 through 1859 Processing helix chain 'D' and resid 1874 through 1879 Processing helix chain 'D' and resid 1880 through 1896 removed outlier: 3.597A pdb=" N PHE D1887 " --> pdb=" O GLN D1883 " (cutoff:3.500A) Processing helix chain 'D' and resid 1918 through 1937 Processing helix chain 'D' and resid 1983 through 2070 removed outlier: 3.807A pdb=" N ASP D1989 " --> pdb=" O PRO D1985 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N SER D2031 " --> pdb=" O GLU D2027 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLN D2038 " --> pdb=" O ARG D2034 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N LEU D2043 " --> pdb=" O ALA D2039 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASP D2044 " --> pdb=" O LEU D2040 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LYS D2048 " --> pdb=" O ASP D2044 " (cutoff:3.500A) Processing helix chain 'D' and resid 2073 through 2092 Processing helix chain 'D' and resid 2093 through 2105 Processing helix chain 'D' and resid 2120 through 2209 Processing helix chain 'D' and resid 2212 through 2249 removed outlier: 3.595A pdb=" N ASP D2232 " --> pdb=" O TYR D2228 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N LEU D2233 " --> pdb=" O ARG D2229 " (cutoff:3.500A) Processing helix chain 'D' and resid 2263 through 2267 Processing helix chain 'D' and resid 2270 through 2290 removed outlier: 3.809A pdb=" N SER D2274 " --> pdb=" O MET D2270 " (cutoff:3.500A) Processing helix chain 'D' and resid 2302 through 2308 Processing helix chain 'D' and resid 2312 through 2319 removed outlier: 4.203A pdb=" N ALA D2318 " --> pdb=" O ALA D2314 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ASP D2319 " --> pdb=" O GLU D2315 " (cutoff:3.500A) Processing helix chain 'D' and resid 2348 through 2353 removed outlier: 3.512A pdb=" N ASN D2353 " --> pdb=" O LYS D2350 " (cutoff:3.500A) Processing helix chain 'D' and resid 2354 through 2358 removed outlier: 3.593A pdb=" N TYR D2358 " --> pdb=" O LYS D2355 " (cutoff:3.500A) Processing helix chain 'D' and resid 2449 through 2457 removed outlier: 4.014A pdb=" N LEU D2453 " --> pdb=" O LYS D2449 " (cutoff:3.500A) Processing helix chain 'E' and resid 22 through 26 removed outlier: 3.703A pdb=" N PHE E 26 " --> pdb=" O THR E 22 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 22 through 26' Processing helix chain 'E' and resid 30 through 37 Processing helix chain 'E' and resid 45 through 70 Processing helix chain 'E' and resid 71 through 80 Proline residue: E 74 - end of helix removed outlier: 4.534A pdb=" N LYS E 78 " --> pdb=" O LEU E 75 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N MET E 80 " --> pdb=" O LYS E 77 " (cutoff:3.500A) Processing helix chain 'E' and resid 115 through 128 Processing helix chain 'E' and resid 138 through 143 Processing helix chain 'E' and resid 152 through 158 Processing helix chain 'E' and resid 162 through 179 removed outlier: 3.695A pdb=" N ALA E 173 " --> pdb=" O GLN E 169 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA E 176 " --> pdb=" O THR E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 191 Processing helix chain 'E' and resid 202 through 215 Processing helix chain 'E' and resid 218 through 222 Processing helix chain 'E' and resid 226 through 228 No H-bonds generated for 'chain 'E' and resid 226 through 228' Processing helix chain 'E' and resid 229 through 239 Processing helix chain 'E' and resid 241 through 249 Processing helix chain 'E' and resid 257 through 268 removed outlier: 3.593A pdb=" N GLU E 261 " --> pdb=" O GLY E 257 " (cutoff:3.500A) Processing helix chain 'E' and resid 272 through 277 Processing helix chain 'E' and resid 278 through 286 Processing helix chain 'E' and resid 289 through 302 Processing helix chain 'E' and resid 404 through 410 removed outlier: 3.522A pdb=" N LEU E 408 " --> pdb=" O ASP E 404 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LYS E 410 " --> pdb=" O LYS E 406 " (cutoff:3.500A) Processing helix chain 'E' and resid 443 through 461 removed outlier: 3.582A pdb=" N LEU E 447 " --> pdb=" O PRO E 443 " (cutoff:3.500A) Processing helix chain 'E' and resid 463 through 470 Processing helix chain 'E' and resid 478 through 495 Processing helix chain 'E' and resid 499 through 507 Processing helix chain 'E' and resid 521 through 528 Processing helix chain 'E' and resid 531 through 535 Processing helix chain 'E' and resid 552 through 562 removed outlier: 3.919A pdb=" N GLU E 556 " --> pdb=" O ASP E 552 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N VAL E 557 " --> pdb=" O PRO E 553 " (cutoff:3.500A) Processing helix chain 'E' and resid 565 through 577 removed outlier: 3.632A pdb=" N TRP E 570 " --> pdb=" O ASN E 566 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASN E 577 " --> pdb=" O LEU E 573 " (cutoff:3.500A) Processing helix chain 'E' and resid 588 through 605 removed outlier: 3.892A pdb=" N LEU E 592 " --> pdb=" O LYS E 588 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA E 602 " --> pdb=" O VAL E 598 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N HIS E 605 " --> pdb=" O LEU E 601 " (cutoff:3.500A) Processing helix chain 'E' and resid 608 through 618 removed outlier: 3.548A pdb=" N GLN E 617 " --> pdb=" O ASP E 613 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ILE E 618 " --> pdb=" O ALA E 614 " (cutoff:3.500A) Processing helix chain 'E' and resid 625 through 629 Processing helix chain 'E' and resid 630 through 651 Processing helix chain 'E' and resid 654 through 663 Processing helix chain 'E' and resid 671 through 683 Processing helix chain 'E' and resid 693 through 707 Proline residue: E 700 - end of helix Processing helix chain 'E' and resid 710 through 724 removed outlier: 3.509A pdb=" N ARG E 719 " --> pdb=" O GLU E 715 " (cutoff:3.500A) Processing helix chain 'E' and resid 731 through 740 Processing helix chain 'E' and resid 749 through 770 removed outlier: 3.543A pdb=" N PHE E 769 " --> pdb=" O VAL E 765 " (cutoff:3.500A) Processing helix chain 'E' and resid 772 through 780 Processing helix chain 'E' and resid 787 through 805 removed outlier: 4.006A pdb=" N ASN E 793 " --> pdb=" O THR E 789 " (cutoff:3.500A) Processing helix chain 'E' and resid 807 through 817 Processing helix chain 'E' and resid 821 through 830 Processing helix chain 'E' and resid 832 through 842 removed outlier: 4.674A pdb=" N GLN E 838 " --> pdb=" O GLU E 834 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N THR E 841 " --> pdb=" O THR E 837 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU E 842 " --> pdb=" O GLN E 838 " (cutoff:3.500A) Processing helix chain 'E' and resid 851 through 855 Processing helix chain 'E' and resid 857 through 868 removed outlier: 3.848A pdb=" N ARG E 861 " --> pdb=" O VAL E 857 " (cutoff:3.500A) Processing helix chain 'E' and resid 871 through 884 removed outlier: 3.578A pdb=" N THR E 876 " --> pdb=" O PRO E 872 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N THR E 877 " --> pdb=" O LYS E 873 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU E 878 " --> pdb=" O ASP E 874 " (cutoff:3.500A) Processing helix chain 'E' and resid 888 through 902 removed outlier: 3.868A pdb=" N GLY E 902 " --> pdb=" O LEU E 898 " (cutoff:3.500A) Processing helix chain 'E' and resid 904 through 931 Proline residue: E 917 - end of helix Processing helix chain 'E' and resid 938 through 947 removed outlier: 3.935A pdb=" N ILE E 942 " --> pdb=" O ASP E 938 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TRP E 943 " --> pdb=" O ARG E 939 " (cutoff:3.500A) Processing helix chain 'E' and resid 959 through 977 removed outlier: 3.512A pdb=" N ASP E 963 " --> pdb=" O THR E 959 " (cutoff:3.500A) Processing helix chain 'E' and resid 984 through 989 Processing helix chain 'E' and resid 990 through 995 Processing helix chain 'E' and resid 1002 through 1015 removed outlier: 3.761A pdb=" N LEU E1012 " --> pdb=" O GLY E1008 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N VAL E1013 " --> pdb=" O VAL E1009 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N TYR E1014 " --> pdb=" O SER E1010 " (cutoff:3.500A) Processing helix chain 'E' and resid 1016 through 1019 Processing helix chain 'E' and resid 1029 through 1039 Processing helix chain 'E' and resid 1045 through 1065 removed outlier: 3.739A pdb=" N PHE E1053 " --> pdb=" O LEU E1049 " (cutoff:3.500A) Processing helix chain 'E' and resid 1113 through 1116 removed outlier: 3.932A pdb=" N TRP E1116 " --> pdb=" O ALA E1113 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 1113 through 1116' Processing helix chain 'E' and resid 1242 through 1247 removed outlier: 3.948A pdb=" N THR E1246 " --> pdb=" O GLY E1242 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL E1247 " --> pdb=" O ILE E1243 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 1242 through 1247' Processing helix chain 'E' and resid 1248 through 1251 removed outlier: 3.558A pdb=" N LEU E1251 " --> pdb=" O THR E1248 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 1248 through 1251' Processing helix chain 'E' and resid 1474 through 1476 No H-bonds generated for 'chain 'E' and resid 1474 through 1476' Processing helix chain 'E' and resid 1571 through 1579 removed outlier: 3.649A pdb=" N ILE E1576 " --> pdb=" O THR E1572 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N GLU E1577 " --> pdb=" O ARG E1573 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ARG E1578 " --> pdb=" O GLN E1574 " (cutoff:3.500A) Processing helix chain 'E' and resid 1582 through 1587 Processing helix chain 'E' and resid 1588 through 1593 removed outlier: 3.716A pdb=" N GLN E1592 " --> pdb=" O SER E1588 " (cutoff:3.500A) Processing helix chain 'E' and resid 1738 through 1747 Processing helix chain 'E' and resid 1747 through 1759 Processing helix chain 'E' and resid 1762 through 1771 removed outlier: 3.724A pdb=" N ARG E1768 " --> pdb=" O THR E1764 " (cutoff:3.500A) Processing helix chain 'E' and resid 1786 through 1791 Processing helix chain 'E' and resid 1798 through 1802 removed outlier: 4.116A pdb=" N ASP E1801 " --> pdb=" O ASP E1798 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N SER E1802 " --> pdb=" O PRO E1799 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 1798 through 1802' Processing helix chain 'E' and resid 1804 through 1812 removed outlier: 3.912A pdb=" N VAL E1808 " --> pdb=" O ASP E1804 " (cutoff:3.500A) Processing helix chain 'E' and resid 1813 through 1838 Processing helix chain 'E' and resid 1840 through 1859 Processing helix chain 'E' and resid 1874 through 1879 Processing helix chain 'E' and resid 1880 through 1896 removed outlier: 3.597A pdb=" N PHE E1887 " --> pdb=" O GLN E1883 " (cutoff:3.500A) Processing helix chain 'E' and resid 1918 through 1937 Processing helix chain 'E' and resid 1983 through 2070 removed outlier: 3.806A pdb=" N ASP E1989 " --> pdb=" O PRO E1985 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N SER E2031 " --> pdb=" O GLU E2027 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLN E2038 " --> pdb=" O ARG E2034 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N LEU E2043 " --> pdb=" O ALA E2039 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASP E2044 " --> pdb=" O LEU E2040 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LYS E2048 " --> pdb=" O ASP E2044 " (cutoff:3.500A) Processing helix chain 'E' and resid 2073 through 2092 Processing helix chain 'E' and resid 2093 through 2105 Processing helix chain 'E' and resid 2120 through 2209 Processing helix chain 'E' and resid 2212 through 2249 removed outlier: 3.595A pdb=" N ASP E2232 " --> pdb=" O TYR E2228 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LEU E2233 " --> pdb=" O ARG E2229 " (cutoff:3.500A) Processing helix chain 'E' and resid 2263 through 2267 Processing helix chain 'E' and resid 2270 through 2290 removed outlier: 3.809A pdb=" N SER E2274 " --> pdb=" O MET E2270 " (cutoff:3.500A) Processing helix chain 'E' and resid 2302 through 2308 Processing helix chain 'E' and resid 2312 through 2319 removed outlier: 4.202A pdb=" N ALA E2318 " --> pdb=" O ALA E2314 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ASP E2319 " --> pdb=" O GLU E2315 " (cutoff:3.500A) Processing helix chain 'E' and resid 2348 through 2353 removed outlier: 3.511A pdb=" N ASN E2353 " --> pdb=" O LYS E2350 " (cutoff:3.500A) Processing helix chain 'E' and resid 2354 through 2358 removed outlier: 3.593A pdb=" N TYR E2358 " --> pdb=" O LYS E2355 " (cutoff:3.500A) Processing helix chain 'E' and resid 2449 through 2457 removed outlier: 4.015A pdb=" N LEU E2453 " --> pdb=" O LYS E2449 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 160 through 161 Processing sheet with id=AA2, first strand: chain 'A' and resid 317 through 323 removed outlier: 3.528A pdb=" N LYS A 327 " --> pdb=" O ASN A 323 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLU A 332 " --> pdb=" O HIS A 438 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 346 through 348 removed outlier: 3.574A pdb=" N PHE A 360 " --> pdb=" O TYR A 397 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 373 through 375 removed outlier: 3.640A pdb=" N THR A 431 " --> pdb=" O ILE A 416 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1120 through 1121 removed outlier: 6.680A pdb=" N ASN A1082 " --> pdb=" O HIS A1073 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N HIS A1073 " --> pdb=" O ASN A1082 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N TRP A1084 " --> pdb=" O GLY A1071 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N GLY A1071 " --> pdb=" O TRP A1084 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ILE A1086 " --> pdb=" O VAL A1069 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASN A1260 " --> pdb=" O GLY A1071 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1106 through 1107 removed outlier: 3.554A pdb=" N GLN A1107 " --> pdb=" O ARG A1110 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1136 through 1137 Processing sheet with id=AA8, first strand: chain 'A' and resid 1195 through 1201 removed outlier: 5.083A pdb=" N ASN A1222 " --> pdb=" O GLN A1214 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1257 through 1258 removed outlier: 3.986A pdb=" N VAL A1257 " --> pdb=" O LEU A1548 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1271 through 1272 removed outlier: 3.941A pdb=" N LYS A1533 " --> pdb=" O THR A1272 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LYS A1517 " --> pdb=" O GLU A1463 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1285 through 1293 removed outlier: 6.411A pdb=" N ALA A1301 " --> pdb=" O GLY A1289 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N TYR A1291 " --> pdb=" O ILE A1299 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N ILE A1299 " --> pdb=" O TYR A1291 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1285 through 1293 removed outlier: 6.411A pdb=" N ALA A1301 " --> pdb=" O GLY A1289 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N TYR A1291 " --> pdb=" O ILE A1299 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N ILE A1299 " --> pdb=" O TYR A1291 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER A1298 " --> pdb=" O ILE A1501 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1595 through 1597 Processing sheet with id=AB5, first strand: chain 'A' and resid 1602 through 1609 Processing sheet with id=AB6, first strand: chain 'A' and resid 1637 through 1643 removed outlier: 6.535A pdb=" N TYR A1627 " --> pdb=" O PRO A1638 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1774 through 1775 Processing sheet with id=AB8, first strand: chain 'A' and resid 2109 through 2111 Processing sheet with id=AB9, first strand: chain 'A' and resid 2113 through 2115 Processing sheet with id=AC1, first strand: chain 'A' and resid 2294 through 2301 removed outlier: 5.544A pdb=" N THR A2467 " --> pdb=" O ILE A2368 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N ILE A2368 " --> pdb=" O THR A2467 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N CYS A2469 " --> pdb=" O ARG A2366 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ARG A2366 " --> pdb=" O CYS A2469 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 2343 through 2345 removed outlier: 4.193A pdb=" N ALA A2387 " --> pdb=" O LEU A2405 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 160 through 161 Processing sheet with id=AC4, first strand: chain 'B' and resid 317 through 323 removed outlier: 3.528A pdb=" N LYS B 327 " --> pdb=" O ASN B 323 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLU B 332 " --> pdb=" O HIS B 438 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 346 through 348 removed outlier: 3.575A pdb=" N PHE B 360 " --> pdb=" O TYR B 397 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 373 through 375 removed outlier: 3.640A pdb=" N THR B 431 " --> pdb=" O ILE B 416 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 1120 through 1121 removed outlier: 6.681A pdb=" N ASN B1082 " --> pdb=" O HIS B1073 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N HIS B1073 " --> pdb=" O ASN B1082 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N TRP B1084 " --> pdb=" O GLY B1071 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N GLY B1071 " --> pdb=" O TRP B1084 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ILE B1086 " --> pdb=" O VAL B1069 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASN B1260 " --> pdb=" O GLY B1071 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 1106 through 1107 removed outlier: 3.553A pdb=" N GLN B1107 " --> pdb=" O ARG B1110 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 1136 through 1137 Processing sheet with id=AD1, first strand: chain 'B' and resid 1195 through 1201 removed outlier: 5.083A pdb=" N ASN B1222 " --> pdb=" O GLN B1214 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 1257 through 1258 removed outlier: 3.986A pdb=" N VAL B1257 " --> pdb=" O LEU B1548 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1271 through 1272 removed outlier: 3.941A pdb=" N LYS B1533 " --> pdb=" O THR B1272 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LYS B1517 " --> pdb=" O GLU B1463 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1285 through 1293 removed outlier: 6.411A pdb=" N ALA B1301 " --> pdb=" O GLY B1289 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N TYR B1291 " --> pdb=" O ILE B1299 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N ILE B1299 " --> pdb=" O TYR B1291 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1285 through 1293 removed outlier: 6.411A pdb=" N ALA B1301 " --> pdb=" O GLY B1289 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N TYR B1291 " --> pdb=" O ILE B1299 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N ILE B1299 " --> pdb=" O TYR B1291 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N SER B1298 " --> pdb=" O ILE B1501 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1595 through 1597 Processing sheet with id=AD7, first strand: chain 'B' and resid 1602 through 1609 Processing sheet with id=AD8, first strand: chain 'B' and resid 1637 through 1643 removed outlier: 6.536A pdb=" N TYR B1627 " --> pdb=" O PRO B1638 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 1774 through 1775 Processing sheet with id=AE1, first strand: chain 'B' and resid 2113 through 2115 Processing sheet with id=AE2, first strand: chain 'B' and resid 2294 through 2301 removed outlier: 5.545A pdb=" N THR B2467 " --> pdb=" O ILE B2368 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N ILE B2368 " --> pdb=" O THR B2467 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N CYS B2469 " --> pdb=" O ARG B2366 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ARG B2366 " --> pdb=" O CYS B2469 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 2343 through 2345 removed outlier: 4.193A pdb=" N ALA B2387 " --> pdb=" O LEU B2405 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 160 through 161 Processing sheet with id=AE5, first strand: chain 'C' and resid 317 through 323 removed outlier: 3.528A pdb=" N LYS C 327 " --> pdb=" O ASN C 323 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLU C 332 " --> pdb=" O HIS C 438 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 346 through 348 removed outlier: 3.575A pdb=" N PHE C 360 " --> pdb=" O TYR C 397 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 373 through 375 removed outlier: 3.640A pdb=" N THR C 431 " --> pdb=" O ILE C 416 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 1120 through 1121 removed outlier: 6.681A pdb=" N ASN C1082 " --> pdb=" O HIS C1073 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N HIS C1073 " --> pdb=" O ASN C1082 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N TRP C1084 " --> pdb=" O GLY C1071 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N GLY C1071 " --> pdb=" O TRP C1084 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ILE C1086 " --> pdb=" O VAL C1069 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASN C1260 " --> pdb=" O GLY C1071 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 1106 through 1107 removed outlier: 3.554A pdb=" N GLN C1107 " --> pdb=" O ARG C1110 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 1136 through 1137 Processing sheet with id=AF2, first strand: chain 'C' and resid 1195 through 1201 removed outlier: 5.082A pdb=" N ASN C1222 " --> pdb=" O GLN C1214 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 1257 through 1258 removed outlier: 3.985A pdb=" N VAL C1257 " --> pdb=" O LEU C1548 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 1271 through 1272 removed outlier: 3.941A pdb=" N LYS C1533 " --> pdb=" O THR C1272 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LYS C1517 " --> pdb=" O GLU C1463 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 1285 through 1293 removed outlier: 6.412A pdb=" N ALA C1301 " --> pdb=" O GLY C1289 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N TYR C1291 " --> pdb=" O ILE C1299 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N ILE C1299 " --> pdb=" O TYR C1291 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 1285 through 1293 removed outlier: 6.412A pdb=" N ALA C1301 " --> pdb=" O GLY C1289 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N TYR C1291 " --> pdb=" O ILE C1299 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N ILE C1299 " --> pdb=" O TYR C1291 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N SER C1298 " --> pdb=" O ILE C1501 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 1595 through 1597 Processing sheet with id=AF8, first strand: chain 'C' and resid 1602 through 1609 Processing sheet with id=AF9, first strand: chain 'C' and resid 1637 through 1643 removed outlier: 6.536A pdb=" N TYR C1627 " --> pdb=" O PRO C1638 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'C' and resid 1774 through 1775 Processing sheet with id=AG2, first strand: chain 'C' and resid 2114 through 2115 Processing sheet with id=AG3, first strand: chain 'C' and resid 2294 through 2301 removed outlier: 5.544A pdb=" N THR C2467 " --> pdb=" O ILE C2368 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N ILE C2368 " --> pdb=" O THR C2467 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N CYS C2469 " --> pdb=" O ARG C2366 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ARG C2366 " --> pdb=" O CYS C2469 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'C' and resid 2343 through 2345 removed outlier: 4.193A pdb=" N ALA C2387 " --> pdb=" O LEU C2405 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'D' and resid 160 through 161 Processing sheet with id=AG6, first strand: chain 'D' and resid 317 through 323 removed outlier: 3.528A pdb=" N LYS D 327 " --> pdb=" O ASN D 323 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLU D 332 " --> pdb=" O HIS D 438 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'D' and resid 346 through 348 removed outlier: 3.574A pdb=" N PHE D 360 " --> pdb=" O TYR D 397 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'D' and resid 373 through 375 removed outlier: 3.640A pdb=" N THR D 431 " --> pdb=" O ILE D 416 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'D' and resid 1120 through 1121 removed outlier: 6.681A pdb=" N ASN D1082 " --> pdb=" O HIS D1073 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N HIS D1073 " --> pdb=" O ASN D1082 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N TRP D1084 " --> pdb=" O GLY D1071 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N GLY D1071 " --> pdb=" O TRP D1084 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ILE D1086 " --> pdb=" O VAL D1069 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASN D1260 " --> pdb=" O GLY D1071 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'D' and resid 1106 through 1107 removed outlier: 3.554A pdb=" N GLN D1107 " --> pdb=" O ARG D1110 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'D' and resid 1136 through 1137 Processing sheet with id=AH3, first strand: chain 'D' and resid 1195 through 1201 removed outlier: 5.082A pdb=" N ASN D1222 " --> pdb=" O GLN D1214 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'D' and resid 1257 through 1258 removed outlier: 3.985A pdb=" N VAL D1257 " --> pdb=" O LEU D1548 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'D' and resid 1271 through 1272 removed outlier: 3.941A pdb=" N LYS D1533 " --> pdb=" O THR D1272 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LYS D1517 " --> pdb=" O GLU D1463 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'D' and resid 1285 through 1293 removed outlier: 6.412A pdb=" N ALA D1301 " --> pdb=" O GLY D1289 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N TYR D1291 " --> pdb=" O ILE D1299 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N ILE D1299 " --> pdb=" O TYR D1291 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'D' and resid 1285 through 1293 removed outlier: 6.412A pdb=" N ALA D1301 " --> pdb=" O GLY D1289 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N TYR D1291 " --> pdb=" O ILE D1299 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N ILE D1299 " --> pdb=" O TYR D1291 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N SER D1298 " --> pdb=" O ILE D1501 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'D' and resid 1595 through 1597 Processing sheet with id=AH9, first strand: chain 'D' and resid 1602 through 1609 Processing sheet with id=AI1, first strand: chain 'D' and resid 1637 through 1643 removed outlier: 6.536A pdb=" N TYR D1627 " --> pdb=" O PRO D1638 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'D' and resid 1774 through 1775 Processing sheet with id=AI3, first strand: chain 'D' and resid 2113 through 2115 Processing sheet with id=AI4, first strand: chain 'D' and resid 2294 through 2301 removed outlier: 5.545A pdb=" N THR D2467 " --> pdb=" O ILE D2368 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N ILE D2368 " --> pdb=" O THR D2467 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N CYS D2469 " --> pdb=" O ARG D2366 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ARG D2366 " --> pdb=" O CYS D2469 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'D' and resid 2343 through 2345 removed outlier: 4.192A pdb=" N ALA D2387 " --> pdb=" O LEU D2405 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'E' and resid 160 through 161 Processing sheet with id=AI7, first strand: chain 'E' and resid 317 through 323 removed outlier: 3.527A pdb=" N LYS E 327 " --> pdb=" O ASN E 323 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLU E 332 " --> pdb=" O HIS E 438 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'E' and resid 346 through 348 removed outlier: 3.575A pdb=" N PHE E 360 " --> pdb=" O TYR E 397 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'E' and resid 373 through 375 removed outlier: 3.641A pdb=" N THR E 431 " --> pdb=" O ILE E 416 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'E' and resid 1120 through 1121 removed outlier: 6.681A pdb=" N ASN E1082 " --> pdb=" O HIS E1073 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N HIS E1073 " --> pdb=" O ASN E1082 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N TRP E1084 " --> pdb=" O GLY E1071 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N GLY E1071 " --> pdb=" O TRP E1084 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ILE E1086 " --> pdb=" O VAL E1069 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASN E1260 " --> pdb=" O GLY E1071 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'E' and resid 1106 through 1107 removed outlier: 3.553A pdb=" N GLN E1107 " --> pdb=" O ARG E1110 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'E' and resid 1136 through 1137 Processing sheet with id=AJ4, first strand: chain 'E' and resid 1195 through 1201 removed outlier: 5.083A pdb=" N ASN E1222 " --> pdb=" O GLN E1214 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'E' and resid 1257 through 1258 removed outlier: 3.985A pdb=" N VAL E1257 " --> pdb=" O LEU E1548 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'E' and resid 1271 through 1272 removed outlier: 3.941A pdb=" N LYS E1533 " --> pdb=" O THR E1272 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LYS E1517 " --> pdb=" O GLU E1463 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'E' and resid 1285 through 1293 removed outlier: 6.412A pdb=" N ALA E1301 " --> pdb=" O GLY E1289 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N TYR E1291 " --> pdb=" O ILE E1299 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N ILE E1299 " --> pdb=" O TYR E1291 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'E' and resid 1285 through 1293 removed outlier: 6.412A pdb=" N ALA E1301 " --> pdb=" O GLY E1289 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N TYR E1291 " --> pdb=" O ILE E1299 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N ILE E1299 " --> pdb=" O TYR E1291 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER E1298 " --> pdb=" O ILE E1501 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'E' and resid 1595 through 1597 Processing sheet with id=AK1, first strand: chain 'E' and resid 1602 through 1609 Processing sheet with id=AK2, first strand: chain 'E' and resid 1637 through 1643 removed outlier: 6.536A pdb=" N TYR E1627 " --> pdb=" O PRO E1638 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'E' and resid 1774 through 1775 Processing sheet with id=AK4, first strand: chain 'E' and resid 2294 through 2301 removed outlier: 5.545A pdb=" N THR E2467 " --> pdb=" O ILE E2368 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N ILE E2368 " --> pdb=" O THR E2467 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N CYS E2469 " --> pdb=" O ARG E2366 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ARG E2366 " --> pdb=" O CYS E2469 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'E' and resid 2343 through 2345 removed outlier: 4.192A pdb=" N ALA E2387 " --> pdb=" O LEU E2405 " (cutoff:3.500A) 4471 hydrogen bonds defined for protein. 12795 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: 48.06 Time building geometry restraints manager: 30.19 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: 26255 1.33 - 1.45: 15098 1.45 - 1.57: 48482 1.57 - 1.69: 5 1.69 - 1.82: 550 Bond restraints: 90390 Sorted by residual: bond pdb=" CA ARG E 128 " pdb=" C ARG E 128 " ideal model delta sigma weight residual 1.522 1.468 0.054 1.43e-02 4.89e+03 1.43e+01 bond pdb=" CA ARG C 128 " pdb=" C ARG C 128 " ideal model delta sigma weight residual 1.522 1.468 0.054 1.43e-02 4.89e+03 1.42e+01 bond pdb=" CA ARG D 128 " pdb=" C ARG D 128 " ideal model delta sigma weight residual 1.522 1.468 0.054 1.43e-02 4.89e+03 1.42e+01 bond pdb=" CA ARG A 128 " pdb=" C ARG A 128 " ideal model delta sigma weight residual 1.522 1.468 0.054 1.43e-02 4.89e+03 1.41e+01 bond pdb=" CA ARG B 128 " pdb=" C ARG B 128 " ideal model delta sigma weight residual 1.522 1.468 0.053 1.43e-02 4.89e+03 1.40e+01 ... (remaining 90385 not shown) Histogram of bond angle deviations from ideal: 97.45 - 105.04: 1638 105.04 - 112.64: 49103 112.64 - 120.23: 36273 120.23 - 127.83: 35024 127.83 - 135.42: 817 Bond angle restraints: 122855 Sorted by residual: angle pdb=" CA GLN E 906 " pdb=" CB GLN E 906 " pdb=" CG GLN E 906 " ideal model delta sigma weight residual 114.10 130.26 -16.16 2.00e+00 2.50e-01 6.53e+01 angle pdb=" CA GLN C 906 " pdb=" CB GLN C 906 " pdb=" CG GLN C 906 " ideal model delta sigma weight residual 114.10 130.25 -16.15 2.00e+00 2.50e-01 6.52e+01 angle pdb=" CA GLN B 906 " pdb=" CB GLN B 906 " pdb=" CG GLN B 906 " ideal model delta sigma weight residual 114.10 130.25 -16.15 2.00e+00 2.50e-01 6.52e+01 angle pdb=" CA GLN A 906 " pdb=" CB GLN A 906 " pdb=" CG GLN A 906 " ideal model delta sigma weight residual 114.10 130.22 -16.12 2.00e+00 2.50e-01 6.50e+01 angle pdb=" CA GLN D 906 " pdb=" CB GLN D 906 " pdb=" CG GLN D 906 " ideal model delta sigma weight residual 114.10 130.21 -16.11 2.00e+00 2.50e-01 6.49e+01 ... (remaining 122850 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 48785 17.99 - 35.99: 4869 35.99 - 53.98: 841 53.98 - 71.97: 215 71.97 - 89.97: 60 Dihedral angle restraints: 54770 sinusoidal: 21435 harmonic: 33335 Sorted by residual: dihedral pdb=" CA TRP E1560 " pdb=" C TRP E1560 " pdb=" N ASP E1561 " pdb=" CA ASP E1561 " ideal model delta harmonic sigma weight residual -180.00 -145.49 -34.51 0 5.00e+00 4.00e-02 4.76e+01 dihedral pdb=" CA TRP D1560 " pdb=" C TRP D1560 " pdb=" N ASP D1561 " pdb=" CA ASP D1561 " ideal model delta harmonic sigma weight residual 180.00 -145.50 -34.50 0 5.00e+00 4.00e-02 4.76e+01 dihedral pdb=" CA TRP C1560 " pdb=" C TRP C1560 " pdb=" N ASP C1561 " pdb=" CA ASP C1561 " ideal model delta harmonic sigma weight residual 180.00 -145.52 -34.48 0 5.00e+00 4.00e-02 4.75e+01 ... (remaining 54767 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 11402 0.064 - 0.128: 2533 0.128 - 0.192: 116 0.192 - 0.256: 24 0.256 - 0.320: 10 Chirality restraints: 14085 Sorted by residual: chirality pdb=" CB VAL B 310 " pdb=" CA VAL B 310 " pdb=" CG1 VAL B 310 " pdb=" CG2 VAL B 310 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.56e+00 chirality pdb=" CB VAL C 310 " pdb=" CA VAL C 310 " pdb=" CG1 VAL C 310 " pdb=" CG2 VAL C 310 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.55e+00 chirality pdb=" CB VAL A 310 " pdb=" CA VAL A 310 " pdb=" CG1 VAL A 310 " pdb=" CG2 VAL A 310 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.51e+00 ... (remaining 14082 not shown) Planarity restraints: 15950 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU A1037 " 0.013 2.00e-02 2.50e+03 2.65e-02 7.02e+00 pdb=" CD GLU A1037 " -0.046 2.00e-02 2.50e+03 pdb=" OE1 GLU A1037 " 0.016 2.00e-02 2.50e+03 pdb=" OE2 GLU A1037 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU B1037 " -0.013 2.00e-02 2.50e+03 2.64e-02 6.99e+00 pdb=" CD GLU B1037 " 0.046 2.00e-02 2.50e+03 pdb=" OE1 GLU B1037 " -0.016 2.00e-02 2.50e+03 pdb=" OE2 GLU B1037 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU C1037 " -0.013 2.00e-02 2.50e+03 2.63e-02 6.94e+00 pdb=" CD GLU C1037 " 0.046 2.00e-02 2.50e+03 pdb=" OE1 GLU C1037 " -0.016 2.00e-02 2.50e+03 pdb=" OE2 GLU C1037 " -0.016 2.00e-02 2.50e+03 ... (remaining 15947 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 901 2.57 - 3.15: 76809 3.15 - 3.74: 139813 3.74 - 4.32: 199125 4.32 - 4.90: 327652 Nonbonded interactions: 744300 Sorted by model distance: nonbonded pdb=" OG SER C 196 " pdb=" OG1 THR C 199 " model vdw 1.989 2.440 nonbonded pdb=" OG SER E 196 " pdb=" OG1 THR E 199 " model vdw 1.989 2.440 nonbonded pdb=" OG SER D 196 " pdb=" OG1 THR D 199 " model vdw 1.989 2.440 nonbonded pdb=" OG SER A 196 " pdb=" OG1 THR A 199 " model vdw 1.989 2.440 nonbonded pdb=" OG SER B 196 " pdb=" OG1 THR B 199 " model vdw 1.990 2.440 ... (remaining 744295 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.470 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: 0.060 Extract box with map and model: 14.780 Check model and map are aligned: 1.000 Set scattering table: 0.610 Process input model: 196.130 Find NCS groups from input model: 4.850 Set up NCS constraints: 0.440 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 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: 224.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 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 : 0.011 0.078 90390 Z= 0.717 Angle : 0.905 16.157 122855 Z= 0.501 Chirality : 0.050 0.320 14085 Planarity : 0.004 0.051 15950 Dihedral : 15.024 89.967 33220 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.40 % Favored : 92.42 % Rotamer: Outliers : 2.83 % Allowed : 11.12 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.04 (0.07), residues: 11365 helix: -1.24 (0.06), residues: 5305 sheet: -2.56 (0.12), residues: 1445 loop : -2.67 (0.08), residues: 4615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D1560 HIS 0.007 0.002 HIS D2191 PHE 0.035 0.002 PHE D1469 TYR 0.043 0.002 TYR B1836 ARG 0.012 0.001 ARG E1099 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22730 Ramachandran restraints generated. 11365 Oldfield, 0 Emsley, 11365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22730 Ramachandran restraints generated. 11365 Oldfield, 0 Emsley, 11365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1597 residues out of total 9715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 267 poor density : 1330 time to evaluate : 7.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 351 GLN cc_start: 0.7387 (mt0) cc_final: 0.7044 (mt0) REVERT: A 613 ASP cc_start: 0.6540 (t0) cc_final: 0.6089 (t0) REVERT: A 674 MET cc_start: 0.6674 (tpp) cc_final: 0.6442 (tpp) REVERT: A 683 ASN cc_start: 0.6902 (p0) cc_final: 0.6583 (p0) REVERT: A 787 THR cc_start: 0.8501 (OUTLIER) cc_final: 0.8275 (p) REVERT: A 1948 LEU cc_start: 0.8047 (OUTLIER) cc_final: 0.7739 (mm) REVERT: B 277 MET cc_start: 0.7632 (mmm) cc_final: 0.7412 (mmm) REVERT: B 613 ASP cc_start: 0.6626 (t0) cc_final: 0.6085 (t0) REVERT: B 674 MET cc_start: 0.6974 (tpp) cc_final: 0.6306 (tpp) REVERT: B 683 ASN cc_start: 0.6894 (p0) cc_final: 0.6586 (p0) REVERT: B 706 MET cc_start: 0.8303 (mmt) cc_final: 0.8068 (mmp) REVERT: B 734 GLU cc_start: 0.8480 (OUTLIER) cc_final: 0.8265 (mm-30) REVERT: B 1596 GLU cc_start: 0.7360 (OUTLIER) cc_final: 0.7080 (tt0) REVERT: B 1948 LEU cc_start: 0.7950 (OUTLIER) cc_final: 0.7611 (mm) REVERT: C 674 MET cc_start: 0.6563 (tpp) cc_final: 0.6289 (tpp) REVERT: C 1232 MET cc_start: 0.8248 (mtm) cc_final: 0.7959 (mtt) REVERT: D 674 MET cc_start: 0.6471 (tpp) cc_final: 0.6265 (tpp) REVERT: D 706 MET cc_start: 0.8343 (mmt) cc_final: 0.8052 (mmp) REVERT: E 658 LEU cc_start: 0.9350 (tp) cc_final: 0.9051 (tp) REVERT: E 674 MET cc_start: 0.6351 (tpp) cc_final: 0.5895 (tpp) REVERT: E 683 ASN cc_start: 0.6832 (p0) cc_final: 0.6456 (p0) REVERT: E 1833 ASP cc_start: 0.7792 (m-30) cc_final: 0.7574 (m-30) outliers start: 267 outliers final: 89 residues processed: 1548 average time/residue: 0.8541 time to fit residues: 2233.7441 Evaluate side-chains 1031 residues out of total 9715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 937 time to evaluate : 7.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain A residue 734 GLU Chi-restraints excluded: chain A residue 787 THR Chi-restraints excluded: chain A residue 834 GLU Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 906 GLN Chi-restraints excluded: chain A residue 1126 VAL Chi-restraints excluded: chain A residue 1181 SER Chi-restraints excluded: chain A residue 1259 VAL Chi-restraints excluded: chain A residue 1471 THR Chi-restraints excluded: chain A residue 1529 THR Chi-restraints excluded: chain A residue 1596 GLU Chi-restraints excluded: chain A residue 1948 LEU Chi-restraints excluded: chain A residue 2085 SER Chi-restraints excluded: chain A residue 2093 ILE Chi-restraints excluded: chain A residue 2156 GLU Chi-restraints excluded: chain A residue 2166 SER Chi-restraints excluded: chain A residue 2249 THR Chi-restraints excluded: chain A residue 2274 SER Chi-restraints excluded: chain A residue 2305 VAL Chi-restraints excluded: chain A residue 2374 THR Chi-restraints excluded: chain A residue 2433 ASP Chi-restraints excluded: chain B residue 398 SER Chi-restraints excluded: chain B residue 734 GLU Chi-restraints excluded: chain B residue 834 GLU Chi-restraints excluded: chain B residue 851 THR Chi-restraints excluded: chain B residue 906 GLN Chi-restraints excluded: chain B residue 960 LEU Chi-restraints excluded: chain B residue 1126 VAL Chi-restraints excluded: chain B residue 1181 SER Chi-restraints excluded: chain B residue 1471 THR Chi-restraints excluded: chain B residue 1529 THR Chi-restraints excluded: chain B residue 1596 GLU Chi-restraints excluded: chain B residue 1948 LEU Chi-restraints excluded: chain B residue 2085 SER Chi-restraints excluded: chain B residue 2093 ILE Chi-restraints excluded: chain B residue 2156 GLU Chi-restraints excluded: chain B residue 2166 SER Chi-restraints excluded: chain B residue 2249 THR Chi-restraints excluded: chain B residue 2305 VAL Chi-restraints excluded: chain B residue 2374 THR Chi-restraints excluded: chain C residue 398 SER Chi-restraints excluded: chain C residue 834 GLU Chi-restraints excluded: chain C residue 851 THR Chi-restraints excluded: chain C residue 906 GLN Chi-restraints excluded: chain C residue 1126 VAL Chi-restraints excluded: chain C residue 1181 SER Chi-restraints excluded: chain C residue 1259 VAL Chi-restraints excluded: chain C residue 1471 THR Chi-restraints excluded: chain C residue 1529 THR Chi-restraints excluded: chain C residue 1591 THR Chi-restraints excluded: chain C residue 1596 GLU Chi-restraints excluded: chain C residue 2085 SER Chi-restraints excluded: chain C residue 2093 ILE Chi-restraints excluded: chain C residue 2156 GLU Chi-restraints excluded: chain C residue 2166 SER Chi-restraints excluded: chain C residue 2249 THR Chi-restraints excluded: chain C residue 2305 VAL Chi-restraints excluded: chain C residue 2374 THR Chi-restraints excluded: chain C residue 2433 ASP Chi-restraints excluded: chain D residue 398 SER Chi-restraints excluded: chain D residue 834 GLU Chi-restraints excluded: chain D residue 851 THR Chi-restraints excluded: chain D residue 906 GLN Chi-restraints excluded: chain D residue 1181 SER Chi-restraints excluded: chain D residue 1259 VAL Chi-restraints excluded: chain D residue 1471 THR Chi-restraints excluded: chain D residue 1529 THR Chi-restraints excluded: chain D residue 1760 GLU Chi-restraints excluded: chain D residue 2085 SER Chi-restraints excluded: chain D residue 2093 ILE Chi-restraints excluded: chain D residue 2156 GLU Chi-restraints excluded: chain D residue 2166 SER Chi-restraints excluded: chain D residue 2249 THR Chi-restraints excluded: chain D residue 2274 SER Chi-restraints excluded: chain D residue 2305 VAL Chi-restraints excluded: chain D residue 2374 THR Chi-restraints excluded: chain E residue 398 SER Chi-restraints excluded: chain E residue 734 GLU Chi-restraints excluded: chain E residue 834 GLU Chi-restraints excluded: chain E residue 851 THR Chi-restraints excluded: chain E residue 906 GLN Chi-restraints excluded: chain E residue 1126 VAL Chi-restraints excluded: chain E residue 1162 SER Chi-restraints excluded: chain E residue 1181 SER Chi-restraints excluded: chain E residue 1259 VAL Chi-restraints excluded: chain E residue 1471 THR Chi-restraints excluded: chain E residue 1529 THR Chi-restraints excluded: chain E residue 1596 GLU Chi-restraints excluded: chain E residue 1652 VAL Chi-restraints excluded: chain E residue 2093 ILE Chi-restraints excluded: chain E residue 2156 GLU Chi-restraints excluded: chain E residue 2166 SER Chi-restraints excluded: chain E residue 2305 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1140 random chunks: chunk 962 optimal weight: 6.9990 chunk 864 optimal weight: 0.5980 chunk 479 optimal weight: 2.9990 chunk 295 optimal weight: 10.0000 chunk 582 optimal weight: 7.9990 chunk 461 optimal weight: 3.9990 chunk 893 optimal weight: 3.9990 chunk 345 optimal weight: 0.9980 chunk 543 optimal weight: 0.9990 chunk 665 optimal weight: 0.9990 chunk 1035 optimal weight: 7.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 HIS ** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 184 ASN ** A 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 209 HIS ** A 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 315 ASN A 351 GLN A 355 GLN A 371 HIS A 528 ASN A 533 ASN A 724 ASN A 816 GLN A 906 GLN ** A 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 934 ASN A1028 GLN A1150 GLN A1250 GLN A1264 ASN A1617 HIS A1620 ASN A1649 ASN A1680 ASN A1811 ASN A2278 ASN A2310 ASN A2328 ASN ** A2344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2394 ASN B 51 HIS B 158 ASN B 184 ASN B 209 HIS B 315 ASN B 371 HIS B 528 ASN B 533 ASN B 724 ASN B 816 GLN B 906 GLN B 910 GLN ** B 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 934 ASN B1028 GLN B1150 GLN B1250 GLN B1264 ASN B1580 ASN B1617 HIS B1620 ASN B1649 ASN B1680 ASN ** B1767 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1811 ASN B2278 ASN B2310 ASN B2328 ASN ** B2344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2394 ASN C 51 HIS ** C 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 184 ASN ** C 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 209 HIS C 315 ASN C 355 GLN C 371 HIS C 528 ASN C 533 ASN C 724 ASN C 816 GLN C 906 GLN C 910 GLN ** C 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 934 ASN ** C1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1150 GLN C1250 GLN C1264 ASN C1617 HIS C1620 ASN C1649 ASN C1680 ASN ** C1767 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1811 ASN C2278 ASN C2310 ASN C2328 ASN ** C2344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C2394 ASN C2420 ASN D 51 HIS D 209 HIS D 315 ASN D 371 HIS D 528 ASN D 533 ASN D 724 ASN D 816 GLN D 904 ASN D 906 GLN ** D 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 934 ASN D1028 GLN D1150 GLN D1250 GLN D1264 ASN D1580 ASN D1617 HIS D1620 ASN D1649 ASN D1680 ASN ** D1767 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1811 ASN D2174 GLN D2278 ASN D2310 ASN D2328 ASN ** D2344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D2394 ASN D2420 ASN E 51 HIS E 158 ASN E 209 HIS ** E 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 315 ASN E 351 GLN E 371 HIS E 528 ASN E 724 ASN E 816 GLN E 904 ASN E 906 GLN ** E 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 934 ASN ** E 973 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1028 GLN E1150 GLN E1250 GLN E1264 ASN E1617 HIS E1620 ASN E1649 ASN E1680 ASN E1767 ASN E1811 ASN E1872 ASN E1997 GLN E2278 ASN E2310 ASN E2328 ASN ** E2344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E2394 ASN E2420 ASN Total number of N/Q/H flips: 135 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 90390 Z= 0.200 Angle : 0.597 8.084 122855 Z= 0.307 Chirality : 0.041 0.199 14085 Planarity : 0.004 0.053 15950 Dihedral : 6.616 103.974 12515 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 2.56 % Allowed : 15.13 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.08), residues: 11365 helix: 0.53 (0.07), residues: 5310 sheet: -1.89 (0.12), residues: 1525 loop : -1.93 (0.09), residues: 4530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D1560 HIS 0.006 0.001 HIS E2191 PHE 0.024 0.001 PHE E1714 TYR 0.020 0.001 TYR A1836 ARG 0.009 0.000 ARG D2034 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22730 Ramachandran restraints generated. 11365 Oldfield, 0 Emsley, 11365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22730 Ramachandran restraints generated. 11365 Oldfield, 0 Emsley, 11365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1380 residues out of total 9715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 241 poor density : 1139 time to evaluate : 7.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1056 TYR cc_start: 0.8695 (t80) cc_final: 0.8434 (t80) REVERT: A 1826 ASP cc_start: 0.7083 (m-30) cc_final: 0.6558 (m-30) REVERT: A 2037 GLU cc_start: 0.6746 (mp0) cc_final: 0.6375 (mp0) REVERT: A 2098 MET cc_start: 0.7957 (tpp) cc_final: 0.7711 (mmm) REVERT: A 2194 ILE cc_start: 0.8932 (OUTLIER) cc_final: 0.8287 (mt) REVERT: B 674 MET cc_start: 0.6875 (tpp) cc_final: 0.6649 (tpp) REVERT: B 706 MET cc_start: 0.8282 (mmt) cc_final: 0.8081 (mmp) REVERT: B 799 ASN cc_start: 0.8586 (t0) cc_final: 0.8375 (t0) REVERT: B 912 GLN cc_start: 0.8253 (tt0) cc_final: 0.7961 (tt0) REVERT: B 1232 MET cc_start: 0.7907 (mtt) cc_final: 0.7601 (mtt) REVERT: C 501 GLU cc_start: 0.6752 (OUTLIER) cc_final: 0.6337 (tp30) REVERT: C 1232 MET cc_start: 0.8043 (mtm) cc_final: 0.7765 (mtt) REVERT: C 1852 MET cc_start: 0.7507 (tpt) cc_final: 0.7264 (tpt) REVERT: C 2027 GLU cc_start: 0.7100 (tm-30) cc_final: 0.6434 (tm-30) REVERT: D 545 LEU cc_start: 0.9026 (OUTLIER) cc_final: 0.8811 (tt) REVERT: D 649 ASN cc_start: 0.8558 (m-40) cc_final: 0.8256 (m-40) REVERT: D 674 MET cc_start: 0.6516 (tpp) cc_final: 0.6255 (tpp) REVERT: D 706 MET cc_start: 0.8623 (mmt) cc_final: 0.8270 (mmp) REVERT: D 1840 GLU cc_start: 0.7339 (OUTLIER) cc_final: 0.6753 (pm20) REVERT: D 1844 LEU cc_start: 0.9138 (mm) cc_final: 0.8903 (mm) REVERT: D 2027 GLU cc_start: 0.7570 (tm-30) cc_final: 0.6875 (tm-30) REVERT: D 2194 ILE cc_start: 0.8863 (OUTLIER) cc_final: 0.8479 (mt) REVERT: E 637 MET cc_start: 0.7444 (ttm) cc_final: 0.7134 (ttm) REVERT: E 674 MET cc_start: 0.6429 (tpp) cc_final: 0.6207 (tpp) REVERT: E 712 GLU cc_start: 0.7104 (mm-30) cc_final: 0.6888 (mm-30) REVERT: E 960 LEU cc_start: 0.9081 (OUTLIER) cc_final: 0.8858 (tt) outliers start: 241 outliers final: 113 residues processed: 1327 average time/residue: 0.8074 time to fit residues: 1860.5173 Evaluate side-chains 1065 residues out of total 9715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 946 time to evaluate : 8.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 653 ILE Chi-restraints excluded: chain A residue 835 VAL Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 1126 VAL Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain A residue 1170 VAL Chi-restraints excluded: chain A residue 1190 SER Chi-restraints excluded: chain A residue 1197 LEU Chi-restraints excluded: chain A residue 1259 VAL Chi-restraints excluded: chain A residue 1529 THR Chi-restraints excluded: chain A residue 1546 ILE Chi-restraints excluded: chain A residue 1584 ASP Chi-restraints excluded: chain A residue 1798 ASP Chi-restraints excluded: chain A residue 1840 GLU Chi-restraints excluded: chain A residue 2073 SER Chi-restraints excluded: chain A residue 2093 ILE Chi-restraints excluded: chain A residue 2166 SER Chi-restraints excluded: chain A residue 2194 ILE Chi-restraints excluded: chain A residue 2249 THR Chi-restraints excluded: chain A residue 2305 VAL Chi-restraints excluded: chain B residue 371 HIS Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 608 THR Chi-restraints excluded: chain B residue 637 MET Chi-restraints excluded: chain B residue 764 LEU Chi-restraints excluded: chain B residue 835 VAL Chi-restraints excluded: chain B residue 851 THR Chi-restraints excluded: chain B residue 960 LEU Chi-restraints excluded: chain B residue 1049 LEU Chi-restraints excluded: chain B residue 1126 VAL Chi-restraints excluded: chain B residue 1190 SER Chi-restraints excluded: chain B residue 1290 ASP Chi-restraints excluded: chain B residue 1304 LEU Chi-restraints excluded: chain B residue 1529 THR Chi-restraints excluded: chain B residue 1546 ILE Chi-restraints excluded: chain B residue 1790 LYS Chi-restraints excluded: chain B residue 2037 GLU Chi-restraints excluded: chain B residue 2073 SER Chi-restraints excluded: chain B residue 2085 SER Chi-restraints excluded: chain B residue 2093 ILE Chi-restraints excluded: chain B residue 2166 SER Chi-restraints excluded: chain B residue 2168 ILE Chi-restraints excluded: chain B residue 2305 VAL Chi-restraints excluded: chain C residue 499 ASP Chi-restraints excluded: chain C residue 501 GLU Chi-restraints excluded: chain C residue 538 THR Chi-restraints excluded: chain C residue 604 VAL Chi-restraints excluded: chain C residue 608 THR Chi-restraints excluded: chain C residue 835 VAL Chi-restraints excluded: chain C residue 851 THR Chi-restraints excluded: chain C residue 960 LEU Chi-restraints excluded: chain C residue 1126 VAL Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain C residue 1190 SER Chi-restraints excluded: chain C residue 1259 VAL Chi-restraints excluded: chain C residue 1290 ASP Chi-restraints excluded: chain C residue 1529 THR Chi-restraints excluded: chain C residue 1546 ILE Chi-restraints excluded: chain C residue 1798 ASP Chi-restraints excluded: chain C residue 2073 SER Chi-restraints excluded: chain C residue 2085 SER Chi-restraints excluded: chain C residue 2093 ILE Chi-restraints excluded: chain C residue 2166 SER Chi-restraints excluded: chain C residue 2249 THR Chi-restraints excluded: chain C residue 2305 VAL Chi-restraints excluded: chain C residue 2420 ASN Chi-restraints excluded: chain D residue 499 ASP Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 600 LEU Chi-restraints excluded: chain D residue 604 VAL Chi-restraints excluded: chain D residue 608 THR Chi-restraints excluded: chain D residue 637 MET Chi-restraints excluded: chain D residue 835 VAL Chi-restraints excluded: chain D residue 851 THR Chi-restraints excluded: chain D residue 1170 VAL Chi-restraints excluded: chain D residue 1190 SER Chi-restraints excluded: chain D residue 1197 LEU Chi-restraints excluded: chain D residue 1259 VAL Chi-restraints excluded: chain D residue 1290 ASP Chi-restraints excluded: chain D residue 1501 ILE Chi-restraints excluded: chain D residue 1529 THR Chi-restraints excluded: chain D residue 1546 ILE Chi-restraints excluded: chain D residue 1840 GLU Chi-restraints excluded: chain D residue 2073 SER Chi-restraints excluded: chain D residue 2093 ILE Chi-restraints excluded: chain D residue 2166 SER Chi-restraints excluded: chain D residue 2194 ILE Chi-restraints excluded: chain D residue 2249 THR Chi-restraints excluded: chain D residue 2305 VAL Chi-restraints excluded: chain D residue 2417 LEU Chi-restraints excluded: chain D residue 2420 ASN Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 278 THR Chi-restraints excluded: chain E residue 608 THR Chi-restraints excluded: chain E residue 654 THR Chi-restraints excluded: chain E residue 711 THR Chi-restraints excluded: chain E residue 835 VAL Chi-restraints excluded: chain E residue 851 THR Chi-restraints excluded: chain E residue 960 LEU Chi-restraints excluded: chain E residue 1126 VAL Chi-restraints excluded: chain E residue 1190 SER Chi-restraints excluded: chain E residue 1259 VAL Chi-restraints excluded: chain E residue 1304 LEU Chi-restraints excluded: chain E residue 1467 THR Chi-restraints excluded: chain E residue 1529 THR Chi-restraints excluded: chain E residue 1546 ILE Chi-restraints excluded: chain E residue 1652 VAL Chi-restraints excluded: chain E residue 1735 SER Chi-restraints excluded: chain E residue 1989 ASP Chi-restraints excluded: chain E residue 2093 ILE Chi-restraints excluded: chain E residue 2166 SER Chi-restraints excluded: chain E residue 2168 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1140 random chunks: chunk 575 optimal weight: 6.9990 chunk 321 optimal weight: 5.9990 chunk 861 optimal weight: 8.9990 chunk 704 optimal weight: 7.9990 chunk 285 optimal weight: 4.9990 chunk 1037 optimal weight: 20.0000 chunk 1120 optimal weight: 5.9990 chunk 923 optimal weight: 7.9990 chunk 1028 optimal weight: 0.5980 chunk 353 optimal weight: 7.9990 chunk 832 optimal weight: 10.0000 overall best weight: 4.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 ASN ** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 214 GLN A 371 HIS A 533 ASN A 910 GLN ** A 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1227 HIS A1279 ASN A1775 GLN A1872 ASN A1883 GLN A2188 GLN B 38 ASN ** B 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 216 ASN B 611 GLN ** B 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1279 ASN B1872 ASN B2188 GLN C 38 ASN ** C 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 216 ASN C 533 ASN C 606 ASN C 799 ASN ** C 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1028 GLN ** C1103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1279 ASN C1580 ASN C1872 ASN C2146 GLN D 38 ASN ** D 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 294 GLN D 371 HIS D 533 ASN ** D 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1103 HIS D1279 ASN D1872 ASN D2188 GLN E 38 ASN ** E 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 533 ASN E 652 ASN ** E 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 724 ASN ** E 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1249 HIS E1279 ASN E1767 ASN E1997 GLN E2146 GLN Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.075 90390 Z= 0.529 Angle : 0.713 8.938 122855 Z= 0.363 Chirality : 0.045 0.214 14085 Planarity : 0.005 0.058 15950 Dihedral : 5.663 54.135 12410 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 3.43 % Allowed : 18.11 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.08), residues: 11365 helix: 0.89 (0.07), residues: 5305 sheet: -1.67 (0.12), residues: 1555 loop : -1.79 (0.09), residues: 4505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E1560 HIS 0.023 0.001 HIS B 371 PHE 0.018 0.002 PHE A 205 TYR 0.025 0.002 TYR A1836 ARG 0.009 0.001 ARG E2307 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22730 Ramachandran restraints generated. 11365 Oldfield, 0 Emsley, 11365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22730 Ramachandran restraints generated. 11365 Oldfield, 0 Emsley, 11365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1274 residues out of total 9715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 323 poor density : 951 time to evaluate : 7.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 TYR cc_start: 0.7419 (OUTLIER) cc_final: 0.5912 (p90) REVERT: A 1630 ASP cc_start: 0.5157 (OUTLIER) cc_final: 0.3798 (t0) REVERT: A 2098 MET cc_start: 0.7968 (tpp) cc_final: 0.7733 (mmm) REVERT: A 2105 MET cc_start: 0.8111 (tpp) cc_final: 0.7860 (mmt) REVERT: A 2174 GLN cc_start: 0.8355 (OUTLIER) cc_final: 0.8127 (mt0) REVERT: A 2411 ASP cc_start: 0.6256 (OUTLIER) cc_final: 0.4453 (p0) REVERT: B 201 TYR cc_start: 0.7660 (OUTLIER) cc_final: 0.6184 (p90) REVERT: B 674 MET cc_start: 0.6891 (tpp) cc_final: 0.6628 (tpp) REVERT: B 706 MET cc_start: 0.8297 (mmt) cc_final: 0.8018 (mmp) REVERT: B 771 LEU cc_start: 0.8138 (OUTLIER) cc_final: 0.7815 (pp) REVERT: B 1630 ASP cc_start: 0.5317 (OUTLIER) cc_final: 0.4832 (t70) REVERT: C 201 TYR cc_start: 0.7518 (OUTLIER) cc_final: 0.6243 (p90) REVERT: C 291 ASP cc_start: 0.7855 (p0) cc_final: 0.7628 (p0) REVERT: C 367 LYS cc_start: -0.2194 (OUTLIER) cc_final: -0.2404 (pttp) REVERT: C 674 MET cc_start: 0.6666 (tpp) cc_final: 0.6227 (tpp) REVERT: C 706 MET cc_start: 0.8368 (mmt) cc_final: 0.7935 (mmp) REVERT: C 771 LEU cc_start: 0.8350 (OUTLIER) cc_final: 0.8061 (pp) REVERT: C 1232 MET cc_start: 0.8288 (mtm) cc_final: 0.8010 (mtt) REVERT: C 1630 ASP cc_start: 0.5809 (OUTLIER) cc_final: 0.4697 (t0) REVERT: C 1852 MET cc_start: 0.7600 (tpt) cc_final: 0.7368 (tpt) REVERT: C 2411 ASP cc_start: 0.6096 (OUTLIER) cc_final: 0.5885 (p0) REVERT: D 201 TYR cc_start: 0.7619 (OUTLIER) cc_final: 0.6316 (p90) REVERT: D 545 LEU cc_start: 0.9116 (OUTLIER) cc_final: 0.8847 (tt) REVERT: D 674 MET cc_start: 0.6766 (tpp) cc_final: 0.6413 (tpp) REVERT: D 1035 MET cc_start: 0.7901 (ttm) cc_final: 0.7699 (ttt) REVERT: D 1630 ASP cc_start: 0.5520 (OUTLIER) cc_final: 0.4233 (t0) REVERT: D 1840 GLU cc_start: 0.7430 (OUTLIER) cc_final: 0.7156 (pm20) REVERT: D 2411 ASP cc_start: 0.5589 (OUTLIER) cc_final: 0.5220 (p0) REVERT: E 201 TYR cc_start: 0.7845 (OUTLIER) cc_final: 0.6784 (p90) REVERT: E 615 LEU cc_start: 0.9381 (OUTLIER) cc_final: 0.9124 (mp) REVERT: E 771 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8108 (pp) REVERT: E 1630 ASP cc_start: 0.6090 (OUTLIER) cc_final: 0.4643 (t0) REVERT: E 2411 ASP cc_start: 0.6228 (OUTLIER) cc_final: 0.4870 (p0) outliers start: 323 outliers final: 199 residues processed: 1207 average time/residue: 0.7970 time to fit residues: 1689.8903 Evaluate side-chains 1092 residues out of total 9715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 221 poor density : 871 time to evaluate : 7.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 TYR Chi-restraints excluded: chain A residue 214 GLN Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 576 THR Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 653 ILE Chi-restraints excluded: chain A residue 764 LEU Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 835 VAL Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 1004 SER Chi-restraints excluded: chain A residue 1063 VAL Chi-restraints excluded: chain A residue 1126 VAL Chi-restraints excluded: chain A residue 1170 VAL Chi-restraints excluded: chain A residue 1185 THR Chi-restraints excluded: chain A residue 1190 SER Chi-restraints excluded: chain A residue 1197 LEU Chi-restraints excluded: chain A residue 1259 VAL Chi-restraints excluded: chain A residue 1290 ASP Chi-restraints excluded: chain A residue 1299 ILE Chi-restraints excluded: chain A residue 1467 THR Chi-restraints excluded: chain A residue 1529 THR Chi-restraints excluded: chain A residue 1546 ILE Chi-restraints excluded: chain A residue 1572 THR Chi-restraints excluded: chain A residue 1584 ASP Chi-restraints excluded: chain A residue 1596 GLU Chi-restraints excluded: chain A residue 1630 ASP Chi-restraints excluded: chain A residue 1639 VAL Chi-restraints excluded: chain A residue 1798 ASP Chi-restraints excluded: chain A residue 1889 ASP Chi-restraints excluded: chain A residue 1930 MET Chi-restraints excluded: chain A residue 2085 SER Chi-restraints excluded: chain A residue 2093 ILE Chi-restraints excluded: chain A residue 2166 SER Chi-restraints excluded: chain A residue 2174 GLN Chi-restraints excluded: chain A residue 2249 THR Chi-restraints excluded: chain A residue 2276 LEU Chi-restraints excluded: chain A residue 2282 MET Chi-restraints excluded: chain A residue 2411 ASP Chi-restraints excluded: chain B residue 201 TYR Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 280 ASP Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 576 THR Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain B residue 624 MET Chi-restraints excluded: chain B residue 637 MET Chi-restraints excluded: chain B residue 679 ASP Chi-restraints excluded: chain B residue 764 LEU Chi-restraints excluded: chain B residue 771 LEU Chi-restraints excluded: chain B residue 835 VAL Chi-restraints excluded: chain B residue 851 THR Chi-restraints excluded: chain B residue 960 LEU Chi-restraints excluded: chain B residue 1049 LEU Chi-restraints excluded: chain B residue 1126 VAL Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain B residue 1185 THR Chi-restraints excluded: chain B residue 1190 SER Chi-restraints excluded: chain B residue 1197 LEU Chi-restraints excluded: chain B residue 1259 VAL Chi-restraints excluded: chain B residue 1262 LEU Chi-restraints excluded: chain B residue 1290 ASP Chi-restraints excluded: chain B residue 1304 LEU Chi-restraints excluded: chain B residue 1450 VAL Chi-restraints excluded: chain B residue 1529 THR Chi-restraints excluded: chain B residue 1546 ILE Chi-restraints excluded: chain B residue 1572 THR Chi-restraints excluded: chain B residue 1630 ASP Chi-restraints excluded: chain B residue 1639 VAL Chi-restraints excluded: chain B residue 1790 LYS Chi-restraints excluded: chain B residue 1840 GLU Chi-restraints excluded: chain B residue 1930 MET Chi-restraints excluded: chain B residue 2037 GLU Chi-restraints excluded: chain B residue 2073 SER Chi-restraints excluded: chain B residue 2085 SER Chi-restraints excluded: chain B residue 2091 THR Chi-restraints excluded: chain B residue 2093 ILE Chi-restraints excluded: chain B residue 2095 VAL Chi-restraints excluded: chain B residue 2166 SER Chi-restraints excluded: chain B residue 2168 ILE Chi-restraints excluded: chain B residue 2420 ASN Chi-restraints excluded: chain C residue 201 TYR Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 367 LYS Chi-restraints excluded: chain C residue 371 HIS Chi-restraints excluded: chain C residue 499 ASP Chi-restraints excluded: chain C residue 538 THR Chi-restraints excluded: chain C residue 544 ILE Chi-restraints excluded: chain C residue 576 THR Chi-restraints excluded: chain C residue 604 VAL Chi-restraints excluded: chain C residue 608 THR Chi-restraints excluded: chain C residue 764 LEU Chi-restraints excluded: chain C residue 771 LEU Chi-restraints excluded: chain C residue 835 VAL Chi-restraints excluded: chain C residue 851 THR Chi-restraints excluded: chain C residue 960 LEU Chi-restraints excluded: chain C residue 1004 SER Chi-restraints excluded: chain C residue 1063 VAL Chi-restraints excluded: chain C residue 1126 VAL Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain C residue 1190 SER Chi-restraints excluded: chain C residue 1240 ILE Chi-restraints excluded: chain C residue 1259 VAL Chi-restraints excluded: chain C residue 1290 ASP Chi-restraints excluded: chain C residue 1304 LEU Chi-restraints excluded: chain C residue 1450 VAL Chi-restraints excluded: chain C residue 1467 THR Chi-restraints excluded: chain C residue 1501 ILE Chi-restraints excluded: chain C residue 1529 THR Chi-restraints excluded: chain C residue 1546 ILE Chi-restraints excluded: chain C residue 1572 THR Chi-restraints excluded: chain C residue 1596 GLU Chi-restraints excluded: chain C residue 1630 ASP Chi-restraints excluded: chain C residue 1639 VAL Chi-restraints excluded: chain C residue 1652 VAL Chi-restraints excluded: chain C residue 1798 ASP Chi-restraints excluded: chain C residue 1840 GLU Chi-restraints excluded: chain C residue 1891 ILE Chi-restraints excluded: chain C residue 2085 SER Chi-restraints excluded: chain C residue 2091 THR Chi-restraints excluded: chain C residue 2093 ILE Chi-restraints excluded: chain C residue 2166 SER Chi-restraints excluded: chain C residue 2249 THR Chi-restraints excluded: chain C residue 2276 LEU Chi-restraints excluded: chain C residue 2411 ASP Chi-restraints excluded: chain C residue 2420 ASN Chi-restraints excluded: chain D residue 201 TYR Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 371 HIS Chi-restraints excluded: chain D residue 459 VAL Chi-restraints excluded: chain D residue 499 ASP Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 544 ILE Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 576 THR Chi-restraints excluded: chain D residue 600 LEU Chi-restraints excluded: chain D residue 604 VAL Chi-restraints excluded: chain D residue 608 THR Chi-restraints excluded: chain D residue 615 LEU Chi-restraints excluded: chain D residue 637 MET Chi-restraints excluded: chain D residue 655 VAL Chi-restraints excluded: chain D residue 764 LEU Chi-restraints excluded: chain D residue 835 VAL Chi-restraints excluded: chain D residue 851 THR Chi-restraints excluded: chain D residue 960 LEU Chi-restraints excluded: chain D residue 1004 SER Chi-restraints excluded: chain D residue 1063 VAL Chi-restraints excluded: chain D residue 1170 VAL Chi-restraints excluded: chain D residue 1190 SER Chi-restraints excluded: chain D residue 1197 LEU Chi-restraints excluded: chain D residue 1259 VAL Chi-restraints excluded: chain D residue 1290 ASP Chi-restraints excluded: chain D residue 1292 THR Chi-restraints excluded: chain D residue 1304 LEU Chi-restraints excluded: chain D residue 1501 ILE Chi-restraints excluded: chain D residue 1503 ILE Chi-restraints excluded: chain D residue 1529 THR Chi-restraints excluded: chain D residue 1546 ILE Chi-restraints excluded: chain D residue 1572 THR Chi-restraints excluded: chain D residue 1630 ASP Chi-restraints excluded: chain D residue 1803 VAL Chi-restraints excluded: chain D residue 1840 GLU Chi-restraints excluded: chain D residue 1891 ILE Chi-restraints excluded: chain D residue 1930 MET Chi-restraints excluded: chain D residue 2093 ILE Chi-restraints excluded: chain D residue 2166 SER Chi-restraints excluded: chain D residue 2249 THR Chi-restraints excluded: chain D residue 2411 ASP Chi-restraints excluded: chain D residue 2417 LEU Chi-restraints excluded: chain D residue 2420 ASN Chi-restraints excluded: chain E residue 77 LYS Chi-restraints excluded: chain E residue 201 TYR Chi-restraints excluded: chain E residue 278 THR Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 576 THR Chi-restraints excluded: chain E residue 615 LEU Chi-restraints excluded: chain E residue 645 THR Chi-restraints excluded: chain E residue 654 THR Chi-restraints excluded: chain E residue 711 THR Chi-restraints excluded: chain E residue 764 LEU Chi-restraints excluded: chain E residue 771 LEU Chi-restraints excluded: chain E residue 835 VAL Chi-restraints excluded: chain E residue 851 THR Chi-restraints excluded: chain E residue 960 LEU Chi-restraints excluded: chain E residue 1126 VAL Chi-restraints excluded: chain E residue 1133 VAL Chi-restraints excluded: chain E residue 1185 THR Chi-restraints excluded: chain E residue 1190 SER Chi-restraints excluded: chain E residue 1255 THR Chi-restraints excluded: chain E residue 1259 VAL Chi-restraints excluded: chain E residue 1292 THR Chi-restraints excluded: chain E residue 1299 ILE Chi-restraints excluded: chain E residue 1304 LEU Chi-restraints excluded: chain E residue 1450 VAL Chi-restraints excluded: chain E residue 1467 THR Chi-restraints excluded: chain E residue 1503 ILE Chi-restraints excluded: chain E residue 1529 THR Chi-restraints excluded: chain E residue 1546 ILE Chi-restraints excluded: chain E residue 1596 GLU Chi-restraints excluded: chain E residue 1630 ASP Chi-restraints excluded: chain E residue 1639 VAL Chi-restraints excluded: chain E residue 1652 VAL Chi-restraints excluded: chain E residue 1930 MET Chi-restraints excluded: chain E residue 1948 LEU Chi-restraints excluded: chain E residue 2093 ILE Chi-restraints excluded: chain E residue 2166 SER Chi-restraints excluded: chain E residue 2168 ILE Chi-restraints excluded: chain E residue 2276 LEU Chi-restraints excluded: chain E residue 2411 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1140 random chunks: chunk 1024 optimal weight: 1.9990 chunk 779 optimal weight: 0.9980 chunk 538 optimal weight: 3.9990 chunk 114 optimal weight: 0.6980 chunk 494 optimal weight: 0.1980 chunk 696 optimal weight: 0.8980 chunk 1040 optimal weight: 10.0000 chunk 1101 optimal weight: 0.9990 chunk 543 optimal weight: 1.9990 chunk 986 optimal weight: 8.9990 chunk 296 optimal weight: 3.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 533 ASN A 910 GLN ** A 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1767 ASN A2052 GLN A2188 GLN ** A2195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 611 GLN B 912 GLN ** B 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1767 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2188 GLN B2195 GLN C 158 ASN ** C 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 216 ASN C 606 ASN ** C 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1767 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2146 GLN C2195 GLN ** C2344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 158 ASN D 184 ASN ** D 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 371 HIS D 606 ASN D 910 GLN ** D 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1767 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2052 GLN D2188 GLN ** D2195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 184 ASN ** E 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 652 ASN ** E 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E2052 GLN E2146 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.2781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 90390 Z= 0.159 Angle : 0.566 9.573 122855 Z= 0.287 Chirality : 0.040 0.196 14085 Planarity : 0.004 0.047 15950 Dihedral : 5.001 48.809 12406 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 2.34 % Allowed : 19.37 % Favored : 78.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.08), residues: 11365 helix: 1.48 (0.07), residues: 5295 sheet: -1.32 (0.13), residues: 1495 loop : -1.57 (0.09), residues: 4575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E1560 HIS 0.030 0.001 HIS D 371 PHE 0.017 0.001 PHE E1714 TYR 0.014 0.001 TYR A1836 ARG 0.010 0.000 ARG E2307 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22730 Ramachandran restraints generated. 11365 Oldfield, 0 Emsley, 11365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22730 Ramachandran restraints generated. 11365 Oldfield, 0 Emsley, 11365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1247 residues out of total 9715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 221 poor density : 1026 time to evaluate : 7.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 674 MET cc_start: 0.6762 (tpp) cc_final: 0.6148 (tpp) REVERT: A 1826 ASP cc_start: 0.7031 (m-30) cc_final: 0.6447 (m-30) REVERT: B 771 LEU cc_start: 0.7996 (OUTLIER) cc_final: 0.7761 (pp) REVERT: C 637 MET cc_start: 0.8299 (tmm) cc_final: 0.8092 (tmm) REVERT: C 674 MET cc_start: 0.6528 (tpp) cc_final: 0.6253 (tpp) REVERT: C 1232 MET cc_start: 0.8188 (mtm) cc_final: 0.7868 (mtt) REVERT: D 545 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8878 (tt) REVERT: D 613 ASP cc_start: 0.6751 (t0) cc_final: 0.6288 (t0) REVERT: D 649 ASN cc_start: 0.8649 (m-40) cc_final: 0.8324 (m-40) REVERT: D 674 MET cc_start: 0.6587 (tpp) cc_final: 0.6380 (tpp) REVERT: D 2105 MET cc_start: 0.8118 (mmm) cc_final: 0.7843 (mmm) REVERT: E 201 TYR cc_start: 0.7550 (OUTLIER) cc_final: 0.6210 (p90) REVERT: E 613 ASP cc_start: 0.7014 (t0) cc_final: 0.6575 (t0) REVERT: E 615 LEU cc_start: 0.9300 (OUTLIER) cc_final: 0.9070 (mp) REVERT: E 658 LEU cc_start: 0.9173 (tp) cc_final: 0.8906 (tp) REVERT: E 771 LEU cc_start: 0.8249 (OUTLIER) cc_final: 0.7926 (pp) REVERT: E 2194 ILE cc_start: 0.8773 (tt) cc_final: 0.8360 (pt) outliers start: 221 outliers final: 130 residues processed: 1193 average time/residue: 0.7986 time to fit residues: 1662.2006 Evaluate side-chains 1041 residues out of total 9715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 906 time to evaluate : 7.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 280 ASP Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 371 HIS Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 653 ILE Chi-restraints excluded: chain A residue 835 VAL Chi-restraints excluded: chain A residue 1032 MET Chi-restraints excluded: chain A residue 1126 VAL Chi-restraints excluded: chain A residue 1170 VAL Chi-restraints excluded: chain A residue 1185 THR Chi-restraints excluded: chain A residue 1190 SER Chi-restraints excluded: chain A residue 1197 LEU Chi-restraints excluded: chain A residue 1259 VAL Chi-restraints excluded: chain A residue 1290 ASP Chi-restraints excluded: chain A residue 1292 THR Chi-restraints excluded: chain A residue 1546 ILE Chi-restraints excluded: chain A residue 1639 VAL Chi-restraints excluded: chain A residue 1840 GLU Chi-restraints excluded: chain A residue 1889 ASP Chi-restraints excluded: chain A residue 1903 VAL Chi-restraints excluded: chain A residue 2085 SER Chi-restraints excluded: chain A residue 2093 ILE Chi-restraints excluded: chain A residue 2249 THR Chi-restraints excluded: chain B residue 280 ASP Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 371 HIS Chi-restraints excluded: chain B residue 499 ASP Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 637 MET Chi-restraints excluded: chain B residue 764 LEU Chi-restraints excluded: chain B residue 771 LEU Chi-restraints excluded: chain B residue 835 VAL Chi-restraints excluded: chain B residue 1049 LEU Chi-restraints excluded: chain B residue 1126 VAL Chi-restraints excluded: chain B residue 1185 THR Chi-restraints excluded: chain B residue 1190 SER Chi-restraints excluded: chain B residue 1259 VAL Chi-restraints excluded: chain B residue 1290 ASP Chi-restraints excluded: chain B residue 1292 THR Chi-restraints excluded: chain B residue 1304 LEU Chi-restraints excluded: chain B residue 1450 VAL Chi-restraints excluded: chain B residue 1529 THR Chi-restraints excluded: chain B residue 1546 ILE Chi-restraints excluded: chain B residue 1639 VAL Chi-restraints excluded: chain B residue 1903 VAL Chi-restraints excluded: chain B residue 1930 MET Chi-restraints excluded: chain B residue 2037 GLU Chi-restraints excluded: chain B residue 2073 SER Chi-restraints excluded: chain B residue 2093 ILE Chi-restraints excluded: chain B residue 2168 ILE Chi-restraints excluded: chain B residue 2420 ASN Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 371 HIS Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 544 ILE Chi-restraints excluded: chain C residue 604 VAL Chi-restraints excluded: chain C residue 608 THR Chi-restraints excluded: chain C residue 835 VAL Chi-restraints excluded: chain C residue 1004 SER Chi-restraints excluded: chain C residue 1126 VAL Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain C residue 1185 THR Chi-restraints excluded: chain C residue 1190 SER Chi-restraints excluded: chain C residue 1259 VAL Chi-restraints excluded: chain C residue 1290 ASP Chi-restraints excluded: chain C residue 1304 LEU Chi-restraints excluded: chain C residue 1450 VAL Chi-restraints excluded: chain C residue 1467 THR Chi-restraints excluded: chain C residue 1546 ILE Chi-restraints excluded: chain C residue 1652 VAL Chi-restraints excluded: chain C residue 1903 VAL Chi-restraints excluded: chain C residue 2093 ILE Chi-restraints excluded: chain C residue 2249 THR Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 371 HIS Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 499 ASP Chi-restraints excluded: chain D residue 544 ILE Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 600 LEU Chi-restraints excluded: chain D residue 604 VAL Chi-restraints excluded: chain D residue 608 THR Chi-restraints excluded: chain D residue 637 MET Chi-restraints excluded: chain D residue 835 VAL Chi-restraints excluded: chain D residue 1004 SER Chi-restraints excluded: chain D residue 1032 MET Chi-restraints excluded: chain D residue 1170 VAL Chi-restraints excluded: chain D residue 1190 SER Chi-restraints excluded: chain D residue 1259 VAL Chi-restraints excluded: chain D residue 1290 ASP Chi-restraints excluded: chain D residue 1304 LEU Chi-restraints excluded: chain D residue 1450 VAL Chi-restraints excluded: chain D residue 1501 ILE Chi-restraints excluded: chain D residue 1503 ILE Chi-restraints excluded: chain D residue 1529 THR Chi-restraints excluded: chain D residue 1546 ILE Chi-restraints excluded: chain D residue 1596 GLU Chi-restraints excluded: chain D residue 1803 VAL Chi-restraints excluded: chain D residue 1903 VAL Chi-restraints excluded: chain D residue 1930 MET Chi-restraints excluded: chain D residue 2093 ILE Chi-restraints excluded: chain D residue 2249 THR Chi-restraints excluded: chain E residue 201 TYR Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 502 THR Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 544 ILE Chi-restraints excluded: chain E residue 615 LEU Chi-restraints excluded: chain E residue 654 THR Chi-restraints excluded: chain E residue 771 LEU Chi-restraints excluded: chain E residue 835 VAL Chi-restraints excluded: chain E residue 1048 THR Chi-restraints excluded: chain E residue 1126 VAL Chi-restraints excluded: chain E residue 1185 THR Chi-restraints excluded: chain E residue 1190 SER Chi-restraints excluded: chain E residue 1259 VAL Chi-restraints excluded: chain E residue 1304 LEU Chi-restraints excluded: chain E residue 1450 VAL Chi-restraints excluded: chain E residue 1529 THR Chi-restraints excluded: chain E residue 1546 ILE Chi-restraints excluded: chain E residue 1596 GLU Chi-restraints excluded: chain E residue 1652 VAL Chi-restraints excluded: chain E residue 1723 THR Chi-restraints excluded: chain E residue 1903 VAL Chi-restraints excluded: chain E residue 2093 ILE Chi-restraints excluded: chain E residue 2166 SER Chi-restraints excluded: chain E residue 2168 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1140 random chunks: chunk 917 optimal weight: 0.9980 chunk 625 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 820 optimal weight: 3.9990 chunk 454 optimal weight: 1.9990 chunk 940 optimal weight: 0.0870 chunk 761 optimal weight: 10.0000 chunk 1 optimal weight: 5.9990 chunk 562 optimal weight: 1.9990 chunk 989 optimal weight: 3.9990 chunk 278 optimal weight: 8.9990 overall best weight: 1.6164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 ASN ** A 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 533 ASN ** A 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 910 GLN ** A 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1767 ASN A1775 GLN ** A2195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 611 GLN B 910 GLN ** B 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1767 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 216 ASN ** C 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1767 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 371 HIS D 533 ASN ** D 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1767 ASN ** D2344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 652 ASN ** E 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.2910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 90390 Z= 0.216 Angle : 0.571 8.712 122855 Z= 0.288 Chirality : 0.040 0.196 14085 Planarity : 0.004 0.048 15950 Dihedral : 4.822 46.402 12391 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 2.82 % Allowed : 19.77 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.08), residues: 11365 helix: 1.66 (0.07), residues: 5295 sheet: -1.19 (0.13), residues: 1445 loop : -1.44 (0.10), residues: 4625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E1560 HIS 0.010 0.001 HIS D 371 PHE 0.015 0.001 PHE E1714 TYR 0.018 0.001 TYR A2216 ARG 0.010 0.000 ARG C2307 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22730 Ramachandran restraints generated. 11365 Oldfield, 0 Emsley, 11365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22730 Ramachandran restraints generated. 11365 Oldfield, 0 Emsley, 11365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1205 residues out of total 9715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 266 poor density : 939 time to evaluate : 8.087 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 TYR cc_start: 0.7372 (OUTLIER) cc_final: 0.5863 (p90) REVERT: A 674 MET cc_start: 0.6870 (tpp) cc_final: 0.6614 (tpp) REVERT: A 1840 GLU cc_start: 0.7461 (OUTLIER) cc_final: 0.7078 (pm20) REVERT: B 201 TYR cc_start: 0.7633 (OUTLIER) cc_final: 0.6216 (p90) REVERT: B 771 LEU cc_start: 0.7972 (OUTLIER) cc_final: 0.7748 (pp) REVERT: B 976 ILE cc_start: 0.8958 (OUTLIER) cc_final: 0.8713 (tt) REVERT: C 201 TYR cc_start: 0.7392 (OUTLIER) cc_final: 0.6001 (p90) REVERT: C 637 MET cc_start: 0.8312 (tmm) cc_final: 0.8048 (tmm) REVERT: C 674 MET cc_start: 0.6567 (tpp) cc_final: 0.6311 (tpp) REVERT: C 1232 MET cc_start: 0.8221 (mtm) cc_final: 0.7913 (mtt) REVERT: C 1924 TYR cc_start: 0.7975 (m-10) cc_final: 0.7618 (m-80) REVERT: D 201 TYR cc_start: 0.7557 (OUTLIER) cc_final: 0.6137 (p90) REVERT: D 674 MET cc_start: 0.6658 (tpp) cc_final: 0.6401 (tpp) REVERT: E 201 TYR cc_start: 0.7667 (OUTLIER) cc_final: 0.6334 (p90) REVERT: E 615 LEU cc_start: 0.9301 (OUTLIER) cc_final: 0.9092 (mp) REVERT: E 658 LEU cc_start: 0.9246 (tp) cc_final: 0.9004 (tp) REVERT: E 771 LEU cc_start: 0.8211 (OUTLIER) cc_final: 0.7849 (pp) REVERT: E 1226 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8591 (tt) outliers start: 266 outliers final: 161 residues processed: 1146 average time/residue: 0.7764 time to fit residues: 1569.4059 Evaluate side-chains 1063 residues out of total 9715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 891 time to evaluate : 7.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 TYR Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 280 ASP Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 371 HIS Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 653 ILE Chi-restraints excluded: chain A residue 764 LEU Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 835 VAL Chi-restraints excluded: chain A residue 1004 SER Chi-restraints excluded: chain A residue 1032 MET Chi-restraints excluded: chain A residue 1063 VAL Chi-restraints excluded: chain A residue 1126 VAL Chi-restraints excluded: chain A residue 1170 VAL Chi-restraints excluded: chain A residue 1185 THR Chi-restraints excluded: chain A residue 1190 SER Chi-restraints excluded: chain A residue 1197 LEU Chi-restraints excluded: chain A residue 1259 VAL Chi-restraints excluded: chain A residue 1290 ASP Chi-restraints excluded: chain A residue 1292 THR Chi-restraints excluded: chain A residue 1304 LEU Chi-restraints excluded: chain A residue 1450 VAL Chi-restraints excluded: chain A residue 1501 ILE Chi-restraints excluded: chain A residue 1529 THR Chi-restraints excluded: chain A residue 1546 ILE Chi-restraints excluded: chain A residue 1572 THR Chi-restraints excluded: chain A residue 1584 ASP Chi-restraints excluded: chain A residue 1775 GLN Chi-restraints excluded: chain A residue 1798 ASP Chi-restraints excluded: chain A residue 1840 GLU Chi-restraints excluded: chain A residue 1889 ASP Chi-restraints excluded: chain A residue 1903 VAL Chi-restraints excluded: chain A residue 1930 MET Chi-restraints excluded: chain A residue 2085 SER Chi-restraints excluded: chain A residue 2093 ILE Chi-restraints excluded: chain A residue 2249 THR Chi-restraints excluded: chain B residue 201 TYR Chi-restraints excluded: chain B residue 280 ASP Chi-restraints excluded: chain B residue 371 HIS Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 499 ASP Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 637 MET Chi-restraints excluded: chain B residue 764 LEU Chi-restraints excluded: chain B residue 771 LEU Chi-restraints excluded: chain B residue 835 VAL Chi-restraints excluded: chain B residue 840 LEU Chi-restraints excluded: chain B residue 976 ILE Chi-restraints excluded: chain B residue 1049 LEU Chi-restraints excluded: chain B residue 1126 VAL Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain B residue 1185 THR Chi-restraints excluded: chain B residue 1190 SER Chi-restraints excluded: chain B residue 1259 VAL Chi-restraints excluded: chain B residue 1290 ASP Chi-restraints excluded: chain B residue 1292 THR Chi-restraints excluded: chain B residue 1304 LEU Chi-restraints excluded: chain B residue 1450 VAL Chi-restraints excluded: chain B residue 1501 ILE Chi-restraints excluded: chain B residue 1531 THR Chi-restraints excluded: chain B residue 1546 ILE Chi-restraints excluded: chain B residue 1639 VAL Chi-restraints excluded: chain B residue 1790 LYS Chi-restraints excluded: chain B residue 1903 VAL Chi-restraints excluded: chain B residue 1930 MET Chi-restraints excluded: chain B residue 2037 GLU Chi-restraints excluded: chain B residue 2073 SER Chi-restraints excluded: chain B residue 2093 ILE Chi-restraints excluded: chain B residue 2168 ILE Chi-restraints excluded: chain B residue 2274 SER Chi-restraints excluded: chain B residue 2420 ASN Chi-restraints excluded: chain C residue 201 TYR Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 371 HIS Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 499 ASP Chi-restraints excluded: chain C residue 538 THR Chi-restraints excluded: chain C residue 544 ILE Chi-restraints excluded: chain C residue 608 THR Chi-restraints excluded: chain C residue 835 VAL Chi-restraints excluded: chain C residue 1004 SER Chi-restraints excluded: chain C residue 1126 VAL Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain C residue 1185 THR Chi-restraints excluded: chain C residue 1190 SER Chi-restraints excluded: chain C residue 1259 VAL Chi-restraints excluded: chain C residue 1290 ASP Chi-restraints excluded: chain C residue 1304 LEU Chi-restraints excluded: chain C residue 1450 VAL Chi-restraints excluded: chain C residue 1467 THR Chi-restraints excluded: chain C residue 1529 THR Chi-restraints excluded: chain C residue 1546 ILE Chi-restraints excluded: chain C residue 1596 GLU Chi-restraints excluded: chain C residue 1639 VAL Chi-restraints excluded: chain C residue 1652 VAL Chi-restraints excluded: chain C residue 1798 ASP Chi-restraints excluded: chain C residue 1903 VAL Chi-restraints excluded: chain C residue 2093 ILE Chi-restraints excluded: chain C residue 2249 THR Chi-restraints excluded: chain D residue 201 TYR Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 499 ASP Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 544 ILE Chi-restraints excluded: chain D residue 600 LEU Chi-restraints excluded: chain D residue 604 VAL Chi-restraints excluded: chain D residue 608 THR Chi-restraints excluded: chain D residue 637 MET Chi-restraints excluded: chain D residue 835 VAL Chi-restraints excluded: chain D residue 1004 SER Chi-restraints excluded: chain D residue 1032 MET Chi-restraints excluded: chain D residue 1170 VAL Chi-restraints excluded: chain D residue 1190 SER Chi-restraints excluded: chain D residue 1259 VAL Chi-restraints excluded: chain D residue 1290 ASP Chi-restraints excluded: chain D residue 1304 LEU Chi-restraints excluded: chain D residue 1313 THR Chi-restraints excluded: chain D residue 1450 VAL Chi-restraints excluded: chain D residue 1501 ILE Chi-restraints excluded: chain D residue 1503 ILE Chi-restraints excluded: chain D residue 1546 ILE Chi-restraints excluded: chain D residue 1560 TRP Chi-restraints excluded: chain D residue 1803 VAL Chi-restraints excluded: chain D residue 1930 MET Chi-restraints excluded: chain D residue 1976 SER Chi-restraints excluded: chain D residue 2089 LEU Chi-restraints excluded: chain D residue 2093 ILE Chi-restraints excluded: chain D residue 2249 THR Chi-restraints excluded: chain E residue 201 TYR Chi-restraints excluded: chain E residue 278 THR Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 499 ASP Chi-restraints excluded: chain E residue 502 THR Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 544 ILE Chi-restraints excluded: chain E residue 615 LEU Chi-restraints excluded: chain E residue 624 MET Chi-restraints excluded: chain E residue 637 MET Chi-restraints excluded: chain E residue 654 THR Chi-restraints excluded: chain E residue 764 LEU Chi-restraints excluded: chain E residue 771 LEU Chi-restraints excluded: chain E residue 835 VAL Chi-restraints excluded: chain E residue 1048 THR Chi-restraints excluded: chain E residue 1126 VAL Chi-restraints excluded: chain E residue 1185 THR Chi-restraints excluded: chain E residue 1190 SER Chi-restraints excluded: chain E residue 1226 LEU Chi-restraints excluded: chain E residue 1259 VAL Chi-restraints excluded: chain E residue 1304 LEU Chi-restraints excluded: chain E residue 1450 VAL Chi-restraints excluded: chain E residue 1503 ILE Chi-restraints excluded: chain E residue 1546 ILE Chi-restraints excluded: chain E residue 1596 GLU Chi-restraints excluded: chain E residue 1652 VAL Chi-restraints excluded: chain E residue 1723 THR Chi-restraints excluded: chain E residue 1903 VAL Chi-restraints excluded: chain E residue 1930 MET Chi-restraints excluded: chain E residue 2093 ILE Chi-restraints excluded: chain E residue 2168 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1140 random chunks: chunk 370 optimal weight: 2.9990 chunk 992 optimal weight: 4.9990 chunk 217 optimal weight: 3.9990 chunk 646 optimal weight: 3.9990 chunk 272 optimal weight: 0.9990 chunk 1102 optimal weight: 0.9990 chunk 915 optimal weight: 0.9990 chunk 510 optimal weight: 20.0000 chunk 91 optimal weight: 0.0050 chunk 364 optimal weight: 8.9990 chunk 579 optimal weight: 10.0000 overall best weight: 1.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 777 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1767 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 611 GLN ** B 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1767 ASN ** C 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 216 ASN C 533 ASN ** C 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1767 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1767 ASN ** D2344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 652 ASN ** E 777 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E2146 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.3117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 90390 Z= 0.182 Angle : 0.560 10.186 122855 Z= 0.282 Chirality : 0.040 0.255 14085 Planarity : 0.004 0.048 15950 Dihedral : 4.638 45.664 12387 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 2.82 % Allowed : 20.46 % Favored : 76.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.08), residues: 11365 helix: 1.81 (0.07), residues: 5295 sheet: -1.02 (0.13), residues: 1485 loop : -1.32 (0.10), residues: 4585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1560 HIS 0.006 0.001 HIS E2191 PHE 0.014 0.001 PHE E1714 TYR 0.015 0.001 TYR C 496 ARG 0.012 0.000 ARG E2307 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22730 Ramachandran restraints generated. 11365 Oldfield, 0 Emsley, 11365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22730 Ramachandran restraints generated. 11365 Oldfield, 0 Emsley, 11365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1237 residues out of total 9715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 266 poor density : 971 time to evaluate : 7.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 TYR cc_start: 0.7361 (OUTLIER) cc_final: 0.5787 (p90) REVERT: A 637 MET cc_start: 0.8159 (tmm) cc_final: 0.7804 (tmm) REVERT: A 674 MET cc_start: 0.6794 (tpp) cc_final: 0.6552 (tpp) REVERT: A 1840 GLU cc_start: 0.7485 (OUTLIER) cc_final: 0.7104 (pm20) REVERT: B 976 ILE cc_start: 0.8932 (OUTLIER) cc_final: 0.8701 (tt) REVERT: B 1232 MET cc_start: 0.7776 (mtt) cc_final: 0.7545 (mtt) REVERT: C 201 TYR cc_start: 0.7459 (OUTLIER) cc_final: 0.5973 (p90) REVERT: C 637 MET cc_start: 0.8326 (tmm) cc_final: 0.8037 (tmm) REVERT: C 674 MET cc_start: 0.6428 (tpp) cc_final: 0.6183 (tpp) REVERT: C 1232 MET cc_start: 0.8278 (mtm) cc_final: 0.7904 (mtt) REVERT: D 201 TYR cc_start: 0.7504 (OUTLIER) cc_final: 0.6019 (p90) REVERT: D 649 ASN cc_start: 0.8632 (m-40) cc_final: 0.8298 (m-40) REVERT: D 674 MET cc_start: 0.6605 (tpp) cc_final: 0.6355 (tpp) REVERT: D 2105 MET cc_start: 0.7941 (mmm) cc_final: 0.7575 (mmm) REVERT: E 201 TYR cc_start: 0.7585 (OUTLIER) cc_final: 0.6165 (p90) REVERT: E 615 LEU cc_start: 0.9307 (OUTLIER) cc_final: 0.9103 (mp) REVERT: E 658 LEU cc_start: 0.9253 (tp) cc_final: 0.9037 (tp) REVERT: E 771 LEU cc_start: 0.8197 (OUTLIER) cc_final: 0.7884 (pp) REVERT: E 1226 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8654 (tt) outliers start: 266 outliers final: 171 residues processed: 1180 average time/residue: 0.8167 time to fit residues: 1711.0823 Evaluate side-chains 1086 residues out of total 9715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 906 time to evaluate : 7.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 201 TYR Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 371 HIS Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 653 ILE Chi-restraints excluded: chain A residue 764 LEU Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 835 VAL Chi-restraints excluded: chain A residue 1004 SER Chi-restraints excluded: chain A residue 1032 MET Chi-restraints excluded: chain A residue 1063 VAL Chi-restraints excluded: chain A residue 1126 VAL Chi-restraints excluded: chain A residue 1170 VAL Chi-restraints excluded: chain A residue 1185 THR Chi-restraints excluded: chain A residue 1190 SER Chi-restraints excluded: chain A residue 1197 LEU Chi-restraints excluded: chain A residue 1259 VAL Chi-restraints excluded: chain A residue 1290 ASP Chi-restraints excluded: chain A residue 1292 THR Chi-restraints excluded: chain A residue 1304 LEU Chi-restraints excluded: chain A residue 1450 VAL Chi-restraints excluded: chain A residue 1529 THR Chi-restraints excluded: chain A residue 1546 ILE Chi-restraints excluded: chain A residue 1584 ASP Chi-restraints excluded: chain A residue 1639 VAL Chi-restraints excluded: chain A residue 1752 MET Chi-restraints excluded: chain A residue 1798 ASP Chi-restraints excluded: chain A residue 1840 GLU Chi-restraints excluded: chain A residue 1889 ASP Chi-restraints excluded: chain A residue 1903 VAL Chi-restraints excluded: chain A residue 2073 SER Chi-restraints excluded: chain A residue 2085 SER Chi-restraints excluded: chain A residue 2091 THR Chi-restraints excluded: chain A residue 2093 ILE Chi-restraints excluded: chain B residue 280 ASP Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 371 HIS Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 637 MET Chi-restraints excluded: chain B residue 835 VAL Chi-restraints excluded: chain B residue 976 ILE Chi-restraints excluded: chain B residue 1049 LEU Chi-restraints excluded: chain B residue 1126 VAL Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain B residue 1185 THR Chi-restraints excluded: chain B residue 1190 SER Chi-restraints excluded: chain B residue 1259 VAL Chi-restraints excluded: chain B residue 1290 ASP Chi-restraints excluded: chain B residue 1292 THR Chi-restraints excluded: chain B residue 1304 LEU Chi-restraints excluded: chain B residue 1450 VAL Chi-restraints excluded: chain B residue 1503 ILE Chi-restraints excluded: chain B residue 1529 THR Chi-restraints excluded: chain B residue 1531 THR Chi-restraints excluded: chain B residue 1545 VAL Chi-restraints excluded: chain B residue 1546 ILE Chi-restraints excluded: chain B residue 1560 TRP Chi-restraints excluded: chain B residue 1630 ASP Chi-restraints excluded: chain B residue 1790 LYS Chi-restraints excluded: chain B residue 1881 LYS Chi-restraints excluded: chain B residue 1903 VAL Chi-restraints excluded: chain B residue 1910 THR Chi-restraints excluded: chain B residue 1930 MET Chi-restraints excluded: chain B residue 1976 SER Chi-restraints excluded: chain B residue 2037 GLU Chi-restraints excluded: chain B residue 2073 SER Chi-restraints excluded: chain B residue 2093 ILE Chi-restraints excluded: chain B residue 2168 ILE Chi-restraints excluded: chain B residue 2274 SER Chi-restraints excluded: chain B residue 2420 ASN Chi-restraints excluded: chain C residue 201 TYR Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 371 HIS Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 499 ASP Chi-restraints excluded: chain C residue 544 ILE Chi-restraints excluded: chain C residue 608 THR Chi-restraints excluded: chain C residue 679 ASP Chi-restraints excluded: chain C residue 835 VAL Chi-restraints excluded: chain C residue 1004 SER Chi-restraints excluded: chain C residue 1126 VAL Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain C residue 1185 THR Chi-restraints excluded: chain C residue 1190 SER Chi-restraints excluded: chain C residue 1259 VAL Chi-restraints excluded: chain C residue 1290 ASP Chi-restraints excluded: chain C residue 1304 LEU Chi-restraints excluded: chain C residue 1450 VAL Chi-restraints excluded: chain C residue 1467 THR Chi-restraints excluded: chain C residue 1501 ILE Chi-restraints excluded: chain C residue 1529 THR Chi-restraints excluded: chain C residue 1531 THR Chi-restraints excluded: chain C residue 1546 ILE Chi-restraints excluded: chain C residue 1619 THR Chi-restraints excluded: chain C residue 1639 VAL Chi-restraints excluded: chain C residue 1652 VAL Chi-restraints excluded: chain C residue 1903 VAL Chi-restraints excluded: chain C residue 2073 SER Chi-restraints excluded: chain C residue 2093 ILE Chi-restraints excluded: chain C residue 2168 ILE Chi-restraints excluded: chain D residue 201 TYR Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 437 ILE Chi-restraints excluded: chain D residue 459 VAL Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 499 ASP Chi-restraints excluded: chain D residue 544 ILE Chi-restraints excluded: chain D residue 600 LEU Chi-restraints excluded: chain D residue 604 VAL Chi-restraints excluded: chain D residue 608 THR Chi-restraints excluded: chain D residue 637 MET Chi-restraints excluded: chain D residue 771 LEU Chi-restraints excluded: chain D residue 1004 SER Chi-restraints excluded: chain D residue 1032 MET Chi-restraints excluded: chain D residue 1170 VAL Chi-restraints excluded: chain D residue 1190 SER Chi-restraints excluded: chain D residue 1240 ILE Chi-restraints excluded: chain D residue 1259 VAL Chi-restraints excluded: chain D residue 1290 ASP Chi-restraints excluded: chain D residue 1304 LEU Chi-restraints excluded: chain D residue 1450 VAL Chi-restraints excluded: chain D residue 1501 ILE Chi-restraints excluded: chain D residue 1503 ILE Chi-restraints excluded: chain D residue 1529 THR Chi-restraints excluded: chain D residue 1545 VAL Chi-restraints excluded: chain D residue 1546 ILE Chi-restraints excluded: chain D residue 1560 TRP Chi-restraints excluded: chain D residue 1652 VAL Chi-restraints excluded: chain D residue 1803 VAL Chi-restraints excluded: chain D residue 1930 MET Chi-restraints excluded: chain D residue 2089 LEU Chi-restraints excluded: chain D residue 2093 ILE Chi-restraints excluded: chain D residue 2249 THR Chi-restraints excluded: chain D residue 2282 MET Chi-restraints excluded: chain E residue 201 TYR Chi-restraints excluded: chain E residue 278 THR Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 459 VAL Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 499 ASP Chi-restraints excluded: chain E residue 502 THR Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 544 ILE Chi-restraints excluded: chain E residue 615 LEU Chi-restraints excluded: chain E residue 624 MET Chi-restraints excluded: chain E residue 637 MET Chi-restraints excluded: chain E residue 654 THR Chi-restraints excluded: chain E residue 771 LEU Chi-restraints excluded: chain E residue 835 VAL Chi-restraints excluded: chain E residue 1048 THR Chi-restraints excluded: chain E residue 1126 VAL Chi-restraints excluded: chain E residue 1185 THR Chi-restraints excluded: chain E residue 1190 SER Chi-restraints excluded: chain E residue 1226 LEU Chi-restraints excluded: chain E residue 1259 VAL Chi-restraints excluded: chain E residue 1304 LEU Chi-restraints excluded: chain E residue 1450 VAL Chi-restraints excluded: chain E residue 1467 THR Chi-restraints excluded: chain E residue 1503 ILE Chi-restraints excluded: chain E residue 1529 THR Chi-restraints excluded: chain E residue 1546 ILE Chi-restraints excluded: chain E residue 1560 TRP Chi-restraints excluded: chain E residue 1619 THR Chi-restraints excluded: chain E residue 1652 VAL Chi-restraints excluded: chain E residue 1723 THR Chi-restraints excluded: chain E residue 1903 VAL Chi-restraints excluded: chain E residue 2093 ILE Chi-restraints excluded: chain E residue 2168 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1140 random chunks: chunk 1063 optimal weight: 7.9990 chunk 124 optimal weight: 9.9990 chunk 628 optimal weight: 2.9990 chunk 805 optimal weight: 0.3980 chunk 624 optimal weight: 0.0000 chunk 928 optimal weight: 0.8980 chunk 615 optimal weight: 3.9990 chunk 1098 optimal weight: 0.9980 chunk 687 optimal weight: 0.9990 chunk 669 optimal weight: 6.9990 chunk 507 optimal weight: 9.9990 overall best weight: 0.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1767 ASN ** A2195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 ASN B 611 GLN ** B 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1767 ASN B2052 GLN ** B2344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 ASN ** C 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1767 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1926 GLN ** C2344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 777 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1767 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2195 GLN ** D2344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D2353 ASN E 652 ASN ** E 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1250 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.3348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 90390 Z= 0.151 Angle : 0.558 10.924 122855 Z= 0.279 Chirality : 0.039 0.281 14085 Planarity : 0.004 0.049 15950 Dihedral : 4.471 43.367 12385 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 2.45 % Allowed : 21.20 % Favored : 76.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.08), residues: 11365 helix: 1.93 (0.07), residues: 5305 sheet: -0.82 (0.13), residues: 1470 loop : -1.29 (0.10), residues: 4590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D1560 HIS 0.006 0.001 HIS E2191 PHE 0.014 0.001 PHE E1520 TYR 0.015 0.001 TYR A1924 ARG 0.011 0.000 ARG E2208 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22730 Ramachandran restraints generated. 11365 Oldfield, 0 Emsley, 11365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22730 Ramachandran restraints generated. 11365 Oldfield, 0 Emsley, 11365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1233 residues out of total 9715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 231 poor density : 1002 time to evaluate : 8.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 637 MET cc_start: 0.8146 (tmm) cc_final: 0.7837 (tmm) REVERT: A 1840 GLU cc_start: 0.7200 (OUTLIER) cc_final: 0.6822 (pm20) REVERT: A 2105 MET cc_start: 0.8061 (tpp) cc_final: 0.7829 (tpt) REVERT: B 1232 MET cc_start: 0.7837 (mtt) cc_final: 0.7593 (mtt) REVERT: C 501 GLU cc_start: 0.6866 (OUTLIER) cc_final: 0.6533 (tp30) REVERT: C 637 MET cc_start: 0.8311 (tmm) cc_final: 0.8018 (tmm) REVERT: C 674 MET cc_start: 0.6545 (tpp) cc_final: 0.5837 (tpp) REVERT: C 1826 ASP cc_start: 0.7220 (m-30) cc_final: 0.6752 (m-30) REVERT: C 1924 TYR cc_start: 0.7837 (m-80) cc_final: 0.7493 (m-80) REVERT: D 649 ASN cc_start: 0.8635 (m-40) cc_final: 0.8349 (m-40) REVERT: D 2105 MET cc_start: 0.7965 (mmm) cc_final: 0.7673 (mmm) REVERT: E 201 TYR cc_start: 0.7484 (OUTLIER) cc_final: 0.6053 (p90) REVERT: E 658 LEU cc_start: 0.9200 (tp) cc_final: 0.8934 (tp) REVERT: E 771 LEU cc_start: 0.8085 (OUTLIER) cc_final: 0.7812 (pp) REVERT: E 1519 ARG cc_start: 0.7183 (ttp80) cc_final: 0.6926 (ttp80) REVERT: E 1833 ASP cc_start: 0.7702 (m-30) cc_final: 0.7434 (m-30) outliers start: 231 outliers final: 171 residues processed: 1178 average time/residue: 0.7747 time to fit residues: 1611.2303 Evaluate side-chains 1108 residues out of total 9715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 933 time to evaluate : 8.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 280 ASP Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 371 HIS Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 764 LEU Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 835 VAL Chi-restraints excluded: chain A residue 845 GLN Chi-restraints excluded: chain A residue 1004 SER Chi-restraints excluded: chain A residue 1032 MET Chi-restraints excluded: chain A residue 1063 VAL Chi-restraints excluded: chain A residue 1126 VAL Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain A residue 1170 VAL Chi-restraints excluded: chain A residue 1185 THR Chi-restraints excluded: chain A residue 1190 SER Chi-restraints excluded: chain A residue 1195 THR Chi-restraints excluded: chain A residue 1197 LEU Chi-restraints excluded: chain A residue 1259 VAL Chi-restraints excluded: chain A residue 1290 ASP Chi-restraints excluded: chain A residue 1292 THR Chi-restraints excluded: chain A residue 1304 LEU Chi-restraints excluded: chain A residue 1450 VAL Chi-restraints excluded: chain A residue 1467 THR Chi-restraints excluded: chain A residue 1501 ILE Chi-restraints excluded: chain A residue 1529 THR Chi-restraints excluded: chain A residue 1545 VAL Chi-restraints excluded: chain A residue 1546 ILE Chi-restraints excluded: chain A residue 1584 ASP Chi-restraints excluded: chain A residue 1639 VAL Chi-restraints excluded: chain A residue 1752 MET Chi-restraints excluded: chain A residue 1840 GLU Chi-restraints excluded: chain A residue 1889 ASP Chi-restraints excluded: chain A residue 1903 VAL Chi-restraints excluded: chain A residue 2085 SER Chi-restraints excluded: chain A residue 2093 ILE Chi-restraints excluded: chain B residue 280 ASP Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 371 HIS Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 671 THR Chi-restraints excluded: chain B residue 835 VAL Chi-restraints excluded: chain B residue 845 GLN Chi-restraints excluded: chain B residue 1126 VAL Chi-restraints excluded: chain B residue 1185 THR Chi-restraints excluded: chain B residue 1190 SER Chi-restraints excluded: chain B residue 1259 VAL Chi-restraints excluded: chain B residue 1290 ASP Chi-restraints excluded: chain B residue 1292 THR Chi-restraints excluded: chain B residue 1304 LEU Chi-restraints excluded: chain B residue 1450 VAL Chi-restraints excluded: chain B residue 1458 ILE Chi-restraints excluded: chain B residue 1465 ASN Chi-restraints excluded: chain B residue 1503 ILE Chi-restraints excluded: chain B residue 1529 THR Chi-restraints excluded: chain B residue 1545 VAL Chi-restraints excluded: chain B residue 1546 ILE Chi-restraints excluded: chain B residue 1560 TRP Chi-restraints excluded: chain B residue 1630 ASP Chi-restraints excluded: chain B residue 1693 LEU Chi-restraints excluded: chain B residue 1752 MET Chi-restraints excluded: chain B residue 1790 LYS Chi-restraints excluded: chain B residue 1903 VAL Chi-restraints excluded: chain B residue 1930 MET Chi-restraints excluded: chain B residue 1976 SER Chi-restraints excluded: chain B residue 1999 MET Chi-restraints excluded: chain B residue 2037 GLU Chi-restraints excluded: chain B residue 2073 SER Chi-restraints excluded: chain B residue 2093 ILE Chi-restraints excluded: chain B residue 2168 ILE Chi-restraints excluded: chain B residue 2420 ASN Chi-restraints excluded: chain C residue 371 HIS Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 499 ASP Chi-restraints excluded: chain C residue 501 GLU Chi-restraints excluded: chain C residue 538 THR Chi-restraints excluded: chain C residue 544 ILE Chi-restraints excluded: chain C residue 608 THR Chi-restraints excluded: chain C residue 835 VAL Chi-restraints excluded: chain C residue 845 GLN Chi-restraints excluded: chain C residue 1126 VAL Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain C residue 1185 THR Chi-restraints excluded: chain C residue 1190 SER Chi-restraints excluded: chain C residue 1259 VAL Chi-restraints excluded: chain C residue 1290 ASP Chi-restraints excluded: chain C residue 1304 LEU Chi-restraints excluded: chain C residue 1450 VAL Chi-restraints excluded: chain C residue 1501 ILE Chi-restraints excluded: chain C residue 1529 THR Chi-restraints excluded: chain C residue 1546 ILE Chi-restraints excluded: chain C residue 1619 THR Chi-restraints excluded: chain C residue 1630 ASP Chi-restraints excluded: chain C residue 1639 VAL Chi-restraints excluded: chain C residue 1652 VAL Chi-restraints excluded: chain C residue 1903 VAL Chi-restraints excluded: chain C residue 2085 SER Chi-restraints excluded: chain C residue 2093 ILE Chi-restraints excluded: chain C residue 2168 ILE Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 371 HIS Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 544 ILE Chi-restraints excluded: chain D residue 600 LEU Chi-restraints excluded: chain D residue 604 VAL Chi-restraints excluded: chain D residue 608 THR Chi-restraints excluded: chain D residue 637 MET Chi-restraints excluded: chain D residue 771 LEU Chi-restraints excluded: chain D residue 845 GLN Chi-restraints excluded: chain D residue 1170 VAL Chi-restraints excluded: chain D residue 1240 ILE Chi-restraints excluded: chain D residue 1259 VAL Chi-restraints excluded: chain D residue 1290 ASP Chi-restraints excluded: chain D residue 1304 LEU Chi-restraints excluded: chain D residue 1450 VAL Chi-restraints excluded: chain D residue 1501 ILE Chi-restraints excluded: chain D residue 1503 ILE Chi-restraints excluded: chain D residue 1529 THR Chi-restraints excluded: chain D residue 1545 VAL Chi-restraints excluded: chain D residue 1546 ILE Chi-restraints excluded: chain D residue 1560 TRP Chi-restraints excluded: chain D residue 1644 LEU Chi-restraints excluded: chain D residue 1803 VAL Chi-restraints excluded: chain D residue 1842 ASP Chi-restraints excluded: chain D residue 1882 THR Chi-restraints excluded: chain D residue 2093 ILE Chi-restraints excluded: chain D residue 2249 THR Chi-restraints excluded: chain E residue 201 TYR Chi-restraints excluded: chain E residue 278 THR Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 459 VAL Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 502 THR Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 544 ILE Chi-restraints excluded: chain E residue 624 MET Chi-restraints excluded: chain E residue 630 ASP Chi-restraints excluded: chain E residue 637 MET Chi-restraints excluded: chain E residue 654 THR Chi-restraints excluded: chain E residue 671 THR Chi-restraints excluded: chain E residue 771 LEU Chi-restraints excluded: chain E residue 835 VAL Chi-restraints excluded: chain E residue 1048 THR Chi-restraints excluded: chain E residue 1126 VAL Chi-restraints excluded: chain E residue 1185 THR Chi-restraints excluded: chain E residue 1190 SER Chi-restraints excluded: chain E residue 1259 VAL Chi-restraints excluded: chain E residue 1304 LEU Chi-restraints excluded: chain E residue 1450 VAL Chi-restraints excluded: chain E residue 1467 THR Chi-restraints excluded: chain E residue 1503 ILE Chi-restraints excluded: chain E residue 1529 THR Chi-restraints excluded: chain E residue 1546 ILE Chi-restraints excluded: chain E residue 1560 TRP Chi-restraints excluded: chain E residue 1596 GLU Chi-restraints excluded: chain E residue 1619 THR Chi-restraints excluded: chain E residue 1630 ASP Chi-restraints excluded: chain E residue 1652 VAL Chi-restraints excluded: chain E residue 1723 THR Chi-restraints excluded: chain E residue 1903 VAL Chi-restraints excluded: chain E residue 2093 ILE Chi-restraints excluded: chain E residue 2168 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1140 random chunks: chunk 679 optimal weight: 7.9990 chunk 438 optimal weight: 1.9990 chunk 656 optimal weight: 0.9980 chunk 330 optimal weight: 0.9990 chunk 215 optimal weight: 8.9990 chunk 212 optimal weight: 20.0000 chunk 698 optimal weight: 3.9990 chunk 748 optimal weight: 20.0000 chunk 543 optimal weight: 0.9990 chunk 102 optimal weight: 2.9990 chunk 863 optimal weight: 2.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1767 ASN ** A2344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 611 GLN ** B 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1767 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 216 ASN ** C 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 777 GLN ** C 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1169 HIS ** C2344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 351 GLN D 355 GLN ** D 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 777 GLN ** D 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1250 GLN ** D1767 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 652 ASN ** E 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1926 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.3354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 90390 Z= 0.215 Angle : 0.577 11.337 122855 Z= 0.290 Chirality : 0.040 0.333 14085 Planarity : 0.004 0.049 15950 Dihedral : 4.509 43.249 12385 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 2.75 % Allowed : 21.59 % Favored : 75.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.08), residues: 11365 helix: 1.92 (0.07), residues: 5330 sheet: -0.76 (0.13), residues: 1470 loop : -1.28 (0.10), residues: 4565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D1560 HIS 0.006 0.001 HIS D2191 PHE 0.014 0.001 PHE E1520 TYR 0.018 0.001 TYR A1924 ARG 0.009 0.000 ARG E2208 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22730 Ramachandran restraints generated. 11365 Oldfield, 0 Emsley, 11365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22730 Ramachandran restraints generated. 11365 Oldfield, 0 Emsley, 11365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1205 residues out of total 9715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 259 poor density : 946 time to evaluate : 9.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 TYR cc_start: 0.7426 (OUTLIER) cc_final: 0.5825 (p90) REVERT: A 637 MET cc_start: 0.8193 (tmm) cc_final: 0.7874 (tmm) REVERT: A 674 MET cc_start: 0.6308 (tpp) cc_final: 0.5670 (tpp) REVERT: A 767 ARG cc_start: 0.7760 (ttm-80) cc_final: 0.7472 (mmt-90) REVERT: A 2105 MET cc_start: 0.8140 (tpp) cc_final: 0.7938 (tpt) REVERT: B 201 TYR cc_start: 0.7674 (OUTLIER) cc_final: 0.6191 (p90) REVERT: B 624 MET cc_start: 0.7162 (tmm) cc_final: 0.6919 (ttp) REVERT: B 630 ASP cc_start: 0.8361 (OUTLIER) cc_final: 0.8048 (p0) REVERT: B 1232 MET cc_start: 0.7859 (mtt) cc_final: 0.7649 (mtt) REVERT: C 201 TYR cc_start: 0.7431 (OUTLIER) cc_final: 0.6052 (p90) REVERT: C 501 GLU cc_start: 0.6850 (OUTLIER) cc_final: 0.6501 (tp30) REVERT: C 637 MET cc_start: 0.8345 (tmm) cc_final: 0.8035 (tmm) REVERT: C 674 MET cc_start: 0.6601 (tpp) cc_final: 0.6345 (tpp) REVERT: C 1032 MET cc_start: 0.7816 (OUTLIER) cc_final: 0.7237 (tmm) REVERT: C 1560 TRP cc_start: 0.8458 (OUTLIER) cc_final: 0.6465 (p-90) REVERT: C 2105 MET cc_start: 0.8220 (mmm) cc_final: 0.8016 (mmm) REVERT: D 201 TYR cc_start: 0.7566 (OUTLIER) cc_final: 0.5933 (p90) REVERT: D 355 GLN cc_start: 0.7093 (OUTLIER) cc_final: 0.6786 (tp-100) REVERT: D 649 ASN cc_start: 0.8643 (m-40) cc_final: 0.8365 (m-40) REVERT: D 712 GLU cc_start: 0.7084 (mp0) cc_final: 0.6839 (mp0) REVERT: E 201 TYR cc_start: 0.7549 (OUTLIER) cc_final: 0.6073 (p90) REVERT: E 771 LEU cc_start: 0.8206 (OUTLIER) cc_final: 0.7867 (pp) REVERT: E 827 GLN cc_start: 0.7949 (tm-30) cc_final: 0.7687 (tm-30) REVERT: E 1833 ASP cc_start: 0.7641 (m-30) cc_final: 0.7362 (m-30) outliers start: 259 outliers final: 198 residues processed: 1149 average time/residue: 0.7660 time to fit residues: 1561.5789 Evaluate side-chains 1125 residues out of total 9715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 209 poor density : 916 time to evaluate : 7.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 201 TYR Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 371 HIS Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 653 ILE Chi-restraints excluded: chain A residue 671 THR Chi-restraints excluded: chain A residue 835 VAL Chi-restraints excluded: chain A residue 845 GLN Chi-restraints excluded: chain A residue 1004 SER Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1032 MET Chi-restraints excluded: chain A residue 1063 VAL Chi-restraints excluded: chain A residue 1126 VAL Chi-restraints excluded: chain A residue 1170 VAL Chi-restraints excluded: chain A residue 1185 THR Chi-restraints excluded: chain A residue 1190 SER Chi-restraints excluded: chain A residue 1195 THR Chi-restraints excluded: chain A residue 1197 LEU Chi-restraints excluded: chain A residue 1259 VAL Chi-restraints excluded: chain A residue 1290 ASP Chi-restraints excluded: chain A residue 1292 THR Chi-restraints excluded: chain A residue 1299 ILE Chi-restraints excluded: chain A residue 1304 LEU Chi-restraints excluded: chain A residue 1450 VAL Chi-restraints excluded: chain A residue 1467 THR Chi-restraints excluded: chain A residue 1501 ILE Chi-restraints excluded: chain A residue 1503 ILE Chi-restraints excluded: chain A residue 1529 THR Chi-restraints excluded: chain A residue 1545 VAL Chi-restraints excluded: chain A residue 1546 ILE Chi-restraints excluded: chain A residue 1639 VAL Chi-restraints excluded: chain A residue 1752 MET Chi-restraints excluded: chain A residue 1798 ASP Chi-restraints excluded: chain A residue 1889 ASP Chi-restraints excluded: chain A residue 1903 VAL Chi-restraints excluded: chain A residue 2085 SER Chi-restraints excluded: chain A residue 2091 THR Chi-restraints excluded: chain A residue 2093 ILE Chi-restraints excluded: chain B residue 201 TYR Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 499 ASP Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 630 ASP Chi-restraints excluded: chain B residue 671 THR Chi-restraints excluded: chain B residue 835 VAL Chi-restraints excluded: chain B residue 845 GLN Chi-restraints excluded: chain B residue 1126 VAL Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain B residue 1185 THR Chi-restraints excluded: chain B residue 1190 SER Chi-restraints excluded: chain B residue 1259 VAL Chi-restraints excluded: chain B residue 1290 ASP Chi-restraints excluded: chain B residue 1292 THR Chi-restraints excluded: chain B residue 1304 LEU Chi-restraints excluded: chain B residue 1450 VAL Chi-restraints excluded: chain B residue 1458 ILE Chi-restraints excluded: chain B residue 1501 ILE Chi-restraints excluded: chain B residue 1503 ILE Chi-restraints excluded: chain B residue 1529 THR Chi-restraints excluded: chain B residue 1531 THR Chi-restraints excluded: chain B residue 1545 VAL Chi-restraints excluded: chain B residue 1546 ILE Chi-restraints excluded: chain B residue 1558 MET Chi-restraints excluded: chain B residue 1560 TRP Chi-restraints excluded: chain B residue 1630 ASP Chi-restraints excluded: chain B residue 1693 LEU Chi-restraints excluded: chain B residue 1752 MET Chi-restraints excluded: chain B residue 1790 LYS Chi-restraints excluded: chain B residue 1881 LYS Chi-restraints excluded: chain B residue 1903 VAL Chi-restraints excluded: chain B residue 1910 THR Chi-restraints excluded: chain B residue 1976 SER Chi-restraints excluded: chain B residue 2037 GLU Chi-restraints excluded: chain B residue 2073 SER Chi-restraints excluded: chain B residue 2093 ILE Chi-restraints excluded: chain B residue 2168 ILE Chi-restraints excluded: chain B residue 2420 ASN Chi-restraints excluded: chain C residue 201 TYR Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 371 HIS Chi-restraints excluded: chain C residue 437 ILE Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 499 ASP Chi-restraints excluded: chain C residue 501 GLU Chi-restraints excluded: chain C residue 538 THR Chi-restraints excluded: chain C residue 544 ILE Chi-restraints excluded: chain C residue 608 THR Chi-restraints excluded: chain C residue 835 VAL Chi-restraints excluded: chain C residue 1004 SER Chi-restraints excluded: chain C residue 1032 MET Chi-restraints excluded: chain C residue 1126 VAL Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain C residue 1185 THR Chi-restraints excluded: chain C residue 1190 SER Chi-restraints excluded: chain C residue 1259 VAL Chi-restraints excluded: chain C residue 1290 ASP Chi-restraints excluded: chain C residue 1304 LEU Chi-restraints excluded: chain C residue 1450 VAL Chi-restraints excluded: chain C residue 1467 THR Chi-restraints excluded: chain C residue 1501 ILE Chi-restraints excluded: chain C residue 1529 THR Chi-restraints excluded: chain C residue 1546 ILE Chi-restraints excluded: chain C residue 1560 TRP Chi-restraints excluded: chain C residue 1575 LEU Chi-restraints excluded: chain C residue 1619 THR Chi-restraints excluded: chain C residue 1630 ASP Chi-restraints excluded: chain C residue 1639 VAL Chi-restraints excluded: chain C residue 1652 VAL Chi-restraints excluded: chain C residue 1798 ASP Chi-restraints excluded: chain C residue 1903 VAL Chi-restraints excluded: chain C residue 2085 SER Chi-restraints excluded: chain C residue 2093 ILE Chi-restraints excluded: chain C residue 2305 VAL Chi-restraints excluded: chain C residue 2353 ASN Chi-restraints excluded: chain D residue 201 TYR Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 355 GLN Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 371 HIS Chi-restraints excluded: chain D residue 437 ILE Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 544 ILE Chi-restraints excluded: chain D residue 600 LEU Chi-restraints excluded: chain D residue 604 VAL Chi-restraints excluded: chain D residue 608 THR Chi-restraints excluded: chain D residue 637 MET Chi-restraints excluded: chain D residue 655 VAL Chi-restraints excluded: chain D residue 671 THR Chi-restraints excluded: chain D residue 771 LEU Chi-restraints excluded: chain D residue 835 VAL Chi-restraints excluded: chain D residue 845 GLN Chi-restraints excluded: chain D residue 1063 VAL Chi-restraints excluded: chain D residue 1170 VAL Chi-restraints excluded: chain D residue 1190 SER Chi-restraints excluded: chain D residue 1240 ILE Chi-restraints excluded: chain D residue 1259 VAL Chi-restraints excluded: chain D residue 1290 ASP Chi-restraints excluded: chain D residue 1292 THR Chi-restraints excluded: chain D residue 1304 LEU Chi-restraints excluded: chain D residue 1450 VAL Chi-restraints excluded: chain D residue 1501 ILE Chi-restraints excluded: chain D residue 1503 ILE Chi-restraints excluded: chain D residue 1529 THR Chi-restraints excluded: chain D residue 1531 THR Chi-restraints excluded: chain D residue 1545 VAL Chi-restraints excluded: chain D residue 1546 ILE Chi-restraints excluded: chain D residue 1560 TRP Chi-restraints excluded: chain D residue 1644 LEU Chi-restraints excluded: chain D residue 1652 VAL Chi-restraints excluded: chain D residue 1803 VAL Chi-restraints excluded: chain D residue 1842 ASP Chi-restraints excluded: chain D residue 1882 THR Chi-restraints excluded: chain D residue 2089 LEU Chi-restraints excluded: chain D residue 2093 ILE Chi-restraints excluded: chain E residue 201 TYR Chi-restraints excluded: chain E residue 202 ASN Chi-restraints excluded: chain E residue 278 THR Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 459 VAL Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 499 ASP Chi-restraints excluded: chain E residue 502 THR Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 544 ILE Chi-restraints excluded: chain E residue 572 LEU Chi-restraints excluded: chain E residue 624 MET Chi-restraints excluded: chain E residue 630 ASP Chi-restraints excluded: chain E residue 637 MET Chi-restraints excluded: chain E residue 654 THR Chi-restraints excluded: chain E residue 671 THR Chi-restraints excluded: chain E residue 764 LEU Chi-restraints excluded: chain E residue 771 LEU Chi-restraints excluded: chain E residue 835 VAL Chi-restraints excluded: chain E residue 845 GLN Chi-restraints excluded: chain E residue 1048 THR Chi-restraints excluded: chain E residue 1126 VAL Chi-restraints excluded: chain E residue 1185 THR Chi-restraints excluded: chain E residue 1190 SER Chi-restraints excluded: chain E residue 1259 VAL Chi-restraints excluded: chain E residue 1304 LEU Chi-restraints excluded: chain E residue 1450 VAL Chi-restraints excluded: chain E residue 1467 THR Chi-restraints excluded: chain E residue 1503 ILE Chi-restraints excluded: chain E residue 1529 THR Chi-restraints excluded: chain E residue 1546 ILE Chi-restraints excluded: chain E residue 1596 GLU Chi-restraints excluded: chain E residue 1619 THR Chi-restraints excluded: chain E residue 1630 ASP Chi-restraints excluded: chain E residue 1652 VAL Chi-restraints excluded: chain E residue 1723 THR Chi-restraints excluded: chain E residue 1903 VAL Chi-restraints excluded: chain E residue 2093 ILE Chi-restraints excluded: chain E residue 2168 ILE Chi-restraints excluded: chain E residue 2329 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1140 random chunks: chunk 999 optimal weight: 1.9990 chunk 1052 optimal weight: 3.9990 chunk 960 optimal weight: 3.9990 chunk 1023 optimal weight: 0.0980 chunk 616 optimal weight: 1.9990 chunk 446 optimal weight: 7.9990 chunk 804 optimal weight: 0.4980 chunk 314 optimal weight: 6.9990 chunk 925 optimal weight: 6.9990 chunk 968 optimal weight: 8.9990 chunk 1020 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 777 GLN ** A 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1767 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 533 ASN ** B 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1767 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 216 ASN ** C 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1103 HIS ** C1767 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1926 GLN ** C2344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 355 GLN ** D 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1767 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 652 ASN ** E 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1926 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.3437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 90390 Z= 0.208 Angle : 0.581 12.530 122855 Z= 0.291 Chirality : 0.040 0.317 14085 Planarity : 0.004 0.050 15950 Dihedral : 4.499 43.256 12384 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 2.68 % Allowed : 21.91 % Favored : 75.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.08), residues: 11365 helix: 1.95 (0.07), residues: 5330 sheet: -0.69 (0.13), residues: 1470 loop : -1.25 (0.10), residues: 4565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D1560 HIS 0.007 0.001 HIS D2191 PHE 0.026 0.001 PHE D 356 TYR 0.017 0.001 TYR A1924 ARG 0.009 0.000 ARG E2307 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22730 Ramachandran restraints generated. 11365 Oldfield, 0 Emsley, 11365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22730 Ramachandran restraints generated. 11365 Oldfield, 0 Emsley, 11365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1206 residues out of total 9715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 253 poor density : 953 time to evaluate : 8.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 TYR cc_start: 0.7424 (OUTLIER) cc_final: 0.5942 (p90) REVERT: A 637 MET cc_start: 0.8202 (tmm) cc_final: 0.7878 (tmm) REVERT: A 674 MET cc_start: 0.6137 (tpp) cc_final: 0.5468 (tpp) REVERT: A 767 ARG cc_start: 0.7816 (ttm-80) cc_final: 0.7545 (mmt-90) REVERT: B 201 TYR cc_start: 0.7648 (OUTLIER) cc_final: 0.6161 (p90) REVERT: B 630 ASP cc_start: 0.8346 (OUTLIER) cc_final: 0.8051 (p0) REVERT: B 914 GLN cc_start: 0.7887 (tm-30) cc_final: 0.7669 (tm-30) REVERT: B 1232 MET cc_start: 0.7854 (mtt) cc_final: 0.7629 (mtt) REVERT: B 1302 LEU cc_start: 0.7585 (mm) cc_final: 0.7375 (mm) REVERT: C 201 TYR cc_start: 0.7431 (OUTLIER) cc_final: 0.6169 (p90) REVERT: C 501 GLU cc_start: 0.6884 (OUTLIER) cc_final: 0.6537 (tp30) REVERT: C 637 MET cc_start: 0.8351 (tmm) cc_final: 0.8035 (tmm) REVERT: C 674 MET cc_start: 0.6612 (tpp) cc_final: 0.6377 (tpp) REVERT: C 1560 TRP cc_start: 0.8402 (OUTLIER) cc_final: 0.6283 (p-90) REVERT: D 201 TYR cc_start: 0.7585 (OUTLIER) cc_final: 0.5978 (p90) REVERT: D 712 GLU cc_start: 0.7122 (mp0) cc_final: 0.6896 (mp0) REVERT: E 201 TYR cc_start: 0.7528 (OUTLIER) cc_final: 0.6060 (p90) REVERT: E 771 LEU cc_start: 0.8248 (OUTLIER) cc_final: 0.7777 (pp) REVERT: E 827 GLN cc_start: 0.7935 (tm-30) cc_final: 0.7671 (tm-30) REVERT: E 1833 ASP cc_start: 0.7717 (m-30) cc_final: 0.7443 (m-30) outliers start: 253 outliers final: 211 residues processed: 1151 average time/residue: 0.7763 time to fit residues: 1583.7790 Evaluate side-chains 1138 residues out of total 9715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 220 poor density : 918 time to evaluate : 7.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 TYR Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 371 HIS Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 653 ILE Chi-restraints excluded: chain A residue 671 THR Chi-restraints excluded: chain A residue 835 VAL Chi-restraints excluded: chain A residue 845 GLN Chi-restraints excluded: chain A residue 1004 SER Chi-restraints excluded: chain A residue 1032 MET Chi-restraints excluded: chain A residue 1063 VAL Chi-restraints excluded: chain A residue 1126 VAL Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain A residue 1170 VAL Chi-restraints excluded: chain A residue 1185 THR Chi-restraints excluded: chain A residue 1190 SER Chi-restraints excluded: chain A residue 1195 THR Chi-restraints excluded: chain A residue 1197 LEU Chi-restraints excluded: chain A residue 1259 VAL Chi-restraints excluded: chain A residue 1290 ASP Chi-restraints excluded: chain A residue 1292 THR Chi-restraints excluded: chain A residue 1299 ILE Chi-restraints excluded: chain A residue 1304 LEU Chi-restraints excluded: chain A residue 1450 VAL Chi-restraints excluded: chain A residue 1467 THR Chi-restraints excluded: chain A residue 1501 ILE Chi-restraints excluded: chain A residue 1503 ILE Chi-restraints excluded: chain A residue 1529 THR Chi-restraints excluded: chain A residue 1545 VAL Chi-restraints excluded: chain A residue 1546 ILE Chi-restraints excluded: chain A residue 1584 ASP Chi-restraints excluded: chain A residue 1639 VAL Chi-restraints excluded: chain A residue 1752 MET Chi-restraints excluded: chain A residue 1798 ASP Chi-restraints excluded: chain A residue 1889 ASP Chi-restraints excluded: chain A residue 1903 VAL Chi-restraints excluded: chain A residue 1930 MET Chi-restraints excluded: chain A residue 2085 SER Chi-restraints excluded: chain A residue 2091 THR Chi-restraints excluded: chain A residue 2093 ILE Chi-restraints excluded: chain B residue 201 TYR Chi-restraints excluded: chain B residue 280 ASP Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 371 HIS Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 499 ASP Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 630 ASP Chi-restraints excluded: chain B residue 671 THR Chi-restraints excluded: chain B residue 835 VAL Chi-restraints excluded: chain B residue 845 GLN Chi-restraints excluded: chain B residue 1004 SER Chi-restraints excluded: chain B residue 1126 VAL Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain B residue 1185 THR Chi-restraints excluded: chain B residue 1190 SER Chi-restraints excluded: chain B residue 1259 VAL Chi-restraints excluded: chain B residue 1290 ASP Chi-restraints excluded: chain B residue 1292 THR Chi-restraints excluded: chain B residue 1304 LEU Chi-restraints excluded: chain B residue 1450 VAL Chi-restraints excluded: chain B residue 1458 ILE Chi-restraints excluded: chain B residue 1503 ILE Chi-restraints excluded: chain B residue 1529 THR Chi-restraints excluded: chain B residue 1531 THR Chi-restraints excluded: chain B residue 1545 VAL Chi-restraints excluded: chain B residue 1546 ILE Chi-restraints excluded: chain B residue 1558 MET Chi-restraints excluded: chain B residue 1560 TRP Chi-restraints excluded: chain B residue 1630 ASP Chi-restraints excluded: chain B residue 1693 LEU Chi-restraints excluded: chain B residue 1723 THR Chi-restraints excluded: chain B residue 1790 LYS Chi-restraints excluded: chain B residue 1881 LYS Chi-restraints excluded: chain B residue 1882 THR Chi-restraints excluded: chain B residue 1903 VAL Chi-restraints excluded: chain B residue 1910 THR Chi-restraints excluded: chain B residue 1976 SER Chi-restraints excluded: chain B residue 2037 GLU Chi-restraints excluded: chain B residue 2073 SER Chi-restraints excluded: chain B residue 2093 ILE Chi-restraints excluded: chain B residue 2168 ILE Chi-restraints excluded: chain B residue 2420 ASN Chi-restraints excluded: chain C residue 201 TYR Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 371 HIS Chi-restraints excluded: chain C residue 437 ILE Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 499 ASP Chi-restraints excluded: chain C residue 501 GLU Chi-restraints excluded: chain C residue 538 THR Chi-restraints excluded: chain C residue 544 ILE Chi-restraints excluded: chain C residue 608 THR Chi-restraints excluded: chain C residue 835 VAL Chi-restraints excluded: chain C residue 1004 SER Chi-restraints excluded: chain C residue 1063 VAL Chi-restraints excluded: chain C residue 1126 VAL Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain C residue 1185 THR Chi-restraints excluded: chain C residue 1190 SER Chi-restraints excluded: chain C residue 1197 LEU Chi-restraints excluded: chain C residue 1259 VAL Chi-restraints excluded: chain C residue 1290 ASP Chi-restraints excluded: chain C residue 1304 LEU Chi-restraints excluded: chain C residue 1450 VAL Chi-restraints excluded: chain C residue 1501 ILE Chi-restraints excluded: chain C residue 1529 THR Chi-restraints excluded: chain C residue 1531 THR Chi-restraints excluded: chain C residue 1546 ILE Chi-restraints excluded: chain C residue 1560 TRP Chi-restraints excluded: chain C residue 1572 THR Chi-restraints excluded: chain C residue 1575 LEU Chi-restraints excluded: chain C residue 1619 THR Chi-restraints excluded: chain C residue 1630 ASP Chi-restraints excluded: chain C residue 1639 VAL Chi-restraints excluded: chain C residue 1652 VAL Chi-restraints excluded: chain C residue 1798 ASP Chi-restraints excluded: chain C residue 1842 ASP Chi-restraints excluded: chain C residue 1903 VAL Chi-restraints excluded: chain C residue 2085 SER Chi-restraints excluded: chain C residue 2093 ILE Chi-restraints excluded: chain C residue 2249 THR Chi-restraints excluded: chain C residue 2305 VAL Chi-restraints excluded: chain C residue 2353 ASN Chi-restraints excluded: chain D residue 201 TYR Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 371 HIS Chi-restraints excluded: chain D residue 437 ILE Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 499 ASP Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 544 ILE Chi-restraints excluded: chain D residue 600 LEU Chi-restraints excluded: chain D residue 604 VAL Chi-restraints excluded: chain D residue 608 THR Chi-restraints excluded: chain D residue 615 LEU Chi-restraints excluded: chain D residue 637 MET Chi-restraints excluded: chain D residue 655 VAL Chi-restraints excluded: chain D residue 671 THR Chi-restraints excluded: chain D residue 771 LEU Chi-restraints excluded: chain D residue 835 VAL Chi-restraints excluded: chain D residue 845 GLN Chi-restraints excluded: chain D residue 1063 VAL Chi-restraints excluded: chain D residue 1170 VAL Chi-restraints excluded: chain D residue 1190 SER Chi-restraints excluded: chain D residue 1240 ILE Chi-restraints excluded: chain D residue 1259 VAL Chi-restraints excluded: chain D residue 1290 ASP Chi-restraints excluded: chain D residue 1292 THR Chi-restraints excluded: chain D residue 1304 LEU Chi-restraints excluded: chain D residue 1450 VAL Chi-restraints excluded: chain D residue 1501 ILE Chi-restraints excluded: chain D residue 1503 ILE Chi-restraints excluded: chain D residue 1529 THR Chi-restraints excluded: chain D residue 1545 VAL Chi-restraints excluded: chain D residue 1546 ILE Chi-restraints excluded: chain D residue 1560 TRP Chi-restraints excluded: chain D residue 1644 LEU Chi-restraints excluded: chain D residue 1652 VAL Chi-restraints excluded: chain D residue 1803 VAL Chi-restraints excluded: chain D residue 1842 ASP Chi-restraints excluded: chain D residue 1882 THR Chi-restraints excluded: chain D residue 2089 LEU Chi-restraints excluded: chain D residue 2093 ILE Chi-restraints excluded: chain E residue 201 TYR Chi-restraints excluded: chain E residue 278 THR Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 437 ILE Chi-restraints excluded: chain E residue 459 VAL Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 499 ASP Chi-restraints excluded: chain E residue 502 THR Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 544 ILE Chi-restraints excluded: chain E residue 572 LEU Chi-restraints excluded: chain E residue 624 MET Chi-restraints excluded: chain E residue 630 ASP Chi-restraints excluded: chain E residue 637 MET Chi-restraints excluded: chain E residue 654 THR Chi-restraints excluded: chain E residue 671 THR Chi-restraints excluded: chain E residue 771 LEU Chi-restraints excluded: chain E residue 835 VAL Chi-restraints excluded: chain E residue 845 GLN Chi-restraints excluded: chain E residue 1048 THR Chi-restraints excluded: chain E residue 1126 VAL Chi-restraints excluded: chain E residue 1185 THR Chi-restraints excluded: chain E residue 1190 SER Chi-restraints excluded: chain E residue 1259 VAL Chi-restraints excluded: chain E residue 1290 ASP Chi-restraints excluded: chain E residue 1304 LEU Chi-restraints excluded: chain E residue 1450 VAL Chi-restraints excluded: chain E residue 1467 THR Chi-restraints excluded: chain E residue 1503 ILE Chi-restraints excluded: chain E residue 1529 THR Chi-restraints excluded: chain E residue 1546 ILE Chi-restraints excluded: chain E residue 1560 TRP Chi-restraints excluded: chain E residue 1596 GLU Chi-restraints excluded: chain E residue 1619 THR Chi-restraints excluded: chain E residue 1630 ASP Chi-restraints excluded: chain E residue 1652 VAL Chi-restraints excluded: chain E residue 1723 THR Chi-restraints excluded: chain E residue 1903 VAL Chi-restraints excluded: chain E residue 2072 VAL Chi-restraints excluded: chain E residue 2093 ILE Chi-restraints excluded: chain E residue 2168 ILE Chi-restraints excluded: chain E residue 2329 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1140 random chunks: chunk 672 optimal weight: 10.0000 chunk 1082 optimal weight: 0.9990 chunk 660 optimal weight: 0.8980 chunk 513 optimal weight: 0.9980 chunk 752 optimal weight: 2.9990 chunk 1135 optimal weight: 8.9990 chunk 1045 optimal weight: 10.0000 chunk 904 optimal weight: 10.0000 chunk 93 optimal weight: 3.9990 chunk 698 optimal weight: 0.9980 chunk 554 optimal weight: 3.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1767 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 611 GLN ** B 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1767 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1767 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1926 GLN ** C2344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1250 GLN ** D1767 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 652 ASN E 707 GLN ** E 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1250 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.3517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 90390 Z= 0.200 Angle : 0.586 12.622 122855 Z= 0.293 Chirality : 0.040 0.321 14085 Planarity : 0.004 0.050 15950 Dihedral : 4.476 42.841 12384 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 2.48 % Allowed : 22.27 % Favored : 75.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.08), residues: 11365 helix: 1.98 (0.07), residues: 5330 sheet: -0.66 (0.13), residues: 1480 loop : -1.22 (0.10), residues: 4555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D1560 HIS 0.007 0.001 HIS D2191 PHE 0.015 0.001 PHE C1469 TYR 0.016 0.001 TYR A1924 ARG 0.016 0.000 ARG B2307 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22730 Ramachandran restraints generated. 11365 Oldfield, 0 Emsley, 11365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22730 Ramachandran restraints generated. 11365 Oldfield, 0 Emsley, 11365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1176 residues out of total 9715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 234 poor density : 942 time to evaluate : 8.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 TYR cc_start: 0.7408 (OUTLIER) cc_final: 0.5921 (p90) REVERT: A 637 MET cc_start: 0.8183 (tmm) cc_final: 0.7907 (tmm) REVERT: A 674 MET cc_start: 0.6247 (tpp) cc_final: 0.5555 (tpp) REVERT: A 767 ARG cc_start: 0.7789 (ttm-80) cc_final: 0.7510 (mmt-90) REVERT: B 201 TYR cc_start: 0.7673 (OUTLIER) cc_final: 0.6180 (p90) REVERT: B 630 ASP cc_start: 0.8355 (OUTLIER) cc_final: 0.8056 (p0) REVERT: B 914 GLN cc_start: 0.7929 (tm-30) cc_final: 0.7711 (tm-30) REVERT: B 1232 MET cc_start: 0.7845 (mtt) cc_final: 0.7627 (mtt) REVERT: B 1302 LEU cc_start: 0.7578 (mm) cc_final: 0.7363 (mm) REVERT: B 2307 ARG cc_start: 0.8181 (mtm110) cc_final: 0.7896 (ptt180) REVERT: C 201 TYR cc_start: 0.7429 (OUTLIER) cc_final: 0.6164 (p90) REVERT: C 501 GLU cc_start: 0.6901 (OUTLIER) cc_final: 0.6562 (tp30) REVERT: C 637 MET cc_start: 0.8347 (tmm) cc_final: 0.8034 (tmm) REVERT: C 674 MET cc_start: 0.6551 (tpp) cc_final: 0.6318 (tpp) REVERT: C 1560 TRP cc_start: 0.8441 (OUTLIER) cc_final: 0.6369 (p-90) REVERT: D 2435 ASP cc_start: 0.6239 (t0) cc_final: 0.5982 (p0) REVERT: E 201 TYR cc_start: 0.7510 (OUTLIER) cc_final: 0.6153 (p90) REVERT: E 827 GLN cc_start: 0.7937 (tm-30) cc_final: 0.7693 (tm-30) REVERT: E 1833 ASP cc_start: 0.7704 (m-30) cc_final: 0.7459 (m-30) outliers start: 234 outliers final: 209 residues processed: 1126 average time/residue: 0.8197 time to fit residues: 1640.8321 Evaluate side-chains 1135 residues out of total 9715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 216 poor density : 919 time to evaluate : 7.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 TYR Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 371 HIS Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 653 ILE Chi-restraints excluded: chain A residue 671 THR Chi-restraints excluded: chain A residue 835 VAL Chi-restraints excluded: chain A residue 845 GLN Chi-restraints excluded: chain A residue 1004 SER Chi-restraints excluded: chain A residue 1032 MET Chi-restraints excluded: chain A residue 1063 VAL Chi-restraints excluded: chain A residue 1126 VAL Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain A residue 1170 VAL Chi-restraints excluded: chain A residue 1185 THR Chi-restraints excluded: chain A residue 1190 SER Chi-restraints excluded: chain A residue 1195 THR Chi-restraints excluded: chain A residue 1197 LEU Chi-restraints excluded: chain A residue 1259 VAL Chi-restraints excluded: chain A residue 1290 ASP Chi-restraints excluded: chain A residue 1292 THR Chi-restraints excluded: chain A residue 1299 ILE Chi-restraints excluded: chain A residue 1304 LEU Chi-restraints excluded: chain A residue 1450 VAL Chi-restraints excluded: chain A residue 1467 THR Chi-restraints excluded: chain A residue 1501 ILE Chi-restraints excluded: chain A residue 1503 ILE Chi-restraints excluded: chain A residue 1529 THR Chi-restraints excluded: chain A residue 1545 VAL Chi-restraints excluded: chain A residue 1546 ILE Chi-restraints excluded: chain A residue 1584 ASP Chi-restraints excluded: chain A residue 1639 VAL Chi-restraints excluded: chain A residue 1752 MET Chi-restraints excluded: chain A residue 1798 ASP Chi-restraints excluded: chain A residue 1803 VAL Chi-restraints excluded: chain A residue 1889 ASP Chi-restraints excluded: chain A residue 1903 VAL Chi-restraints excluded: chain A residue 1930 MET Chi-restraints excluded: chain A residue 2085 SER Chi-restraints excluded: chain A residue 2091 THR Chi-restraints excluded: chain A residue 2093 ILE Chi-restraints excluded: chain B residue 201 TYR Chi-restraints excluded: chain B residue 280 ASP Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 499 ASP Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 630 ASP Chi-restraints excluded: chain B residue 637 MET Chi-restraints excluded: chain B residue 671 THR Chi-restraints excluded: chain B residue 835 VAL Chi-restraints excluded: chain B residue 845 GLN Chi-restraints excluded: chain B residue 1126 VAL Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain B residue 1185 THR Chi-restraints excluded: chain B residue 1190 SER Chi-restraints excluded: chain B residue 1259 VAL Chi-restraints excluded: chain B residue 1290 ASP Chi-restraints excluded: chain B residue 1292 THR Chi-restraints excluded: chain B residue 1304 LEU Chi-restraints excluded: chain B residue 1450 VAL Chi-restraints excluded: chain B residue 1458 ILE Chi-restraints excluded: chain B residue 1465 ASN Chi-restraints excluded: chain B residue 1503 ILE Chi-restraints excluded: chain B residue 1529 THR Chi-restraints excluded: chain B residue 1531 THR Chi-restraints excluded: chain B residue 1545 VAL Chi-restraints excluded: chain B residue 1546 ILE Chi-restraints excluded: chain B residue 1558 MET Chi-restraints excluded: chain B residue 1560 TRP Chi-restraints excluded: chain B residue 1630 ASP Chi-restraints excluded: chain B residue 1693 LEU Chi-restraints excluded: chain B residue 1723 THR Chi-restraints excluded: chain B residue 1790 LYS Chi-restraints excluded: chain B residue 1881 LYS Chi-restraints excluded: chain B residue 1882 THR Chi-restraints excluded: chain B residue 1903 VAL Chi-restraints excluded: chain B residue 1910 THR Chi-restraints excluded: chain B residue 2037 GLU Chi-restraints excluded: chain B residue 2073 SER Chi-restraints excluded: chain B residue 2093 ILE Chi-restraints excluded: chain B residue 2168 ILE Chi-restraints excluded: chain B residue 2274 SER Chi-restraints excluded: chain B residue 2420 ASN Chi-restraints excluded: chain C residue 201 TYR Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 371 HIS Chi-restraints excluded: chain C residue 437 ILE Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 499 ASP Chi-restraints excluded: chain C residue 501 GLU Chi-restraints excluded: chain C residue 538 THR Chi-restraints excluded: chain C residue 544 ILE Chi-restraints excluded: chain C residue 608 THR Chi-restraints excluded: chain C residue 835 VAL Chi-restraints excluded: chain C residue 1004 SER Chi-restraints excluded: chain C residue 1063 VAL Chi-restraints excluded: chain C residue 1126 VAL Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain C residue 1185 THR Chi-restraints excluded: chain C residue 1190 SER Chi-restraints excluded: chain C residue 1259 VAL Chi-restraints excluded: chain C residue 1290 ASP Chi-restraints excluded: chain C residue 1304 LEU Chi-restraints excluded: chain C residue 1450 VAL Chi-restraints excluded: chain C residue 1529 THR Chi-restraints excluded: chain C residue 1531 THR Chi-restraints excluded: chain C residue 1546 ILE Chi-restraints excluded: chain C residue 1560 TRP Chi-restraints excluded: chain C residue 1572 THR Chi-restraints excluded: chain C residue 1575 LEU Chi-restraints excluded: chain C residue 1619 THR Chi-restraints excluded: chain C residue 1630 ASP Chi-restraints excluded: chain C residue 1639 VAL Chi-restraints excluded: chain C residue 1652 VAL Chi-restraints excluded: chain C residue 1798 ASP Chi-restraints excluded: chain C residue 1842 ASP Chi-restraints excluded: chain C residue 1903 VAL Chi-restraints excluded: chain C residue 2073 SER Chi-restraints excluded: chain C residue 2085 SER Chi-restraints excluded: chain C residue 2093 ILE Chi-restraints excluded: chain C residue 2249 THR Chi-restraints excluded: chain C residue 2353 ASN Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 371 HIS Chi-restraints excluded: chain D residue 437 ILE Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 499 ASP Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 544 ILE Chi-restraints excluded: chain D residue 600 LEU Chi-restraints excluded: chain D residue 604 VAL Chi-restraints excluded: chain D residue 608 THR Chi-restraints excluded: chain D residue 615 LEU Chi-restraints excluded: chain D residue 637 MET Chi-restraints excluded: chain D residue 655 VAL Chi-restraints excluded: chain D residue 671 THR Chi-restraints excluded: chain D residue 771 LEU Chi-restraints excluded: chain D residue 835 VAL Chi-restraints excluded: chain D residue 845 GLN Chi-restraints excluded: chain D residue 1170 VAL Chi-restraints excluded: chain D residue 1190 SER Chi-restraints excluded: chain D residue 1240 ILE Chi-restraints excluded: chain D residue 1259 VAL Chi-restraints excluded: chain D residue 1290 ASP Chi-restraints excluded: chain D residue 1304 LEU Chi-restraints excluded: chain D residue 1450 VAL Chi-restraints excluded: chain D residue 1501 ILE Chi-restraints excluded: chain D residue 1503 ILE Chi-restraints excluded: chain D residue 1529 THR Chi-restraints excluded: chain D residue 1545 VAL Chi-restraints excluded: chain D residue 1546 ILE Chi-restraints excluded: chain D residue 1560 TRP Chi-restraints excluded: chain D residue 1575 LEU Chi-restraints excluded: chain D residue 1644 LEU Chi-restraints excluded: chain D residue 1652 VAL Chi-restraints excluded: chain D residue 1803 VAL Chi-restraints excluded: chain D residue 1842 ASP Chi-restraints excluded: chain D residue 1882 THR Chi-restraints excluded: chain D residue 1976 SER Chi-restraints excluded: chain D residue 2089 LEU Chi-restraints excluded: chain D residue 2093 ILE Chi-restraints excluded: chain E residue 201 TYR Chi-restraints excluded: chain E residue 278 THR Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 437 ILE Chi-restraints excluded: chain E residue 459 VAL Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 499 ASP Chi-restraints excluded: chain E residue 502 THR Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 544 ILE Chi-restraints excluded: chain E residue 572 LEU Chi-restraints excluded: chain E residue 624 MET Chi-restraints excluded: chain E residue 637 MET Chi-restraints excluded: chain E residue 654 THR Chi-restraints excluded: chain E residue 671 THR Chi-restraints excluded: chain E residue 835 VAL Chi-restraints excluded: chain E residue 845 GLN Chi-restraints excluded: chain E residue 1048 THR Chi-restraints excluded: chain E residue 1126 VAL Chi-restraints excluded: chain E residue 1185 THR Chi-restraints excluded: chain E residue 1190 SER Chi-restraints excluded: chain E residue 1259 VAL Chi-restraints excluded: chain E residue 1299 ILE Chi-restraints excluded: chain E residue 1304 LEU Chi-restraints excluded: chain E residue 1450 VAL Chi-restraints excluded: chain E residue 1467 THR Chi-restraints excluded: chain E residue 1503 ILE Chi-restraints excluded: chain E residue 1529 THR Chi-restraints excluded: chain E residue 1546 ILE Chi-restraints excluded: chain E residue 1560 TRP Chi-restraints excluded: chain E residue 1596 GLU Chi-restraints excluded: chain E residue 1619 THR Chi-restraints excluded: chain E residue 1630 ASP Chi-restraints excluded: chain E residue 1652 VAL Chi-restraints excluded: chain E residue 1723 THR Chi-restraints excluded: chain E residue 1903 VAL Chi-restraints excluded: chain E residue 2072 VAL Chi-restraints excluded: chain E residue 2093 ILE Chi-restraints excluded: chain E residue 2168 ILE Chi-restraints excluded: chain E residue 2276 LEU Chi-restraints excluded: chain E residue 2329 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1140 random chunks: chunk 718 optimal weight: 20.0000 chunk 963 optimal weight: 0.7980 chunk 277 optimal weight: 0.9980 chunk 833 optimal weight: 0.9980 chunk 133 optimal weight: 1.9990 chunk 251 optimal weight: 0.8980 chunk 905 optimal weight: 10.0000 chunk 379 optimal weight: 2.9990 chunk 930 optimal weight: 2.9990 chunk 114 optimal weight: 5.9990 chunk 166 optimal weight: 0.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 777 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1767 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1767 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 773 ASN ** C 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1250 GLN ** C1767 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1926 GLN ** C2344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1767 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 652 ASN E 707 GLN ** E 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.106897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.075294 restraints weight = 215581.385| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 3.13 r_work: 0.2937 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.3649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 90390 Z= 0.171 Angle : 0.580 12.444 122855 Z= 0.289 Chirality : 0.040 0.322 14085 Planarity : 0.004 0.055 15950 Dihedral : 4.397 41.421 12384 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 2.41 % Allowed : 22.55 % Favored : 75.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.08), residues: 11365 helix: 2.06 (0.07), residues: 5325 sheet: -0.59 (0.13), residues: 1455 loop : -1.22 (0.10), residues: 4585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C1560 HIS 0.007 0.001 HIS D2191 PHE 0.016 0.001 PHE C1469 TYR 0.015 0.001 TYR A 481 ARG 0.014 0.000 ARG B2307 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 24774.35 seconds wall clock time: 434 minutes 48.67 seconds (26088.67 seconds total)