Starting phenix.real_space_refine on Fri Dec 15 01:18:39 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yew_10796/12_2023/6yew_10796.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yew_10796/12_2023/6yew_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_10796/12_2023/6yew_10796.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yew_10796/12_2023/6yew_10796.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yew_10796/12_2023/6yew_10796.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yew_10796/12_2023/6yew_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-1.21rc1-5172/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: 37.54, per 1000 atoms: 0.42 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: 25.78 Conformation dependent library (CDL) restraints added in 11.8 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: 9.16 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: 49.53 Time building geometry restraints manager: 28.50 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: 4.240 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: 0.080 Extract box with map and model: 14.840 Check model and map are aligned: 1.010 Set scattering table: 0.660 Process input model: 196.920 Find NCS groups from input model: 4.580 Set up NCS constraints: 0.410 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 225.200 ------------------------------------------------------------------------------- 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 : 8.027 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 outliers start: 267 outliers final: 89 residues processed: 1548 average time/residue: 0.8910 time to fit residues: 2339.0204 Evaluate side-chains 1025 residues out of total 9715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 936 time to evaluate : 7.706 Switching outliers to nearest non-outliers outliers start: 89 outliers final: 0 residues processed: 89 average time/residue: 0.6523 time to fit residues: 120.6811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 665 optimal weight: 0.9990 chunk 1035 optimal weight: 7.9990 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 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 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 209 HIS B 315 ASN B 371 HIS B 528 ASN B 533 ASN ** B 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 724 ASN B 816 GLN B 910 GLN ** B 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 934 ASN B1028 GLN B1150 GLN B1250 GLN B1264 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 209 HIS C 315 ASN C 355 GLN C 371 HIS C 528 ASN C 533 ASN C 724 ASN C 816 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 C1169 HIS 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 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 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 757 GLN E 816 GLN ** E 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 934 ASN ** E 973 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1150 GLN E1250 GLN E1264 ASN E1617 HIS E1620 ASN E1649 ASN E1680 ASN E1767 ASN E1811 ASN E1872 ASN E1883 GLN E1997 GLN E2278 ASN E2310 ASN E2328 ASN E2394 ASN E2420 ASN Total number of N/Q/H flips: 127 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.1769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 90390 Z= 0.219 Angle : 0.613 8.591 122855 Z= 0.316 Chirality : 0.041 0.211 14085 Planarity : 0.004 0.052 15950 Dihedral : 5.088 28.442 12365 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 2.09 % Allowed : 15.28 % Favored : 82.63 % 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: -1.31 (0.08), residues: 11365 helix: 0.43 (0.07), residues: 5305 sheet: -1.94 (0.12), residues: 1515 loop : -2.02 (0.09), residues: 4545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D1560 HIS 0.006 0.001 HIS C2191 PHE 0.023 0.001 PHE E1714 TYR 0.020 0.001 TYR A1836 ARG 0.007 0.000 ARG E2307 *********************** 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 1298 residues out of total 9715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 197 poor density : 1101 time to evaluate : 8.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 197 outliers final: 87 residues processed: 1245 average time/residue: 0.8692 time to fit residues: 1887.1423 Evaluate side-chains 1020 residues out of total 9715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 933 time to evaluate : 7.641 Switching outliers to nearest non-outliers outliers start: 87 outliers final: 0 residues processed: 87 average time/residue: 0.6570 time to fit residues: 119.4901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1140 random chunks: chunk 575 optimal weight: 0.6980 chunk 321 optimal weight: 5.9990 chunk 861 optimal weight: 9.9990 chunk 704 optimal weight: 5.9990 chunk 285 optimal weight: 0.9990 chunk 1037 optimal weight: 20.0000 chunk 1120 optimal weight: 6.9990 chunk 923 optimal weight: 2.9990 chunk 1028 optimal weight: 0.0980 chunk 353 optimal weight: 4.9990 chunk 832 optimal weight: 8.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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 214 GLN A 351 GLN A 371 HIS A 533 ASN ** A 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1279 ASN A1775 GLN A2052 GLN ** A2344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 184 ASN B 611 GLN ** B 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1279 ASN B1580 ASN ** B1767 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 158 ASN ** C 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 216 ASN ** C 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 533 ASN C 606 ASN C 799 ASN ** C 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1028 GLN C1279 ASN C1580 ASN ** 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 371 HIS D 533 ASN D 910 GLN ** D 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1279 ASN ** D1767 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 158 ASN ** E 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 533 ASN E 652 ASN E 724 ASN ** E 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1279 ASN E1767 ASN E2052 GLN E2146 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 90390 Z= 0.252 Angle : 0.591 8.749 122855 Z= 0.301 Chirality : 0.041 0.217 14085 Planarity : 0.004 0.048 15950 Dihedral : 4.824 26.210 12365 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 1.65 % Allowed : 17.70 % Favored : 80.65 % 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: -0.54 (0.08), residues: 11365 helix: 1.16 (0.07), residues: 5265 sheet: -1.61 (0.12), residues: 1485 loop : -1.71 (0.09), residues: 4615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1560 HIS 0.006 0.001 HIS D2191 PHE 0.017 0.001 PHE E1714 TYR 0.018 0.001 TYR A1836 ARG 0.010 0.000 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 1182 residues out of total 9715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 1026 time to evaluate : 7.577 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 outliers start: 156 outliers final: 52 residues processed: 1149 average time/residue: 0.8368 time to fit residues: 1698.6494 Evaluate side-chains 972 residues out of total 9715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 920 time to evaluate : 7.590 Switching outliers to nearest non-outliers outliers start: 52 outliers final: 0 residues processed: 52 average time/residue: 0.6920 time to fit residues: 79.8292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 538 optimal weight: 0.6980 chunk 114 optimal weight: 5.9990 chunk 494 optimal weight: 0.9980 chunk 696 optimal weight: 1.9990 chunk 1040 optimal weight: 6.9990 chunk 1101 optimal weight: 1.9990 chunk 543 optimal weight: 3.9990 chunk 986 optimal weight: 0.0270 chunk 296 optimal weight: 6.9990 overall best weight: 1.1442 ------------------------------------------------------------------------------- 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 533 ASN ** A 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 910 GLN ** A 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 351 GLN B 611 GLN ** B 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1767 ASN B2170 GLN ** C 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 216 ASN ** C 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 606 ASN C 799 ASN ** C 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1767 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2146 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 533 ASN ** D 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1767 ASN ** D2195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 184 ASN E 652 ASN ** E 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E2146 GLN ** E2266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.2658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 90390 Z= 0.179 Angle : 0.565 10.203 122855 Z= 0.286 Chirality : 0.040 0.198 14085 Planarity : 0.004 0.048 15950 Dihedral : 4.573 26.039 12365 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 1.52 % Allowed : 18.54 % Favored : 79.95 % 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: -0.06 (0.08), residues: 11365 helix: 1.55 (0.07), residues: 5295 sheet: -1.31 (0.13), residues: 1465 loop : -1.53 (0.09), residues: 4605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1560 HIS 0.005 0.001 HIS E2191 PHE 0.016 0.001 PHE D1520 TYR 0.013 0.001 TYR A1836 ARG 0.006 0.000 ARG A1841 *********************** 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 1177 residues out of total 9715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 1034 time to evaluate : 7.688 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 outliers start: 143 outliers final: 70 residues processed: 1135 average time/residue: 0.8179 time to fit residues: 1622.7502 Evaluate side-chains 985 residues out of total 9715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 915 time to evaluate : 7.623 Switching outliers to nearest non-outliers outliers start: 70 outliers final: 0 residues processed: 70 average time/residue: 0.6480 time to fit residues: 98.0467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1140 random chunks: chunk 917 optimal weight: 0.0000 chunk 625 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 820 optimal weight: 1.9990 chunk 454 optimal weight: 8.9990 chunk 940 optimal weight: 6.9990 chunk 761 optimal weight: 7.9990 chunk 1 optimal weight: 4.9990 chunk 562 optimal weight: 1.9990 chunk 989 optimal weight: 10.0000 chunk 278 optimal weight: 2.9990 overall best weight: 2.1992 ------------------------------------------------------------------------------- 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 ** A 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 920 ASN ** 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** ** B1103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1767 ASN C 38 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** ** C1103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C2146 GLN ** 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** D1103 HIS D1767 ASN E 652 ASN E 910 GLN ** E 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.2801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 90390 Z= 0.267 Angle : 0.586 8.346 122855 Z= 0.296 Chirality : 0.041 0.234 14085 Planarity : 0.004 0.046 15950 Dihedral : 4.598 25.890 12365 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 1.33 % Allowed : 20.01 % Favored : 78.66 % 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: 0.13 (0.08), residues: 11365 helix: 1.65 (0.07), residues: 5295 sheet: -1.10 (0.13), residues: 1455 loop : -1.39 (0.10), residues: 4615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E1560 HIS 0.006 0.001 HIS D2191 PHE 0.014 0.001 PHE E1714 TYR 0.018 0.001 TYR B1836 ARG 0.011 0.000 ARG E2307 *********************** 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 1082 residues out of total 9715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 957 time to evaluate : 8.610 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 outliers start: 125 outliers final: 57 residues processed: 1048 average time/residue: 0.8232 time to fit residues: 1520.0266 Evaluate side-chains 955 residues out of total 9715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 898 time to evaluate : 7.579 Switching outliers to nearest non-outliers outliers start: 57 outliers final: 0 residues processed: 57 average time/residue: 0.6550 time to fit residues: 81.9265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1140 random chunks: chunk 370 optimal weight: 0.9990 chunk 992 optimal weight: 9.9990 chunk 217 optimal weight: 4.9990 chunk 646 optimal weight: 3.9990 chunk 272 optimal weight: 9.9990 chunk 1102 optimal weight: 2.9990 chunk 915 optimal weight: 0.9980 chunk 510 optimal weight: 0.0270 chunk 91 optimal weight: 2.9990 chunk 364 optimal weight: 9.9990 chunk 579 optimal weight: 6.9990 overall best weight: 1.6044 ------------------------------------------------------------------------------- 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 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1028 GLN ** 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 910 GLN ** B 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1767 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1926 GLN ** C 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 GLN C 216 ASN ** C 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 606 ASN C 799 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** C2146 GLN ** C2344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 571 GLN ** D 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1767 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2052 GLN ** D2195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** E1250 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.3002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 90390 Z= 0.213 Angle : 0.570 9.240 122855 Z= 0.288 Chirality : 0.040 0.196 14085 Planarity : 0.004 0.048 15950 Dihedral : 4.511 27.899 12365 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 1.21 % Allowed : 20.33 % 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: 0.29 (0.08), residues: 11365 helix: 1.78 (0.07), residues: 5295 sheet: -0.95 (0.13), residues: 1490 loop : -1.33 (0.10), residues: 4580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP D1560 HIS 0.006 0.001 HIS D2191 PHE 0.014 0.001 PHE E1714 TYR 0.012 0.001 TYR A1924 ARG 0.006 0.000 ARG D1841 *********************** 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 1072 residues out of total 9715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 958 time to evaluate : 7.706 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 outliers start: 114 outliers final: 43 residues processed: 1045 average time/residue: 0.8436 time to fit residues: 1556.8384 Evaluate side-chains 947 residues out of total 9715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 904 time to evaluate : 7.592 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 0 residues processed: 43 average time/residue: 0.6942 time to fit residues: 66.9915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1140 random chunks: chunk 1063 optimal weight: 6.9990 chunk 124 optimal weight: 9.9990 chunk 628 optimal weight: 8.9990 chunk 805 optimal weight: 0.9990 chunk 624 optimal weight: 0.0980 chunk 928 optimal weight: 0.9990 chunk 615 optimal weight: 0.0000 chunk 1098 optimal weight: 0.8980 chunk 687 optimal weight: 2.9990 chunk 669 optimal weight: 7.9990 chunk 507 optimal weight: 4.9990 overall best weight: 0.5988 ------------------------------------------------------------------------------- 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 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1767 ASN A1944 GLN ** 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 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 910 GLN ** B 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1767 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2052 GLN ** 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** ** 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 777 GLN ** D 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 652 ASN ** E 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E2146 GLN ** E2344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.3294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 90390 Z= 0.148 Angle : 0.557 11.295 122855 Z= 0.279 Chirality : 0.039 0.304 14085 Planarity : 0.003 0.047 15950 Dihedral : 4.322 25.634 12365 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 0.91 % Allowed : 20.99 % Favored : 78.10 % 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: 1.95 (0.07), residues: 5300 sheet: -0.79 (0.13), residues: 1485 loop : -1.28 (0.10), residues: 4580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP E1560 HIS 0.006 0.001 HIS E2191 PHE 0.014 0.001 PHE E1714 TYR 0.017 0.001 TYR E 286 ARG 0.007 0.000 ARG E2307 *********************** 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 1105 residues out of total 9715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 1019 time to evaluate : 8.468 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 outliers start: 86 outliers final: 41 residues processed: 1082 average time/residue: 0.8963 time to fit residues: 1715.9293 Evaluate side-chains 966 residues out of total 9715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 925 time to evaluate : 7.666 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 0 residues processed: 41 average time/residue: 0.6819 time to fit residues: 64.3012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1140 random chunks: chunk 679 optimal weight: 20.0000 chunk 438 optimal weight: 0.9990 chunk 656 optimal weight: 2.9990 chunk 330 optimal weight: 0.9990 chunk 215 optimal weight: 0.0670 chunk 212 optimal weight: 20.0000 chunk 698 optimal weight: 4.9990 chunk 748 optimal weight: 7.9990 chunk 543 optimal weight: 4.9990 chunk 102 optimal weight: 3.9990 chunk 863 optimal weight: 3.9990 overall best weight: 1.8126 ------------------------------------------------------------------------------- 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 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 777 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1028 GLN ** 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 ** 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 799 ASN ** 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** C1926 GLN ** 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 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** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.3287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 90390 Z= 0.234 Angle : 0.586 11.659 122855 Z= 0.294 Chirality : 0.040 0.310 14085 Planarity : 0.004 0.048 15950 Dihedral : 4.373 27.792 12365 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 0.83 % Allowed : 21.70 % Favored : 77.48 % 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: 0.49 (0.08), residues: 11365 helix: 1.94 (0.07), residues: 5325 sheet: -0.74 (0.13), residues: 1480 loop : -1.29 (0.10), residues: 4560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C1560 HIS 0.005 0.001 HIS D2191 PHE 0.012 0.001 PHE E1714 TYR 0.016 0.001 TYR B2216 ARG 0.008 0.000 ARG B2011 *********************** 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 1023 residues out of total 9715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 945 time to evaluate : 8.844 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 outliers start: 78 outliers final: 39 residues processed: 994 average time/residue: 0.8134 time to fit residues: 1432.8269 Evaluate side-chains 952 residues out of total 9715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 913 time to evaluate : 7.594 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 0 residues processed: 39 average time/residue: 0.6810 time to fit residues: 61.2552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1140 random chunks: chunk 999 optimal weight: 0.7980 chunk 1052 optimal weight: 1.9990 chunk 960 optimal weight: 0.6980 chunk 1023 optimal weight: 0.5980 chunk 616 optimal weight: 2.9990 chunk 446 optimal weight: 8.9990 chunk 804 optimal weight: 0.0060 chunk 314 optimal weight: 7.9990 chunk 925 optimal weight: 6.9990 chunk 968 optimal weight: 7.9990 chunk 1020 optimal weight: 1.9990 overall best weight: 0.8198 ------------------------------------------------------------------------------- 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 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 777 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1028 GLN ** 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 226 ASN ** B 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 723 ASN B 910 GLN ** B 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1767 ASN ** B2344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 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** ** D 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 351 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 ** D2195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 652 ASN ** E 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.3497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 90390 Z= 0.162 Angle : 0.568 11.865 122855 Z= 0.284 Chirality : 0.040 0.233 14085 Planarity : 0.004 0.049 15950 Dihedral : 4.277 25.631 12365 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 0.38 % Allowed : 22.16 % Favored : 77.45 % 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: 0.63 (0.08), residues: 11365 helix: 2.07 (0.07), residues: 5300 sheet: -0.66 (0.13), residues: 1465 loop : -1.21 (0.10), residues: 4600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E1560 HIS 0.005 0.001 HIS E2191 PHE 0.013 0.001 PHE D1520 TYR 0.015 0.001 TYR E 286 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 1005 residues out of total 9715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 969 time to evaluate : 7.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 11 residues processed: 996 average time/residue: 0.8938 time to fit residues: 1573.0262 Evaluate side-chains 935 residues out of total 9715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 924 time to evaluate : 7.692 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.7423 time to fit residues: 26.0415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1140 random chunks: chunk 672 optimal weight: 4.9990 chunk 1082 optimal weight: 4.9990 chunk 660 optimal weight: 5.9990 chunk 513 optimal weight: 3.9990 chunk 752 optimal weight: 3.9990 chunk 1135 optimal weight: 0.8980 chunk 1045 optimal weight: 1.9990 chunk 904 optimal weight: 10.0000 chunk 93 optimal weight: 4.9990 chunk 698 optimal weight: 1.9990 chunk 554 optimal weight: 6.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- 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 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1767 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1944 GLN ** 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 ** B 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1767 ASN ** C 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 777 GLN C 799 ASN ** C 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1250 GLN 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 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1767 ASN E 652 ASN ** E 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1103 HIS E1250 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.3375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 90390 Z= 0.302 Angle : 0.623 11.847 122855 Z= 0.313 Chirality : 0.042 0.261 14085 Planarity : 0.004 0.051 15950 Dihedral : 4.482 29.629 12365 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 0.35 % Allowed : 22.53 % Favored : 77.12 % 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: 0.54 (0.08), residues: 11365 helix: 1.92 (0.07), residues: 5335 sheet: -0.65 (0.13), residues: 1490 loop : -1.21 (0.10), residues: 4540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP C1560 HIS 0.009 0.001 HIS D 522 PHE 0.013 0.001 PHE A 205 TYR 0.023 0.001 TYR C1924 ARG 0.017 0.000 ARG B1983 ********************** 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 953 residues out of total 9715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 920 time to evaluate : 7.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 18 residues processed: 938 average time/residue: 0.8475 time to fit residues: 1404.2343 Evaluate side-chains 916 residues out of total 9715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 898 time to evaluate : 7.698 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.7049 time to fit residues: 34.2334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1140 random chunks: chunk 718 optimal weight: 7.9990 chunk 963 optimal weight: 0.8980 chunk 277 optimal weight: 6.9990 chunk 833 optimal weight: 0.6980 chunk 133 optimal weight: 0.9990 chunk 251 optimal weight: 0.9990 chunk 905 optimal weight: 8.9990 chunk 379 optimal weight: 6.9990 chunk 930 optimal weight: 0.9990 chunk 114 optimal weight: 3.9990 chunk 166 optimal weight: 1.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- 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 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1028 GLN ** 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 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 910 GLN ** 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 351 GLN ** 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** ** C1767 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1926 GLN C2052 GLN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2195 GLN ** 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** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.106746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.075567 restraints weight = 215655.160| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 3.13 r_work: 0.2928 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.3581 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= 0.172 Angle : 0.584 12.446 122855 Z= 0.292 Chirality : 0.040 0.238 14085 Planarity : 0.004 0.051 15950 Dihedral : 4.352 25.795 12365 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 0.18 % Allowed : 22.66 % Favored : 77.16 % 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: 2.04 (0.07), residues: 5340 sheet: -0.59 (0.13), residues: 1465 loop : -1.20 (0.10), residues: 4560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E1560 HIS 0.005 0.001 HIS D2191 PHE 0.014 0.001 PHE E1714 TYR 0.015 0.001 TYR C 496 ARG 0.015 0.000 ARG D2307 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 25203.00 seconds wall clock time: 453 minutes 6.70 seconds (27186.70 seconds total)